Search Results - EGA European Genome-Phenome Archive

Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance

The treatment outcome of glioma patients remains disappointing, and more studies are needed to improve therapeutic strategies. In particular, it is crucial to understand the mechanisms underlying resistance to treatment and malignant transformation, as well as the intratumoral heterogeneity and interaction of tumor cells and host immunity. Recent advances in omics analysis techniques, such as next-generation sequencing (NGS), have enabled us to obtain omics data more easily and accelerated our ability to integrate this information and precisely characterize cases. In our project, we have already collected more than 100 pairs of human glioma/normal tissue samples, of which some are multiple specimens collected from initial and recurrent tumors, and some include multiple specimens collected from different regions within a single tumor. We used our in-house algorithms, composed of alignment and variant calling programs, to analyze omics data from multiple platforms, such as whole-exome sequencing (WES), RNA sequencing (RNA-seq), and methylation array, with our original cohort of glioma patients. Using several informatics tools, the information about genetic and epigenetic status and expression signatures were analyzed. Those data are expected to provide key information for investigating the mechanisms discussed above. Through this project, we hope to improve strategies for personalized therapy based on comprehensive omics data.

Study JGAS000004

Phylogenetic analysis of paired breast carcinomas identifies genetic events associated with clonal recurrence and invasive progression

Development of ipsilateral breast carcinoma following diagnosis of breast ductal carcinoma in situ (DCIS) has been assumed to represent recurrence of the primary tumour. However, this may not be the case and it is important to know how often recurrences are new tumours. Ipsilateral primary-recurrence pairs (n=78) were sequenced to test their clonal relatedness. Shared genetic events were identified from whole exome sequencing (n=54 pairs) using haplotype-specific copy number and phylogenetic analysis. The remaining pairs were sequenced by a targeted panel or low-coverage whole genome sequencing. We included 32 non-recurrent DCIS to compare recurrent and non-recurrent disease. We found that 7% of DCIS recurrences were non-clonal by whole exome sequencing, indicative of a new breast carcinoma. Lower resolution methods detected a higher non-clonality rate (29%). Comparing primary DCIS with their recurrences found that evolution of DCIS to invasive disease was associated with increased ploidy and copy number events. TP53 mutations were enriched in DCIS with clonal recurrence compared with non-recurrent DCIS. Our results verify that de novo “recurrent tumours” of independent origin occur in patients who may be at high risk. (https://www.biorxiv.org/content/10.1101/2024.05.19.594731v2.full)

Study EGAS50000001298

LySeqST: A targeted sequencing assay for robust genomic classification of diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) is a biologically heterogeneous disease. Two genomic classification systems, LymphGen and DLBclass, are capable of reproducibly classifying single tumors into subtypes with prognostic relevance in the context of standard-of-care R-CHOP chemoimmunotherapy. Preliminary data from subgroup analyses of clinical trials suggest that the distinct biological features are targetable with drugs that exploit subtype-specific vulnerabilities, and large clinical trials are being designed to test this hypothesis. Although whole exome sequencing (WES) remains the gold standard for each of these classification systems, many laboratories may opt for smaller targeted sequencing panels that reduce costs associated with sequencing, data storage, and processing. Here, we describe the design and validation of a targeted sequencing panel (LySeqST) that captures the genomic features required specifically for LymphGen classification. We perform in silico and real-world validation vs. WES data and demonstrate that LySeqST can be used to accurately classify DLBCL tumors. In an unselected population-based cohort, we determine the real-world proportions and validate the prognostic relevance of LymphGen subtypes, confirming that only tumors expressing the dark zone gene expression signature are consistently associated with inferior outcomes. Our results support the use of LySeqST for accurate genomic classification of DLBCL.

Study EGAS50000001601

Genentech Colon Cancer Screen

Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics. Here we analyse systematically more than 70 pairs of primary human colon tumours by applying next-generation sequencing to characterize their exomes, transcriptomes and copy-number alterations. We have identified 36,303 protein-altering somatic changes that include several new recurrent mutations in the Wnt pathway gene TCF7L2, chromatin-remodelling genes such as TET2 and TET3 and receptor tyrosine kinases including ERBB3. Our analysis for significantly mutated cancer genes identified 23 candidates, including the cell cycle checkpoint kinase ATM. Copy-number and RNA-seq data analysis identified amplifications and corresponding overexpression of IGF2 in a subset of colon tumours. Furthermore, using RNA-seq data we identified multiple fusion transcripts including recurrent gene fusions involving R-spondin family members RSPO2 and RSPO3 that together occur in 10% of colon tumours. The RSPO fusions were mutually exclusive with APC mutations, indicating that they probably have a role in the activation of Wnt signalling and tumorigenesis. Consistent with this we show that the RSPO fusion proteins were capable of potentiating Wnt signalling. The R-spondin gene fusions and several other gene mutations identified in this study provide new potential opportunities for therapeutic intervention in colon cancer.

Study EGAS00001000288

Single cell sequencing of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

The quantity of tumor infiltrating lymphocytes (TILs) in breast cancer (BC) is a robust prognostic factor for improved patient survival particularly in triple negative and HER2-overexpressing BC subtypes. Whilst T cells are the predominant TIL population, the relationship between quantitative and qualitative differences in T cell subpopulations and patient prognosis remains unknown. We performed single-cell RNA sequencing (scRNA-seq) of 6311 T cells isolated from human BCs, and show for the first time that significant heterogeneity exists in the infiltrating T cell population. We demonstrated that high TIL BCs contained significant numbers of CD8+ T cells with features of tissue-resident memory T (TRM) cell differentiation and that these CD8+ TRM cells expressed high levels of immune checkpoint molecules and effector proteins. A CD8+ TRM gene signature developed from the scRNA-seq data was significantly associated with improved patient survival in early-stage triple negative breast cancer (TNBC) and provided better prognostication compared with CD8 expression alone. Our data suggests that CD8+ TRM contribute to BC immunosurveillance and are the key targets of modulation through immune checkpoint inhibition. Further understanding of the development, maintenance and regulation of TRM cells will be crucial for successful immunotherapeutic development in BC.

Study EGAS00001002845

Molecular characteristics in Burkitt lymphoma over age groups

Treatment optimization has improved the overall survival in Burkitt lymphoma (BL) patients but there are still relevant outcome differences between pediatric and adult patients. In both age groups survival remains poor for patients who suffer relapse. Therefore, new treatment approaches are warranted to improve survival. Thus, we conducted a comparative study in the largest pediatric cohort to date including 191 cases and 97 samples from adult patients and analyzed the mutational landscape. We detected overlapping molecular profiles but also significant differences in the mutational pattern. Samples from pediatric patients show a higher frequency of mutations in ID3, DDX3X and BAF-complex components ARID1A and SMARCA4, while YY1AP1 and BCL2 are more frequently mutated in cases from adult BL patients. Correlation of the mutational profile with clinical data was available for the pediatric cohort and identified TP53 mutations to be highly significantly associated with the incidence of relapse thus identifying the first molecular marker to be associated with the incidence of relapse in pediatric BL. As the hotspot analysis of TP53 mutations showed mostly gain of function mutations, it is tempting to speculate that drugs decreasing the amount of malignant TP53 or increase the abundance of wildtype TP53 could be a promising approach for future treatment regimens to further improve prognosis.

Study EGAS00001005270

Ethiopia_Genome_Project__high_coverage_

The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity.This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum.The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.

Study EGAS00001000237

Allele Balance Bias Identifies Systematic Genotyping Errors and False Disease Associations

In recent years, Next Generation Sequencing (NGS) has become a cornerstone of clinical genetics and diagnostics. Many clinical applications require high precision, especially if rare events such as somatic mutations in cancer or genetic variants causing rare diseases need to be identified. Although random sequencing errors can be modeled statistically and deep sequencing minimizes their impact, systematic errors remain a problem even at high depth of coverage. Understanding their source is crucial to increase precision of clinical NGS applications. In this work, we studied the relation between recurrent biases in allele balance (AB), systematic errors and false positive variant calls across a large cohort of human samples analyzed by whole exome sequencing (WES). We have modeled the allele balance distribution for biallelic genotypes in 987 WES samples in order to identify positions recurrently deviating significantly from the expectation, a phenomenon we termed allele balance bias (ABB). Furthermore, we have developed a genotype callability score based on ABB for all positions of the human exome, which detects false positive variant calls that passed state-of-the-art filters. Finally, we demonstrate the use of ABB for detection of false associations proposed by rare variant association studies (RVAS).

Study EGAS00001003027

The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias

Pediatric de novo acute myeloid leukemia (AML) is a heterogeneous disease that can be divided into clinically distinct subtypes based on the presence of specific chromosomal abnormalities or gene alterations. One of the best characterized subtypes of AML involves leukemias with alterations of the core-binding factor (CBF)-complex, which comprises the FAB subtypes M2 and M4Eo and associates with a favorable outcome. Patients with the AML M2 subtype harbor a translocation between chromosomes 8 and 21 [t(8;21)] that yields the chimeric fusion gene RUNX1(AML1)-RUNX1T1(ETO), while patients with AML M4Eo express the chimeric fusion gene CBFβ-SMMHC(MYH11) as a result of an inversion/translocation event of chromosome 16 [inv(16)/t(16;16)]. In an effort to define the total complement of genetic changes in CBF-leukemia, we performed paired-end whole genome sequencing (WGS) on diagnostic leukemia blasts and matched germ line samples from 17 pediatric CBF-leukemia patients using the Illumina platform. Somatic alterations, including single nucleotide variations (SNVs) and structural variations (SVs), including insertions, deletions, inversions, and inter- and intra-chromosomal rearrangements, were detected using complementary analysis pipelines (Bambino, CREST and CONSERTING). Recurrent screening of identified mutations will be performed in a cohort of approximately 94 cases of CBF-leukemias.

Study EGAS00001000349

An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup

Effective treatment of diffuse large B cell lymphoma (DLBCL) is plagued by heterogeneous responses to standard therapy, and molecular mechanisms underlying unfavorable outcomes in lymphoma patients remain elusive. Here, we profiled 148 genomes with 91 matching transcriptomes in an R-CHOP-treated DLBCL cohort to uncover molecular subgroups linked to treatment failure. Systematic integration of high-resolution genotyping arrays and RNA-seq data revealed novel deletions in RCOR1 to be associated with unfavorable progression free survival (P = 0.001). Integration of expression data from the clinical samples with data from RCOR1 knockdowns in the lymphoma cell lines KM-H2 and Raji yielded an RCOR1 loss-associated gene signature comprising of 233 genes. This signature identified a subgroup of patients with unfavorable overall survival (OS) (P = 0.023). The prognostic significance of the 233-gene signature for OS was reproduced in an independent cohort comprising of 195 R- CHOP treated patients (P = 0.039). Additionally, we discovered that within the IPI low risk group, the gene signature provides additional prognostic value that was independent of the cell-of-origin phenotype. Taken together, we present a novel and reproducible molecular subgroup of DLBCL, impacting risk-stratification of R- CHOP treated DLBCL patients and revealing a new avenue for therapeutic intervention strategies.

Study EGAS00001001000

Rapid identification of somatic genome rearrangements as personalized biomarkers for blood-based cancer monitoring

Increasing evidence shows the value of circulating tumour DNA (ctDNA) to detect cancer and monitor its progression. Somatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of ctDNA in liquid biopsies. However, accurate, affordable, and fast identification of such SV biomarkers is challenging, which hinders routine use in the clinic. Here, we demonstrate a novel approach - termed SHARC - for rapid discovery of somatic SV breakpoints as personalized tumour biomarkers. SHARC combines low-coverage cancer genome sketching by using Oxford Nanopore portable sequencing with a random forest classification and a dedicated filtering pipeline to enrich for somatic SVs. Our method leverages the real-time and long-read capabilities of Nanopore sequencing to identify somatic SV breakpoints at nucleotide resolution from a tumour biopsy within two days. We applied SHARC to tumour samples of high-grade ovarian and prostate cancer and validated on average 10 somatic SVs per sample with the use of PCR mini-amplicons. Finally, we demonstrate that these somatic SV biomarkers can be used to detect tumour presence from liquid biopsies in a quantitative manner and we retrospectively monitored treatment response in patients with prostate cancer, demonstrating its potential benefit for clinical practice.

Study EGAS00001003963

Genomics of enteropathy associated T cell lymphoma (EATL)

Enteropathy-associated T cell lymphoma (EATL) is a lethal and the most common neoplastic complication of celiac disease. In this study, we applied whole exome sequencing in 69 EATL tumors to define the genetic landscape of EATLs. The most frequently mutated gene in EATL was SETD2 (32% of cases), with loss of function mutations comprising a large proportion (41%) of those mutations. The JAK-STAT pathway was the most frequently mutated signaling pathway, with mutations in STAT5B being the most common, followed by JAK1, JAK3, STAT3, and the negative regulator of the pathway, SOCS1. We also identified mutations in NRAS and KRAS, as well as TP53 and TERT. Interestingly, the two types of EATL had highly overlapping genetic alterations indicating shared mechanisms underlying their pathogenesis. Gene expression analysis of the two types of EATL identify robust differences in transcriptional profiles. We further modeled the effects of SETD2 loss in vivo by developing a T cell specific knockout mouse model. These mice manifested an expansion of γδ T cells that identify novel roles for SETD2 in T cell development and lymphomagenesis. Together, our data render the most comprehensive genetic portrait yet of this uncommon but lethal disease, and may inform future classification schemes.

Study EGAS00001001954

Comparison of structural variations from 10X Genomics linked-reads and conventional Illumina short-reads sequencing

Structural variations (SVs) are large genomic rearrangements that can drive many diseases. Conventional short-reads whole genome sequencing (cWGS) allows their identification with base-pair resolution, but suffers from high false discovery rate. cWGS taps in short-range information from short-reads while linked-reads sequencing (10XWGS) utilizes long-range information. 10XWGS allows linkage of short-reads originating from the same large DNA molecule with a unique barcode captured in a gel bead in emulsion. This mitigates alignment-based artefacts from cWGS especially in repetitive regions. However, the false discovery rate of this technology is unclear. In this study, we performed a comprehensive analysis of different type and size of SVs predicted from these two technologies. The SVs common between both technologies were found to be highly specific by PCR and Sanger sequencing while validation rate dropped for uncommon events. Further, we propose a novel enrichment approach for filtering out false positive calls from both the technologies independently. To this end, we trained a machine learning model for respective technologies and used it to characterise SVs from MCF7 cell line and a primary breast cancer tumor with high precision. This approach would be valuable in understanding true mechanisms driven by SVs in various diseases.

Study EGAS00001004093

High Grade Serous Ovarian Carcinomas Originate in the Fallopian Tube

High-grade serous ovarian carcinoma (HGSOC) is the most frequent type of ovarian cancer and has a poor outcome. It has been proposed that fallopian tube cancers may be precursors of HGSOC but evolutionary evidence for this hypothesis has been limited. To provide insights into the origins of HGSOC, we We performed whole-exome sequence and copy number analyses of laser-capture microdissected fallopian tube lesions (p53 signatures, serous tubal intraepithelial carcinomas (STICs), and fallopian tube carcinomas), ovarian cancers, and metastases from nine patients with HGSOC. The majority of tumor-specific sequence and structural alterations in ovarian cancers were present in STICs, including those affecting TP53, BRCA1, BRCA2 or PTEN genes. An eEvolutionary analyseis revealed that p53 signatures and STICs were are the precursors of ovarian carcinoma which in turn gave rise to metastatic lesionsand identify a. In one patient we identified a second STIC as a metastasis in the fallopian tube opposite from the affected ovary. These analyses revealed a window of seven years between the development of a STIC and the initiation of ovarian carcinomas, with development of metastases following rapidly thereafter. Our results provide insights into the etiology of ovarian cancer and have implications for the prevention, early detection and therapeutic intervention of this disease.

Study EGAS00001002589

Mapping_gene_environment_interactions_in_macrophages

Immune cells sense and respond to external stimuli such as pathogens and initiate an inflammatory response. Genetic variants altering the behaviour and responses of immune cells may inform the results of disease association studies and provide an insight into the regulation of immune response. Studies mapping quantitative trait loci (QTL) are usually performed in quiescent or naïve cells and therefore any variants with a condition-specific manner (e.g. those with an effect only detectable in a specific time-point after cell stimulation) are likely to remain undiscovered. So far, only a handful of studies have attempted to study QTL in multiple states and even on those studies the number of states has remained relatively low (<5). Only very recently Horst and colleagues published the largest study to date investigating the effect of host variable (e.g. age, sex, contraceptive use etc.) on protein levels in macrophages stimulated with 19 different conditions (Horst et al, 2016). This project aims to develop a high-throughput experimental platform to detect QTL in a large number of states using iPSC derived macrophages. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Study EGAS00001002268

Reconstituting the transcriptome and DNA methylome landscapes of human implantation at single-cell resolution

Implantation is a milestone event during mammalian embryogenesis. Due to the extreme difficulty of obtaining in vivo human early post-implantation embryos, the gene regulatory network and epigenetics controlling human embryo implantation remains elusive. Here, combining an in vitro culture system for human post-implantation development and single-cell omics sequencing technologies, over 10,000 single cells at five representative stages of pre/post-implantation development were systematically analyzed. Unsupervised dimensionality reduction and clustering algorithm of the transcriptome data show stepwise implantation routes for the epiblast, primitive endoderm, and trophectoderm lineages, suggesting preparation for the establishment of a mother-to-offspring connection after implantation. Female embryos showed asynchronous progress of dosage loss of X chromosomes during implantation. Furthermore, using the single cell trio-Seq (scTrio-Seq) strategy, re-methylation of the genomes of all the three lineages was unambiguously revealed. Surprisingly, the genome re-methylation of PE lineage were much slower than both EPI and TE lineages during the implantation process, indicating distinct methylome features between EPI and PE although both of which were derived from ICM. Collectively, our work paves the way for understanding the complex molecular mechanisms that regulate human embryo implantation, informing new insights and future efforts in early embryonic development and reproductive medicine.

Study EGAS00001003443

Comprehensive genomic profiles of small cell lung cancer

We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. We found bi-allelic inactivation of TP53 and RB1 in nearly all the tumors analyzed, sometimes by complex genomic rearrangements. Two tumors with wild-type RB1 had evidence of chromothripsis leading to overexpression of Cyclin D1, revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumor suppressors TP53 and RB1 is obligatory in SCLC. We further discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Δex2/3. In few cases, SCLC tumors exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signaling in a pre-clinical SCLC mouse model dramatically reduced the number of tumors and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.

Study EGAS00001000925

Clonal selection and double hit events involving tumor suppressor genes underlie relapse from total therapy

In order to gain insights into the mechanisms of disease progression in multiple myeloma (MM) patients treated with multi-agent and high-dose chemotherapy we have performed a longitudinal study of 33 patients entered into Total Therapy protocols using gene expression profiling, high resolution copy number analyses and whole exome sequencing. The results of this study show the importance of acquired mutations in MM driver genes, bi-allelic events affecting tumor suppressor genes and increased proliferation rates in driving relapse, which is enhanced by intra-clonal heterogeneity and Darwinian type clonal evolution. Branching was the most frequent evolution pattern, characterized by clonal loss and appearance of new clones. We found a higher number of lost and acquired copy number aberrations and an excess of bi-allelic inactivation of tumor suppressor genes in GEP70 high risk (HiR) cases, consistent with genomic instability being a key feature of HiR MM. In conclusion, our study further stresses the impact of known prognostic markers and driver genes on the fitness level of MM cells to survive multi-agent chemotherapy. The frequent bi-allelic loss of tumor suppressor genes in HiR cases and the potentially resulting failure of treatment with DNA damaging agents highlight the need for new therapies for HiR MM.

Study EGAS00001001810

Ethiopia_Genome_Project__low_coverage_

The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity.This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum.The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.

Study EGAS00001000238

Large-scale viral genome analysis identifies novel clinical associations between hepatitis B virus and chronically infected patients

Despite the high global prevalence of chronic hepatitis B (CHB) infection, datasets covering the whole hepatitis B viral genome from large patient cohorts are lacking, greatly limiting our understanding of the viral genetic factors involved in this deadly disease. We performed deep sequencing of viral samples from patients chronically infected with HBV to investigate the association between viral genome variation and patients’ clinical characteristics. We discovered novel viral variants strongly associated with viral load and HBeAg status. Patients with viral variants C1817T and A1838G had viral loads nearly three orders of magnitude lower than patients without those variants. These patients consequently experienced earlier viral suppression while on treatment. Furthermore, we identified novel variants that either independently or in combination with precore mutation G1896A were associated with the transition from HBeAg positive to negative phase of infection. These observations are consistent with the hypothesis that mutation of the HBeAg open reading frame is an important factor driving CHB patient’s HBeAg status. This analysis provides a detailed picture of HBV genetic variation in the largest patient cohort to date and highlights the diversity of plausible molecular mechanisms through which viral variation affects clinical phenotype.

Study EGAS00001003689

The_Genomic_Advances_in_SepsisGAinSRNA_seq

Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. This cohort comprises a subset of patients enrolled in the Genomic Advances in Sepsis (GAinS) study, an established biobank of adult sepsis patients. Patients with sepsis due to community acquired pneumonia or faecal peritonitis were recruited from 34 hospitals across the UK from 2005-2018, with samples for functional genomics and detailed clinical information collected on the first, third and/or fifth day following ICU admission. RNA was extracted from leukocytes isolated at the bedside using LeukoLOCK kits. We have previously identified sepsis response signatures (SRSs), transcriptomic endotypes that are associated with differential early mortality (Davenport et al, Lancet Respir Med, 2016; Burnham et al, AJRCCM, 2017) and response to treatment in a clinical trial (Antcliffe et al, AJRCCM, 2018). We generated RNA sequencing data on 903 samples, including 134 samples repeated from our previously released microarray data. Libraries were prepared using NEB Ultra II Library Prep kits (Illumina) and sequenced on a NovaSeq 6000. Reads were aligned to the reference genome (GRCh38) using STAR and gene counts quantified using featureCounts (annotation Ensembl v99). Counts were TMM-normalised and log-transformed. Following QC, processed data were available on 864 samples from 667 unique patients.

Study EGAS00001003772

Extreme phenotypes define epigenetic and metabolic signatures in cardiovascular diseases.

Improving the understanding of cardiometabolic syndrome pathophysiology and its relationship with thrombosis are ongoing healthcare challenges. Using plasma biomarkers analysis coupled with the transcriptional and epigenetic characterisation of cell types involved in thrombosis, obtained from two extreme phenotype groups (obese and lipodystrophy) and comparing these to lean individuals and blood donors, the present study identifies the molecular mechanisms at play, highlighting patterns of abnormal activation in innate immune phagocytic cells and shows that extreme phenotype groups could be distinguished from lean individuals, and from each other, across all data layers. The characterisation of the same obese group, six months after bariatric surgery shows the loss of the patterns of abnormal activation of innate immune cells previously observed. However, rather than reverting to the gene expression landscape of lean individuals, this occurs via the establishment of novel gene expression landscapes. Netosis and its control mechanisms emerge amongst the pathways that show an improvement after surgical intervention. Taken together, by integrating across data layers, the observed molecular and metabolic differences form a disease signature that is able to discriminate, amongst the blood donors, those individuals with a higher likelihood of having cardiometabolic syndrome, even when not presenting with the classic features.

Study EGAS00001003780

THE GENOMIC LANDSCAPE OF ACTINIC KERATOSIS

Actinic keratoses (AK) are lesions of epidermal keratinocyte dysplasia and are pre-cursor lesions to invasive cutaneous squamous cell carcinoma (cSCC). Identifying the specific genomic alterations driving the progression of normal skin to AK and invasive cSCC is challenging due to the massive, ultraviolet radiation-induced mutational burden characteristic to these lesions. Here, we present the largest whole exome sequencing study to date on AK with matched cSCC and demonstrate that AK and cSCC are almost indistinguishable at the genomic level, in terms of mutational burden, patterns of driver gene mutations and copy number alterations. We identified 44 significantly mutated AK driver genes through our established bioinformatics pipeline and demonstrate these genes are similarly mutated in cSCC. We also identified mutational signature-32 exclusively in AK from patients exposed to azathioprine, providing further, compelling evidence for this drug’s role in keratinocyte carcinogenesis, likely through its blocking of transcription coupled repair. We demonstrated that cSCC had higher levels of intra-sample heterogeneity than AK and that several signaling pathways, including immune-related signaling and TGF-beta signaling were significantly more mutated in cSCC. Integrating our findings with independent gene expression data confirms that dysregulated TGF-beta signaling may represent the critical pathway in the progression from AK to cSCC.

Study EGAS00001004243

Hypoxia acts as an environmental cue for the human TRM differentiation program

Tissue-resident memory T-cells (TRM) provide frontline defense against infectious diseases and contribute to anti-tumor immunity; however, aside from the necessity of TGF-β, knowledge regarding TRM-inductive cues remains incomplete, particularly for human cells. Oxygen tension is an environmental cue that distinguishes peripheral tissues from the circulation and here, we demonstrate that differentiation of human CD8+ T-cells in the presence of hypoxia and TGF-β1 led to the development of a TRM phenotype, characterized by a greater than five-fold increase in CD69+CD103+ cells expressing human TRM hallmarks and enrichment for endogenous human TRM gene signatures, including increased adhesion molecule expression and decreased expression of genes involved in recirculation. Hypoxia and TGF-β1 synergized to produce a significantly larger population of TRM phenotype cells than either condition alone, and comparison of these cells from the individual and combination conditions revealed distinct phenotypic and transcriptional profiles, indicating a programming response to milieu rather than a mere expansion. Our findings identify a previously unreported cue for the TRM differentiation program and can enable facile generation of human TRM phenotype cells in vitro for basic studies and translational applications such as adoptive cellular therapy.

Study EGAS00001005286

The Molecular Landscape of Asian Breast Cancers Reveals Clinically Relevant Population-Specific Differences

Molecular profiles of breast cancer have contributed to an improved understanding of the disease, enabled development of molecular prognostic signatures to guide treatment decisions and unveiled new or more accurate therapeutic options for breast cancer patients. However, the extent to which differences in genetic, environmental and lifestyle factors influence molecular profiles in different populations remains poorly characterised, as relatively few large-scale molecular studies of breast tumours in non-Caucasian populations have hitherto been reported. Here, we present the molecular profiles of 560 Asian breast tumours and a comparative analysis of breast cancers arising in Asian and Caucasian women. Compared to the breast tumours in predominantly Caucasian women reported in TCGA and METABRIC, we show an increased prevalence of Her2-enriched molecular subtypes and higher prevalence of TP53 somatic mutations in ER+ Asian breast tumours. Using gene expression and immunohistochemistry, we observed elevated immune scores in Asian breast tumours, suggesting potential clinical response to immune checkpoint inhibitors. Whilst Her2-subtype and enriched immune score are associated with improved survival, presence of TP53 somatic mutations is associated with poorer survival in ER+ tumours. Taken together, these population differences unveil new opportunities to improve the understanding of this disease and lay the foundation for precision medicine in different populations.

Study EGAS00001004518

Whole genome, exome and transcriptome analysis to guide individualized cancer interpretation

Study Design: The Cancer Alliance study was a collaboration of nine academic medical institutions in the New York city area and led by the New York Genome Center. Tumor-normal paired samples were submitted by the institutions for whole genome, whole exome and transcriptome sequencing and bioinformatics analysis at New York Genome Center. Relevant clinical histories were also collected. Raw sequence files were available to all collaborators. Variant call files were analyzed both manually by interpreters at NYGC and by IBM Watson Genome Analytics. This study was approved by a central institutional review board (IRB), Biomedical Research Alliance of New York, and by local IRBs, including Stony Brook University and Northwell Health. The study was supported in part by a grant from the IBM corporation (IBM Watson Health) to the New York Genome Center, New York Genome Center philanthropic funds and Rockefeller University grant # UL1TR000043 from the National Center for Advancing Translational Sciences (NCATS), and the National Institutes of Health (NIH) Clinical and Translational Science Award (CTSA) program. The principal investigator Robert B. Darnell MD, PhD., is a Howard Hughes Medical Institute Investigator. Results: Pending Publication of Analysis of Study Conclusions: Pending Publication of Analysis of Study

Study EGAS00001004013

A recessive PRDM13 mutation results in congenital hypogonadotropic hypogonadism and cerebellar hypoplasia

The PRDM13 (PR Domain containing 13) putative chromatin modifier and transcriptional regulator functions downstream of the transcription factor PTF1A, which controls GABAergic fate in the spinal cord and neurogenesis in the hypothalamus. Here, we report a novel, recessive syndrome associated with PRDM13 mutation. Patients exhibited intellectual disability, ataxia with cerebellar hypoplasia, scoliosis and delayed puberty with congenital hypogonadotropic hypogonadism (CHH). Expression studies revealed Prdm13/PRDM13 transcripts in the developing hypothalamus and cerebellum in mouse and human. An analysis of hypothalamus and cerebellum development in mice homozygous for a Prdm13 mutant allele revealed a significant reduction in the number of Kisspeptin (Kiss1) neurons in the hypothalamus and PAX2+ progenitors emerging from the cerebellar ventricular zone. The latter was accompanied by ectopic expression of the glutamatergic lineage marker TLX3. Prdm13-deficient mice displayed cerebellar hypoplasia, normal gonadal structure, but delayed pubertal onset. Together, these findings identify PRDM13 as a critical regulator of GABAergic cell fate in the cerebellum and of hypothalamic kisspeptin neuron development, providing a mechanistic explanation for the co-occurrence of CHH and cerebellar hypoplasia in this syndrome. To our knowledge, this is the first evidence linking disrupted PRDM13-mediated regulation of Kiss1 neurons to CHH in humans.

Study EGAS00001005878

Comprehensive Genomic Characterization of Refractory Multiple Myeloma Reveals a Complex Mutational and Structural Landscape Associated with Drug Resistance (H067)

Outcome of patients with multiple myeloma (MM) refractory to immunomodulatory agents (IMiDs) and proteasome inhibitors (PIs) is still very poor. To elucidate the genetic landscape of relapsed/refractory MM (RRMM) we performed whole genome and transcriptome sequencing of 39 heavily pretreated RRMM patients with at least double refractoriness revealing complex structural changes and a high mutational load (H067/K08K). We found a median of 67 structural variants and 116 nonsynonymous exonic mutations per patient. Assessment of oncogenic drivers showed NRAS, BRAF, TP53, KRAS, SLC4A7, FAM46C, DIS3, RB1, KMT2C, MLLT4, EWSR1, HCFC2, and COPS3 as significantly mutated. We found multiple genomic regions with bi-allelic events affecting known tumor suppressor genes, most frequently TP53, RB1, and TRAF3. Supervised analysis of mutational signatures showed a major contribution of Cosmic signature 6 associated with deficiency in DNA mismatch repair and the ‘BRCAness’ signature which coincided with mutations in genes known to confer PARP inhibitor sensitivity. Recurrently mutated gene networks included genes with relevance for PI and IMiD activity, the latter including in particular members of the Cereblon and the COP9 signalosome complex. In conclusion, this comprehensive genomic characterization revealed a complex mutational and structural landscape in RRMM and highlights potential implications for therapeutic strategies.

Study EGAS00001004363

Multi-omics integration reveals only minor long-term molecular and functional sequelae in immune cells of individuals recovered from COVID-19

The majority of COVID-19 patients experience mild to moderate disease course and recover within a few weeks. An increasing number of studies characterized the long-term changes in the specific anti-SARS-CoV-2 immune responses, but how COVID-19 shapes the innate and heterologous adaptive immune system after recovery is less well known. To comprehensively investigate the post-SARS-CoV-2 infection sequelae on the immune system, we performed a multi-omics study by integrating single-cell RNA-sequencing, single-cell ATAC-sequencing, genome-wide DNA methylation profiling, and functional validation experiments in convalescent COVID-19 and healthy individuals. We showed that immune responses generally recover without major sequelae after COVID-19. However, subtle differences persist at the transcriptomic level in monocytes, with downregulation of the interferon pathway, while DNA methylation also displays moderate changes in convalescent COVID-19 individuals. However, these differences did not affect the cytokine production capacity of PBMCs upon different bacterial, viral, and fungal stimuli, although baseline release of IL-1RA and IFN?? was higher in convalescent individuals. In conclusion, despite minor differences in epigenetic and transcriptional programs, the immune system of convalescent COVID-19 patients largely recovers to the homeostatic level of healthy individuals.

Study EGAS00001005529

Proteogenomics of chronic lymphocytic leukemia

Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterized the proteome and transcriptome in-depth alongside genetic and ex-vivo drug response profiling in a clinically well annotated CLL discovery cohort (n= 68). Unsupervised clustering of the proteome data revealed six subgroups. Five of these proteomic groups were associated with genetic features, while one group was only detectable at the proteome level. This new group was characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). We developed classifiers to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n= 165, n= 169) and confirmed that ASB-CLL comprises about 20 % of CLL patients. The inferior overall survival observed in ASB-CLL was independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling. This is the transcriptomics data of the discovery cohort.

Study EGAS00001005746

Whole genome sequencing delineates regulatory, structural, and cryptic splice variants in early onset cardiomyopathy

Cardiomyopathy (CMP) is a heritable disorder. Over 50% cases are gene-elusive on clinical gene panel testing. The contribution of variants in non-coding DNA elements that result in cryptic splicing and regulate gene expression has not been explored. We analyzed whole genome sequencing (WGS) data in a discovery cohort of 209 pediatric CMP patients and 1,953 independent replication genomes and exomes. We searched for protein-coding variants, and non-coding variants predicted to affect the function or expression of genes. Thirty-nine % cases harbored pathogenic coding variants in known CMP genes, and 5% harbored high-risk loss-of-function (LoF) variants in additional candidate CMP genes. Fifteen % harbored high-risk regulatory variants in promoters and enhancers of CMP genes (Odds ratio 2.25, p=6.70×10-7 versus controls). Genes involved in α-dystroglycan glycosylation (FKTN, DTNA) and desmosomal signaling (DSC2, DSG2) were most highly enriched for regulatory variants (Odds ratio 6.7-58.1). Functional effects were confirmed in patient myocardium and reporter assays in human cardiomyocytes, and in zebrafish CRISPR knockouts. We provide strong evidence for the genomic contribution of functionally active variants in new genes and in regulatory elements of known CMP genes to early-onset CMP.

Study EGAS00001004929

Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

Molecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), were missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we used Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis revealed genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells (MDCs). Importantly, we detected heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observed remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies.

Study EGAS00001004943

Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation

Accurate assessment of treatment response and residual disease is indispensable for the evaluation of cancer treatment efficacy. However, performing tissue biopsies for longitudinal follow-up poses a major challenge in the management of solid tumours like neuroblastoma. In the present study, we evaluated whether circulating miRNAs are suitable to monitor neuroblastoma tumour burden and whether treatment-induced changes of miRNA abundance in the tumour are detectable in serum. We performed small RNA sequencing on longitudinally collected serum samples from mice carrying orthotopic neuroblastoma xenografts that were exposed to treatment with idasanutlin or temsirolimus. We identified 57 serum miRNAs to be differentially expressed upon xenograft tumour manifestation, out of which 21 were also found specifically expressed in the serum of human high-risk neuroblastoma patients. The murine serum levels of these 57 miRNAs correlated with tumour tissue expression and tumour volume, suggesting potential utility for monitoring tumour burden. In addition, we describe serum miRNAs that dynamically respond to p53 activation following treatment of engrafted mice with idasanutlin. We identified idasanutlin-induced serum miRNA expression changes upon one day and 11 days of treatment. By limiting to miRNAs with a tumour-related induction, we put forward hsa-miR-34a-5p as a potential pharmacodynamic biomarker of p53 activation in serum.

Study EGAS00001006678

T cell landscape definition by multi-omics identifies galectin-9 as novel immunotherapy target in chronic lymphocytic leukemia (CLL)

Failure of immunotherapy after applying checkpoint inhibitors or CAR-T cells is linked to T cell exhaustion. Here, we explored the T cell landscape in chronic lymphocytic leukemia (CLL) by single-cell omics analyses of blood, bone marrow and lymph node samples of patients and spleen samples of a CLL mouse model. By single-cell RNA- sequencing, mass cytometry (CyTOF), and multiplex image analysis of tissue microarrays, we defined the spectrum of phenotypes and transcriptional programs of T cells and and their differentiation state trajectories. We identified disease-specific accumulation of distinct regulatory T cell subsets and T cells harboring an exhausted phenotype exclusively in the CLL lymph node tissue. Integration of TCR data revealed a clonal expansion of CD8+ precursor exhausted T cells, suggesting their reactivity for CLL cells. Interactome analyses identified the TIM3 ligand Galectin-9 as novel immunoregulatory molecule in CLL. Blocking of Galectin-9 in CLL-bearing mice slowed down disease development and reduced the number of TIM3 expressing T cells. Galectin-9 expression correlated with shorter survival of CLL patients. Thus, Galectin-9 contributes to immune escape in CLL and represents a novel target for immunotherapy.

Study EGAS00001006864

Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities WGS

Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically uniquely defined by alterations in the SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be further classified in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT-MYC and ATRT-SHH subgroups. Whereas ATRT-MYC universally displayed high sensitivity to multi-targeted tyrosine kinase inhibitors, ATRT-SHH showed a more heterogeneous response with a subset showing high sensitivity to Notch inhibitors, which corresponded to high expression of Notch receptors. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing a representative pre-clinical model which enables the development of subgroup-specific therapies.

Study EGAS00001006865

Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities RNA-Seq

Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically uniquely defined by alterations in the SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be further classified in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT-MYC and ATRT-SHH subgroups. Whereas ATRT-MYC universally displayed high sensitivity to multi-targeted tyrosine kinase inhibitors, ATRT-SHH showed a more heterogeneous response with a subset showing high sensitivity to Notch inhibitors, which corresponded to high expression of Notch receptors. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing a representative pre-clinical model which enables the development of subgroup-specific therapies.

Study EGAS00001006866

Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities DNA-Methylation

Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically uniquely defined by alterations in the SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be further classified in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT-MYC and ATRT-SHH subgroups. Whereas ATRT-MYC universally displayed high sensitivity to multi-targeted tyrosine kinase inhibitors, ATRT-SHH showed a more heterogeneous response with a subset showing high sensitivity to Notch inhibitors, which corresponded to high expression of Notch receptors. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing a representative pre-clinical model which enables the development of subgroup-specific therapies.

Study EGAS00001006881

Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection

SARS-CoV-2 vaccine immunogenicity varies between individuals, and immune responses correlate with vaccine efficacy. Using data from 1,076 participants enrolled in ChAdOx1 nCov-19 vaccine efficacy trials in the United Kingdom, we find that inter-individual variation in normalised antibody responses against SARS-CoV-2 spike (S) and its receptor binding domain (RBD) at 28 days following first vaccination shows genome-wide significant association with major histocompatibility complex (MHC) class II alleles. The most statistically significant association with higher levels of anti-RBD antibody was HLA-DQB1*06 (P=3.2 x 10-9), which we replicate in 1,677 additional vaccinees. Individuals carrying HLA-DQB1*06 alleles were less likely to experience PCR-confirmed breakthrough infection during the Wuhan and Alpha-variant waves compared to non-carriers (HR 0.63, 0.42-0.93, P=0.02). We identify a distinct S-derived peptide that is predicted to bind effectively to HLA-DQB1*06 compared to other equivalent alleles, and find evidence of increased spike-specific memory B-cell responses in HLA-DQB1*06 carriers at 84 days post first vaccination. Our results demonstrate association of HLA type with COVID-19 vaccine antibody response and risk of breakthrough infection, with implications for future vaccine design and implementation.

Study EGAS00001006909

Long-term organoid culture of a small intestinal neuroendocrine tumor rna-seq

Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare and highly heterogeneous neoplasms whose incidence has markedly increased over the last decades. A grading system based on the tumor cells' proliferation index predicts high-risk for G3 NETs. However, low-to-intermediate grade (G1/G2) NETs have an unpredictable clinical course that varies from indolent to highly malignant. Cultures of human cancer cells enable to perform functional perturbation analyses that are instrumental to enhance our understanding of cancer biology. To date, no tractable and reliable long-term culture of G1/G2 NET has been reported to permit disease modeling and pharmacological screens. Here, we report of the first long-term culture of a G2 metastatic small intestinal NET that preserves the main genetic drivers of the tumor and retains expression patterns of the endocrine cell lineage. Replicating the tissue, this long-term culture showed a low proliferation index, and yet it could be propagated continuously without dramatic changes in the karyotype. The model was readily available for pharmacological screens using targeted agents and as expected, showed low tumorigenic capacity in vivo. Overall, this is the first long-term culture of NETs to faithfully recapitulate many aspects of the original neuroendocrine tumor.

Study EGAS00001007108

Patient-derived pediatric brain tumor organoids faithfully recapitulate primary tumors

Extensive molecular analysis by many groups has revealed a heterogeneous landscape of embryonal brain tumors, including medulloblastoma (MB) and atypical teratoid/rhabdoid tumor (ATRT). MB, the most common malignant pediatric brain tumor, is comprised of four molecularly distinct subgroups: Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3), and Group 4 (G4). Among these, MB-SHH harboring MYCN amplification and TP53 mutation and MB-G3 with MYC overexpression or amplification constitute the most aggressive tumors, have the poorest clinical outcomes, and lack effective therapeutic options for recurrent disease. Here we describe the establishment of tumor organoid (TO) models from patient-derived orthotopic xenografts (PDOX) of MYCN-amplified and TP53-mutant MB-SHH, MYC-amplified MB-G3 and two ATRT which all grew in mice when reimplanted into the cortices of naïve recipient animals (TOX). Methylation, bulk and single-cell RNA sequencing, and whole genome sequencing demonstrated that TOs and TOXs faithfully recapitulated the molecular landscape and heterogeneity of PDOXs and primary patient tumors compared to established cell lines. The development of TOs will facilitate in vitro high-throughput drug or CRISPR screens without the need for use tumor-bearing mice. This will also accelerate the identification and validation of new vulnerabilities and in vivo preclinical testing toward clinical trials.

Study EGAS00001008305

Long-term organoid culture of a small intestinal neuroendocrine tumor

Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare and highly heterogeneous neoplasms whose incidence has markedly increased over the last decades. A grading system based on the tumor cells' proliferation index predicts high-risk for G3 NETs. However, low-to-intermediate grade (G1/G2) NETs have an unpredictable clinical course that varies from indolent to highly malignant. Cultures of human cancer cells enable to perform functional perturbation analyses that are instrumental to enhance our understanding of cancer biology. To date, no tractable and reliable long-term culture of G1/G2 NET has been reported to permit disease modeling and pharmacological screens. Here, we report of the first long-term culture of a G2 metastatic small intestinal NET that preserves the main genetic drivers of the tumor and retains expression patterns of the endocrine cell lineage. Replicating the tissue, this long-term culture showed a low proliferation index, and yet it could be propagated continuously without dramatic changes in the karyotype. The model was readily available for pharmacological screens using targeted agents and as expected, showed low tumorigenic capacity in vivo. Overall, this is the first long-term culture of NETs to faithfully recapitulate many aspects of the original neuroendocrine tumor.

Study EGAS00001007093

Transcriptomics identifies blunted immunomodulatory effects of vitamin D in people with multiple sclerosis

Vitamin D deficiency is a risk factor for developing multiple sclerosis (MS). However, the immune effects of vitamin D in people with MS are not well understood. We analyzed transcriptomic datasets generated by RNA sequencing of immune cell subsets (CD4+, CD8+ T cells, B cells, monocytes) from 33 healthy controls and 33 untreated MS cases. We utilized a traditional bioinformatic pipeline and weighted gene co-expression network analysis (WGCNA) to determine genes and pathways correlated with endogenous vitamin D. In controls, CD4+ and CD8+ T cells had 1079 and 1188 genes, respectively, whose expressions were correlated with plasma 25-hydroxyvitamin D level (P<0.05). Functional enrichment analysis identified association with TNF-alpha and MAPK signaling. In CD4+ T cells of controls, vitamin D level was associated with expression levels of several genes proximal to multiple sclerosis risk loci (P=0.01). Genes differentially associated with endogenous vitamin D by case-control status were enriched in TNF-alpha signaling via NF-κB. WGCNA suggested a blunted response to vitamin D in cases relative to controls. Collectively, our findings provide further evidence for the immune effects of vitamin D, and demonstrate a differential immune response to vitamin D in cases relative to controls, highlighting a possible mechanism contributing to MS pathophysiology.

Study EGAS00001007254

Targeting TRIP13 in Wilms Tumor with Nuclear Export Inhibitors

Wilms tumor (WT) is the most common renal malignancy of childhood. Despite improvements in the overall survival, relapse occurs in ~15% of patients with favorable histology WT (FHWT). Half of these patients will succumb to their disease. Identifying novel targeted therapies in a systematic manner remains challenging in part due to the lack of faithful preclinical in vitro models. We established ten short-term patient-derived WT cell lines and characterized these models using low-coverage whole genome sequencing, whole exome sequencing and RNA-sequencing, which demonstrated that these ex-vivo models faithfully recapitulate WT biology. We then performed targeted RNAi and CRISPR-Cas9 loss-of-function screens and identified the nuclear export genes (XPO1 and KPNB1) as strong vulnerabilities. We observed that these models are sensitive to nuclear export inhibition using the FDA approved therapeutic agent, selinexor (KPT-330). Selinexor treatment of FHWT suppressed TRIP13 expression, which was required for survival. We further identified in vitro and in vivo synergy between selinexor and doxorubicin, a chemotherapy used in high risk FHWT. Taken together, we identified XPO1 inhibition with selinexor as a potential therapeutic option to treat FHWTs and in combination with doxorubicin, leads to durable remissions in vivo.

Study EGAS00001007389

Cancer Genetic Markers of Susceptibility (CGEMS) Prostate Cancer Genome-Wide Association Study (GWAS) - Primary Scan (Stage 1) - PLCO Screening Trial

The Cancer Genetic Markers of Susceptibility (CGEMS) prostate cancer genome-wide association study (GWAS) included genotyping approximately 550,000 SNPs (Phase 1A with HumanHap300 and Phase 1B HumanHap240, both from Illumina, San Diego, CA) in 1,172 prostate cancer patients and 1,157 controls of European ancestry from the Prostate, Lung, Colon and Ovarian (PLCO, http://www.cancer.gov/prevention/plco/) Cancer Screening Trial. The original analysis published in Nature Genetics [PMID: 17401363] included 2,282 subjects. After improvement and revisions of the original analysis, 2,252 subjects were submitted to dbGaP.

Study phs000207

SUM-seq data for spontaneously differentiated iPSCs to EBs

Clonal CRISPRi/a hiPS cell lines were plated to induce spontaneous differentiation in KSR medium (KSR medium: knockout DMEM/F12 (Gibco, 12660012), 2 mM GlutaMAX, 1× NEAAs, 20% knockout serum replacement (Gibco, 10828010) and 0.1 mM β-mercaptoethanol (Merck-Millipore)). non-TC plates and dishes were used. At the day of plating, KSR medium was supplemented with Y-27632 (10 µM). The next day, medium was replaced with fresh KSR medium. Medium changes were performed every other day. EBs were transferred to 15 ml conical tubes and allowed to sediment at room temperature for 5 min. The supernatant was replaced with fresh KSR medium and cells were transferred onto non-TC treated plates and maintained at 37 °C, 5% CO2. On day 12 of differentiation, the KSR medium was replaced with Essential 6 medium (Gibco, A1516401). EBs were collected and subjected to SUM-seq library preparation as described in Lobato-Moreno et al. 2025 Nature Methods.

Dataset EGAD50000001589

Estonian Microbiome Project second time point dataset

Out of the 2,509 Estonian Microbiome Project participants, a sub-cohort of over 300 individuals provided an additional stool sample after a median follow-up period of 4.4 years. All participants of the EstMB cohort gave informed consent for the data and samples to be used for scientific purposes. In the second time point, the participants were instructed to send the samples by post immediately after taking the sample and time their sample collection to avoid shipping on the weekends. The median time between sampling and arrival at the freezer in the core facility for the second time point was 53 hours and 1 minute (mean: 59 hours and 22 minutes; minimum: 34 minutes; maximum: 168 hours and 7 minutes [note: additionally, one outlying measurement was 508 hours and 27 minutes. The shotgun metagenomics paired-end sequencing was performed by Novogene Bioinformatics Technology Co., Ltd., using Illumina NovaSeq6000 platform, resulting in 4.62 ± 0.44 Gb of data per sample (insert size 350 bp, read length 2 × 250 bp).

Dataset EGAD50000001686

Single-cell RNA sequencing of control and Notch inhibitor treated HCC PDX model

We generated single-cell RNA-seq data for anti-Notch2 (n=3), anti-JAG1 (n=1) and anti-gD (n=4) treated LIV78 tumors. NCR nude mice bearing similarly sized LIV78 tumors (volumes between 300-900mm3) were injected intravenously with 30mg/kg body weight of either anti-Notch2, anti-Jag1 or anti-gD control antibody 72hrs prior to tumor harvest and tumor cell isolation. Following the depletion of CD45+ and Ter119+ cells, the samples were processed for single-cell RNA-seq (scRNAseq) as described previously (Long et al., 2019) using the Chromium Single Cell 3’ Library and Gel bead kit v2, following the manufacturer’s manual. cDNAs and libraries were prepared following the manufacturer’s manual (10X Genomics). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq 2500 (Illumina) following the manufacturer’s sequencing specification (10X Genomics) to produce the resulting FASTQ files.

Dataset EGAD50000000738

Somatic mutation in edited cholangiocyte organoids

Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.

Dataset EGAD00001015455

Autozygosity pilot - Born in Bradford (2017-05-11)

The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing cohort samples from the Born In Bradford study will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples. This dataset contains all the data available for this study on 2017-05-11.

Dataset EGAD00001003329

The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

Telomere fusions (TFs) can trigger the accumulation of oncogenic alterations leading to malignant transformation and drug resistance. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancers remains limited. Here, we characterize the rates and spectrum of somatic TFs across >30 cancer types using whole-genome sequencing data. TFs are pervasive in human tumours with rates varying markedly across and within cancer types. In addition to end-to-end fusions, we find novel patterns of TFs that we mechanistically link to the activity of the alternative lengthening of telomeres (ALT) pathway. We show that TFs can be detected in the blood of cancer patients, which enables cancer detection with high specificity and sensitivity even for early-stage tumours and cancers of high unmet clinical need. Overall, we report a novel genomic footprint that enables characterization of the telomere maintenance mechanism of tumours and liquid biopsy analysis.

Dataset EGAD00001012101

RNA sequencing in primary inflammatory (TPP) macrophages following deletion of a disease-associated gene desert at chr21q22, disruption of ETS2, or treatment of ETS2-edited macrophages with a HIF1α stabiliser.

This dataset comprises raw RNA sequencing data (FASTQs) from primary inflammatory (TPP) macrophages that were unedited (non-targeting control, NTC), edited to delete the disease-associated chr21q22 enhancer region (n=5), or edited to disrupt ETS2 with 1 of 2 independent gRNAs (n=9). We also performed RNA-sequencing in NTC or ETS2-edited TPP macrophages that were treated for 12 hours with vehicle (DMSO) or roxadustat (30 uM, n=3). Macrophages were detached using Accutase and lysed. RNA was extracted from cell lysates using an AllPrep DNA/RNA Mini Kit (Qiagen). Sequencing libraries were prepared from 10ng RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s instructions. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 and the libraries were sequenced on a NextSeq500. Raw data are provided as 50 bp paired-end Illumina reads.

Dataset EGAD00001011338

Single cell transcriptomes of childhood renal tumours

This data set contains single cell transcriptomes generated using the chromium 10X platform from both fresh cells and nuclei. The samples measured are derived from children with Wilms tumour, Clear Cell Sarcoma of the Kidney (CCSK), or Malignant Rhabdoid Tumours.

Dataset EGAD00001007572

Whole-genome sequence data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

Each tumor sample was cut into three pieces, yielding two end-pieces for cryovials and a middle portion placed in 10% buffered formalin. End pieces were homogenized manually and with a paddle blender (Stomacher). All paraffin-embedded blocks, including formalin-fixed tumor samples and molecular-fixed fallopian tubes, were sectioned and stained with hematoxylin and eosin prior to expert histopathological review to confirm the presence of high grade serous carcinoma. Homogenized end pieces were then flash frozen and later used for WGS. For all tumor and matched normal (peripheral blood) samples, DNA was extracted with the Qiagen AllPrep DNA/RNA kit (tumor samples from patients 25,26,28-32) or the Qiagen Blood and Tissue Extraction Kit (tumor samples from patients 1-4,7,9-17, and all blood samples). For all tumor and normal samples, DNA extraction was followed by library construction and sequencing using Illumina HiSeq2500 whole genome shotgun v4 chemistry with paired-end 125bp reads.

Dataset EGAD00001003984

Somatic mutation in edited cholangiocyte organoids

Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.

Dataset EGAD00001015457

Single cell transcriptional evolution of myeloid leukaemia of Down syndrome – WGS

Abstract: Children with Down syndrome have a 150-fold increased risk of developing myeloid leukaemia (ML-DS). Unusually for a childhood leukaemia, ML-DS arises from a preleukaemic state, termed transient abnormal myelopoiesis (TAM), and via a conserved sequence of mutations. Here, we examined the relationship between the genetic and transcriptional evolution of ML-DS from a rich collection of primary patient samples through single cell mRNA sequencing, complemented by phylogenetic analyses in progressive disease. We distilled the transcriptional consequence of each genetic step in the evolution of ML-DS, showing that TAM-defining GATA1 mutations account for most of the ML-DS transcriptome, including those of progressive disease. This transcriptional backbone may thus represent a common vulnerability in ML-DS. We extracted the transcriptional difference between TAM and ML-DS which, unexpectedly, reflected features shared across childhood leukaemia. Our approach delineates the transcriptional evolution of ML-DS and provides an analytical blueprint for distilling consequences of mutations directly from patient samples.

Dataset EGAD00001015453

A Heterozygous Missense Mutation in the Coiled-Coil Domain of STAT5B is Associated with Leukocytosis, Lymphadenopathy, Splenomegaly, Necrotizing Granulomas, Hyper-IgM and Thrombocytopenia

We describe one patient with a heterozygous missense mutation in the coiled-coil domain of STAT5B. This patient presented with leukocytosis, lymphadenopathy, splenomegaly, necrotizing granulomas, hyper-IgM and autoimmune thrombocytopenia. Mutant STAT5B protein was shown to dominantly-interfere with IL2-induced transcriptional activity resulting in global downregulation of STAT5-regulated genes in patient T cells. The patient exhibited an increase in CD4+ T effector memory cells in the peripheral blood and these cells were resistant to restimulation-induced cell death in vitro.

Study phs001479

16S rRNA gene V4 region sequencing data, ASV profiles, and sample metadata of human faecal samples predominantly from the Estonian population

This dataset comprises 16S rRNA gene V4 region amplicon sequencing data generated from 1,826 human faecal samples, predominantly from the Estonian population. The dataset includes raw sequencing reads and processed amplicon sequence variant (ASV) outputs, consisting of ASV abundance tables, representative ASV sequences, and taxonomic assignments. In addition, a sample metadata table is provided, containing sample and host information, including sample identifier, sequencing run identifier, date of sampling, sex, age, height, weight, nationality, disease status, and Bristol stool type. Sequencing was performed using the Illumina MiSeq and iSeq 100 platforms. The cohort includes individuals with no reported disease (n = 889), gastrointestinal diseases (n = 217), allergies and asthma (n = 194), thyroid gland disorders (n = 117), cardiovascular diseases (n = 103), various general health conditions (n = 139), cancer (n = 28), diabetes (n = 20), gynaecological issues (n = 7). Disease status was unavailable for 112 samples.

Dataset EGAD50000002306

Whole-genome methylation profiling of menstrual stem cells identifies novel biomarkers for endometriosis

Endometriosis, despite its high prevalence, is underdiagnosed and poorly managed due to lack of clinically validated biomarkers and pathophysiological insight. Menstrual bloodderived stem cells (MenSCs) have been implicated in disease pathogenesis, but their diagnostic potential remains unexplored. We conducted a clinical study (n=42; 19 endometriosis, 23 controls) to assess whether DNA methylation profiles of freshly isolated MenSCs can identify disease-specific biomarkers. Whole-genome methylation sequencing revealed differentially methylated regions (DMRs) enriched in genes linked to hallmarks of endometriosis (e.g., inflammation, tissue remodelling, development). These DMRs robustly distinguished cases from controls, independent of technical and clinical variables. Machine learning models trained and validated on these DMRs achieved high diagnostic performance (specificity 83%, sensitivity 79%). Integration with an independent single-cell RNA sequencing dataset showed that the DMRs may modulate gene expression, further supporting their biological relevance. These findings position MenSC DNA methylation profiling as a promising, non-invasive approach for early endometriosis diagnosis and personalised care.

Dataset EGAD50000002353

DRIP-seq data for Molecular Characterization of ETMRs

This dataset contains DRIP-seq data from 2 patients. DNA–RNA hybrids were extracted from tissue derived from ETMR patient-derived xenograft (PDX) models (BT183) that were treated using topotecan or saline as described previously27. Tumours were subsequently frozen and pelleted using ultracentrifugation. DNA–RNA hybrids were extracted as described previously using the same protocol that is applied for cultured cells21. DNA was extracted using proteinase K followed by phenol–chloroform extraction and ethanol precipitation. Subsequently the DNA was fragmented using the restriction enzymes HindIII, EcoRI, BsrGI, XbaI and SspI (New England Biolabs). Digested DNA was subsequently incubated with the anti-DNA–RNA hybrid anti- body S9.6 (Merck, MABE1095) and immunoprecipitated using agarose beads. Bound DNA–RNA hybrids were eluted and incubated with pro- teinase K and cleaned with an additional phenol–chloroform–ethanol extraction. The DNA was subsequently sonicated and sequenced using a Hiseq 2000 machine with a 50-bp single-read protocol. Each treat- ment condition was performed in duplicate and both RNase H and the input was included as negative controls resulting in 10 Fastq files.

Dataset EGAD00001006219

WGS dataset of Characterization of UV DNA damage in B-cell precursor acute lymphoblastic leukemia

We characterized B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients that present with the mutational signature SBS7a. We found clear subtype specificity, but presence of SBS7a did not seem linked to heterogeneity within subtypes. To further distinguish the incidence of SBS7a in pediatric cancer we analyzed a pan-cancer WGS cohort and identified frequent SBS7a in anaplastic large cell lymphomas. As SBS7a is commonly found in skin cancers and has been linked to UV-light induced DNA damage, we compared the features of UV-light induced DNA damage in skin cancer and SBS7a in ALL, and found high similarity. We found no defects in UV damage response pathways in SBS7a-positive samples, indicating no additional UV vulnerability. Additionally, transcriptomic data showed no differences between samples with and without SBS7a. Finally we looked into the moment of exposure to the source of SBS7a by deep sequencing of diagnosis-relapse pairs and single cell whole genome sequencing of diagnosis samples with high SBS7a.

Dataset EGAD00001015600

Co-amplification of MYC and CCNE1 in aggressive childhood osteosarcoma

Osteosarcoma, the most common primary malignant tumour of bone, affects children and adults alike. No fundamental biological differences between paediatric and adult osteosarcoma are known. Here, we apply multi-region whole genome sequencing to an index case of a four-year old child whose aggressive tumour harboured high level, focal amplifications of MYC and CCNE1 connected by translocations. We re-analysed copy number readouts of 258 cases of high-grade osteosarcoma from three different cohorts and identified an additional three cases with MYC and CCNE1 co-amplification, confined to children and associated with aggressive disease. Examining the age distribution of MYC and CCNE1 amplicons across all cases revealed a significant enrichment of focal MYC amplification in children, whereas CCNE1 amplification is not strictly restricted to children. Our findings indicate that amplification of the MYC oncogene, known to be associated with a poor outcome, delineates a variant of osteosarcoma specific to childhood. When co-amplified with CCNE1, it may herald an aggressive disease course.

Dataset EGAD00001006859

Integrated genomic characterization of adrenocortical carcinoma

Adrenocortical carcinomas (ACC) are aggressive cancers originating in the cortex of the adrenal glands. Despite the overall poor prognosis, ACC outcome is heterogeneous. CTNNB1 and TP53 mutations are frequent in these tumors, but the complete spectrum of genetic changes remains undefined. Exome sequencing and SNP array analysis of 45 ACC revealed recurrent alterations in known drivers (CTNNB1, TP53, CDKN2A, RB1, MEN1) and genes not previously reported to be altered in ACC (ZNRF3, DAXX, TERT and MED12), which were validated in an independent cohort of 77 ACC. The cell-surface transmembrane E3 ubiquitin ligase ZNRF36 was the gene the most frequently altered (21%), and appears as a potential novel tumor suppressor gene related to the ß-catenin pathway.Our integrated genomic analyses led to the identification of two distinct molecular subgroups with opposite outcome. The C1A group of poor outcome ACC was characterized by numerous mutations and DNA methylation alterations, whereas the C1B group with good prognosis displayed a specific deregulation of two miRNA clusters. Thus, aggressive and indolent ACC correspond to two distinct molecular entities, driven by different oncogenic alterations.

Dataset EGAD00001000764

A practical guide for mutational signature analysis in hematological malignancies

Analysis of mutational signatures is becoming routine in cancer genomics, with implications for pathogenesis, classification, prognosis, and even treatment decisions. However, the field lacks a consensus on analysis and result interpretation. Using whole-genome sequencing of multiple myeloma (MM), chronic lymphocytic leukemia (CLL) and acute myeloid leukemia, we compare the performance of public signature analysis tools. We describe caveats and pitfalls of de novo signature extraction and fitting approaches, reporting on common inaccuracies: erroneous signature assignment, identification of localized hyper-mutational processes, overcalling of signatures. We provide reproducible solutions to solve these issues and use orthogonal approaches to validate our results. We show how a comprehensive mutational signature analysis may provide relevant biological insights, reporting evidence of c-AID activity among unmutated CLL cases or the absence of BRCA1/BRCA2-mediated homologous recombination deficiency in a MM cohort. Finally, we propose a general analysis framework to ensure production of accurate and reproducible mutational signature data.

Dataset EGAD00001005028

Mechanisms of patient response to Dabrafenib in Melanoma

Samples will be from the BRF113683 (BREAK-3) study which is a Phase III Randomized, Open-label Study Comparing GSK2118436 to Dacarbazine (DTIC) in Previously Untreated Subjects With BRAF Mutation Positive Advanced (Stage III) or Metastatic (Stage IV) Melanoma (n=250 enrolled)*NGS [Agilent capture (Sanger V2 panel): 360 genes and 20 gene fusions; Illumina HiSEQ Sequencing]*CNV: [via NGS or Affy SNP 6.0 or Illumina Omni (TBD)]Bioinformatics: Analysis will be performed using core Sanger informatics pipelines similar to those previously described (Papaemmanuil E et al. (2013) Blood. 22:3616 -3627). Briefly, copy number analysis will be performed using the ASCAT algorithm, and base substitutions, small insertions and deletions using the CAVEMAN and Pindel algorithms, respectively. Statistical approaches including generalized linear models will be used to predict clinical variables such as maximum clinical response and duration of response using genetic data. Sanger and EBI to conduct analysis; Raw data and correlation with clinical endpoints to be analyzed by both EBI/Sanger and GSK (unique pipeline analyses to increase call confidence)

Dataset EGAD00001001375

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver

Chronic liver injury predisposes to cirrhosis and hepatocellular carcinoma, but how somatic mutations accumulate in liver disease is unexplored. We sequenced whole genomes of 400 microdissections of 100-500 hepatocytes from 5 normal and 6 cirrhotic livers. Compared to normal liver, cirrhotic liver had higher mutation burden, especially structural variants, including chromothripsis. Cirrhotic nodules were oligoclonal; sometimes entirely derived from a single, recent common ancestor. Clonal expansions millimeters in diameter occurred in cirrhosis in the absence of known driver mutations. Endogenous mutational processes predominated, although signatures of polycyclic aromatic hydrocarbon and aristolochic acid exposure occurred in some samples. Up to 10-fold within-patient variation in activity of exogenous signatures existed between adjacent cirrhotic nodules, with both clone-specific and microenvironmental forces shaping this heterogeneity. Synchronous hepatocellular carcinomas drew from the same repertoire of mutational signatures as background cirrhotic liver, but with higher burden. Somatic mutations chronicle the exposures, toxicity, regeneration and clonal structure of liver tissue as it progresses from health to disease.

Dataset EGAD00001004578

Download Metadata

Metadata Distribution Welcome to the realm of Metadata Distribution within the EGA ecosystem! Our Metadata REST API empowers you to effortlessly retrieve metadata from the expansive landscape of EGA. By utilising this API, you gain access to publicly available insights across various EGA domains, including studies, samples, experiments, runs, analyses, policies, DACs, and datasets. Furthermore, this API facilitates cross-referencing of objects, enabling you to gather, for example, all the datasets associated with a specific DAC, seamlessly. In addition, we have added the ability to query private data using the metadata API. If you possess the necessary permissions, you can access behind-the-login private data for a specified list of datasets. Metadata Distribution Index Identifiers Dataset Mappings Website Download Metadata API - Private Identifiers At the core of EGA's organisational structure are unique accessions that serve as essential tags for our diverse objects. Here's a quick overview of the accessions and their corresponding object types: EGA Accession ID EGA Object description EGAS EGA Study Accession ID EGAC EGA DAC Accession ID EGAP EGA Policy Accession ID EGAN EGA Sample Accession ID EGAR EGA Run Accession ID EGAX EGA Experiment ID EGAZ EGA Analysis Accession ID EGAD EGA Dataset Accession ID EGAB EGA Submission ID EGAF EGA File Unique Accession ID For further information check our metadata schema documentation. Dataset Mappings For authorised datasets, comprehensive mappings reveal meaningful connections: Sample_file: This file presents information about the linkage between samples and files available in the dataset. Study_experiment_run_sample: This file presents information about the linkage between studies, experiments, runs, and samples within the dataset. Study_analysis_sample: This file presents information about the linkage between studies, analyses, and samples contained within the dataset. Run_sample: This file presents information about the linkage between runs and samples within the dataset. Analysis_sample: This file presents information about the linkage between analyses and samples within the dataset. An empty file indicates the absence of corresponding information. Website Download Our website serves as your gateway to downloading metadata. Simply navigate to the dataset page, and you'll find a blue Metadata button. Once authenticated, you can click this button for authorised datasets. If you lack permissions for a particular dataset, request access by clicking the 'Request Access' button. For authorised datasets, choose your preferred metadata format: CSV, TSV, or JSON. Metadata API - Private Leverage the power of programmatic metadata downloads! Start by authenticating yourself with your credentials to obtain an access token. With this token, programmatically query private information. Queries mirror the structure of the Public Metadata API. However, behind the login, you can delve into specific mapping information (as mentioned above in dataset mappings) alongside object-level exploration. Authentication An active session is required to work with the API. Each time you log in with your credentials a new session is started, which is identified by an access_token. Below an example on how to obtain one using curl: curl https://idp.ega-archive.org/realms/EGA/protocol/openid-connect/token \ -d 'client_id=metadata-api' \ -d 'username=...' \ --data-urlencode 'password=...' \ -d 'grant_type=password' All responses from the API are in JSON format. A successful response should include a new token to be used for the session: {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiA...TNw", "expires_in":300, "refresh_expires_in":1800, "refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiA...pTX10", "token_type":"Bearer", ... } Save the access_token value and include it in the API call headers. Example query usage Below you can find some example of queries available behing authentication and authorisation. Querying study-experiment-run-sample mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/study_experiment_run_sample \ -H 'Authorization: Bearer access_token' Querying run-sample mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/run_sample \ -H 'Authorization: Bearer access_token' Querying study-analysis-sample mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/study_analysis_sample \ -H 'Authorization: Bearer access_token' Querying analysis-sample mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/analysis_sample \ -H 'Authorization: Bearer access_token' Querying sample-file mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/sample_file \ -H 'Authorization: Bearer access_token' You can get a different output format by adding one of these options to the curl command: -H 'Accept: text/tsv' -H 'Accept: application/json' -H 'Accept: text/csv' For more detailed information, refer to the Metadata API Specification.

Documentation access/download/metadata

CIDR: NINDS High Throughput Genotyping Resource Access for Structural Hindbrain Disorders

Recessive forms for many structural brain disorders (SBDs), including cerebellar hypoplasia (CBH), corpus callosum hypoplasia (CCH), cobblestone lissencephaly (COB), classical lissencephaly (LIS), microcephaly (MIC), and pontocerebellar hypoplasia (PCH), have been described. Patients usually present to the clinic with neurodevelopmental disorders (NDDs), including autism, epilepsy, intellectual disability, and cerebral palsy. Subsequent brain MRI usually leads to the diagnosis of an SBD. While a handful of genes that cause these diseases have been identified, most patients do not have mutations in these genes, suggesting that there is still much work to be done in identifying the genetic causes of these disorders. We have recruited a cohort of families with inherited SBDs, most from families with documented parental consanguinity with more than one affected member. Current approaches utilizing exome sequencing of SBD affected members still leave most cases unsolved, in part because there are too many possible variants to consider. Linkage analysis will allow us to extract all the useful genetic information from the family, taking advantage of each genetically informative meiosis in each family. We propose to analyze up to 100 SBD families for 500 samples per year for 4 years, through the CIDR SNP Genotyping Service, in parallel with already-funded exome sequencing of affects, leveraging off an already funded Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) effort to identify new causes of SBDs. Understanding the pathogenetic mechanisms underlying recessive pediatric SBDs will lead to better diagnostic and therapeutic opportunities for patients, and may shed light on complex NDDs. Ultimately, this work will identify new genetic disease loci to provide insight into pediatric SBD, with the hope to mitigate the impact of SBD worldwide.Public Health Significance: NDDs affect approximately 4-6% of the general population, most notably children, and are evident in disorders, such as intellectual disability, epilepsy, and autism, with estimated yearly costs of $51.2B for intellectual disability, $11.5B for cerebral palsy, and $2.5B for visual impairment, making up >5% of total health care costs. Recessive NDDs impose enormous personal, social, and economic costs because of the early onset and the lifetime of medical dependence that often ensues. Genetic testing is critical to the diagnosis and treatment of these diseases. Many of the diseases under study have no treatment or cure. Structural brain diseases (SBDs) underlie a large percentage of these diseases, and are defined loosely as any condition in which defects in the structure or volume of a key brain component. SBDs are divided into major categories based upon the anatomical brain location. The major types involve the anatomical structures of the developing neural tube, forebrain, hindbrain, cerebral cortex, and those affecting overall brain size. For the purposes of this application, we have excluded SBDs resulting from environmental causes (i.e. prematurity-induced), those below the brainstem, or those unlikely to be due to a germline or de novo mutation (i.e. focal SBDs or simplex disease).

Study phs002621

Genome-Wide Association of Type 2 Diabetes in Africans: The AADM Study

The Africa America Diabetes Mellitus (AADM) study is a genetic epidemiological study of type 2 diabetes in Sub-Saharan Africa. Study participants were enrolled through university medical centers in Nigeria, Ghana, and Kenya. Ethical approval for the study was obtained from the Institutional Review Board (IRB) of each participating institution. All subjects provided written informed consent for the collection of samples and subsequent analysis. The case definition of type 2 diabetes was based on the American Diabetes Association (ADA) criteria. After providing informed consent, participants underwent the same enrollment procedures, which included collection of demographic information, medical history, clinical examination and a blood draw. Genome-wide SNP genotyping was done on either the Axiom™ PanAFR SNP array (n=1,808) or the Multi-Ethnic Global Array (MEGA) (n=3,423). After appropriate quality control, in silico imputation was done using the African Genome Resources Haplotype Reference Panel (at the Sanger Imputation Service). Imputed genotypes were filtered for variants with minor allele frequency (MAF)≥ 0.01 and information score (info) ≥ 0.3 for genetic association analysis. Genome-wide association analysis between type 2 diabetes and the imputed genotype dosages was done using a generalized linear mixed model, which adjusted for age, gender, body mass index, the genetic relatedness matrix and the first three principal components (PCs) of the genotypes.Metabolomics profiling of plasma samples of type 2 diabetes (T2D) cases and controls in Nigerians (West Africa) was done in the AADM Study. Plasma metabolites were measured in a total of 580 individuals (N=310 for the discovery phase and N=270 for the replication stage) using the global/untargeted approach on the Metabolon platform and following the manufacturer's standard operation protocols. The analytic methods are described in detail in Doumatey et al. [Genome Med 2024]. The measured metabolites level represented by peak areas are relative values. The peak area data were batch-normalized to remove the instrument batch effects (batch variability) and the batch-normalized data correspond to the median-scaled raw data. For each identified metabolite, the minimum value across all batches in the batch-normalized was imputed for the missing values. The batch-normalized and imputed data are natural log-transformed and consist of 1116 metabolites for the discovery cohort and 1071 metabolites for the replication. Welch's two-sample t-test on the log-transformed data was used to identify metabolites differentially expressed between T2D cases and controls . All other statistical analyses conducted on both the replication and discovery cohorts used the log-transformed data. To merge the discovery and replication, the same quality control samples (bridge samples) were run with each batch of the experimental samples in both cohorts and used to correct for additional variability and uniformize the procedures. The resulting merged data is the QC-normalized and imputed data that contains only metabolites that were common to both cohorts and successfully bridged for all batches (n= 891 metabolites).

Study phs001844

Longitudinal Study of Genetic Causes of Intrahepatic Cholestasis

This longitudinal observational study will investigate the natural history and progression of four genetic causes of intrahepatic cholestasis of childhood, including alpha-1 antitrypsin deficiency (α1-AT), Alagille syndrome (AGS), progressive familial intrahepatic cholestasis (PFIC), and bile acid synthesis defects (BAD). This study will be conducted as part of the Cholestatic Liver Disease Consortium (CLiC), an NIH-funded multi-centered Rare Disease Clinical Research Consortium. In this study, we will collect defined data elements in a uniform fashion at fixed intervals for five years over a relatively large number of patients with these rare disorders. In addition, a biobank of patient specimens and DNA samples will be established for use in ancillary studies to be performed in addition to this study. By comparing outcome measures between the four liver diseases (i.e., using each disorder as a disease-control for the other disorders), the full impact of each disorder can best be determined in comparison to the other liver diseases. Using the longitudinal database in this fashion, this study will provide an improved understanding of the effects of the cholestatic liver during childhood irrespective of the underlying etiology as well as to the pathophysiology, outcome, and complications of each of the disorders. This initial characterization will allow calculation of sample sizes for future therapeutic intervention clinical trials and provide the baseline to which interventions should be compared.

Study phs001288

Human CD4 Memory T Cell Activation Time Course

We performed a high-resolution time course RNA-seq experiment on CD4+ memory T cells during activation with anti-CD3/CD28 beads. We performed this in 24 adult individuals of European ancestry with no autoimmune diseases. We used 1 million cells as starting material, per time point (up to 8 time points per individual from 0 to 72 hours). We identified widespread dynamic allele-specific expression (dynASE) across the genome, i.e. ASE that changes with time after activation, which reflects cell state-dependent genetic regulatory effects. DynASE events were enriched in risk loci for multiple autoimmune diseases. This highlights the importance of studying multiple cellular states in order to elucidate the mechanisms of autoimmune disease. It also provides a successful framework to do it in other cellular systems relevant for other traits. We also showed an unprecedented amount of regulatory variation for HLA genes. HLA-DQB1 has 3 distinct regulatory haplotypes with expression profiles that could come from 3 different genes. We performed ATAC-seq in replicate for CD4+ memory T cells stimulated for 72 hours from another healthy individual. These data, together with genetic fine-mapping, CRISPR editing, EMSA and luciferase assays, helped us find a SNP in the promoter of HLA-DQB1 that causes at least part of the large cell state-dependent change in expression, at the RNA and protein levels.

Study phs002259

MAESTRO-Pool Enables Highly Parallel and Specific Mutation-Enrichment Sequencing for Minimal Residual Disease Detection in Cohort Studies

MAESTRO-Pool builds upon the technology MAESTRO (Minor Allele Enriched Sequencing Through Recognition Oligonucleotides) by pooling tumor-specific MAESTRO probes from multiple patients and applying these to all samples from all patients. In this study, MAESTRO-Pool was applied to a cohort of 9 melanoma patients where 98 plasma samples were screened for 22,333 mutations. Additionally, a new dynamic minimal residual disease (MRD) caller was used to estimate the likelihood of MRD detection based on the number mutations and cell-free DNA molecules interrogated which allowed each bespoke MRD test to be properly calibrated against false detection. These developments led to sensitive detection in patient-matched samples down to 0.78 parts per million (ppm) while limiting false detection in negative controls to 1/784 (tumor fraction=2.7 ppm). MAESTRO-Pool and the dynamic MRD caller enable a unique blend of sensitivity, specificity, and efficiency, which will improve the ability to detect MRD.The data contained in this repository consists of:Tumor and normal whole genome sequencing data used to call patient-specific tumor mutations and design the MRD Tracker and MAESTRO-Pool fingerprintsMAESTRO-Pool data (enriched duplex sequencing via hybrid capture) of tumor gDNA, normal gDNA and cfDNA MRD Tracker data (duplex sequencing via hybrid capture) of tumor gDNA, normal gDNA and cfDNA

Study phs003447

Brain Cell Type-Specific Enhancer-Promoter Connectivity Maps and Disease Risk Association

These studies map the epigenetic landscape of microglia, neurons, astrocytes and oligodendrocytes. The initial study compared acutely isolated microglia to cultured microglia from the same donors, to identify changes that occur when microglia are removed from the brain microenvironment. In collaboration with the Rady Children's Hospital, we obtained brain tissue samples from pediatric patients representing putative normal tissue resected to gain access to brain tumors as well as tissue resected to remove epileptic foci. We assayed microglia isolated from these samples using RNA-seq, ATAC-seq and ChIP-seq for PU.1, H3K4me2, and H3K27ac. For patients from whom a sufficient cell number was obtained, we additionally cultured their microglia for up to 7 days and subjected these to the same suite of assays. In a follow-up study, we obtained brain tissue from a comparable cohort of pediatric epilepsy patients from Rady Children's Hospital. We isolated nuclei from microglia, neurons, astrocytes and oligodendrocytes, and assayed for ATAC-seq, ChIP-seq for H3K4me3, and H3K27ac, and PLAC-seq (Proximity Ligated ChIP-seq). We isolated microglia from human fetal and postnatal sample and assayed for bulk RNA-seq, bulk ATAC-seq, bulk H3K27ac ChIP-seq, single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq. For these studies, human microglia are defined by signature genes/proteins, such as P2RY12, SALL1, and CX3CR1.

Study phs001373

NHLBI TOPMed: Pulmonary Hypertension and the Hypoxic Response in SCD (PUSH)

During Visit One, the PUSH Study will perform echocardiography on 600 children and adolescent with patients with sickle cell disease (SCD) and 100 control children and adolescents at three Field Centers, namely Howard University, Children's National Medical Center and University of Michigan. Patients or their parents will be approached and asked to give informed consent. If they appear to have a difficult reading, reading of the consent will be offered. Patients or their parents not appearing to comprehend the consent will not be eligible. As a part of this visit, each participant or parent will sign informed consent, complete a Participant Contact Information Form, complete a Medical History Form, undergo physical examination with completion of a Physical Examination Form and have blood drawn. Each participant must have echocardiography performed with measurement of Tricuspid Regurgitant Jet Velocity (TRV). In addition, attempts will be made 1) to perform a six-minute walk test, 2) to collect information from a recent (within six months) Transcranial Doppler Study (TCD) or to perform TCD, and 3) to perform pulmonary function tests. Study personnel will review all forms for completeness and conduct phlebotomy. Blood will be shipped to the Central Lab. Results of all procedures and tests will be transmitted to the Data Manager at Howard University. Sequencing was only done on sickle cell participants.

Study phs001682

Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer

The discovery of frequent 8p11-p12 amplifications in squamous cell lung cancer (SQLC) has fueled hopes that FGFR1, located inside this amplicon, might be a therapeutic target. In a clinical trial, only 11% of patients with 8p11 amplification (detected by FISH) responded to FGFR kinase inhibitor treatment. To understand the mechanism of FGFR1 dependency, we performed deep genomic characterization of 52 SQLCs with 8p11-p12 amplification, including 10 tumors obtained from patients who had been treated with FGFR inhibitors. We discovered somatically altered variants of FGFR1 with deletion of exons 1-8 that resulted from intragenic tail-to-tail rearrangements. These ectodomain-deficient FGFR1 variants (ΔEC-FGFR1) were expressed in the affected tumors and were tumorigenic in both in vitro and in vivo models of lung cancer. Mechanistically, breakage-fusion-bridges were the source of 8p11-p12 amplification, resulting from frequent head-to-head and tail-to-tail rearrangements. Generally, tail-to-tail rearrangements within or in close proximity upstream of FGFR1 were associated with FGFR1 dependency. Thus, the genomic events shaping the architecture of the 8p11-p12 amplicon provide a mechanistic explanation for the emergence of FGFR1-driven SQLC. Specifically, we believe that FGFR1 ectodomain-deficient and FGFR1-centered amplifications caused by tail-to-tail rearrangements are a novel somatic genomic event that might be predictive of therapeutically relevant FGFR1 dependency.

Study EGAS50000001368

Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Atherosclerosis Risk in Communities Study (ARIC)

Cohort Description The Atherosclerosis Risk in Communities (ARIC) study began in the mid-1980s with the initial aims being to describe the presence of subclinical atherosclerosis, the progression of atherosclerosis to clinical cardiovascular disease (CVD), and the association of novel risk factors with CVD. ARIC recruited its cohort of men and women aged 45-64 in 1987-89 from four communities (Forsyth County, NC; Jackson, MS; suburban Minneapolis, MN; and Washington County, MD). As of 2025, ARIC counts over 4,000 participants.Data Submitted Wave 1 questionnaire data includes 356 variables for up to 5763 ARIC participants in C4R. Wave 2 questionnaire data includes 367 variables for up to 5000 ARIC participants in C4R. Wave 3 questionnaire data includes 81 variables for up to 3450 participants in C4R.Dried Blood Spot/Serosurvey data includes 8 variables for up to 2437 ARIC participants in C4R. Derived data includes 62 variables for up to 18765 observations. Phenotype data includes 163 variables for up to 5937 ARIC participants in C4R. Brain MRI data includes 13 variables for up to 2550 participants in C4R.HCU data includes 21 variable for up to 631 ARIC participants in C4R.Lung CT data includes 15 variables for 1329 ARIC participants in C4R.Neurocognitive data includes 16 variables and 49826 observations.Serosurvey data includes 20 variables for 1707 ARIC participants in C4R.

Study phs002988

Inherited chromosomally-integrated human herpesvirus 6A/B (HHV-6A/B) genome sequences in the Japanese population

The deposited sequences represent inherited chromosomally-integrated human herpesvirus 6 (iciHHV-6) genomes identified from 10 BioBank Japan (BBJ) subjects based on the analysis of the whole-genome sequencing (WGS) data. In brief, we re-aligned unmapped reads from the WGS to HHV-6A genome (Genbank accession number: KJ123690.1) using BWA-MEM algorithm. Ten out of 3,256 subjects were identified with high depth of coverage of HHV-6. We further distinguished subjects with integrated HHV-6A subtypes from those with integrated HHV-6B based on phylogenetic analysis of concatenated sequences of three viral genes (U27/U43/U83, which show high divergence between viral species). We reconstructed the HHV-6 viral genome of 10 subjects. First, reads that mapped to a reference HHV-6A genome (KJ123690.1) were further aligned against the integrated HHV-6A genome derived from a Japanese individual NA18999 (GenBank Accession number: KY316047.1) using BWA-MEM. Based on the alignment, variant calling was performed using freebayes (version: v1.2.0-2-g29c4002) with parameters ploidy = 1 and min-alternate-fraction = 0.8 {Garrison, 2012}. We generated subject-specific iciHHV-6 viral sequences by applying the resulting variants to the KY316047.1 reference genome using the FastaAlternateReferenceMaker function in the Genome Analysis Toolkit (GATK) v3.7. Please note that HHV-6B-specific variants are unlikely to be sensitively reconstructed using this method.

Study JGAS000240

INSPIRE - Investigator-initiated Phase 2 Study of Pembrolizumab Immunological Response in Metastatic Solid Tumors

Whole exome and RNA sequencing source data for: Clouthier, D.L., Lien, S.C., Yang, S.Y.C. et al. An interim report on the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE). j. immunotherapy cancer 7, 72 (2019). https://doi.org/10.1186/s40425-019-0541-0 Bratman S*, Yang SYC*, Iafolla MAJ, Liu Z, Hansen AR, Bedard P, Lheureux S, Spreafico A, Razak AA, Shchegrova S, Louie M, Billings P, Zimmerman B, Sethi H, Aleshi A, Torti D, Marsh K, Eagles J, Cirlan I, Hanna Y, Clouthier D, Lien SC, Ohashi PS, Xu W, Siu LL, Pugh TJ. Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab. Nature Cancer. 2020:1:873-881. https://doi.org/10.1038/s43018- 020-0096-5. Yang SYC, Lien SC, Wang BX, Clouthier DL, Hanna Y, Cirlan I, Zhu K, Bruce JP, El Ghamrasni S, Iafallo MAJ, Oliva M, Hansen AR, Spreafico A, Bedard PL, Lheureux S, Razak A, Speers V, Berman HK, Aleshin A, Haibe-Kains B, Brooks DG, McGaha TL, Butler MO, Bratman SV, Ohashi PS, Siu LL, and Pugh TJ. Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. Nature Comm 2021:12, 5137. https://doi.org/10.1038/s41467-021-25432-7

Study EGAS00001003280

Comparison of 133/144bp dominant phenotype vs 166bp dominant phenotype.

Background: Previous studies found that cell-free DNA (cfDNA) generated from tumors was shorter than that from healthy cells, and selecting short cfDNA could enrich for tumor cfDNA and improve its usage in early cancer diagnosis and treatment monitoring; however, the underlying mechanism of shortened tumor cfDNA was still unknown, which potentially limits its further clinical application.Results: Using targeted sequencing of cfDNA in a large cohort of solid tumor patient, sequencing reads harboring tumor-specific somatic mutations were isolated to examine the exact size distribution of tumor cfDNA. For the majority of studied cases, 166bp remained as the peak size of tumor cfDNA, with tumor cfDNA showing an increased proportion of short fragments (100-150bp). Less than 1% of cfDNA samples were found to be peaked at 134/144bp and independent of tumor cfDNA purity. Using whole-genome sequencing of cfDNA, we discovered a positive correlation between cfDNA shortening and the magnitude of chromatin inaccessibility, as measured by transcription, DNase I hypersensitivity, and histone modifications. Tumor cfDNA shortening occurred simultaneously at both 5’ and 3’ ends of the DNA wrapped around nucleosomes. Conclusions: Tumor cfDNA shortening exhibited two distinctive modes. Tumor cfDNA purity and chromatin inaccessibility were contributing factors but insufficient to trigger a global transition from 166bp dominant to 134/144bp dominant phenotype.

Study EGAS00001004135

Comprehensive analysis of atypical teratoid rhabdoid tumour (ATRT) using genomic, epigenomic and transcriptomic techniques.

ATRTs (Atypical teratoid rhabdoid tumours) represent one of the most aggressive pediatric brain cancers, but intriguingly exhibit few other recurrently mutated loci except for SMARCB1/hSNF5. We integrated whole genome (n=15), exome, copy number, gene expression and methylation analyses to comprehensively interrogate 64 ATRTs and observed that structural events were relatively frequent in the ATRT genome (~3 tumour). In addition to SMARCB1, which was targeted by structural events in a majority (49/64) of tumours, recurrent structural alterations targeting the LRP1B, CDH13, BCR and MKL1 loci were observed. We observed novel translocation events, including 2 targeting SMARCB1 which were detected only by NGS analyses. Significantly, integration of gene expression and methylation profiles with genomic analyses revealed ATRT comprise two sub-groups with distinct clinical and genetic features. Group 1 tumours were characterized by supra-tentorial brain location, focal intragenic alterations of SMARCB1 and a pro-neural gene expression signature with evidence of NOTCH pathway activation. While Group 2 ATRTs were characterized by infra-tentorial brain location, broad SMARCB1 alterations and an activation of the BMP signalling pathway. Our findings highlight epigenetic mechanisms as important determinants of ATRT tumour phenotypes, and demonstrate for the first time that ATRTs arising in different anatomical compartments comprise distinct molecular and therapeutic sub-groups.

Study EGAS00001000506

Transcriptional and DNA binding profiling of CEBPE in REH acute lymphoblastic leukaemia cells using shRNA RNA-Seq and ChIP-Seq

ChIP-Seq - CEBPE - REH. The ETV6/RUNX1 translocated acute lymphoblastic leukaemia cell line REH was used to perform ChIP-Seq using a CEBPE antibody. Cells were fixed in 1% formaldehyde for 10mins, prior to preparation of chromatin using Active Motif Express ChIP-IT. 2ug of antibody (anti CEBPE Atlas Antibodies HPA002928)was added to 25ug of chromatin O/N at 4C with rotation. Duplicate reactions were pooled and purified. 10ng of ChIPd and input DNA used for Illumina NGS preparation (NEBNext ChIP-Seq Library kit; New England Biolabs), CEBPE and Input DNA ChIP samples were sequenced on a MiSeq using 150bp Kit v3 paired end and a HiSeq 2500 using 2x101 version 4 paired end (Illumina) respectively. Reactions performed in duplicate. shCEBPE RNA-Seq - REH. REH cells were lentivirally transduced with a pTRIPZ shRNA vector for transcriptional profiling of CEBPE. Two controls (empty and non-targeting) and two CEBPE shRNAs (V3THS_150517(A13), V3THS_404312(G3) Dharmacon, GE) were transduced into REH cells. Cells were treated with 1ug/ml doxycyclin for 144hrs and total RNA purified. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on an Illuimna HiSeq 2500 using 2x101 version 4 paired end chemistry. 3 biological replicates of each samples were prepared.

Study EGAS00001002877

scRNA-seq of HGSC tumor and ascites

Immune regulatory metabolites are key features of the tumor microenvironment (TME), yet with a few notable exceptions, their identities remain largely unknown. We uncovered the immune regulatory metabolic states and metabolomes of sorted tumor and stromal, CD4+, and CD8+ cells from the tumor and ascites of patients with high-grade serous ovarian cancer (HGSC) using high-dimensional flow cytometry and metabolomics supplemented with single cell RNA sequencing. Flow cytometry revealed that tumor cells show a consistently greater uptake of glucose than T cells, but similar mitochondrial activity. Cells within the ascites and tumor had pervasive metabolite differences, with a striking enrichment in 1-methylnicotinamide (MNA) in T cells infiltrating the tumor compared to ascites. Despite the elevated levels of MNA in T cells, the expression of nicotinamide N-methyltransferase, the gene encoding the enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to nicotinamide, was restricted to fibroblasts and tumor cells. Treatment of T cells with MNA resulted in an increase in T cell-mediated secretion of the tumor promoting cytokine tumor necrosis factor alpha. Thus, the TME-derived metabolite MNA contributes to an alternative and non-cell autonomous mechanism of immune modulation of T cells in HGSC. Collectively, uncovering the tumor-T cell metabolome may reveal metabolic vulnerabilities that can be exploited using T cell-based immunotherapies to treat human cancer.

Study EGAS00001004829

Ultrasensitive detection of minor allele fractions in maternal samples based on microhaplotype analysis

Background: Tools for quantifying and studying genetic variation in heterogeneous cell populations have a limited sensitivity. However, many biological problems require ultrasensitive genetic deconvolution of cell mixtures. The detection of fetal cells in cervical samples from pregnant women presents such a challenge. Methods: Using deep sequencing of microhaplotype loci and analysis of the error profiles in genetically pure and mixed samples, we increase the sensitivity for minor allele detection and demonstrate the potential for paternal allele detection in cervical samples from pregnant women. Results: Using artificial DNA mixtures, we show that unique alleles can be readily identified in mixtures with a ratio of 1 in 10,000 (0.01%). By applying this method on ten non-invasive cervical samples from pregnant women we could identify the presence of paternal alleles in half of the samples. Unexpectedly, we demonstrate those alleles not to be of fetal origin but of sperm. Conclusions: We developed a novel method that can deconvolute genetic mixtures to at least 0.01%, which can be applied to study minor allele fractions in genetic mixtures and, for example, could aid in trophoblast cell detection in maternal blood or cervix. Our results demonstrate the importance of discriminating fetal and paternal alleles when analyzing cervical fetal cells and may pinpoint a potential cause of erroneous results in previous trophoblast isolation studies.

Study EGAS00001007057

Germline whole genome sequencing of patients with Li-Fraumeni syndrome

Five hundred ng to 1 ug of genomic DNA was submitted to The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children for genomic library preparation and whole genome sequencing. DNA samples were quantified using the Qubit High Sensitivity Assay and purity was assessed using the Nanodrop OD 260/280 ratio. Approximately 500-700 ng of DNA was used as input material for library preparation using the Illumina TruSeq PCR-free DNA Library Prep Kit following the manufacturer’s recommended protocol. In brief, DNA was fragmented to 400 bp on average using sonication on a Covaris LE220 instrument. Fragmented DNA was end-repaired, A-tailed and indexed TruSeq Illumina adapters with overhang-T were added to the DNA. Libraries were then validated on a Bioanalyzer DNA High Sensitivity chip to check for size and absence of primer dimers and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). Validated libraries were pooled in equimolar quantities and paired-end sequenced on an Illumina HiSeq X platform following Illumina’s recommended protocol to generate paired-end reads of 150-bases in length and an average depth of 40X. FASTQ files were aligned to the hg19 reference genome using BWA-mem v0.78. PCR duplicates were marked with Picard MarkDuplicates v1.1.08, and base recalibration and realignment was performed using GATK v2.8.1.

Study EGAS00001007061

Towards standardized whole exome sequencing (WES) for cancer patients: lessons from a multicentric pilot study

A growing number of druggable targets and national initiatives for precision oncology necessitate broader genomic profiling for many cancer patients. Whole exome sequencing (WES) offers unbiased analysis of the entire coding sequence, segmentation-based detection of copy number alterations (CNAs), and accurate determination of complex biomarkers including tumor mutational burden (TMB), homologous recombination repair deficiency (HRD), and microsatellite instability (MSI). To assess the inter-institution variability of clinical WES, we performed a comparative pilot study between German Centers of Personalized Medicine (ZPMs) from five participating institutions. Tumor and matched normal DNA from 30 patients were analyzed using custom sequencing protocols and bioinformatic pipelines. Calling of somatic variants was highly concordant with a sensitivity between 91-95% and a positive predictive value (PPV) of 82-95% compared with a three-institution consensus and full agreement for 16 of 17 druggable targets. Deviations were observed for cases with low VAF or coverage, differing annotations, and different filter protocols. CNAs showed overall agreement in 76% for the genomic sequence with high wet-lab variability. Complex biomarkers correlated strongly between institutions (HRD: 0.79-1, TMB: 0.97-0.99) and all institutions agreed on microsatellite instability. This study will contribute to the development of quality control frameworks for comprehensive genomic profiling and sheds light onto parameters that require stringent standardization.

Study EGAS00001007363

Knoll et al Identification of drug candidates targeting monocyte reprogramming in people living with HIV

Introduction People living with HIV (PLHIV) are characterized by functional reprogramming of innate immune cells even after long-term antiretroviral therapy (ART). In order to assess technical feasibility of omics technologies for application to larger cohorts, we compared multiple omics layers. Methods Bulk and single-cell transcriptomics, flow cytometry, proteomics, chromatin landscape analysis by ATAC-seq as well as ex vivo drug stimulation was performed in a small number of blood samples derived from PLHIV and healthy controls from the 200-HIV cohort study. Results Single-cell RNA-seq analysis revealed that most immune cells in peripheral blood of PLHIV are altered in their transcriptomes and that a specific functional monocyte state previously described in acute HIV infection is still existing in PLHIV while other monocyte cell states are only occurring acute infection. Moreover, a reverse transcriptome approach on a rather small number of PLHIV was sufficient to identify drug candidates for reversing the transcriptional phenotype of monocytes in PLHIV. Discussion These scientific findings and technological advancements for clinical application of single-cell transcriptomics form the basis for the larger 2000-HIV multicenter cohort study on PLHIV, for which a combination of bulk and single-cell transcriptomics will be included as the leading technology to determine disease endotypes in PLHIV and to predict disease trajectories and outcomes.

Study EGAS00001007460

Genetics of Chemotherapy Induced Peripheral Neuropathy in N08C1 and N08CB

Chemotherapy-induced peripheral neuropathy (CIPN) is a common and potentially dose-limiting toxicity of chemotherapy treatment. CIPN severity varies widely between cancer patients, and previous studies had found evidence of genes and single nucleotide variants (SNV) being associated with CIPN. The goal of this study was to further identify genetic markers and pathways associated with CIPN severity using whole exome sequencing (WES) and whole genome sequencing (WGS) of participants in two clinical studies which collected longitudinal patient-reported outcome (PRO) measures of CIPN. NCCTG/Alliance study N08C1 was a prospective cohort study of the natural history of paclitaxel-associated acute pain syndrome (P-APS) and CIPN. NCCTG/Alliance trial N08CB was a randomized, placebo-controlled trial of calcium and magnesium for prevention of oxaliplatin-induced sensory neuropathy in which the treatment had no significant effect on either acute pain or sensory neuropathy. Both N08C1 and N08CB collected patient assessments of CIPN symptoms before each cycle of chemotherapy using the EORTC QLQ-CIPN20 instrument. For this study, CIPN cases were selected from each of N08C1 and N08CB as those patients with the most severe CIPN symptoms (assessed longitudinally). CIPN controls were selected as those with the least severe symptoms. WGS was obtained for N08C1 samples (WES had been obtained and analyzed previously), and WES was obtained for N08CB samples.

Study phs001480

Genetic and Phenotypic Analysis of Multiple Sclerosis in Hispanics

We sought to identify MS susceptibility variants specific to the Major Histocompatibility Complex and to assess the effect of ancestral risk modification within 2652 Latinx and Hispanic individuals, as well as 2435 Black and African American individuals ascertained in collaboration with the Alliance for Research in Hispanic MS (ARHMS). All DNA samples were obtained through whole blood extraction and were genotyped on the MS Chip, an Illumina Infinium custom genotyping array that contains targeted and dense coverage of the extended MHC, specifically designed for imputation. Classical HLA alleles, SNPs, and amino acid residues were imputed simultaneously from genotyped SNPs using HLA-TAPAS and a multi-ethnic reference panel of 2504 samples from the 1000 Genomes Project. We have identified several novel susceptibility alleles which are rare in European populations including HLA-B*53:01, and we have identified an independent role for HLA-DRB1*15:01 and HLA-DQB1*06:02 on MS risk. We found a decrease in Native American ancestry in MS cases vs controls across the MHC, peaking near the previously identified MICB locus; and we have identified several susceptibility variants for which MS risk is modified by global or local ancestry. We are making data on all genotyped and imputed SNPs, classical HLA alleles, and amino acid residues available through dbGaP for the Hispanic and African American samples utilized in these analyses.

Study phs003105

Evaluation of Hybridization Capture versus Amplicon-based Methods for Whole Exome Sequencing

Next generation sequencing has aided characterization of genomic variation. While whole genome sequencing may capture all possible mutations, whole exome sequencing is more cost-effective and captures most phenotype-altering mutations. Initial strategies for exome enrichment utilized a hybridization-based capture approach. Recently, amplicon-based methods were designed to simplify preparation and utilize smaller DNA inputs. We appraised two hybridization capture-based and two amplicon-based whole exome sequencing methods, utilizing both Illumina and Ion Torrent sequencers, comparing on-target alignment, uniformity, and variant calling. While the amplicon methods had higher on-target rates, the hybridization capture-based approaches showed better uniformity. All methods identified many of the same single nucleotide variants, but each amplicon-based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform-specific variant calling algorithms. All methods demonstrated effective copy number variant calling when compared against a single nucleotide polymorphism array. This study illustrates some differences between various whole exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach.

Study phs000938

Genetic Components of Knee Osteoarthritis (GeCKO) Study: The Osteoarthritis Initiative

The Osteoarthritis Initiative (OAI) is a publicly and privately funded prospective longitudinal cohort with a primary objective of identifying risk factors for incidence and progression of tibiofemoral knee OA. The OAI utilized a focused population-based recruitment to enroll 4,674 men and women between the ages of 45-79 years who either had radiographic symptomatic knee OA or who were without radiographic symptomatic OA in both knees but were considered high risk for OA because they had two or more known risk factors for knee OA. Subjects were recruited into the baseline phase of the OAI at multiple sites throughout the US between 2004 and 2006. All subjects were invited back for follow-up examinations to assess incidence or progression of OA annually, for up to 5 years. Phenotype data from the baseline and follow-up examinations are available for public access from the Osteoarthritis Initiative (OAI) database at http://www.oai.ucsf.edu/. The Genetic Components of Knee Osteoarthritis (GeCKO) Study was initiated in 2009 as a genetic ancillary study to perform a genome-wide association study to identify genetic variants associated with radiographic osteoarthritis. This study included 4,482 individuals participating in the parent OAI study. Following sample cleaning (e.g., removal of duplicates, sex mismatches, poor sample quality, etc.), the final sample set included 4,129 individuals.

Study phs000955

Whole Exome Sequencing and RNA-Seq to Characterize the Somatic Breast Cancer Landscape Among Latinas in California

Somatic mutational profiles are increasingly being used to guide treatment. However, there is a dearth of data from non-European populations. To address this gap, we conducted paired tumor/normal whole exome paired-end sequencing and tumor RNA-Seq on 146 breast tumors from 140 Hispanic/Latina (H/L) women with breast cancer. We characterized somatic mutations, copy number alterations, tumor subtypes [Prediction Analysis of Microarray 50 (PAM50)], Catalogue Of Somatic Mutations In Cancer (COSMIC) mutation signatures and expression profiles, and compared them to breast tumors from non-Hispanic White (White) women in The Cancer Genome Atlas (TCGA). Using MutSigCV, we found that the most commonly mutated genes, including TP53, RUNX1, PTEN, PIK3CA, MAP3K1, GATA3, CDH1 and CBFB, were similar to those in breast tumors from non-Hispanic white women. Novel findings were that outliers of BLTP2 (aka KIAA0100) over-expression and COSMIC mutational signature 16 were more common in tumors from H/L women than White women. We also identified that the known germline APOBEC3A/B deletion variant was significantly more common in H/L women and was associated with indigenous American ancestry. Data available through dbGaP will be whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) data, as well as phenotypic data, including estrogen receptor, progesterone receptor, and HER2 receptor status, tumor histology, stage, and grade, and age at diagnosis.

Study phs003218

NIMH Human Middle Temporal Gyrus (MTG) Cell Types

Elucidating the cellular architecture of the human neocortex is central to understanding our cognitive abilities and susceptibility to disease. In this study, we applied single nucleus RNA sequencing to perform a comprehensive analysis of cell types in the middle temporal gyrus of human cerebral cortex. We identify a highly diverse set of excitatory and inhibitory neuronal types, many of which are relatively sparse. Additionally, we found that excitatory types are less layer-restricted than expected based prior knowledge from cell morphologies and from mouse studies. Comparison to a similar mouse cortex single cell RNA-sequencing dataset revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of human cell type properties. Despite this general conservation, we also find extensive differences between homologous cell types in human and mouse, including dramatic alterations in proportions, laminar distributions, gene expression, and morphology. These species-specific features emphasize the importance of directly studying human brain. This study conducted by the Allen Institute for Brain Science was supported by the Allen Institute for Brain Science and by US National Institutes of Health grant U01 MH114812-02 to E.S.L. Collaborators request that publications resulting from these data cite their original publication: Hodge RD, Bakken TE, et al. Conserved cell types with divergent features between human and mouse cortex. bioRxiv. 2018 doi: 10.1101/384826.

Study phs001790

eMERGE Geisinger eGenomic Medicine (GeM) - MyCode Project Controls

A research cohort of adult Geisinger Clinic patients was enrolled from community-based primary care clinics of the Geisinger Health System. Patients were eligible for enrollment if they were a primary care patient of a Geisinger Clinic physician and were scheduled for a non-emergent clinic visit. All participants provided written informed consent and HIPAA authorization. Consenting patient agreed to provide blood samples for broad biomedical research use, and permission to access data in their Geisinger electronic medical record for research. The enrollment rate was 90% of patients approached. The demographics of the cohort approximate those of the Geisinger Clinic outpatient population. Research blood samples were collected during an outpatient clinical phlebotomy encounter. Research blood samples are coded and stored in a central biorepository. Samples are linkable to clinical data in a de-identified manner for research via an IRB-approved data broker process. For genomic analysis, DNA is extracted from EDTA-anticoagulated whole blood. For the initial eMERGE Geisinger eGenomic Medicine (GeM) genotyping project, a subset of 1,232 unique samples were genotyped using Illumina HumanOmniExpress-12 v1.0 arrays, and used as population controls for other Geisinger Clinic case cohorts, including abdominal aortic aneurysm and gastric bypass surgery cases. These samples were selected from a larger subset of approximately 6,000 MyCode DNA samples using a partial matching algorithm that included age, sex, and body mass index as variables.

Study phs000381

Evolution of Core Archetypal Phenotypes in High-Grade Serous Ovarian Cancer (HGSOC)

The evolution of resistance in high-grade serous ovarian cancer (HGSOC) cells in response to chemotherapy is only partially understood. To uncover phenotypic changes associated with chemotherapy resistance, we performed single-cell RNA-sequencing (scRNA-seq) or whole-genome sequencing of 23 total patients, with longitudinal samples collected from 9, treatment-naïve samples from 8 patients, and post-treatment samples from 6 patients. Our study revealed that the HGSOC transcriptome could be described using three core archetypal phenotypes, defined as oncogenic tasks that describe majority of the transcriptional data. We implemented a multi-task learning approach to identify the biological tasks of each archetype and identified metabolism and proliferation, cellular defense response, and DNA repair signaling. The “metabolism and proliferation” archetype evolved during treatment and was enriched in cancer cells from patients that received multiple-lines of treatment and had elevated tumor burden indicated by CA-125 levels. The emergence of archetypes was not consistently linked to specific whole-genome driver mutations. However, archetypes were closely associated with sub-clonal clusters at the single-cell level, indicating that cancer cell sub-populations specialize in particular biological tasks. Our study reveals a defining principle of ovarian tumor evolution using temporal scRNA-seq profiles, identifies the key phenotypic features across patients and links metabolic shifts with a response to chemotherapy.

Study phs002294

Aurora US Metastatic Breast Cancer Retrospective Project

The AURORA US Metastatic Breast Cancer project is funded by the Breast Cancer Research Foundation (BCRF) Evelyn H. Lauder Founder's Fund for Metastatic Breast Cancer Research. This multi-center effort conducted within the Translational Breast Cancer Research Consortium (TBCRC) and cancer researchers to better understand the metastatic process through the study of both the primary and metastatic tissue. In the retrospective phase, TBCRC sites submitted matched primary and metastatic tissues and blood from previous collections for piloting the process. Samples were profiled using whole genome DNA sequencing, whole exome DNA sequencing, DNA methylation arrays, and RNA sequencing. The final freeze set for samples with successful nucleic acid extraction and molecular assays included 55 patients with 31 primary tissues and 102 metastases. Twenty patients had tissue collected at autopsy and included 19 with more than one metastasis. Metastases were from 20 different tissue locations with the most common sites being liver, lung, lymph node, and brain. The median age at primary diagnosis was 49 years. The clinical subtypes of the primary tumors were 34% Triple Negative, 30% ER+HER2-, 11% ER+HER2+, and 7% ER-HER2+. Patients received an average of 3 lines of therapy in the metastatic setting. The median overall survival from primary diagnosis was 4.5 years and overall survival from metastatic diagnosis was 2 years.

Study phs002622

The Human Gut Microbiome and Recurrent Abdominal Pain in Children

This project explores the nature of the human intestinal microbiome in healthy children and children with recurrent abdominal pain. The overall goal is to obtain a robust knowledge-base of the intestinal microbiome in children without evidence of pain or gastrointestinal disease, children with functional abdominal pain, and children with abdominal pain and changes in bowel habits (irritable bowel syndrome). Multiple strategies have been deployed to navigate and understand the nature of the intestinal microbiome in childhood. These strategies include 454 pyrosequencing-based strategies to sequence 16S rRNA genes and understand the detailed composition of microbes in healthy and disease groups. Microarray-based hybridization with the PhyloChip and quantitative real-time PCR (qPCR) probes are being applied as complementary strategies to gain an understanding of the intestinal microbiome from various perspectives. Data collected and analyzed during the HMP UH2 and UH3 Demo project, from a set of healthy and IBS children may enable the identification of core microbiomes in children in addition to variable components that may distinguish healthy from diseased pediatric states. We are currently analyzing the dataset for the presence of disease-specific signatures in the human microbiome, and correlating these microbial signatures with pediatric health or IBS disease status. This study explores the nature of core and variable human microbiomes in pre-adolescent healthy children and children with recurrent abdominal pain.

Study phs000265

Epigenomics of Human CD8 T cell Differentiation and Aging

The efficacy of the adaptive immune response declines dramatically with age, but the cell-intrinsic mechanisms driving the changes characteristic of immune aging in humans remain poorly understood. One hallmark of immune aging is the loss of self-renewing naive cells and the accumulation of differentiated but dysfunctional cells within the CD8 T cell compartment. Using ATAC-seq, we first inferred the transcription factor binding activities that maintain the naive and central and effector memory CD8 T cell states in young adults. Integrating our results with RNA-seq, we determined that BATF, ETS1, Eomes, and Sp1 govern transcription networks associated with specific CD8 T cell subset properties, including activation and proliferative potential. Extending our analysis to aged humans, we found that the differences between memory and naive CD8 T cells were largely preserved across age, but that naive and central memory cells from older individuals exhibited a shift toward a more differentiated pattern of chromatin openness. Additionally, aged naive cells displayed a loss in chromatin openness at gene promoters, a phenomenon that appears to be due largely to a loss in binding by NRF1, leading to a marked drop-off in the ability of the naive cell to initiate transcription of mitochondrial genes. Our findings identify BATF- and NRF1-driven gene regulation as targets for delaying CD8 T cell aging and restoring T cell function.

Study phs001187

Center for Common Disease Genomics [CCDG] - Cardiovascular: Genetics of Coronary Heart Disease - Characterizaton of Coronary Prone Pedigrees

The primary cohort includes samples from 499 men and 154 women who survived a myocardial infarction, percutaneous transluminal angioplasty, or coronary artery bypass grafting (CABG) by age 55 years for men or age 65 years for women. Patients were seen at least six months after their acute event. Samples from another 488 men and 541 women that showed a nearly identical age, gender, and measured blood pressure distribution were collected as population-based controls. These controls tended to live in urban Salt Lake City, where the vast majority of the population is Caucasian. Blood samples were collected in the morning after 12h to 16h of fasting and prepared according to guidelines of the Lipid Research Clinic's program Manual of Laboratory Operations. All samples have serum, DNA and/or white blood cells, and a host of measurements (e.g. standard clinical chemistries, LDL and HDL cholesterol, triglycerides, glucose, HbA1C, insulin, blood pressures, anthropometric data, information on medical conditions and drug use, etc.). Additional details about the cohort or sample preparation were published previously. Here we present in total 1,475 patients that were successfully sequenced. This number includes 228 women, 419 men, and 7 of unreported gender survivors as well as 339 women and 482 men that served as population-based controls.

Study phs001901

Children's Hospital of Philadelphia (CHOP) Control Copy Number Variation (CNV) Study

We present a database of copy number variations (CNVs) detected in 2,026 disease-free individuals, using high-density, SNP-based oligonucleotide microarrays. This large cohort analyzed for CNVs in a single study using a uniform array platform and computational tools, comprises mainly of Caucasians (65.2%) and African-Americans (34.2%), We have catalogued and characterized 54,462 individual CNVs, 77.8% of which were identified in multiple unrelated individuals. These non-unique CNVs mapped to 3,272 distinct regions of genomic variation spanning 5.9% of the genome; 51.5% of these were previously unreported, and >85% are rare. Our annotation and analysis confirmed and extended previously reported correlations between CNVs and several genomic features such as repetitive DNA elements, segmental duplications and genes. We demonstrate the utility of this data set in distinguishing CNVs with pathologic significance from normal variants. Together, this analysis and annotation provides a useful resource to assist with the assessment of CNVs in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics. The CNV resource is available at: http://cnv.chop.edu. Reprinted from Shaikh T., et al., High-Resolution Mapping and Analysis of Copy Number Variations in the Human Genome: A Data Resource for Clinical and Research Applications Genome Research. 2009, with permission from Genome Research. CHOP CNVs from 2,026 disease-free individuals are available through dbVar at http://www.ncbi.nlm.nih.gov/dbvar/studies/nstd21.

Study phs000199

Etiological Investigation of Cancer Susceptibility in Inherited Bone Marrow Failure Syndromes: A Natural History Study

Background: A prospective cohort of Inherited Bone Marrow Failure Syndrome (IBMFS) will provide new information regarding cancer rates and types in these disorders. Mutations in IBMFS genes are relevant to carcinogenesis in sporadic cancers. Patients with IBMFS who develop cancer differ in their genetic and/or environmental features from patients with IBMFS who do not develop cancer. These cancer-prone families are well suited for cancer screening and prevention trials targeting those at increased genetic risk of cancer. Carriers of IBMFS gene mutations are at increased risk of cancer. The prototype disorder is Fanconi Anemia (FA); other IBMFS will also be studied. Objectives: To determine the types and incidence of specific cancers in patients with an IBMFS. To investigate the relevance of IBMFS gene mutations in the carcinogenesis pathway of the sporadic counterparts of IBMFS-associated cancers. To identify risk factors for IBMFS-related cancers in addition to the primary germline mutations. To determine the risk of cancer in IBMFS carriers. Design: Natural history study, with questionnaires, clinical evaluations, clinical and research laboratory tests, review of medical records, cancer surveillance. Primary endpoints are all cancers, solid tumors, and cancers specific to each type of IBMFS. Secondary endpoints are markers of pre-malignant conditions, such as leukoplakia, serum or tissue evidence of carcinogenic viruses, and bone marrow morphologic myelodyplastic syndrome or cytogenetic clones.

Study phs001481

Transformation of Dysplasia in Barrett's Esophagus

Complex chromosomal alterations are a hallmark of advanced cancers but rarely seen in normal tissue. The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations that can drive their transformation through focal oncogenic amplifications. However, the etiology and evolution dynamics of these alterations are poorly understood. Here we study chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) by multi-regional whole-genome sequencing analysis of BE samples with dysplasia and microscopic EAC foci. Through haplotype-specific copy-number analysis of BE genome evolution, we identified distinct patterns of episodic copy-number evolution consistent with the outcomes of abnormal mitosis and dicentric chromosome breakage. While abnormal mitosis, including whole-genome duplication, accounts for most chromosome or arm-level copy-number changes, segmental copy-number alterations display signatures of multi-generational evolution of unstable dicentric chromosomes. Continuous evolution of dicentric chromosomes through breakage-fusion-bridge cycles and chromothripsis rapidly increases genomic complexity and diversity among BE cells, culminating in the generation of distinct focal amplifications. These mutational processes enable multiple subclones within small dysplastic areas to undergo parallel transformation to cancer following acquisition of distinct oncogenic amplifications. Our results demonstrate how chromosomal instability drives clonal diversification in precancer evolution and promotes tumorigenesis in primary human samples.

Study phs002706

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Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance

Phylogenetic analysis of paired breast carcinomas identifies genetic events associated with clonal recurrence and invasive progression

LySeqST: A targeted sequencing assay for robust genomic classification of diffuse large B-cell lymphoma

Genentech Colon Cancer Screen

Single cell sequencing of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

Molecular characteristics in Burkitt lymphoma over age groups

Ethiopia_Genome_Project__high_coverage_

Allele Balance Bias Identifies Systematic Genotyping Errors and False Disease Associations

The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias

An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup

Rapid identification of somatic genome rearrangements as personalized biomarkers for blood-based cancer monitoring

Genomics of enteropathy associated T cell lymphoma (EATL)

Comparison of structural variations from 10X Genomics linked-reads and conventional Illumina short-reads sequencing

High Grade Serous Ovarian Carcinomas Originate in the Fallopian Tube

Mapping_gene_environment_interactions_in_macrophages

Reconstituting the transcriptome and DNA methylome landscapes of human implantation at single-cell resolution

Comprehensive genomic profiles of small cell lung cancer

Clonal selection and double hit events involving tumor suppressor genes underlie relapse from total therapy

Ethiopia_Genome_Project__low_coverage_

Large-scale viral genome analysis identifies novel clinical associations between hepatitis B virus and chronically infected patients

The_Genomic_Advances_in_Sepsis__GAinS__RNA_seq

Extreme phenotypes define epigenetic and metabolic signatures in cardiovascular diseases.

THE GENOMIC LANDSCAPE OF ACTINIC KERATOSIS

Hypoxia acts as an environmental cue for the human TRM differentiation program

The Molecular Landscape of Asian Breast Cancers Reveals Clinically Relevant Population-Specific Differences

Whole genome, exome and transcriptome analysis to guide individualized cancer interpretation

A recessive PRDM13 mutation results in congenital hypogonadotropic hypogonadism and cerebellar hypoplasia

Comprehensive Genomic Characterization of Refractory Multiple Myeloma Reveals a Complex Mutational and Structural Landscape Associated with Drug Resistance (H067)

Multi-omics integration reveals only minor long-term molecular and functional sequelae in immune cells of individuals recovered from COVID-19

Proteogenomics of chronic lymphocytic leukemia

Whole genome sequencing delineates regulatory, structural, and cryptic splice variants in early onset cardiomyopathy

Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation

T cell landscape definition by multi-omics identifies galectin-9 as novel immunotherapy target in chronic lymphocytic leukemia (CLL)

Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities WGS

Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities RNA-Seq

Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities DNA-Methylation

Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection

Long-term organoid culture of a small intestinal neuroendocrine tumor rna-seq

Patient-derived pediatric brain tumor organoids faithfully recapitulate primary tumors

Long-term organoid culture of a small intestinal neuroendocrine tumor

Transcriptomics identifies blunted immunomodulatory effects of vitamin D in people with multiple sclerosis

Targeting TRIP13 in Wilms Tumor with Nuclear Export Inhibitors

Cancer Genetic Markers of Susceptibility (CGEMS) Prostate Cancer Genome-Wide Association Study (GWAS) - Primary Scan (Stage 1) - PLCO Screening Trial

SUM-seq data for spontaneously differentiated iPSCs to EBs

Estonian Microbiome Project second time point dataset

Single-cell RNA sequencing of control and Notch inhibitor treated HCC PDX model

Somatic mutation in edited cholangiocyte organoids

Autozygosity pilot - Born in Bradford (2017-05-11)

The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

RNA sequencing in primary inflammatory (TPP) macrophages following deletion of a disease-associated gene desert at chr21q22, disruption of ETS2, or treatment of ETS2-edited macrophages with a HIF1α stabiliser.

Single cell transcriptomes of childhood renal tumours

Whole-genome sequence data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

Somatic mutation in edited cholangiocyte organoids

Single cell transcriptional evolution of myeloid leukaemia of Down syndrome – WGS

A Heterozygous Missense Mutation in the Coiled-Coil Domain of STAT5B is Associated with Leukocytosis, Lymphadenopathy, Splenomegaly, Necrotizing Granulomas, Hyper-IgM and Thrombocytopenia

16S rRNA gene V4 region sequencing data, ASV profiles, and sample metadata of human faecal samples predominantly from the Estonian population

Whole-genome methylation profiling of menstrual stem cells identifies novel biomarkers for endometriosis

DRIP-seq data for Molecular Characterization of ETMRs

WGS dataset of Characterization of UV DNA damage in B-cell precursor acute lymphoblastic leukemia

Co-amplification of MYC and CCNE1 in aggressive childhood osteosarcoma

Integrated genomic characterization of adrenocortical carcinoma

A practical guide for mutational signature analysis in hematological malignancies

Mechanisms of patient response to Dabrafenib in Melanoma

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver

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CIDR: NINDS High Throughput Genotyping Resource Access for Structural Hindbrain Disorders

Genome-Wide Association of Type 2 Diabetes in Africans: The AADM Study

Longitudinal Study of Genetic Causes of Intrahepatic Cholestasis

Human CD4 Memory T Cell Activation Time Course

MAESTRO-Pool Enables Highly Parallel and Specific Mutation-Enrichment Sequencing for Minimal Residual Disease Detection in Cohort Studies

Brain Cell Type-Specific Enhancer-Promoter Connectivity Maps and Disease Risk Association

NHLBI TOPMed: Pulmonary Hypertension and the Hypoxic Response in SCD (PUSH)

Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer

Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Atherosclerosis Risk in Communities Study (ARIC)

Inherited chromosomally-integrated human herpesvirus 6A/B (HHV-6A/B) genome sequences in the Japanese population

INSPIRE - Investigator-initiated Phase 2 Study of Pembrolizumab Immunological Response in Metastatic Solid Tumors

Comparison of 133/144bp dominant phenotype vs 166bp dominant phenotype.

The_Genomic_Advances_in_SepsisGAinSRNA_seq