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• CIDR/NICHD Genetic Basis of Recessive Pediatric Brain Diseases - Group 2

  The purpose of this study is to identify new genetic causes of recessive forms of pediatric neurodevelopmental disorders (NDDs) including Cerebellar hypoplasia (CBH), Lissencephaly (LIS), Microcephaly (MIC), Corpus callosum hypoplasia (CCH), Pontocerebellar hypoplasia (PCH), Pontine tegemental cap dysplasia (PTCD), and Aicardi syndrome among many others. Using whole exome sequencing on one or two affected members per family, we are able to identify many pathogenic genes for these families. Using Human SNP Linkage Scans, which takes advantage of the Illumina HumanCore Array, and parametric linkage analysis software (Genehunter, Allegro, and others), we seek to identify pathogenic loci utilizing 60-70 families per year. Through the combination of parametric linkage analysis with exome sequencing and bioinformatics approaches, we will refine our search for superior sensitivity and accuracy when investigating candidate genes and identifying causative mutations for disease.

  Study phs001267

• CIDR/NICHD Genetic Basis of Recessive Pediatric Brain Diseases

  The purpose of this study is to identify new genetic causes of recessive forms of pediatric neurodevelopmental disorders (NDDs) including cerebellar hypoplasia (CBH), lissencephaly (LIS), microcephaly (MIC), corpus callosum hypoplasia (CCH), pontocerebellar hypoplasia (PCH), pontine tegmental cap dysplasia (PTCD), and Aicardi syndrome among many others. Using whole exome sequencing on one or two affected members per family, we are able to identify many pathogenic genes for these families. Using Human SNP Linkage Scans, which takes advantage of the Illumina HumanCore Array, and parametric linkage analysis software (Genehunter, Allegro, and others), we seek to identify pathogenic loci utilizing 60-70 families per year. Through the combination of parametric linkage analysis with exome sequencing and bioinformatics approaches, we will refine our search for superior sensitivity and accuracy when investigating candidate genes and identifying causative mutations for disease.

  Study phs001060

• CIDR NICHD Genetic Basis of Recessive Pediatric Brain Diseases - Group 4

  The purpose of this study is to identify new genetic causes of recessive forms of pediatric neurodevelopmental disorders (NDDs) including Cerebellar hypoplasia (CBH), Lissencephaly (LIS), Microcephaly (MIC), Corpus callosum hypoplasia (CCH), Pontocerebellar hypoplasia (PCH), Pontine tegmental cap dysplasia (PTCD), and Aicardi syndrome among many others. Using whole exome sequencing (WES) on one or two affected members per family, we are able to identify many pathogenic genes for these families. Using Human SNP Linkage Scans, which takes advantage of the Illumina HumanCore Array, and parametric linkage analysis software (Genehunter, Allegro, and others), we seek to identify pathogenic loci utilizing 60-70 families per year. Through the combination of parametric linkage analysis with exome sequencing and bioinformatics approaches, we will refine our search for superior sensitivity and accuracy when investigating candidate genes and identifying causative mutations for disease.

  Study phs001822

• CIDR NICHD Genetic Basis of Recessive Pediatric Brain Disease - Group 3

  The purpose of this study is to identify new genetic causes of recessive forms of pediatric neurodevelopmental disorders (NDDs) including Cerebellar hypoplasia (CBH), Lissencephaly (LIS), Microcephaly (MIC), Corpus callosum hypoplasia (CCH), Pontocerebellar hypoplasia (PCH), Pontine tegmental cap dysplasia (PTCD), and Aicardi syndrome among many others. Using whole exome sequencing (WES) on one or two affected members per family, we are able to identify many pathogenic genes for these families. Using Human SNP Linkage Scans, which takes advantage of the Illumina HumanCore Array, and parametric linkage analysis software (Genehunter, Allegro, and others), we seek to identify pathogenic loci utilizing 60-70 families per year. Through the combination of parametric linkage analysis with exome sequencing and bioinformatics approaches, we will refine our search for superior sensitivity and accuracy when investigating candidate genes and identifying causative mutations for disease.

  Study phs001510

• ABCB1 expression in HCC biopsies

  We analyzed the ABCB1 expression in RNA-seq data of 134 HCCs (120 of these were previously published), including the biopsies from which the 3 doxorubicin-sensitive and 3 doxorubicin-resistant HCCOs were derived.

  Study EGAS50000000041

• Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia [scRNAseq]

  This dataset contains single-cell RNA, individually reference-aligned data from 203 individuals representing four Indonesian populations: the general urban population of Denpasar and the traditional community of Pedawa Village in Bali, as well as the traditional community of Yoboi Village (in Lake Sentani) and Sereh Village (individuals from highland Papua residing near Lake Sentani) in Papua. The dataset was produced as part of the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia, a study aimed at characterizing how genetic background and environmental context shape immune cell states across diverse Indonesian communities.

  Dataset EGAD50000002385

• Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia [TCR]

  This dataset contains single-cell TCR, individually reference-aligned data from 203 individuals representing four Indonesian populations: the general urban population of Denpasar and the traditional community of Pedawa Village in Bali, as well as the traditional community of Yoboi Village (in Lake Sentani) and Sereh Village (individuals from highland Papua residing near Lake Sentani) in Papua. The dataset was produced as part of the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia, a study aimed at characterizing how genetic background and environmental context shape immune cell states across diverse Indonesian communities.

  Dataset EGAD50000002383

• Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands

  Identification and quantification of low-frequency mutations remain challenging despite improvements in the baseline error rate of next-generation sequencing technologies. Here, we describe a method, termed SaferSeqS, that addresses this challenge by (1) efficiently introducing identical molecular barcodes in the Watson and Crick strands of template molecules and (2) enriching target sequences with strand-specific PCR. The method achieves high sensitivity and specificity and detects variants at frequencies below 1 in 100,000 DNA template molecules with a background mutation rate of <5 × 10-7 mutants per base pair (bp). We demonstrate that it can evaluate mutations in a single amplicon or simultaneously in multiple amplicons, assess limited quantities of cell-free DNA with high recovery of both strands and reduce the error rate of existing PCR-based molecular barcoding approaches by >100-fold.

  Study EGAS00001005048

• Variant Calling used in ABB project

  This dataset has two Variants Files in VCF format used in ABB project (https://github.com/Francesc-Muyas/ABB). One has the variants found in a Rare Variant Association Study performed in CLL patients. This has 1217 samples represented. The other variant file has 209 SNPs predicted in 10 samples by GATK HaplotypeCaller and selected for Sanger Sequencing Validation. Raw reads were aligned against the Human Reference genome (Hg19) with BWA mem and variants were obtained using GATK HaplotypeCaller.

  Dataset EGAD00001004132

• WES profiles from the CheckMate-274 clinical trial

  The dataset contains WES profiles of 487 patients from the CA209-274 clinical trial. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. Normalized WES libraries were pooled and sequenced on Illumina NovaSeq 6000 at a plex level appropriate to the coverage of tumor: 2 × 100 bp PE 100 M reads, germline: 2 × 100 bp PE 25 M reads.

  Dataset EGAD50000000792

• RNAseq profiles from the CheckMate-274 clinical trial

  The dataset contains RNAseq profiles of 370 patients from the CA209-274 clinical trial. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. RNAseq libraries (75PE, 50M) were sequenced on Illumina NovaSeq 6000 at a plex-level appropriate to the coverage of 2 × 50 base pair (bp) paired end (PE) 50M reads. Fastq files are included.

  Dataset EGAD50000000793

• EED inhibition of organoid development

  Transcriptomics and epigenomics after chemical inhibition of EED during early human brain organoid development. To investigate the role of H3K27me3 inhibition during neuroectoderm induction, we treated brain organoids with 3 concentrations of EED inhibitor (and control) during the transition of pluripotency to neuroepithelium. At the neuroepithelium stage, we profiled the organoids using scRNA-seq (transcriptome) and bulk Cut&Tag (H3K27me3, H3K27ac). Library preparation for scRNA-seq was carried out with the 10x genomics platform.

  Dataset EGAD50000000224

• Long read whole genome sequencing data from brain postmortem tissue

  Chart genetic variation in the human brain in healthy controls and Parkinson’s disease (PD) patients.

  Study EGAS50000000921

• PBMC scRNA-seq data using 10X Genomics platform

  Matrices of counts from single-cell RNA-seq data and single-cell CITE-seq data collected from 16 patients enrolled in GO30103 trial, and the cell level annotation. Specifically, PBMCs at C1D1, C1D15 (2 weeks after treatment), C2D1 (3 weeks after treatment) and C4D1 (9 weeks after treatment) were collected and subject to 10x Genomics protocol. Associated metadata also included.

  Dataset EGAD50000000370

• BLUEPRINT Whole-genome fingerprint of the DNA methylome during human B-cell differentiation

  We used whole-genome bisulfite sequencing (WGBS) to generate unbiased DNA methylation maps of six purified B-cell subpopulations: hematopoietic progenitor cells (HPC); pre-B-II cells (preB2C); naive B cells from peripheral blood (naiBC); germinal center B cells (gcBC); memory B cells from peripheral blood (memBC) and plasma cells from bone marrow (bm-PC). WGBS was performed in 2 biological replicates from each subpopulation.

  Dataset EGAD00001001304

• Dataset for urologic_cancer-EXON

  Rare cancer sequencing data of 112 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008904

• Latency and interval therapy affect the evolution in metastatic colorectal cancer

  While comparison of primary tumor and metastases has highlighted genomic heterogeneity in colorectal cancer (CRC), previous studies have focused on a single metastatic site or limited genomic testing. Combining data from whole exome and ultra-deep targeted sequencing, we explored possible evolutionary trajectories beyond the status of these mutations, particularly among patient-matched metastatic tumors. Our findings confirm the persistence of known clinically-relevant mutations (e.g. those of RAS family of oncogenes) in CRC primary and metastases, yet reveal that latency and interval systemic therapy affect the course of evolutionary events within metastatic lesions. Specifically, our analysis of patient-matched primary and multiple metastatic lesions, developed over time, showed a similar genetic composition for liver metastatic tumors, which were 21-months apart. This genetic makeup was different from those identified in lung metastases developed before manifestation of the second liver metastasis. These results underscore the role of dormancy in the evolutionary path of metastatic CRC.

  Study EGAS00001003646

• Immune cell atlas of environmental and ancestral diversity in Indonesia [scRNAseq]

  Island Southeast Asia (ISEA) remains consistently underrepresented in large-scale human genomic resources despite its rich ancestral and lifestyle diversity. The region's complex population history and environmental/pathogen pressures could have shaped its populations' unique immune responses. Here, we generated single-cell PBMC profiles from 199 Indonesians sampled across four populations in the islands of Bali and New Guinea. The dataset consists of low-pass whole genome sequencing and pooled single-cell PBMC transcriptome sequencing. These groups capture diversity in regional genetic ancestries (West ISEA-like and Papuan-like) and lifestyle contrasts (urban versus rural communities in Bali; highland versus lowland communities in New Guinea), providing a window into how ancestry and environment jointly shape immune variation across ISEA. Together, this study provides the first large-scale single-cell immune atlas of ISEA, highlighting how ancestral and environmental diversity jointly shape human immunity in this globally important yet understudied region.

  Study EGAS50000001656

• Immune cell atlas of environmental and ancestral diversity in Indonesia [WGS]

  Island Southeast Asia (ISEA) remains consistently underrepresented in large-scale human genomic resources despite its rich ancestral and lifestyle diversity. The region's complex population history and environmental/pathogen pressures could have shaped its populations' unique immune responses. Here, we generated single-cell PBMC profiles from 199 Indonesians sampled across four populations in the islands of Bali and New Guinea. The dataset consists of low-pass whole genome sequencing and pooled single-cell PBMC transcriptome sequencing, including T-cell receptor (TCR). These groups capture diversity in regional genetic ancestries (West ISEA-like and Papuan-like) and lifestyle contrasts (urban versus rural communities in Bali; highland versus lowland communities in New Guinea), providing a window into how ancestry and environment jointly shape immune variation across ISEA. Together, this study provides the first large-scale single-cell immune atlas of ISEA, highlighting how ancestral and environmental diversity jointly shape human immunity in this globally important yet understudied region.

  Study EGAS50000001655

• NHLBI TOPMed: Determining the Association of Chromosomal Variants with Non-PV Triggers and Ablation-Outcome in AF (DECAF)

  The DECAF trial was conducted at the Texas Cardiac Arrhythmia Institute (TCAI) in 2013 in collaboration with the University of Texas at Austin. Four hundred consecutive AF patients undergoing catheter ablation were enrolled. All participants provided voluntary informed consents. Blood samples were collected before the ablation procedure and labeled with anonymous patient identifier. The researchers at UT Austin responsible for DNA extraction and genetic analysis were blinded about the clinical characteristics and identification of the study participants. AF cases included adults >18 years of age from both sex and all AF types.

  Study phs001546

• Genome Sequencing and Variant Calling of HCM Patients with MYH7 Variants

  To investigate potential genetic causes of cardiomyopathy we recruited 48 patients harboring rare MYH7 variants identified from panel-based testing and with a clinical manifestation of cardiomyopathy. Genome sequencing was performed to identify other potential causative variants and genetic modifiers of the cardiomyopathy phenotype, which varied among patients.

  Study phs004024

• LongVar low-coverage data

  This dataset includes sequencing data from participants of the LongVar study. Specifically, it comprises low-coverage whole genome sequencing (WGS) data which was derived from cell-free DNA from blood samples. These data were generated to compare imputation accuracy. 133 individuals agreed to share their data, and are healthy volunteers.

  Study EGAS50000001114

• Single cell chromatin accessibility profiles from myelofibrosis patients

  To explore how JAK2V617F disrupts cell-fate and the regulatory chromatin landscape of HSCs, we applied GoT-ChA to CD34+ sorted progenitor cells from 21 human primary samples, comprising 18 patients with JAK2V617F-mutated MF (no additional mutations, except for Pt-08), who either had no treatment (n = 12; including three longitudinal samples from a PV patient who progressed to MF) or who were treated with ruxolitinib (n = 6), a JAK1/2 inhibitor. We included a JAK2V617F CH sample (Pt-19) to explore early epigenetic changes, before the onset of overt hematological abnormality.

  Dataset EGAD50000000234

• RNAseq of Sjögren's Syndrome and Healthy Volunteers' Salivary Glands

  Mechanistic genetic and inflammatory endpoints were studied to gain insight into the molecular mechanisms of Sjögren's syndrome. Transcriptomic studies allowed the exploration of molecular alterations that might cause or influence the studied salivary gland pathology and potentially elucidate druggable pathways for intervention.

  Study phs001842

• Human_Evolution_3

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.

  Study EGAS00001000315

• RNA-Seq on OCIAML-22 Fractions

  The donor AML patient (unsorted) that was used to generate OCI-AML22 was expanded for the indicated number of days (Donor: 0 day, 12d: 12 days, 2m: 2 months, 3m: 3 months), then sorted for the indicated fraction (CD34p: CD34+; CD34m: CD34-, CD38m: CD38-, CD38m: CD38-).

  Study EGAS00001006512

• Reference exome data for Australian Aboriginal populations from Western Australia and the Northern Territory

  Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) population of Martu origin. Sequence data for both NT and WA samples were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. The data is provided as 2 VCF files, one for the WA population and one for the NT population.

  Dataset EGAD00001005189

• DECONVOLUTION OF HEMATOPOIETIC STEM/PROGENITOR CELL SIGNALING IN HUMAN AML

  A comprehensive taxonomy of the predicted interactions between LEPR + stromal niches, HSPCs and adaptive/innate immune cells in the human NBM and AML

  Study EGAS00001007330

• Long read mRNA sequencing of human neural retinal samples - Usher syndrome transcript landscape

  Long-read (PacBio) RNA sequencing dataset of three neural retinal samples. Three PacBio libraries were prepared according the 'standard workflow' optimized for sequencing transcripts centered around 2kb. Additionally one Library (input HNR_S2) was prepared according an optimized 'long workflow' to enrich for larger transcripts up to >10kb. To further enhance the capture of full-length transcripts for USH2A and ADGRV1 (USH2C) genes, we also employed a targeted enrichment approach using the Samplix Xdrop System, followed by PacBio long-read sequencing. USH2A and ADGRV1 enrichment was performed by targeting '5- mid and 3' targets of the respective genes. Finally, we also added ONT (Oxford Nanopore technology) long-read mRNA sequencing of three independent neural retina samples. These data were used for the validation of events observed from the Iso-Seq and Samplix data. The ONT datasets contain sequencing data of the Usher-associated genes. Files are raw BAM, and CRAM format files generated by a Sequel II machine. Additionally, the ccs3 BAM format files are included.

  Dataset EGAD50000000720

• Whole genome sequencing data of paediatric patients with BCR::ABL1 acute lymphoblastic leukemia

  The BCR::ABL1 fusion results from the t(9;22)(q34;11.2) translocation, also known as the Philadelphia chromosome. In children, BCR::ABL1-positive leukemia is rare, accounting for approximately 3% of cases. The BCR::ABL1 oncoprotein activates multiple signaling pathways that drive cell proliferation. Historically, this subtype was associated with an extremely poor prognosis; however, the incorporation of tyrosine kinase inhibitors into therapy has markedly improved outcomes, with overall survival now approaching 80% in pediatric patients. Relapse most commonly occurs through the emergence of clones harboring kinase domain mutations, yet 30–40% of relapses arise in the absence of such mutations, a phenomenon that remains poorly understood.

  Study EGAS50000001512

• Single Cell Omics Resolves Transcriptional Alterations in Sjogren's Syndrome

  Single cell omics resolves transcriptional alterations in Sjogren's Syndrome. This data compares the single cell transcriptional profiles of the minor salivary glands between Sjogren’s Syndrome patients and non-Sjogren’s Syndrome subjects. Portions of this data were reported in two separate publications: Huang & Perez, et al., 2021 Nature Medicine and Yin, et al., 2021, Frontiers in Immunology . 

  Study phs002446

• CentralAfricanCMC_Pemberton

  The CentralAfricanCMC_Pemberton dataset encompasses 153,798 SNPs from the Illumina Cardio-MetaboChip (Voight et al. 2012) genotyped in 406 individuals from 19 Central African Populations from Gabon, Cameroon, Centralafrican Republic and Uganda). Individual phenotypic and cultural information at the individual level for this data set encompass gender, lifestyle (hunter-gatherer or farmer), and, when available, stature phenotype (standing height in cm, sitting-height in cm, and weight in kg). Other cultural, linguistic, and geographical location information about the sampled populations can be found in Pemberton et al. , Human Genetics, 2018 (https://doi.org/10.1007/s00439-018-1902-3).This dataset can only be accessed and used for non-commercial research purposes with a finality complying with the informed consent provided by Central African donors for the study of human evolutionary history only.

  Dataset EGAD00010001584

• MYOSEQ

  The MYOSEQ project focuses on the application of next generation sequencing, in particular whole exome sequencing (WES), in a large cohort of patients with unexplained limb‐girdle weakness (LGW). Focusing on undiagnosed patients with a clearly defined clinical phenotype enables increased diagnostic rates for known genes (in particular Pompe disease, GNE related pathologies and other known LGMD subtypes) in this cohort, while the use of WES provides scope both for new gene discovery and for additional research into disease modifiers and genotype‐phenotype correlation with substantial cost effectiveness. The LGW patient cohort was collated by Newcastle University in collaboration with clinical centers across Europe. The sequencing was performed at the Broad Institute and jointly analyzed with Newcastle University.

  Dataset EGAD00001006158

• Oesophageal adenocarcinoma WGS from LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19)

  This dataset contains whole genome sequencing (WGS) generated from the inoperable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19). WGS data were generated with the aim to assess previously reported (e.g. tumour mutational burden) and novel predictive genomic markers for immunochemotherapy treatment in this setting. Using these data, mutation and copy number profiles were generated for the LUD2015-005 study, which were assessed for correlation with patient outcomes from this trial.

  Dataset EGAD00001009400

• CXCL8 secreted by immature granulocytes inhibits wildtype hematopoiesis in chronic myelomonocytic leukemia

  CXCL8 secreted by immature granulocytes inhibits wildtype hematopoiesis in chronic myelomonocytic leukemia [Abstract] In chronic myelomonocytic leukemia, blocking CXCL8 produced by clonal dysplastic granulocytes is a potential therapeutic strategy to slow disease progression. [Data provided] Exome-sequencing, bulk mRNA-seq and single-cell RNA-seq of iGRAN, monocytes and PBMC of CMML patients and controls.

  Dataset EGAD50000000789

• Cutaneous Melanoma GWAS Combining Multiple Populations and Risk Phenotypes

  Most genetic susceptibility to cutaneous melanoma (CM) remains to be discovered. Meta-analysis genome-wide association study (GWAS) of 36,760 melanoma cases (67% newly-genotyped) and 375,188 controls identified 54 significant loci with 68 independent SNPs. Analysis of risk estimates across geographical regions and host factors suggests the acral melanoma subtype is uniquely unrelated to pigmentation. Combining this meta-analysis with nevus count and hair colour GWAS, and transcriptome association approaches, uncovered 31 potential secondary loci, for a total of 85 CM susceptibility loci. These findings provide substantial insights into CM genetic architecture, reinforcing the importance of nevogenesis, pigmentation, and telomere maintenance together with identifying potential new pathways for CM pathogenesis.

  Study phs001868

• Single-cell gene expression profiling of human iPSCs-derived cortical organoids

  To investigate the relationships between cerebral cortical organoid morphological characteristics and cellular composition, we morphologically classifi ed human iPSC-derived cortical organoids and analyzed the cellular makeup of each morphological type by single-cell gene expression profi ling.

  Study JGAS000726

• Whole-genome sequencing study of uveal melanoma

  Uveal melanoma is the most common primary intraocular cancer, characterized by metastasis-related mortality. Here, we explored whole-genome sequences from 40 primary uveal melanomas to illustrate the landscape of genomic mutations and investigate their association with prognosis.

  Study EGAS50000001603

• WNT7B-reporter organoids sorted

  Transcriptomic data from pancreatic ductal adenocarcinoma (PDAC) organoids to investigate the role of WNT7B. This dataset includes: - Bulk mRNA sequencing of WNT7B-reporter pancreatic ductal adenocarcinoma (PDAC) organoids sorted for cells displaying low, medium and high expression of the reporter

  Study EGAS50000001543

• scRNA-seq data set for 13 AML patients

  This dataset includes single cell (sc)RNA-seq of N=13 AML patients. The dataset includes bam files that have been purged of reads mapping to cells where a majority of the reads from that cell mapped to the human genome. All scRNA-seq data were generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) from 10X Genomics.

  Dataset EGAD50000001346

• Evaluation_of_size_selection_on_cancer_specific_sequencing_libraries

  A couple of previously characterized and sequenced libraries will be repeated using a couple of differing size selection criteria and skim sequenced using an Illumina HiSeq. The resulting sequence will be analyzed to determine the optimal DNA library size for our specific downstream analysis.

  Study EGAS00001000293

• Childhood cerebellar tumors mirror conserved fetal transcriptional programs

  We used single-cell transcriptomics to study >60,000 cells from the developing murine cerebellum, and show that different molecular subgroups of childhood cerebellar tumors mirror the transcription of cells from distinct, temporally restricted cerebellar lineages.

  Study EGAS00001003170

• Whole-exome sequencing of BCP HD ALL on Illumina HiSeq 2000, 100 bp paired-end

  Genomic DNA from leukemic and remission bone marrow mononuclear cells was isolated with the QIAamp DNA Blood Extraction Kit (Qiagen, Venlo, The Netherlands). Libraries were prepared with the Illumina TruSeq DNA Sample Prep and TruSeq Exome Enrichment Kits (Illumina, San Diego, CA, USA) according to the manufacturer's recommendations. 100 bp paired-end sequencing was performed on a HiSeq 2000 (Illumina) to about 80x coverage.

  Dataset EGAD00001002653

• Y-phylogeny-haplogroupDE (2019-04-03)

  High-coverage whole genome sequences using Hiseq X for 4 individuals to investigate their Y chrosmosmes' relationship to the known phylogeny. 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/ . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004892

• Loss-of-activity-mutation in the cardiac chloride-bicarbonate exchanger AE3 causes short QT syndrome

  Patients with short QT syndrome (SQTS) may present with syncope, ventricular fibrillation or sudden cardiac death. Six SQTS susceptibility genes, encoding cation channels, explain less than 25% of SQTS cases. Here we identify a missense mutation in the anion exchanger (AE3)-encoding SLC4A3 gene in two unrelated families with SQTS. The mutation causes reduced surface expression of AE3 and reduced membrane bicarbonate transport. Slc4a3 knockdown in zebrafish causes increased cardiac pHi, short QTc, and reduced systolic duration, which is rescued by wildtype but not mutated SLC4A3. Mechanistic analyses suggest that an increase in pHi and decrease in [Cl-]i shortened the action potential duration. However, other mechanisms may also play a role. Altered anion transport represents a mechanism for development of arrhythmia and may provide new therapeutic possibilities.

  Study EGAS00001002632

• TNBC ctDNA Targeted Panel

  Circulating tumour DNA (ctDNA) detection in liquid biopsy is an emerging alternative to tissue biopsy, but its utility in treatment response monitoring and prognosis in triple negative breast cancer (TNBC) remains to be well understood. In this study, we determined the presence of early stage TNBC ctDNA detectable actionable mutations with a clinically validated hotspot treatment indication panel. Sequencing of plasma DNA from 130 TNBC patients collected within 7 months of primary treatment completion revealed that 7.7% had detectable residual disease with a hotspot panel. Among neoadjuvant treated patients, we observed a trend where patients with incomplete pathologic response and positive ctDNA within 7 months of treatment completion were at risk of reduced progression free survival. We propose that a high risk subset of early TNBC patients treated in NAT protocols may be identifiable by combining tissue response and sensitive ctDNA detection.

  Study EGAS00001006937

• The RNA, ChIP and whole exome sequencing analysis of human colorectal cancer organoids and normal colon organoids treated with (+)-JQ1

  To reveal the mechanism of anti-tumor effect of (+)-JQ1, we performed RNA, ChIP and whole exome sequencing using human colorectal cancer and normal colon organoids.

  Study JGAS000378

• shallow whole genome sequencing BAM files aligned to the human reference genome GRCh38

  We profiled large B-cell lymphoma (LBCL) patient plasma samples with ultra-low-pass (shallow) whole genome sequencing. The DNA sequencing was performed on pre-capture genomic libraries, with an intended mean coverage of at least 0.1X, FASTQ files were cleaned by fastp and mapped to the reference human genome (GRCh38) with bwa.

  Dataset EGAD50000001497

• RNA-Sequencing data of patient derived normal fibroblasts (NFs), cancer associated fibroblasts (CAFs) and tumor spheroid samples

  RNA-Sequencing data of patient derived normal fibroblasts (NFs), cancer associated fibroblasts (CAFs) and tumor spheroid samples performed in the context of the characterization of an IL1R1 positive CAF population in CRC tumour samples.

  Study EGAS00001007205

• Insights from genome-wide data from Thailand and Laos

  We provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies

  Study EGAS00001006053

• RNAseq of 76 samples from Uveal Melanoma tumors

  Hotspot mutations in the spliceosome gene SF3B1 are reported in 20% of uveal melanomas. SF3B1 is involved in 3'-splice site (3'ss) recognition during RNA splicing; however, the molecular mechanisms of its mutation have remained unclear. Here we show, using RNA-Seq analyses of uveal melanoma, that the SF3B1 R625/K666 mutation results in deregulated splicing at a subset of junctions, mostly by the use of alternative 3'ss.

  Dataset EGAD00001004398

• Whole genome sequencing of Xeroderma Pigmentosum leukemias samples

  In the current study we report for the first time the unique collection of 6 leukemias and two sarcomas from XP-C. Comprehensive WGS-based mutational analysis provides genetic explanation for the increased incidence of leukemia in XP-C and describes an unique mutational process in internal tumors associated with NER deficiency. Raw data are provided in FASTQ format and variant analysis as VCF files.

  Dataset EGAD00001006322

• Diet driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome

  This study profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events. Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline.

  Study EGAS00001006982

• Whole exome sequencing of ETV::RUNX1 positive acute lymphoblastic leukemia

  This dataset contains whole exome sequencing of ETV::RUNX1 positive acute lymphoblastic leukemia. Germline and leukemia samples were sequenced in pairs. A total of 94 samples were sequenced and reads were aligned to hg19 genome reference. Aligned bam files are provided in this data set.

  Dataset EGAD50000001184

• Gene expression in human monocyte differentiation

  This dataset consists of RNA-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 63 samples.

  Dataset EGAD00001007956

• Epi_Tax_targeted_sequencing

  Sequencing of 350 cancer genes in BC samples from patients treated with either Epirubicin or Paclitaxel monotherapy in the neoadjuvant setting.

  Study EGAS00001000587

• DUX4 activates novel intergenic transcripts and isoforms in a tissue-specific context

  DUX4, a transcription factor driving zygotic genome activation during the embryonic cleavage stage in mammals, regulates the expression of genic and non-genic elements and modulates chromatin accessibility. Its misexpression in skeletal muscle causes Facioscapulohumeral muscular dystrophy (FSHD). The sporadic expression of DUX4 in FSHD muscle and the limitations of short-read RNA sequencing challenge, however, a comprehensive grasp of its consequences on the muscle transcriptome. Here, leveraging full-length isoform RNA sequencing with short-read RNA sequencing on DUX4-inducible myoblasts, we elucidated DUX4-induced transcriptomic changes within a myogenic context. DUX4 yields a complex transcriptome featuring numerous unannotated isoforms from known and novel loci. Moreover, we observed distinct isoform usage of DUX4 target genes between myogenic and embryonic cleavage states highlighting the distinct differences between DUX4 transcription factor activity in skeletal muscle and during the cleavage stage. We also identified ~1,400 unannotated intergenic isoforms predominantly originating from repetitive elements such as LTRs, LINEs, and SINEs. Integration with available datasets delineates the transcriptional and epigenetic landscape of these loci across myogenic and embryonic backgrounds. Like the cell type-specific isoform production, the usage of DUX4 binding sites at these intergenic loci is in part cell type-specific. Collectively, these findings demonstrate substantial and context-specific transcriptomic alterations induced by DUX4 further enriching our understanding of DUX4-induced muscle pathology.

  Study EGAS50000000503

• Transdisciplinary Studies of Genetic Variation in Colorectal Cancer(CORECT): Axiom GWAS

  This study is part 1 of 2 for Schumacher et al, Nat Commun. 2015 Jul 7;6:7138. Part 1 is the original GWAS data for 9,259 participants on the Affymetrix Axiom platform of the studies listed below in the Inclusion Criteria.

  Study phs001856

• Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma

  Angiosarcomas are rare malignant tumors of the endothelium, arising commonly from the head and neck region (AS-HN) and recently associated with ultraviolet (UV) exposure and human herpesvirus-7 (HHV-7) infection. We examined 81 cases of angiosarcomas, including 47 cases of AS-HN, integrating information from whole genome sequencing, gene expression profiling and spatial transcriptomics (10X Visium). In the AS-HN cohort, we observed recurrent somatic mutations in CSMD3 (18%), LRP1B (18%), MUC16 (18%), POT1 (16%) and TP53 (16%). UV-positive AS-HN harbored significantly higher tumor mutation burden (TMB) than UV-negative cases (p=0.0294). NanoString profiling identified three clusters with distinct tumor inflammation signature (TIS) scores (p<0.001). Spatial transcriptomics revealed topological profiles of the tumor microenvironment, identifying dominant but tumor-excluded inflammatory signals in “immune-hot” cases and immune foci even in otherwise “cold” cases. In conclusion, spatial transcriptomics reveal the tumor immune landscape of angiosarcoma, and in combination with multi-omic information, may improve implementation of treatment strategies.

  Study EGAS00001007083

• Microbial signatures and innate immune gene expression in lamina propria phagocytes of inflammatory bowel diseases patients

  The microbial populations associated with the lamina propria phagocyte population in CD and UC patients was examined. Specifically, the differences between phagocyte-associated microbiota (PAM) and mucosa-associated microbiota were determined.

  Study EGAS00001003105

• Analysis of the relationship between disease phenotype and genotype in patients with Alzheimer's disease

  In this study, we explored the genetic background of Alzheimer's disease by intercomparative analysis of the genetic background of sporadic Alzheimer's disease and disease phenotypes derived from iPS cells.

  Study JGAS000383

• Rearrangements of Viral and Human Genomes at Human Papillomavirus Integration Events and Their Allele-Specific Impacts on Cancer Genome Regulation

  We discovered genomic and epigenomic dysregulation originating at sites of human papillomavirus (HPV) integration following the Oxford Nanopore long-read analysis of 72 cervical cancer genomes. The integration events had allele-specific effects on the genome, methylome, and transcriptome, which sometimes resulted in the activation of cancer genes. We also examined the 72 samples using Illumina short-read analysis in phs000528.

  Study phs003780

• Exome-wide analysis identifies three low-frequency missense variants associated with pancreatic cancer risk in Chinese populations

  Germline coding variants have not been systematically investigated for pancreatic ductal adenocarcinoma (PDAC). Here, we report an exome-wide investigation using the Illumina Human Exome Beadchip with 943 PDAC cases and 3,908 controls in the Chinese population, followed by two independent replicate samples including 2,142 cases and 4,697 controls. We identify three low-frequency missense variants associated with the PDAC risk: rs34309238 in PKN1 (OR = 1.77, 95% CI: 1.48-2.12, P = 5.35 X 10-10), rs2242241 in DOK2 (OR = 1.85, 95% CI: 1.50-2.27, P = 4.34 X 10-9) and rs183117027 in APOB (OR = 2.34, 95% CI: 1.72-3.16, P = 4.21 X 10-8).

  Study EGAS00001003040

• Shared disease specific B cell clones in Crohn’s disease

  We performed deep sequencing of the B cell receptor (BCR) repertoire in four cohorts of patients with Crohn’s disease (CD) together with healthy and disease controls. Using sequence homology, we identified BCR clones that were shared between patients with CD but not found in healthy individuals nor in patients with ulcerative colitis (UC), indicating CD-associated B cell immune responses. Shared clones were present in inflamed gut mucosa, draining intestinal lymph nodes and blood, suggesting the presence of common CD-associated antigens that drive B cell responses in CD patients.

  Study EGAS50000000912

• Genomics analysis of mucinous tumours of the ovary and related neoplasms

  To perform genetic and gene expression analyses on mucinous ovarian tumours to determine a progression model, cell of origin and novel therapeutic targets.

  Study EGAS00001003545

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence (RNA-seq)

  Understanding how prostate cancer cells adapt to AR-targeted interventions is critical for identifying novel drug targets to improve the clinical management of treatment-resistant disease. Our study revealed an enzalutamide-induced epigenetic plasticity towards pro-survival signaling, and uncovered circadian regulator ARNTL as an acquired vulnerability after AR inhibition, presenting a novel clinical lead for therapeutic development.

  Study EGAS00001006016

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence (ChIP-seq)

  Understanding how prostate cancer cells adapt to AR-targeted interventions is critical for identifying novel drug targets to improve the clinical management of treatment-resistant disease. Our study revealed an enzalutamide-induced epigenetic plasticity towards pro-survival signaling, and uncovered circadian regulator ARNTL as an acquired vulnerability after AR inhibition, presenting a novel clinical lead for therapeutic development.

  Study EGAS00001006017

• scRNA-seq of a 3D human cortical tissue model from human iPSCs exploring 2D versus 3D co-culturing

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model, as well as 2D co-cultures for comparison. Samples include distinct conditions as described in the Study section. The dataset was generated using the BD Rhapsody technology and sequenced paired-end with Illumina NovaSeq2000. Information on the multiplexing of samples is reported in the Analyses section.

  Dataset EGAD50000002021

• Ashkenazi Jewish Leukoencephalopathy

  Genetic leukoencephalopathies (gLEs) are a group of heterogeneous disorders with white matter abnormalities in the central nervous system (CNS). Patients affected with gLEs have brain white matter defects that can be seen in MRI and exhibit variable neurologic phenotypes including motor impairment, hypotonia, pyramidal dysfunction, dystonia and/or dyskinesias, ataxia, seizures, cortical blindness, optic atrophy, and impaired cognitive development. The exact causes in half of gLEs are unknown. We studied three unrelated families affected with an undiagnosed gLE and discovered a homozygous germline mutation c.2536T>G in VPS11 by whole exome sequencing, a gene involved in membrane trafficking and fusion of the lysosomes and endosomes, as a novel cause of a new gLE syndrome.

  Study EGAS00001001767

• A Phase I/IB Study of Ipilimumab or Nivolumab in Patients With Relapsed Hematologic Malignancies After Allogeneic Hematopoietic Cell Transplantation

  Relapse after allogeneic hematopoietic stem cell transplantation (HSCT) is characterized by poor outcomes and novel therapeutic options are urgently needed. Immune checkpoint blockade using CTLA-4 and PD-1 blocking antibodies are a potential concept for reinstating a dormant graft-versus-leukemia (GvL) effect.This study investigated transcriptomic changes in biopsies obtained from patients who received immune checkpoint blockade for relapsed hematologic malignancy post-HSCT and elucidated transcriptional programs associated with successful reinvigoration of GvL. Differential gene expression analysis showed evidence of increased T cell infiltration in biopsies of responders to ipilimumab treatment and demonstrated shared gene programs between GvL and GvHD.

  Study phs002377

• Impact of germline pathogenic variants in 27 cancer-predisposing genes on the risk of lymphoma

  The application of advanced molecular technology has significantly expanded lymphoma classification, allowing risk stratification and treatment optimization. Limited evidence suggests the presence of a genetic predisposition in lymphoma, indicating the potential for better individualized clinical management based on a novel lymphoma classification. Herein, we examined the impact of germline pathogenic variants in 27 cancer-predisposing genes with lymphoma risk and explored the clinical characteristics of pathogenic variant carriers. This study included 2,066 lymphoma patients and 38,153 cancer-free controls from the Japanese population. Following quality control of sequencing data, samples from 1,982 lymphoma patients and 37,592 controls were further analyzed. Sequencing data of controls were obtained from JGAD000721. Germline pathogenic variants in some cancer-predisposing genes were associated with a high risk of lymphoma. Furthermore, germline pathogenic variants in these genes were especially associated with the higher risk of a certain subtype. These results would provide novel insights concerning monogenic form into lymphoma classification. Some lymphoma patients may benefit from surveillance and targeted treatment like other neoplasms.

  Study JGAS000347

• Exceptional Outcomes in a Phase Ib Study Combining PARP and MEK Inhibition, With or Without Anti-PD-L1, for BRCA-Wildtype Platinum-Sensitive Recurrent Ovarian Cancer

  To evaluate regimens combining PARP and MEK inhibition, with or without PD-L1 inhibition, for BRCA-wildtype platinum-sensitive recurrent ovarian cancer (PSROC).

  Study EGAS00001007496

• Whole genome, whole exome and transcriptome sequencing of 10 ccRCC with Von Hippel-Lindau disease

  The aim of this study is to investigate genetic and transcriptomic profiles of inherited ccRCC with Von Hippel-Lindau disease.

  Study JGAS000544

• Fluctuating DNA methylation tracks cancer evolution at clinical scale

  Long-read Nanopore data of fCpGs from Gabbutt & Duran-Ferrer (2025) for developing the EVOFLUx method to study cancer evolution via DNA methylation fluctuations.

  Study EGAS50000001192

• 16S rRNA Rectal Mucus

  16S rRNA sequencing of rectal mucus samples from patients suspected to have colorectal cancer. This is 1 of 4 sequencing experiments on the same sample type.

  Study EGAS50000001262

• Whole genome sequencing of ATCWGS42

  WGS of patient ATCWGS42, a patient who responded to BRAF/MEK targeted therapy but relapsed. This folder includes multi-region sequencing from the patient.

  Study EGAS50000001489

• Enzymatic Methyl-Seq Rectal Mucus

  Enzymatic methyl sequencing of rectal mucus samples from patients suspected to have colorectal cancer. This is 1 of 4 sequencing experiments on the same sample type.

  Study EGAS50000001314

• miRNA

  The purpose is to perform miRNA analysis on FACS sorted target immune cell populations to uncover novel potential miRNA diagnostic markers biomarkers predictive of therapy response but also possibly identify perturbed signaling pathways or miRNA targets of intervention with the use of agomirs/antagomirs.

  Dataset EGAD50000002025

• Matched_Pair_Cancer_Cell_line_Whole_Genomes

  We propose to definitively characterise the somatic genetics of 29 matched pair cell lines through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000160

• Breast cancer sequential sampling study

  This study aims to whole genome sequence DNA derived from breast cancer patients who received neo-adjuvany chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Dataset EGAD00001000387

• Mitochondrial DNA mosaicism in human somatic cells

  Genomic alterations accumulate in the somatic cells throughout an individual’s lifetime. Recent sequencing studies have documented widespread mutations in the nuclear genome and the frequent clonal competition of normal cells carrying mutations. However, the landscape of mitochondrial DNA (mtDNA) heteroplasmy in normal human tissues is poorly understood. This study investigated the whole genome sequences (WGSs) of 2,096 clones established from non-neoplastic healthy single cells obtained from 31 donors. In addition, we analyzed 31 WGSs of neoplastic cells, including 12 clones established from adenomatous polyps from one individual with MUTYH-associated polyposis and 19 matched colorectal carcinomas from individuals who donated normal colorectal clones.

  Dataset EGAD50000000373

• input

  Input dataset of human islets. To be used in conjuction with Cohesin and Mediator ChIP-Seq datasets.

  Dataset EGAD00001005209

• Accumulation of copy number alterations and clinical progression across advanced prostate cancer

  The burden of copy number alterations positively associated with radiologically-evident distant metastases at diagnosis (P=0.00006) and showed a non-linear relationship with clinical outcome on univariable and multivariable analysis, characterised by a sharp increase in the relative risk of progression (P=0.003) and death (P=0.045) for each unit increase, stabilising into more modest increases with higher burdens. This association between copy number burden and outcome was similar in each of the four metastatic states. Copy number loss occurred significantly more frequently than gain at the lowest copy number burden quartile (q=4.1X10-6). Loss of segments in chromosome 5q21-22 and gains at 8q21-24, respectively including CHD1 and cMYC, occurred more frequently in cases with higher copy number alteration (for either region: Kolmogorov–Smirnov distance, 0.5; adjusted P<0.0001). Copy number alterations showed variability across tumor regions in the same prostate. This variance associated with increased risk of distant metastases (Kruskal-Wallis test P=0.037).

  Study EGAS00001006251

• 120 individuals from the TEENAGE study (Ntalla et al., 2013) have been genotyped on the Illumina HumanCoreExome-12v1-1_A array. This is a population-based study of adolescents from the Attica region in Greece

  120 individuals from the TEENAGE study (Ntalla et al., 2013) have been genotyped on the Illumina HumanCoreExome-12v1-1_A array. This is a population-based study of adolescents from the Attica region in Greece

  Study EGAS00001001733

• DCIS Whole Exome & Whole Genome Sequencing Data

  Primary DCIS and recurrent DCIS/IBC (total n=82, ipsilateral n=78 and contralateral n=4) as well as non-recurrent DCIS (n=32) cases were identified through hospital databases from Royal Melbourne Hospital (RMH), Nottingham City Hospital (UK), the LifePool cohort and Peter MacCallum Cancer Centre (PMCC). All cases were micro-dissected from haematoxylin stained sections (range 4-20 sections) by manual micro-dissection to achieve >50% tumour tissue purity. DNA was extracted using the FFPE AllPrep kit (Qiagen, MD, USA). Depending on the success and timing of DNA extraction (Figure 1), cases were analysed by a targeted sequencing panel (n=46, samples pre-2020), whole exome sequencing (WES, n=67), or low-coverage whole genome sequencing (LCWGS). WES: DNA was processed by the Australian Genome Research Facility (AGRF) using the Twist Bioscience Human Comprehensive Exome v1 or v2 (Twist Bioscience HQ, South San Francisco, CA, USA) according to the Twist Target Enrichment Standard Hybridisation Protocol. Sequencing was performed on the Illumina NovaSeq 6000 with 150 bp paired-end reads for a median depth of 101.29x, range: 20.39-247x. Whole Genome Sequencing (WGS): Libraries for four paired samples with matched stromal DNA were made, processed and sequenced by AGRF using the IDT xGen Kit (USA) according to the manufacturer’s protocol, aiming to achieve 60x depth for tumour DNA and 30x for matched normal. File type: Paired-end FASTQ.

  Dataset EGAD50000001846

• ICGC_Benchmarking_Exercise

  The main objective of this benchmark is the comparison of the full sequencing pipeline of different ICGC partners, including procedures, methods and performance of library preparation and whole-genome deep-sequencing. A secondary objective will be a follow-up comparison of data analysis pipelines for identification of germline and somatic variants subsequent to the results of the ICGC Somatic Variant Calling Pipeline Benchmark.

  Study EGAS00001000433

• Multiple_Myeloma_Diagnosis_to_Relapse_study_samples

  The study will investigate serial samples from the same patient taken at the time of MGUS or SMM diagnosis, and later at the time of evolution towards MM. Samples will be sequenced by whole genome along with a matched normal to obtain the highest possible amount of information toinvestigate genomic changes at disease evolution.

  Study EGAS00001001299

• Whole exome DNA sequence profiling of spatial biopsies of high grade serous epithelial ovarian cancer

  The study aims at dissecting the heterogeneity across multiple biopsies of high grade serous epithelial ovarian cancer (HGS-EOC) through a comprehensive characterization of variants and structural changes at the whole exome level. To this aim, the study uses samples from multiple bioptic sites taken from eight HGS-EOC patients.

  Study EGAS00001003048

• Circulating Tumor DNA in Checkpoint Inhibitor treated Lung Cancer

  BackgroundImmune checkpoint inhibitors (ICI) are increasingly used to treat non-small cell lung cancer (NSCLC) and there is a critical need for novel predictive/prognostic biomarkers. We evaluated whether dynamics of circulating tumor (ctDNA) can identify NSCLC patients who benefit from single agent ICI.MethodsCirculating cell-free DNA (cfDNA) from 177 patients was analyzed prior ICI and at first treatment evaluation using a Commercial 77-gene panel. We performed de novo mutation calling and corrected for variants related clonal hematopoiesis. ctDNA changes were evaluated as predictors of tumor response estimated with PET/diagnostic CT and survival.ResultsMutations were detected in 159 of 174 (91.4%) analyzable patients. Most responders presented decreasing ctDNA levels, while non-responders had mixed molecular responses. Patients with a >50% molecular ctDNA decrease or no detectable ctDNA demonstrated improved PFS (5.9 versus 1.8 months; HR 0.49, 95%CI, 0.35-0.67, P < .001), and OS (18.9 versus 9.9 months; HR 0.41, 95%CI, 0.30-0.57, P < .001) compared to patients not achieving these endpoints. Clearance of mutations (and no detected ctDNA) had a similar effect (PFS HR 0.45, 95%CI, 0.32-0.61, P < .001; OS 0.37,95%CI, 0.27-0.52, P < .001) compared to patients having stable or additional mutations. After adjusting for clinical factors both >50% ctDNA decrease (HR 0.4, 95% CI, 0.3-0.6, P < .001) and clearance of mutations (HR 0.42, 95% CI, 0.3-0.6, P < .001) remained independent predictors for PFS and OS.ConclusionsctDNA testing reveals significant prognostic albeit not predictive information in ICI treated advanced NSCLC. This relevant information can be obtained with a commercial easy-to-implement ctDNA test that will facilitate extensive testing.

  Study EGAS00001004847

• RNAseq of primary mesothelioma cell lines

  Mesothelioma is an aggressive cancer associated with previous exposure to asbestos and dismal prognosis. Since a pemetrexed/cisplatin combination was introduced for treatment of mesothelioma, no new first- or second-line therapies have been discovered. Thus, to better understand what drives mesothelioma carcinogenesis and to identify potential targets for therapy, in this project we aim at performing RNAseq analysis of a panel of mesothelioma cells lines.

  Dataset EGAD00001009642

• NHLBI TOPMed: Boston Early-Onset COPD Study

  Chronic obstructive pulmonary disease (COPD) is the third leading cause of death in the United States and the only leading cause of death that is steadily increasing in frequency. This project collected a set of extended pedigrees ascertained through subjects with severe, early-onset COPD. This study has enrolled subjects with severe COPD (forced expiratory volume in one second (FEV1) < 40% predicted) at an early age (< 53 years) without alpha-1 antitrypsin deficiency (a known Mendelian risk factor for COPD). Extended pedigrees are enrolled, primarily in New England, although some more geographically distant subjects have been included. This study has been used for epidemiological studies, familial aggregation analysis, linkage analysis, and candidate gene association analysis. Approximately 80 of the severe, early-onset COPD probands will undergo whole genome sequencing in this project with sequencing data available through dbGaP.

  Study phs000946

• Exome sequencing data from two myelosarcomas

  Isolated myeloid sarcoma (MS, i.e. acute myeloid leukemia without detectable bone marrow infiltration) is rare and most patients subsequently develop overt AML. We prospectively performed whole exome sequencing of uterine MS, concomitant morphologically normal bone marrow (BM) and subsequently developing AML from two women. Both patients harbored preleukemic clones in the morphologically normal BM, including DNMT3A mutations. In addition, recurrent mutations were identified in the NFE2 gene, a gene not previously associated with AML or isolated MS. Retrospective studies of further MS samples, twelve with and four without preceding or concomitant bone marrow AML, revealed NFE2 mutations in two additional cases, both with isolated MS and prior myeloid malignancies. We conclude that DNMT3A mutated preleukemia may predispose for the frequent bone marrow relapses following isolated MS and that recurrent NFE2 mutations may have a role in the development of isolated MS.

  Study EGAS00001002562

• Feasibility of Ultra-Rapid Exome Sequencing in Critically Ill Infants and Children With Suspected Monogenic Conditions in the Australian Public Health Care System

  Critically ill infants and children with suspected monogenic conditions underwent ultra-rapid whole exome genetic testing. A molecular diagnosis was established in 51% of the patients. This study suggests feasibility of ultra-rapid genomic testing in critically ill pediatric patients.

  Study EGAS00001005430

• Juvenile Idiopathic Arthritis exome sequencing in a consanguineous family

  Identify the causative gene defect in three affected patients with JIA.

  Study EGAS00001003510

• Identification Of Pathogenic Mutations And Application Of Polygenic Risk Scores In Early-Onset Diabetes Patients

  Maturity-onset Diabetes of the Young (MODY) presents a diagnostic challenge. In this study we investigate the genetic background of Latvian early-onset diabetes patients, using whole-genome sequencing data. Additionally, we investigate the utility of previously published and available type 1 diabetes (T1D) and type 2 diabetes (T2D) polygenic risk scores in differentiating monogenic diabetes (MODY) from T1D and T2D cases.

  Study EGAS50000000991

• This agreement governs the terms on which access will be granted to the data generated by the United Kingdom Brain Expression Consortium.

  Dac EGAC00001001408

• A single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

  Nodal B-cell non-Hodgkin lymphomas (B-NHL) are a clinically diverse set of cancers thought to originate from distinct stages of B-cell maturation. To characterize intratumor heterogeneity across B-NHL entities, we performed CITE-Seq (cellular indexing of transcriptomes and epitopes) on 51 lymph node samples including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL) and marginal zone lymphoma (MZL, n = 11) tumors, in addition to non-malignant reactive lymph nodes (rLN, n = 8). We also performed 5 prime scRNA-seq with immune receptor profiling for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL, and 2 MZL).

  Study EGAS50000000342

• Tissue DNA, WBC DNA and cfDNA (deep-)sequencing of mCRC patients treated with doublet chemotherapy and anti-EGFR in the CAIRO5 study

  This study assessed whether ctDNA based treatment response monitoring could be performed in a tumor tissue-independent manner by combining ultra-deep targeted sequencing analyses of cfDNA with patient-matched white blood cell (WBC) derived DNA. In total, 183 cfDNA and 49 WBC samples, along with 28 tissue samples, from 52 metastatic colorectal cancer patients participating in the prospective phase III CAIRO5 clinical trial (NCT02162563) were analyzed using the PGDx elio plasma resolve assay.

  Study EGAS00001006695

• Measurement of the Male Germline Mutation Rate Using Sequential Sperm Samples

  We recalled 23 sperm donors with prior banked samples to provide a new sperm sample. The old and new sequential sperm samples were then profiled by high-fidelity duplex sequencing to measure individual-specific mutation rates and patterns. We also performed deep whole-genome sequencing of sequential sperm samples from two individuals followed by targeted validation, which measured remarkably stable mosaicism of clonal mutations that likely arose during embryonic and germline development.

  Study phs003716

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  To elucidate the feature of age-associated helper T (ThA) cells and its contribution to autoimmune diseases, CD4+ T cell subsets from 19 rheumatoid arthritis (RA), 62 systemic lupus erythematosus (SLE), 40 idiopathic inflammatory myopathy (IIM) and 64 healthy controls (HC) were collected (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA). RNA-seq was performed with each CD4+ T cell subset samples.

  Study JGAS000626