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• JAK and STAT alterations in CD30 positive LPD

  JAK and STAT alterations in CD30 positive LPD, panel sequencing, 12 cutaneous lymphoma patients, 40 samples

  Dataset EGAD00001005801

• An isoform quantitative trait locus in SBNO2 links genetic susceptibility to Crohn’s disease with defective antimicrobial activity

  Despite major advances in linking single genetic variants to single causal genes, the significance of genetic variation on transcript-level regulation of expression, transcript-specific functions, and relevance to human disease has been poorly investigated. Strawberry notch homolog 2 (SBNO2) is a candidate gene in a susceptibility locus with different variants associated with Crohn’s disease and bone mineral density. The SBNO2 locus is also differentially methylated in Crohn’s disease but the functional mechanisms are unknown. Here we show that the isoforms of SBNO2 are differentially regulated by lipopolysaccharide and IL-10. We identify Crohn’s disease associated isoform quantitative trait loci that negatively regulate the expression of the noncanonical isoform 2 corresponding with the methylation signals at the isoform 2 promoter in IBD and CD. The two isoforms of SBNO2 drive differential gene networks with isoform 2 dominantly impacting antimicrobial activity in macrophages. Our data highlight the role of isoform quantitative trait loci to understand disease susceptibility and resolve underlying mechanisms of disease. This dataset contains RNAseq raw data from CD14+ monocyte-derived macrophages and siRNA-mediated knockdown experiments, as well as RNAseq raw data from THP-1 monocytes-derived macrophages following ectopic expression of SBNO2 isoforms.

  Dataset EGAD50000000264

• Impact of Mobile Element Insertions on Human Transcriptome Variation

  Mobile DNA elements are ubiquitous in nearly all species and mobile element insertions can affect nearby gene expression through many mechanisms, from disrupting coding regions to initiating DNA methylation to altering RNA splicing patterns. Thousands of mobile element insertions are still polymorphic in human populations, and these polymorphic mobile element insertions (pMEIs) can contribute to transcriptome and phenotypic variation in humans. We identified and genotyped pMEIs using the whole genome sequencing (WGS) data from the Genotype-Tissue Expression (GTEx) project. We then used the extensive multi-tissue transcriptome data from the GTEx project to systematically assess the effects of pMEIs on human transcriptome variation.

  Study phs002030

• Intercepting Progression from Pre-Invasive to Invasive Lung Adenocarcinoma

  An improved understanding of the biology of lung cancer is needed to intercept the disease at an early point in its progression. In this project we have used multidimensional methods to profile the tumor microenvironment (TME) and to determine the crosstalk between cancer cells and the TME in pre-invasive to invasive human lung non-solid adenocarcinomas. Comparative analysis of the cellular and molecular events associated with the distinct histological stages will lead to identification of the critical events triggering progression and thereby identify targets to intercept disease progression. The data being submitted represents the genomic profiles of patient samples with pre-invasive and invasive human lung adenocarcinomas.

  Study phs002818

• Genomic Landscape of Pediatric Germ Cell Tumors

  Germ cell tumors (GCTs) are cancers of the testis, ovary and extragonadal sites that occur in infants, children, adolescents, and adults. Post-pubertal (type II) malignant GCTs may present as a seminoma, non-seminoma or with mixed histologies. In contrast, pre-pubertal (type I) GCTs are limited to (benign) teratomas and (malignant) yolk sac tumors (YST). Epidemiologic and molecular data have shown that pre- and post-pubertal GCTs arise by distinct mechanisms. Dedicated studies of the genomic landscape of type I and II GCTs in children and adolescents are lacking. Here we present an integrated genomic analysis of extracranial GCTs across the age spectrum from 0-24 years.

  Study phs002009

• Derivation and Investigation of The First Human Cell-Based Model of Beckwith-Wiedemann Syndrome

  Beckwith-Wiedemann Syndrome (BWS) is the most common human imprinting disorder, and phenotypes include hepatomegaly and hepatoblastoma development. In approximately 20% of patients, this syndrome is caused by uniparental isodisomy of the paternal allele across chromosome 11p15 (pUPD11). From fibroblasts cultured from 2 BWS patients with pUPD11, we derived induced pluripotent stem cells (iPSC) and differentiated to hepatocytes to study a model of the BWS liver transcriptome through RNA-Seq. Compared to 2 similarly derived controls, we observed differential expression in insulin signaling, cell proliferation, and cell cycle pathways, indicating their potential importance in the liver overgrowth and oncogenesis associated with BWS.

  Study phs002365

• Systematic immune cell dysregulation and molecular subtypes revealed by single cell RNA-seq of subjects with type 1 diabetes

  Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting beta-cells. A comprehensive immune cell phenotype evaluation in T1DM has not been performed thus far at the single. In this cross-sectional analysis, we generated a single-cell transcriptomic dataset of peripheral blood mononuclear cells (PBMCs) from 46 manifest T1DM (Stage 3) cases and 31 matched controls.Our study reveals a surprisingly strong systemic dimension at the level of immune cell network in T1DM, defines disease-relevant molecular subtypes and has the potential to guide non-invasive test development and patient stratification.

  Study EGAS50000000231

• Association of Oxidative Stress Pathway Alterations with Risk of Treatment Failure in RTOG9512: A Randomized Trial of Hyperfractionation Versus Conventional Fractionation in T2 Squamous Cell Carcinoma of the Vocal Cord

  Based on the growing body of retrospectively collected and heterogeneously treated clinical cohorts and preclinical models, we investigated the clinical importance of NRF2 pathway alteration in an independent set of patients treated uniformly in the large prospective phase III trial RTOG 9512. We tested the hypothesis that patients with T2 glottic squamous cell carcinoma (SCC) harboring NRF2 pathway mutations would show radioresistance and have more local failure (LF) and locoregional failure (LRF) compared to those who did not have these mutations, using patients who received radiotherapy alone, thus removing potentially confounding effects of other therapies, like surgery or chemotherapy.

  Study phs003274

• NHLBI TOPMed: Chicago Initiative to Raise Asthma Health Equity (CHIRAH)

  The CHIRAH project was a community-based study of the factors associated with asthma morbidity in the African American population. CHIRAH evaluated the role of various variables (biologic/environmental, psychologic/behavioral, and socioeconomic) on asthma morbidity and the function of changes in these variables on asthma morbidity in a longitudinal fashion. This involved collection of a cohort-based on school screening which was sampled to include similar numbers of underprivileged and non-underprivileged subjects which roughly equally represented self-reported African Americans and self-reported non-African Americans. Subjects were followed up every 3 months of this cohort over the course of 2 years.

  Study phs001605

• DNTR sequencing data of paediatric acute lymphoblastic leukemia

  This study used the DNTR-seq method in leukaemia samples to profile the whole-genome and mRNA jointly in single cells. Direct tagmentation is used in a collection of single-cell whole genome sequencing (scWGS) methods, including DNTR-seq, which provide high quality data at ultra-low to low coverage. The overall goal was to characterize the genetic and transcriptional heterogeneity of cancer samples. To infer clonal structure and evolutionary history, copy number analysis based workflows were implemented. Bone marrow mononuclear cells from pediatric acute lymphoblastic leukemia samples were FACS sorted into 384 plates to generate the DNA and RNA profiles.

  Study EGAS50000001247

• Genomic analysis Nasopharyngeal cancer through whole exome sequencing and whole genomic sequencing.

  Nasopharyngeal carcinoma (NPC) is a squamous-cell carcinoma and has remarkable ethnic and geographic distribution, with a high prevalence in southern China, southeast Asia, northern Africa and Alaska. Although there are previous studies implicated NF-κB pathway play an important role in NPC. Newer research also found several important cellular processes and pathways in NPC, including chromatin modification, ERBB-PI3K signaling and autophagy machinery. Put these studies together, although, NPC is still poorly understood at the genetic level. Here we determined the mutational landscape of 553 cases with NPC using whole-genomic and whole-exome sequencing. These approaches revealed a distinct mutational signature and significantly mutated genes.

  Study EGAS00001002788

• Chordoma_Sequencing_Project_RNAseq

  This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

  Study EGAS00001000410

• ICGC Oesophageal adenocarcinoma - 100 tumour samples

  The oesophageal project will focus on adenocarcinoma which is increasing in incidence in the UK and other developed countries and has a very poor outcome. The primary aims of this project are to deeply sequence tumour and normal genomic DNA (including the precursor condition Barrett’s oesophagus when material is available) to provide a comprehensive catalogue of somatic mutations. This will be achieved through a UK-wide network of hospitals involved in a research collaboration called the OCCAMS consortium. The goal of this project is to use high quality clinical material with accurately annotated clinic-pathological, treatment and outcome data.

  Study EGAS00001000724

• Genetics and transcriptomes of pediatric B cell precursor leukemia with gain of chromosome 21

  Down syndrome (DS, constitutive trisomy 21) children have a 27-fold increased risk of developing B-ALL (DS-ALL), face a worse outcome due to treatment-related morbidities, and an increased rate of relapses compared to other children. This highlights the need to better understand the mechanisms of DS-associated leukemogenesis to develop more adapted treatment. In this study, we characterized the genetic and transcriptomic landscapes of DS-ALL and found a high incidence of somatic mutations leading to RAS/MAPK pathway activation in DS-ALL, as seen in other pediatric B-ALL presenting somatic gains of the chromosome 21 (B-ALL+21).

  Study EGAS00001003760

• Ovarian carcinosarcoma genomics and eribulin response

  Ovarian carcinosarcoma (OCS) is an aggressive and rare tumour type with limited treatment options. OCS is hypothesised to develop via the combination theory, with a single progenitor resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). In this study, we analysed DNA variants from isolated carcinoma and sarcoma components to show that OCS from 18 women is monoclonal. RNA sequencing indicated the carcinoma components were more mesenchymal when compared with pure epithelial ovarian carcinomas, supporting the conversion theory and suggesting that EMT is important in the formation of these tumours.

  Study EGAS00001006555

• NHLBI GO-ESP: Early-Onset Myocardial Infarction Exome Chip (Broad EOMI)

  The NHLBI "Grand Opportunity" Exome Sequencing Project (GO-ESP), a signature project of the NHLBI Recovery Act investment, was designed to identify genetic variants in coding regions (exons) of the human genome (the "exome") that are associated with heart, lung and blood diseases. These and related diseases that are of high impact to public health and individuals from diverse racial and ethnic groups will be studied. These data may help researchers understand the causes of disease, contributing to better ways to prevent, diagnose, and treat diseases, as well as determine whether to tailor prevention and treatments to specific populations. This could lead to more effective treatments and reduce the likelihood of side effects. GO-ESP is comprised of five collaborative components: 3 cohort consortia - HeartGO, LungGO, and WHISP - and 2 sequencing centers - BroadGO and SeattleGO. As part of this initiative, the Broad has performed genotyping on several thousand subjects from 4 different cohorts on Illumina's ExomeChip platform as described below: The Duke Study: The Duke study enrolled cases from the Duke University Medical Center with myocardial infarction or coronary artery stenosis > 50%. Controls were individuals who were > 50 years old without coronary stenosis > 30% and without history of myocardial infarction, coronary artery bypass grafting, percutaneous coronary intervention, or heart transplant. The InterMountain Heart Study: The Intermountain Heart Study is an observational registry of individuals with coronary artery disease and healthy controls who received care at participating Intermountain Healthcare facilities. The Ottawa Heart Study: The Ottawa heart study enrolled cases with angiographically confirmed coronary artery disease (> 1 coronary artery with > 50% stenosis) who did not have type 2 diabetes and were ≤ 50 years old for males and ≤ 50 years old for females. Controls were also enrolled who were asymptomatic males > age 65 and females > age 70. PennCATH: PennCATH is a case-control study that recruited individuals undergoing coronary angiography at the University of Pennsylvania Hospital. Cases had angiographically confirmed coronary artery disease (>1 coronary artery with 50% stenosis) and were ≤ 55 years old if male and ≤ 60 years old if female. Controls were men > 40 years old and women > 45 years old with normal coronary angiography.

  Study phs000936

• 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

• 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

• Whole-Genome Sequencing (WGS) of a Malignant Granular Cell Tumor (GCT) with Metabolic Response to Pazopanib

  We report one case study of a malignant granular cell tumor patient with metabolic response to pazopanib. In this study, we used whole-genome sequencing of the tumor with the matched blood to characterize the somatic mutation profile in this tumor. This is the first reported whole-genome sequencing study of the rare malignant granular cell tumor.

  Study phs000978

• Whole-genome variant calling of individuals from the study of allergic diseases in the Canary Islands

  Research study of genetic susceptibility and analyses of polygenic risk scores in allergic diseases. This dataset consists of variant data derived from whole-genome sequencing in reference samples from one of the parental populations (i.e., North Africans). The dataset consist of 15 VCF files (and corresponding index files) with a total of 1.58 million variants called using GATK v4 and following the Broad Variant Calling Best Practices, from a set of unrelated individuals sequenced in paired-read mode 2x150 bp using an Illumina HiSeq 4000 sequencer.

  Dataset EGAD50000000429

• WGS of cord blood hematopoietic stem and progenitor cells

  In this study, the mutational effects of prenatal chemotherapy exposure on cord blood hematopoietic stem and progenitor cells was investigated in cord blood samples taken from 10 healthy pregnant women, 4 pregnant cancer patients receiving no systemic anti-cancer treatment during pregnancy and 12 pregnant cancer patients receiving chemotherapy during pregnancy. Sequencing was performed on Illumina platforms.

  Study EGAS50000000288

• Spatial transcriptome analysis of aging of healthy skin samples

  Previous studies have revealed that skin T cells accumulate and maintain immune responses in the elderly. However, we questioned why these functional T cells fail to recognize and eliminate malignant cells, making elderly skin more prone to developing malignant tumors. To address this question, we examined the overall skin microenvironment in aging using Xenium digital spatial RNA sequencing.

  Study JGAS000771

• BulkRNAseq - Notch Signaling Maintains a Progenitor-Like Subclass of Hepatocellular Carcinoma

  To identify the Notch signaling components expressed in both the human cancer cells and mouse stromal cells that typically comprise PDX tumors, we performed bulk RNA sequencing. Our results demonstrate that a JAG1-NOTCH2 signaling axis within the human cancer cell population drives the Notch dependency in the super-responder models, with NOTCH2 serving as the functionally relevant receptor.

  Study EGAS50000000515

• Genome-wide copy number analysis of neuroblastoma

  Neuroblastoma is the most common extracranial solid tumor in childhood. Despite the improvement of risk-stratified therapies, overall survival rate of high-risk group is still as low as 40-50%. To investigate genome-wide copy number profiles of neuroblastoma, we performed SNP array analysis and PCR-based amplicon deep sequencing of neuroblastoma-related genes in 522 neuroblastoma samples.

  Study JGAS000046

• Bulk-mRNA sequencing comparing hiPSC derived vascular cells from CADASIL patient lines

  CADASIL is a hereditary brain small vessel disease caused by pathogenic variants in the NOTCH3 gene and causes degenration of Vascular Smooth Muscle cells in the brain. We performed bulk-mRNA sequencing and transcriptomic analysis from hiPSC derived vascular cells (hiPSC;Endothelial Cells; Neural Crest Cells; Vascular Smooth Muscle Cells) comparing CADASIL patient lines and respective isogenic-controls.

  Study EGAS50000001507