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• Integrative Analysis of Pediatric Acute Leukemia Identifies Acute Myeloid/T-Lymphoblastic Leukemia Subtype that Spans a T Lineage and Myeloid Continuum with Distinct Prognoses

  Genomic characterization of pediatric patients with acute myeloid leukemia (AML) has revealed age specific mutational spectrums, distinguishing it biologically from adult patients. While gene expression profiling signatures can differentiate subsets of pediatric AML, its clinical utility in risk stratification has remained limited.

  Study EGAS00001004701

• snRNA-seq schizophrenia control Prefrontal cortex

  Human Brodmann Area 8/9 tissue from 43 schizophrenia subjects and 42 control individuals was obtained from three sources, NBB (Netherlands Brain Bank), Craig A. Stockmeier (University of Mississippi Medical Center), Macedonian/New York State Psychiatric Institute Brain Collection (Andrew J. Dwork, Columbia University). All subjects included in the study were matched between the two groups for age, gender, and postmortem interval. Nuclei were isolated and enriched for 85% neuronal nuclei before single nucleus RNA sequencing was performed with 10x Genomics Chromium Single Cell protocol v3.

  Dataset EGAD50000002447

• ovarian cancer sample exome seq

  Tissue samples were collected from 18 ovarian cancer patients. After mechanical and enzymatic dissociation, a part of these tissues underwent growth factoromics analysis. For four cases, single-cell sequencing analysis was conducted under conditions with or without estradiol. Additionally, the remains of the tissues were frozen and subsequently subjected to exome sequencing on 16 of these samples. Sixteen cases were diagnosed as HGSOC, while two samples were clear cell or mucinous type (Extended Data Table 1). All cases were grade 3, and none had received neoadjuvant chemotherapy.

  Dataset EGAD50000002057

• Enzymatic methylation sequencing of rectal mucus from patients suspected to have colorectal cancer

  This dataset contains comprises enzymatic methylation sequencing (EM-Seq) data generated from 208 rectal mucus samples from patients suspected to have colorectal cancer and healthy controls. Targeted CpG sites were enriched using a panel of genes implicated in colorectal cancer, and libraries were prepared with NEBNext EM-Seq prior to Illumina sequencing. Sequencing was performed on the Illumina NovaSeq6000 platform, producing paired-end FASTQ files. These data support analyses of DNA methylation patterns in CRC detection and progression

  Dataset EGAD50000001871

• Sequencing data for the manuscript "Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas"

  Mapping the spatial organization of DNA-level somatic copy number changes in tumors can provide insight to understanding higher-level molecular and cellular processes that drive pathogenesis. We describe an integrated framework of spatial transcriptomics, tumor/normal DNA sequencing, and bulk RNA sequencing to identify shared and distinct characteristics of an initial cohort of eleven gliomas of varied pathology and a replication cohort of six high-grade glioblastomas.

  Dataset EGAD50000001394

• (RNA-seq) Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  Raw and processed RNA-seq data from a patient-derived xenograft (yielding 18 samples) and the VOA1066 undifferentiated endometrial carcinoma cell-line (yielding 15 samples). PDX samples were treater with either compound-14, dBRD9, or were untreated. VOA1066 samples were treated with either compound-12, dBRD9, or were untreated. Samples were sequenced on an Illumina NextSeq 500 using 37-bp single-end sequencing. Raw fastq files and gene count tables are included for each sample.

  Dataset EGAD50000001471

• Single-cell multi-omics and mtDNA genotyping of human peripheral blood cells

  This dataset comprises two mtscATAC-seq libraries (customized 10X ATAC-seq) generated from donor M80 and donor H05, and one DOGMA-seq library (customized 10X multiome) generated from donor H05, all derived from primary human peripheral blood mononuclear cells. Patient M80 is an 80-year-old male with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), while donor H05 is a healthy 5-year-old pediatric donor. The raw FASTQ files have been provided.

  Dataset EGAD50000001489

• Transcriptomic analyisis of 54 samples of AC16 cells exposed to trastuzumab

  Data of 54 samples with their 54 paired fastaq files that were sequenced in a Novaseq 6000 platform. Samples correspond to the three biological replicates of AC16 cells (i.e. AC16, C1, C2). Each biological replicate was edited to carry either of the three different genotypes of the rs1136201 variant (i.e. AA, AG, GG) and each genotype was enriched to express HER2 protein in three levels (i.e. low, medium and high expression) as selected by FACS. Additionally, treatment of each sample was performed and sequenced in duplicates (i.e. 1 and 2)

  Dataset EGAD50000001705

• Fragmentomics profiling and quantification of plasma Epstein-Barr virus DNA enhance prediction of future nasopharyngeal carcinoma.

  This dataset included human plasma EBV DNA target-capture sequencing data. The capture probes were designed to cover the entire EBV genome and selected human autosomal regions. After enrichment, the products were sequenced on the NextSeq500 System (Illumina) and aligned to the EBV genome (AJ507799.2) and the human genome (hg19) in BAM format. A total of 558 cases were analyzed, including seven subjects who developed NPC in the second-round screening, 431 non-NPC subjects with first-round transiently positive EBV, and 120 non-NPC subjects with first-round persistently positive EBV.

  Dataset EGAD50000001449

• BAM file s of WGS data of Progressive supranuclear palsy patients

  BAM files of healthy controls (3) and Progressive supranuclear palsy (PSP) patients (4). Genomic DNA from donors was fragmented, end-polished, A-tailed, and ligated with Illumina adapters, followed by size selection. Libraries were PCR-amplified (unless PCR-free), purified with AMPure XP, assessed on the Agilent Fragment Analyzer, and quantified using Qubit and qPCR. Qualified libraries were pooled and sequenced on Illumina platforms, and low-quality reads or adapter-contaminated reads were removed. Clean data were then mapped to the hg38 reference genome using BWA.

  Dataset EGAD50000001758

• SATB1 KO Treg and Teff cells: ATAC-seq

  We expanded human Treg and CD4+ Teff cells for 9 days, re-activated the cells and performed CRISPR/Cas9 RNP-mediated KO at day 11. The cells were treated with a pro-inflammatory cytokine IL-12 on day 12. 4 days after editing, living cells were FACS-sorted, the cell nuclei were extracted and prepared for ATAC-seq. AAVS1 KO served as control. The transcription factors SATB1 and two other targets (included to increase the robustness of the dataset) were knocked-out. Three biological replicates have been applied.

  Dataset EGAD50000001276

• SATB1 KO Treg and Teff cells: RNA-seq

  We expanded human Treg and CD4+ Teff cells for 9 days, re-activated the cells and performed CRISPR/Cas9 RNP-mediated KO at day 11. The cells were treated with a pro-inflammatory cytokine IL-12 on day 12. 4 days after editing, living cells were FACS-sorted, the RNA was extracted and prepared for RNA-seq. AAVS1 KO served as control. The transcription factors SATB1 and two other targets (included to increase the robustness of the dataset) were knocked-out. Three biological replicates have been applied.

  Dataset EGAD50000001277

• FASTQ Data from In Situ Hi-C on Medulloblastoma Tissue Samples

  29 Hi-C datasets [8 G3 (MB3667, MB3687, MB3690, MB3692, MB3693, MB4010, MB4037, MB4141), 13 G4 (MB0558, MB3510, MB3670, MB3689, MB3716, MB3760, MB3761, MB3807, MB4079, MB4132, MB4174, MBSF7, SNC_2_5), 7 SHH (MB3612, MB3661, MB3662, MB3695, MB3697, MB3724, MB4143), and 1 WNT (MB4036)]. Fresh tissue samples were obtained from The Hospital for Sick Children (Toronto, ON). In situ Hi-C libraries were generated using approximately 2.5 million dissociated cells as input. All Hi-C libraries were sequenced at 150 bp PE with a Hi-Seq X instrument (Illumina) at McGill Genome Centre (Montreal, QC).

  Dataset EGAD50000000771

• Chromatin profiling of baseline and Notch inhibitor treated HCC PDX model

  We generated chromatin accessibility profiles for anti-Notch2 (n=3) and anti-gD (n=3) treated LIV78 tumors. Tumors were isolated, snap frozen in liquid nitrogen and stored at -80C. Tumor tissue was pulverized using a Covaris CP02 CryoPrep Pulverizer. Flash frozen pulverized tumor samples were sent to Active Motif to perform the ATAC-seq assay. Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina) to produce FASTQ sequencing files.

  Dataset EGAD50000000735

• RNA sequencing of primary B-cells infected with Epstein-Barr virus (EBV), treated with heat-inactivated EBV, CpG or BCR-crosslinking in presence or absence of Linrodostat

  B cells were isolated from buffy coat preparations of healthy donors using CD19 magnetic beads. B cells were then infected with EBV using spinoculation or activated with heat-inactivated EBV, respectively. Additionally cells were treated with 5ng/ml CpG or a BCR-crosslinking mixture in presence or absence of 10 µM Linrodostat (IDO1 inhibitor). RNA samples were isolated at 2 days post-infection / post-activation and one day 0 control with non-infected B cells was included.

  Dataset EGAD50000000306

• RNA-Seq data from study: Molecular underpinnings of dedifferentiation and aggressiveness in chromophobe renal cell carcinoma

  The ChRCC study RNA-Seq dataset contains raw whole transcriptome sequencing data of 16 tumor and 6 adjacent normal samples from 7 UTSW patients, who have consented to depositing their genomic data to public repository. RNA-Seq was performed using 50bp single-end on a HiSeq2500 platform (Illumina, San Diego, CA, USA). 50M reads per sample on average. The raw data is in fastq format.

  Dataset EGAD50000000416

• Epigenomic timecourse of brain organoid development

  Single-cell Cut&Tag of three histone modifications and chromatin accessibility over a timecourse of brain organoid development from pluripotency. We profiled 5 time points of brain organoid development and 2 time points of retinal organoid development. At each time point used scCut&Tag to profile histone modifications (H3K27me3, H3K27ac, H3K4me3) as well as multiome-seq (10X) to jointly profile transcriptome and chromatin accessibility from the same cell suspension. Library preparation was carried out with the 10x genomics platform.

  Dataset EGAD50000000222

• Perturb-seq dataset

  We performed a systematic, genome-wide investigation of enhancer regions in colorectal cancer (CRC). We identified 12,117 putative enhancer regions using H3K27ac and H3Kme1 ChIP-seq and ATAC-seq. We performed scRNA-seq in HT29 and SW480 (MSS CRC cell lines) using the Parse Biosciences WT-mega kit with CRISPRi/dCas9 inhibition of these regions (Perturb-seq). The Parse split-pipe pipeline was used to demultiplex the raw fastq files into the processed files (mtx files for genes and gRNA) for each cell line.

  Dataset EGAD50000000375

• Analysis of Cell-Free DNA to Predict Outcome to Bevacizumab Combination Therapy in Metastatic Colorectal Cancer Patients

  This dataset includes FASTQ files of low coverage whole genome sequencing of normal tissue (n = 8), tumor tissue (n = 55) and cell free DNA from plasma samples (n=101) from patients with metastatic colorectal cancer treated with bevacizumab. A total of 164 samples are present from two different cohorts. The first batch of samples (n = 139, sample names sAPD302T until sAPD502_P0) were collected from the AC-Angiopredict Phase 2 trial (NCT01822444), the second batch of samples (n = 25m, sample names sAPD503_P0 until sAPD527_P0) were collected from the UMM cohort.

  Dataset EGAD50000000176

• Pharmacological improvement of CFTR function rescues airway epithelial homeostasis and host defense in children with cystic fibrosis

  This dataset encompasses single-cell RNA sequencing data derived from nasal swabs of a paired cohort of school-aged children with cystic fibrosis. The study includes samples both before (n=13) and after initiation (n=13) of elexacaftor/tezacaftor/ivacaftor (ETI) treatment. Additionally, age- and sex-matched controls were included (n=12). Detailed information about the study design and methodology can be found in the manuscript: “Pharmacological improvement of CFTR function rescues airway epithelial homeostasis and host defense in children with cystic fibrosis”.

  Dataset EGAD50000000173

• ctgap-G-1

  Illumina HumanCoreExome-12v1-1_A chip typing in a Greek adolescent population

  Dataset EGAD00010001005

• Exploiting evolutionary steering in cancer therapy

  This dataset contains 9 bam files of exome sequencing for an experiment of evolved resistance. Here a barcoded cell line (HCC827 - POT) has been treated under high concentrations of gefitinib (GEF) and trametinib (TRM) until resistance has evolved, as well as under control conditions (DMSO). The dataset contains exome sequencing of confluent cells for three replicates for each anti-cancer drug as well as two replicates of growth under DMSO conditions. The original barcoded cell line (POT) was also exome sequenced and is included in the cohort. Sequencing was performed on the Illumina NovaSeq platform.

  Dataset EGAD00001005782

• SCAT_Osteosarcoma_Validation

  This experiment is to validate putative somatic substitutions and indels identified in an exome screen of ~50 osteosarcoma tumour/normal pairs. It is the first stage in our ICGC commitment to study osteosarcoma. The validation process is an important component of our analysis to clarify the data prior to looking for evidence of new cancer genes, or subverted pathways important in the development of cancer. 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/

  Dataset EGAD00001000280

• Transcriptomics of human olfactory mucosa

  The olfactory gene repertoire is largely species-specific, shaped by the nature and necessity of chemosensory information for survival in each species' niche. We are intrigued by this interspecific variation and started to investigate the olfactory transcriptome in primates for evidence of selection at the level of receptor gene choice. Having collected this data from two primates, we now wish to extend the analysis to humans. 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/

  Dataset EGAD00001003213

• SOFT study - sequencing premenopausal breast cancer (2017-11-22)

  Our project will examine the role of PIK3CA mutations and their sensitivity to endocrine therapies and its role, with the addition of complete ovarian suppression. We plan to test our hypotheses using tumour samples collected from patients enrolled in the SOFT/IBCSG24-02 clinical study (Suppression of Ovarian Function Trial - (NCT00066690). SOFT is a phase III trial that randomised 3066 premenopausal women to evaluate if adding ovarian suppression to adjuvant endocrine therapy will improve clinical outcomes. This dataset contains all the data available for this study on 2017-11-22.

  Dataset EGAD00001003811

• Adenoma development in familial adenomatous polyposis and MUTYH‐associated polyposis: somatic landscape and driver genes

  Familial adenomatous polyposis (FAP) and MUTYH‐associated polyposis (MAP) are inherited disorders associated with multiple colorectal adenomas that lead to a very high risk of colorectal cancer. The somatic mutations that drive adenoma development in these conditions have not been investigated comprehensively. In this study we performed analysis of paired colorectal adenoma and normal tissue DNA from individuals with FAP or MAP, sequencing 14 adenoma whole exomes (eight MAP, six FAP), 55 adenoma targeted exomes (33 MAP, 22 FAP) and germline DNA from each patient.

  Dataset EGAD00001004332

• Genomic and transcriptomic determinants of therapy resistance and immune landscape evolution during anti-EGFR treatment in colorectal cancer

  Genomic and transcriptomic data from a cohort of 35 RAS wild-type colorectal cancers. All 35 cases were DNA sequenced at baseline (BL) before treatment with single agent cetuximab. Progressive disease (PD)-biopsies were taken shortly after radiological progression and successfully exome sequenced from 24/35 cases. mRNA sequencing is available for 25 Baseline and 15 PD samples. ctDNA from 9 cases that progressed after prolonged cetuximab benefit were also deep sequenced.

  Dataset EGAD00001004501

• Mannheim Liquid Biopsy Unit, Heidelberg University & DKFZ

  The dataset consists of sequenced cell free DNA (cfDNA) samples from colorectal cancer patients. The samples were sequenced on an Illumina MiSeq machine using a custom amplicon sequencing approach. These amplicons were designed to cover the most common mutation hotspots in colorectal cancer. The data include 138 cfDNA samples from 34 different patients. For each patient several samples are available derived from blood drawn at different time points during treatment. In addition the data include samples from 22 histology slides and 30 samples derived from HT29/HCT116 cell lines that were used as controls.

  Dataset EGAD00001004574

• 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.

  Dataset EGAD00001000653

• Chondromyxoid fibroma

  Chondromxoid fibroma is a benign tumour of bone with unknown underlying pathogenesis. To determine pathognomic genomic event in chondromyxoid fibroma whole genome sequencing will be undertaken to reconstruct rearrangements and find underlying mutations.

  Dataset EGAD00001001063

• PKD1 capture-by-hybridization resequencing for genetic diagnostics of polycystic kidney disease

  We established and validated a sequence capture based NGS testing approach for PKD1. The presence of six PKD1 pseudogenes and tremendous allelic heterogeneity make molecular genetic testing of PKD1 variants challenging. In the publication accompaying this dataset (An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease, Eisenberger et.al., PLoS one), we demonstrate that the applied standard mapping algorithm specifically aligns reads to the PKD1 locus and overcomes the complication of unspecific capture of pseudogenes. This dataset contains the raw PKD1 reads of all patients from the publication.

  Dataset EGAD00001001091

• 463 newly diagnosed patients paired samples (Tumor/Normal)

  463 newly diagnosed patients from the UK Myeloma XI clinical trial (NCT01554852) underwent whole exome sequencing plus targeted capture of the IGH/K/L and MYC loci. 200 ng of DNA were processed using NEBNext DNA library prepartion kit and hybridised to the SureSelect Human All Exon V5 Plus. Four samples were pooled and run on one lane of a HiSeq 2000 using 76-bp paired end reads. DNA from CD138+ selected bone marrow cells (myeloma tumour) as well as peripheral white blood cells were analysed and somatic mutations detected.

  Dataset EGAD00001001358

• Transcriptome and Exome from longitudinal samples of human glioblastoma

  We obtained paired longitudinal specimens from a total of 38 glioblastoma (GBM) patients (34 primary and 4 secondary GBM patients). Treatment-naive initial tumors were available for 35 cases; for the other 3 cases, we used the first available recurrent tumors in lieu of initial tumors. Tumor specimens were subjected to whole-exome sequencing (27 of 38 cases, with the matched normal/blood for 22 of the 27 cases) and transcriptome sequencing (30 of 38 cases).

  Dataset EGAD00001001424

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (ChIP-Seq for mature neutrophil, on genome GRCh37)

  ChIP-Seq data for 182 mature neutrophil sample(s). 2847 run(s), 366 experiment(s), 355 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002670

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (RNA-Seq for mature neutrophil, on genome GRCh37)

  RNA-Seq data for 205 mature neutrophil sample(s). 205 run(s), 205 experiment(s), 205 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816

  Dataset EGAD00001002675

• Whole-genome bisulfite sequencing

  Raw reads from whole-genome bisulfite sequencing. Whole-genome bisulfite sequencing library preparations and Illumina sequencing of DNA samples from TET2 mutation carriers (Ly9, Ly11, Ly14, Id1) and their age-matched controls (Ly8, Ly10, Ly13, Id2, Id3) was done as a service at BGI (BGI Tech Solutions Co., Ltd., China). Bisulfite treatment was done with EZ DNA Methylation-Gold Kit (Zymo Research, CA, USA) for 300-400bp size-range fragments with methylated adapters in 5' and 3' ends. Sequencing was done with the HiSeq X-Ten platform using paired-end 150 base-pair read length.

  Dataset EGAD00001004779

• The British Autozygosity Populations BioResource (2019-08-14)

  This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. 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 2019-08-14.

  Dataset EGAD00001005253

• The identification of genetic vulnerabilities in head and neck cancers for the development of novel therapies (2020-01-15)

  CRISPR/Cas9 lethality screens in a set of Asian head and neck cancer cell lines to identify novel targets. . This dataset contains all the data available for this study on 2020-01-15.

  Dataset EGAD00001005784

• RNA sequencing of CD8 T cells from melanoma patients prior to and during checkpoint immunotherapy and untreated healthy controls

  We are interested in inter-individual variation in transcriptional response to immune checkpoint blockade. We have analysed poly A purified RNA expression from CD8 T cells (297 transcriptomes in total) isolated from metastatic melanoma patients (n=106) prior to and during treatment with either single agent (Pembrolizumab) or combination (Ipilimumab/ Nivolumab) immune checkpoint blockade. We compare expression at different stages of treatment and additionally contrast this with that from healthy controls (n=68).

  Dataset EGAD00001005973

• Whole Genome Sequencing of Human Organoid Lines (2020-02-20)

  The study will use WGS to aid in benchmarking different culture conditions in a set of genetically annotated human organoid lines. The data will be used to assess whether there is any clonal differences introduced when culturing these lines in different conditions. . This dataset contains all the data available for this study on 2020-02-20.

  Dataset EGAD00001005995

• miRNA-seq data for Molecular Characterization of ETMR

  This dataset contains miRNA-seq data from 10 patients. Small RNAs were isolated as described previously57,58 from fresh-frozen tumour material. In brief, total RNA was extracted using guanidinium isothiocyanate/phenol extraction followed by 3′-adaptor ligation of barcoded adenylated adaptors. Samples were pooled in two sets of five samples. Subsequently, gel electrophoresis was used to isolate small RNAs (19–35 nt) and purified using ethanol precipitation. Fragments were then amplified using standard PCR, isolated using gel electropho- resis and purified using ethanol precipitation. Samples were sequenced on a HiSeq 2000 v.4 machine resulting in 10 Fastq files.

  Dataset EGAD00001006218

• RNA-seq data from 121 tumor samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). RNA-seq was performed using the QuantSeq kit FWD HT kit (Lexogen) using 500 ng input RNA from 121 tumor samples. Data provided here consist of 780 fastq files for RNA-seq.

  Dataset EGAD00001006238

• Raw microarray gene expression data from NPC samples_Cohort 1

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006273

• Raw microarray gene expression data from NPC samples_Cohort 2

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006272

• Processed microarray gene expression data from NPC samples_Cohort 2

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006274

• Processed microarray gene expression data from NPC samples_Cohort 1

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006275

• Genomic Landscape of Malignant Peripheral Nerve Sheath Tumor-like Melanoma

  Malignant peripheral nerve sheath tumor (MPNST)-like melanoma is a rare malignancy with overlapping characteristics of both neural sarcoma and melanoma. The genomics of MPNST-like melanoma have not been previously described. In this study, we performed whole exome sequencing analysis in 8 samples from 6 patients diagnosed with MPNST-like melanoma. Our results demonstrate that, although MPNST-like melanoma shares oncogenic alterations common to both cutaneous melanoma and MPNST, it also presents unique genomic alterations not previously described in neither of the malignancies.

  Dataset EGAD00001006999

• 252 human breast cancer samples in WGS and WES

  We analyzed chromothripsis in 252 human breast cancers from two patient cohorts (149 metastatic breast cancers, 63 untreated primary tumors, 29 local relapses, 11 longitudinal pairs) using whole-genome and whole-exome (paired) sequencing. A lot of the WGS samples were sequenced on Illumina HiSeq X-Ten using Illumina TruSeq Nano DNA. For exome sequencing Agilent_SureSelect_V5+UTRs has been used (sequencing on Hiseq2000, Hiseq2500 and Hiseq4000). For exome sequencing Agilent_SureSelect_V5+UTRs has been used (sequencing on Hiseq2000, Hiseq2500 and Hiseq4000).

  Dataset EGAD00001007563

• Single-cell RNA-seq of matched primary GBM tumours, patient-derived organoids, and gliomasphere lines

  Single-cell RNA-seq of primary GBM tumours and matched patient-derived organoids and gliomasphere lines. Obtained using the 10X Genomics single-cell 3' expression solution (v2 chemistry). Primary samples and PDOs from 12 tumours from 10 patients (10 primary, two recurrent), and gliomasphere lines from a subset of five tumours. Samples were obtained from two spatially distinct regions of each tumour.

  Dataset EGAD00001007936

• Sequence data for study: Mobilization of tissue-resident memory CD4+ T lymphocytes from bone marrow and their contribution to a systemic secondary immune reaction

  Short Description: This study contains 7 RRBS samples, including 3 ex vivo CD4+ Trm (2 x spleen and 1 x bone marrow) and 4 blood tetanus (TT) and measles (Me) antigen-reactive memory CD4+ cells before and one day post DTaP (diphtheria-tetanus-pertussis) and MMR (measles-mumps-rubella) vaccination, respectively (1 x tetanus D0, 1 x tetanus D1, 1 x measles D0, 1 x measles D1). Technology: Illumina HiSeq 2500 Filetype: fastq format

  Dataset EGAD00001007886

• HCA Female Reproductive Adult WSSS RNA

  HCA Endometrium_LM The endometrium regenerates monthly and its transformation is executed through dynamic changes in states and interactions of multiple cell types. Using transcriptomics methods we seek to profile changes of the endometrium across the menstrual cycle. Our map will have implications in women's health and cancer, by enabling the interpretation of GWAS analyses or the studying functional consequences of somatic mutations. 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/

  Dataset EGAD00001007909

• Risk alleles of membranous nephropathy and recurrence of the disease on the grafted kidney

  Samples are from patients enrolled in an international multicentric study aimed to define the genetic determinants of recurrence of membranous nephropathy in the kidney graft. They include 248 samples from patients with MN including 105 patients who received a graft, their 105 graft donors, and 192 controls all of Caucasian origin. Files from targeted-capture of HLA and PLA2R loci are available as fastq files.

  Dataset EGAD00001007831

• Exploring the heterogeneity of sarcoma using single cell sequencing

  Multi region samples are collected from patients, with consent, immediately after resection of the tumour. Samples are digested and sorted using FACS as single cells into lysis buffer. Cells are then stored until further processing for G&T-seq. After sequencing, we will explore intra-tumour heterogeneity using computational approaches to integrate RNA and DNA data onto the tumour 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/ .

  Dataset EGAD00001006786

• single cell RNA sequencing of resting and IAV-stimulated mononuclear phagocytes of Africans and Europeans

  CD14+ monocytes from 4 African and 4 Europeans individuals with varying degree of ex-vivo susceptibility to Influenza, were either stimulated with Influenza A virus, or left resting. Cells from all 16 samples were collected at 4 time points (0, 2, 4, 6h post infection), and pooled across 13 libraries. Samples were processed on the 10x chromium with 3' reagents kits, V3 chemistry and sequenced with Hiseq X ten.

  Dataset EGAD00001006938

• Relapse series of two Pediatric ALL patients

  In this proof of principle study, we performed whole genome sequencing of two cases with multiple relapses in order to investigate whether groups of mutations separated in time show distinct mutational signatures. In patient 1, who experienced two relapses, the analysis unraveled a continuous interplay of aberrant AID/APOBEC-associated activities. Patient 2 had three relapses. We identified episodic mutational processes at diagnosis and first relapse leading to mutations resembling UV light-driven DNA damage, and thiopurine-associated damage at first relapse.

  Dataset EGAD00001006948

• DNA-seq BAM files from 16 patients affected by acute intermittent porphyria

  Paired-end BAM files from 16 patients affected by acute intermittent porphyria. Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). FASTQ files were processed at the CNAG (Barcelona) using the GEM short-read aligner on the human genome version hs37d5, producing a total of 16 BAM files.

  Dataset EGAD00001006951

• 12 Pediatric B-cell precursor acute lymphoblastic leukemia samples with very early relapse

  Sequencing data (BAM/CRAM) of diagnosis-relapse pairs of 12 children who relapsed very early, followed by a deep-sequencing validation of all identified mutations.

  Dataset EGAD00001008309

• Human normal esophagus and Barrett's esophagus mtDNA sequencing

  BAM files containing paired-end mtDNA sequencing data from human esophageal samples of individuals that had progressed to dysplasia or developed Barrett's esophagus (BE) post-esophagectomy. BE biopsies and the background mucosa were analysed. Each patient (JE*) has associated mtDNA sequencing data from biopsies of stroma, BE and squamous and cardia tissue. Two technical replicates, denoted "A" and "B", were analysed for each biopsy. Libraries were sequenced via the Illumina MiSeq platform v2 (Illumina, San Diego, CA, USA) 300 cycles (150 nt paired-end).

  Dataset EGAD00001008310

• Hubrecht Organoid Technology Colon Cancer Study

  Functional screening on patient-derived organoids identifies a therapeutic bispecific antibody that triggers EGFR degradation in LGR5+ tumor cells

  Dataset EGAD00001008445

• HELIUS virome sequencing

  The dataset contains fecal WGS samples of 196 participants to the HELIUS study, as well as VLP filtrate sequencing for a subset of 48 participants.

  Dataset EGAD00001008765

• RNA-seq Revision

  The dataset comprises bulk RNA‑seq libraries generated on the Illumina NextSeq 500 platform, including primary human hepatocytes (four donors), colon tissue (four masked replicates), and a comprehensive set of iPSC‑derived samples from the JHU106, ChiPSC18, ChiPSC22, and H9 lines. The collection covers multiple differentiation stages from iPSC to DE to HLC and cultivation protocols (CEL, HAY, SPH) with at least three replicates per condition. All sequencing data are provided as raw FASTQ files, with colon samples delivered as masked FASTQ in accordance with patient consent requirements.

  Dataset EGAD00001008951

• Systematic Identification of Somatic Non-coding Alterations

  Profiling of 12 megabases of human non-coding DNA (including enhancers, promoters, and boundaries of topologically associating domains) in a longitudinal cohort of patients treated with endocrine therapies. For each patient, DNA from the primary and relapsed (metastatic) tumour, along with normal matched DNA, were profiled.

  Dataset EGAD00001009064

• ATAC-seq in hiPSC-derived neurons after BDNF and KCl stimulations

  Brain-Derived Neurotrophic Factor (BDNF) is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. Molecular mechanisms of BDNF promoting cellular survival and synaptic plasticity have been intensely studied, yet its role in genome regulation is obscure. Using human induced pluripotent stem cell (hiPSC)-derived neurons via lentiviral delivery of the neuronal transcription factor Ngn2, we performed a temporal profiling (1h, 6h and 10h) of chromatin accessibility upon BDNF treatment or depolarization (KCl) to identify BDNF-specific chromatin-to-gene expression programs.

  Dataset EGAD00001009100

• TRACERx Reduced-representation bisulfite sequencing (RRBS)

  RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue. TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Dataset EGAD00001009707

• Single-cell RNA and DNA sequencing data obtained after genome-and-transcriptome separation.

  This dataset contains single-cell RNA and DNA sequencing data (fastq, n=928) obtained after genome-and-transcriptome separation. The RNA-seq data was obtained by Smart-seq2 amplification and Nextera XT library preparation. The DNA-seq data was obtained either by Gtag library preparation and amplification or by PicoPlex whole-genome amplification followed by Nextera XT library preparation. The single cells originate from a human PDX melanoma model and from HCC38 and HCC38 BL cell lines. The sequencing libraries were sequenced with Illumina instruments.

  Dataset EGAD00001010096

• untargeted whole genome sequencing - Evaluation and correction of GC biases in cell-free DNA at the fragment level

  These are aligned paired-end reads from Illumina NovaSeq 6000 whole-genome sequencing of 4 cfDNA samples extracted from blood plasma (plasma-Seq). Three samples from patients with breast cancer, prostate cancer, or colorectal cancer and one sample from a healthy individual were aligned to GRCh38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set). The observed GC bias is different in each of these cfDNA samples which leads to different average GC content per sample. This bias is corrected using the GCparagon commandline tool.

  Dataset EGAD00001010100

• 10x Genomics VDJ single cell sequencing and 10x Genomics sc RNA-Seq (5 individuals/17 VDJ runs,19 scRNA runs))

  single cell RNAseq and TCR sequencing data of 5 individuals. 10x Genomics VDJ single cell sequencing (17 runs) and 10x Genomics sc RNA-Seq (19 runs). The VDJ sequencing was done on a Nextseq 550 using the Chromium Single Cell VDJ Reagent Kit. The RNA-Seq was done either on HiSeq4000 or NovaSeq 6000 using the Chromium Single Cell 5 Reagent Kit.

  Dataset EGAD00001009986

• RNA-seq analysis of CCO+/CCO- hepatocytes in normal human liver

  RNAseq data from Passman et al 2023. Clonal CCO-deficient hepatocyte patches and nearby CCO-proficient hepatocytes were identified in morphologically normal human livers and sampled at varying distances along the PT-CV axis. Samples are characterised according to their location within the liver lobule, with "PT" denoting samples abutting the portal triad, "CV" denoting samples abutting the central hepatic vein, and "Mid" sampled acquired midway between these structures. Analysis was performed on an Illumina Nextseq using a high output kit and 100 single-end cycles.

  Dataset EGAD00001010033

• T-cell receptor targeting FLT3 D835Y mutation study

  We identified a T-cell receptor (TCR) reactive to the recurrent FLT3 D835Y mutation in the tyrosine-kinase domain. To validate the elimination efficacy of leukemia cells, we transplanted human acute myeloid leukemia (AML) cells with FLT3 D835Y mutations into NSG-SGM3 mice and treated either with TCR FLT3 D835Y redirected T cells, or control TCR (TCR 1G4). After treatment, we performed flow sorting of AML blasts (CD3-CD19-) and primary T cells (CD3+CD8+orCD4+CD19-CD33-) and performed whole-exome sequencing.

  Dataset EGAD00001011258

• Whole genome sequencing of Osteosarcoma clonal evolution

  Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. Here, we conducted longitudinal whole-genome sequencing of 37 tumor samples from eight patients with osteosarcoma that relapsed or became refractory to initial therapy. We found that the chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.

  Dataset EGAD00001011285

• Sequencing data for oesophageal and related samples - Zamani et al

  Data supporting: "Genomic and epidemiological similarities between phenotypically distinct esophageal adenocarcinoma suggest a single entity" Zamani et al

  Dataset EGAD00001015435

• Lung Cell Atlas: Paediatric RNA (2025-10-02)

  Single cell sequencing will be carried out by multiome profiling (RNAseq and ATACseq). Additonal modalities may be examined. Spatial profiling may involve Visium, Curio and other technologies. This data set will feed into a larger analysis of the human lungs over development, that aims to detail all the cell types of the human lungs and airways and will extend current knowledge by providing chromatin accessibility data that will allow us to link GWAS data and identify regulatory networks and then compare these against fetal and adult data sets . This dataset contains all the data available for this study on 2025-10-02.

  Dataset EGAD00001015722

• Lung Cell Atlas: Paediatric Spatial (2025-10-02)

  Single cell sequencing will be carried out by multiome profiling (RNAseq and ATACseq). Additonal modalities may be examined. Spatial profiling may involve Visium, Curio and other technologies. This data set will feed into a larger analysis of the human lungs over development, that aims to detail all the cell types of the human lungs and airways and will extend current knowledge by providing chromatin accessibility data that will allow us to link GWAS data and identify regulatory networks and then compare these against fetal and adult data sets . This dataset contains all the data available for this study on 2025-10-02.

  Dataset EGAD00001015723

• A rare CTSC mutation in Papillon-Lefèvre Syndrome

  Papillon-Lefèvre Syndrome (PLS) is an autosomal recessive monogenic disease caused by loss-of-function mutations in the CTSC gene. In this study we performed whole genome sequencing on two siblings, with the PLS-typical symptoms. After sequencing the CTSC gene was analyzed to confirm the PLS diagnosis genetically.

  Study EGAS00001005040

• ARST17B2-Q Germline and Somatic Genetic Landscape of Pediatric Rhabdomyosarcoma

  Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. While these malignancies display aberrant myogenic differentiation, relatively little is known about genetic susceptibility to RMS, or how genetic variants influence subsequent somatic events and may be used in risk stratification strategies. A small percentage of cases are associated with mutations in TP53 (Li-Fraumeni syndrome), HRAS (Costello syndrome), and PTCH1 (nevoid basal cell carcinoma syndrome/Gorlin syndrome), suggesting the genetic origins of childhood RMS. In spite of this, little work has been done to characterize genetic susceptibility to this malignancy. We plan to leverage samples collected as part of D9902 to conduct one of the largest germline genomic studies of RMS. We anticipate that once genetic associations are identified, researchers can use the information to develop better strategies to detect, treat, and prevent childhood RMS.

  Study phs003192

• Differential Gene Expression in Cryptorchid Testes

  Differential Gene Expression in Cryptorchid Testes Study uses whole-genome RNA profiling of testicular biopsies to determine a potential causative role of isolated congenital cryptorchidism in azoospermia and/or infertility in the context of our previously published GeneChip data. Cryptorchid patients, aged 7 months to 5 years and otherwise healthy, were enrolled in this prospective study. During surgery, testicular tissue biopsies were obtained for histological examination and RNA-sequencing (RNA-seq). Fifteen patients were selected based on the histological results and were divided into two groups. Seven were classified as belonging to the high infertility risk (HIR) and eight to the low infertility risk (LIR) group. Cryptorchid boys in the high infertility risk group lacked transformation of gonocytes into Ad spermatogonia due to impaired mini puberty. This group of patients will be infertile despite successful surgery.

  Study phs001275

• Genotyping NIGMS Chromosomal Aberration and Inherited Disorder Samples

  As part of an effort to correlate molecular copy number variation determinations with state of the art karyotype analyses, 716 samples derived from 697 individuals from the Chromosomal Aberrations and Inherited Disorders collections of the NIGMS Human Genetic Cell Repository were genotyped and analyzed for CNV determination by the Microarray Center at the Coriell Institute for Medical Research. Karyotyping is performed on all cell cultures in the Repository with reported chromosome abnormalities. The samples chosen for genotyping in this study are intended to represent a diverse set of copy number variants, but the selection was also weighted to over-sample commonly manifested types of aberrations. When available, the ISCN description of the sample based on G-banding and FISH analysis is included in the phenotypic data. Karyotypes for these cells can be viewed in the online Repository catalog (http://ccr.coriell.org/Sections/Collections/NIGMS/?SsId=8).

  Study phs000269

• Genetic analysis of patients with Inherited Retinal Dystrophies (IRDs) using next generation sequencing to identify the causative variants

  Genetic analysis of patients with Inherited Retinal Dystrophies (IRDs) was carried out by performing Whole Genome Sequencing (WGS). The main purpose of this study is to identify simple and complex mutations responsible for IRD in patients. WGS was performed on selected affected and unaffected individuals using the Illumina HiSeqX10. The reads were aligned to human genome 19 (hg19) and variant calling was performed using Genome Analysis Toolkit (GATK). The genotyping quality of single nucleotide variants (SNVs) and indels was assessed using the variant quality score recalibration approach implemented in GATK. Copy number variations (CNVs) were called using Genome STRiP and SpeedSeq. This large set of whole genome sequencing data from different ethnicity can be stored and shared through dbGaP. This data could serve as a source for checking frequencies of variants or the pathogenicity of selected variants in different ethnicities.

  Study phs001619

• Polygenic Risk Score for the Prediction of Breast Cancer Is Related to Lesser Terminal Duct Lobular Unit Involution of the Breast

  The Susan G. Komen Tissue Bank (KTB) at the Indiana University Simon Cancer Center is an annotated biobank, which has recruited healthy women who provided demographic, lifestyle, and cancer-related information via self-administered questionnaire, blood samples and normal breast tissues. H&E slides of the normal breast tissues were scanned for image analysis and a pathologist measured the number of terminal duct lobular units (TDLUs) ("TDLU count"). The acini count per TDLU was quantified using the TDLU analyzer software. In this analysis, we computed the recently developed polygenic risk score (PRS) based on 313 common variants for the prediction of breast cancer and related this PRS to TDLU count and acini count per TDLU. We did this for the overall PRS, the ER-positive PRS and the ER-negative PRS.

  Study phs002062

• Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing

  Current methods available for pre-implantation genetic diagnosis (PGD) of in vitro fertilized (IVF) embryos do not detect de novo. Detection of these types of mutations requires whole genome sequencing (WGS). In this study advanced massively parallel WGS was performed on three 5-10 cell biopsies from two blastocyst-stage embryos. Overall, greater than 95% of each genome was called and experimentally derived haplotypes and barcoded read data were used to detect and phase up to 82% of de novo single base mutations with a false positive rate of ~1 error per Gb. These results suggest that phased WGS using barcoded DNA could be used in the future as part of the PGD process to maximize comprehensiveness in detecting disease causing mutations and reduce the incidence of genetic diseases.

  Study phs000858

• Genomic Factors Involved in Chromosome Rearrangements

  Approximately 15-20% of children referred for chromosomal microarray analysis (CMA) testing have a clinically relevant CNV that in many cases explains their phenotype. The goal of this study is to discover the genomic factors that mediate chromosome rearrangements and the phenotypic effects of chromosome rearrangements. We hypothesize that particular DNA sequences are susceptible to breakage and rearrangement. To this end, we fine-map chromosome breakage sites and analyze the DNA motifs that underlie double-strand breaks (DSBs). Our studies will also capture the genomic structure of breakpoint junctions, which will allow us to determine the mechanisms of DNA repair that shape different types of chromosome rearrangements. We also correlate chromosome rearrangements with clinical features to establish genotype-phenotype correlations. Defining critical regions of deletion or duplication is the first step to identifying candidate genes responsible for particular phenotypes.

  Study phs000845

• Anorexia Nervosa Genetics Initiative (ANGI)

  The Anorexia Nervosa Genetics Initiative (ANGI) is an international collaboration that recruited individuals with a lifetime history of anorexia nervosa from the United States (US), Australia/New Zealand (ANZ), Sweden (SE), and Denmark (DK). Matched controls, with no history of eating disorders, were also recruited from the US, SE, and DK. Recruitment avenues included national registers (SE, DK), treatment centers (US, ANZ, SE, DK), and social and traditional media (US, ANZ, SE). Participants provided blood samples and clinical information. Diagnoses were based on DSM-IV or ICD-10 criteria (amenorrhea was not required). Genotype data are available for 12,918 participants. *NOTE: Denmark data cannot be shared openly but require prior and individual permission by the data owner: The Head of the National Center for Register Based Research Aarhus, DK. Genotyping of samples from Denmark was completed using the Illumina PsychArray (data not supplied).

  Study phs001541

• Massachusetts General Hospital (MGH) Atrial Fibrillation Study

  The Massachusetts General Hospital (MGH) Atrial Fibrillation Study was initiated in 2001. The study has enrolled serial probands, unaffected and affected family members with atrial fibrillation. At enrollment participants undergo a structured interview to systematically capture their past medical history, AF treatments, and family history. An electrocardiogram is performed; the results of an echocardiogram are obtained; and blood samples are obtained. The Massachusetts General Hospital (MGH) Atrial Fibrillation Study is utilized in the following dbGaP substudies. To view genotypes, analysis, other molecular data, and derived variables collected in these substudies, please click on the following substudies below or in the "Substudies" box located on the right hand side of this top-level study page phs001001 Massachusetts General Hospital (MGH) Atrial Fibrillation Study. phs001116 MGH AF CHARGE-S phs001117 MGH AF Exome Sequencing phs001118 MGH AF Medical Resequencing

  Study phs001001

• Genomic Correlates of Response and Resistance to Immune Checkpoint Blockade in Solid Tumors

  Immune checkpoint inhibitors yield clinical benefit in many cancer types, but molecular predictors of response have not yet been robustly characterized. In this study, we pursued whole exome sequencing (WES) of pre-treatment tumors from patients treated with immune checkpoint therapies - including monoclonal antibodies targeting programmed cell death-1 (PD-1) and cytotoxic T-lymphocyte-associated protein-4 (CTLA-4). Using these data, we aim to apply computational pipelines for mutation-calling, neoantigen prediction, and other analyses to validate pre-existing hypotheses regarding response to immune checkpoint therapies and discover new relationships with greater power. Further, by pursuing genomic characterization of tumors from patients with a variety of cancer types, we hope to describe molecular features of intrinsically sensitive or resistant tumors that are both context-specific and shared across cancer types.

  Study phs001565

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): Covidseeker and COVID-19 Citizen Science: Leveraging Citizen Science and Real-Time Geospatial Temporal Mobile Data for Digital Contact Tracing and SARS-CoV-2 Hotspotting

  The Covidseeker and COVID-19 Citizen Science Study integrates a retrospectively-determined geolocation digital program into an established digital infrastructure housed within the NIH-funded Eureka platform to enroll SARS-CoV-2 positive and negative individuals. The solution also leverages the ongoing COVID-19 Citizen Science Study cohort both in-person and remotely to test and implement existing technology to enhance readily accessible contact tracing methods and identify “hot spots” of transmission of SARS-CoV-2. The tools are designed to alert users regarding overlap with SARS-CoV-2 infected individuals, identifying businesses that were visited by someone who later tested positive for COVID-19, and working with those businesses and public health departments on strategies to reduce the spread of the virus. DOI: https://rapids.ll.mit.edu/10.57895/me7r-vp06

  Study phs002519

• International Collaboration of Incident HIV and HCV in Injecting Cohorts (InC3)

  This study represents a merged international multi-cohort project of pooled biological and behavioral data from ten prospective cohorts of injection drug users (Grebely J, Morris MD, Rice TM, Bruneau J, Cox AL, Kim AY, et al., 2012, PMID: 23203695). Of the 10 cohorts, six provided data and samples for the genome wide association study (GWAS) entitled “Genetic Analysis of Opioid Addiction in People Who Inject Drugs”. The InC3 cohorts included in the GWAS were: i) Australian Trial in Acute Hepatitis C (ATAHC-I, Sydney); ii) Hepatitis C Incidence and Transmission Study in Prison (HITS-p) (Sydney); iii) Hepatitis C Incidence and Transmission Study in Community (HITS-c) (Sydney); iv) HepCo Study (Montreal); v) SuperMIX Study (combining the Networks II & MIX studies, Melbourne); and vi) the UFO Study (San Francisco).

  Study phs002310

• Characterization of X Chromosome Inactivation Using Integrated Analysis of Whole-Exome and mRNA Sequencing

  This study of DNA and RNA sequencing of 5 parent-offspring trios is a single center study. The goal of this study is to characterize X chromosome inactivation (XCI) ratio in females using phased genomic variations obtained through whole genome or exome sequencing in trios, followed by allele-specific expression analysis of the phased, heterozygous alleles in the mRNA of the female offspring, and to apply this method to clinical diagnosis. The distribution of allele ratios across X obtained from mRNA sequencing allows for the estimation of X inactivation status of inherited X chromosomes, and the parameters of each parental allele distributions in the offspring's mRNA data can be used as determinants for XCI ratio. This approach was used to evaluate the contribution of skewed XCI ratio to phenotypic heterogeneity in an undiagnosed, mild neurological condition.

  Study phs000816

• Dynamics of Genomic and Immune Responses During Primary Immunotherapy Resistance in Mismatch Repair Deficient Tumors

  We study a patient with dMMR lung cancer refractory to immunotherapy. Post-treatment tumor demonstrated compound heterozygous frameshift deletions located upstream of the kinase domain in the gene encoding JAK1 protein, downregulation of JAK1 and mediators of its signal transduction, and total loss of JAK1 phosphorylation. Importantly, one of the JAK1 mutations, despite not being detected in the pre-treatment tumor, was found at low variant allele frequency in the pre-treatment circulating tumor DNA, suggesting clonal selection of the mutation. This report provides the most detailed look yet of defective JAK1 signaling in the context of dMMR and immunotherapy-resistance. Together with observations of JAK1 frameshift indels being enriched in dMMR compared with MMR-proficient tumors, our findings demonstrate the critical function of JAK1 in immunological surveillance of dMMR cancer.

  Study phs002089

• Pancreatic Cancer Case Control Association Study

  Pancreatic cancer is the fourth leading cause of cancer death in the United States. This is in large part due to the rapidly fatal course of this disease, as the vast majority of patients die within months of diagnosis and the five-year survival rate is less than 5. We have brought together over 8000 participants from 9 studies of pancreatic cancer, to conduct a GWAS of pancreatic cancer. The studies were drawn from the Pancreatic Cancer Case-Control consortium and include case-control studies from the United States, Europe and Australia. Sites include: Johns Hopkins National Familial Pancreas Tumor Registry, Mayo Clinic Biospecimen Resource for Pancreas Research, Ontario Pancreas Cancer Study (OPCS), Yale University, MD Anderson Case Control Study, Queensland Pancreatic Cancer Study, University of California San Francisco Molecular Epidemiology of Pancreatic Cancer Study, International Agency of Cancer Research and Memorial Sloan Kettering Cancer Center.

  Study phs000648

• Host Response to Respiratory Infections

  In this study, we describe a strategy to identify undiagnosed respiratory viral infections through screening nasopharyngeal (NP) swabs for the chemokine CXCL10, which is highly induced in the nasopharynx as part of the host antiviral response. Using this strategy, we conducted two screens: first, we screened NP swabs collected at Yale New Haven Hospital (YNHH) in January 2017 from patients with undiagnosed respiratory viral infections and identified patients infected with seasonal coronaviruses and the relatively uncommon influenza C virus. Second, we screened samples from the beginning of March 2020 in the weeks before YNHH tested for SARS-CoV-2 and identified four patients that had undiagnosed SARS-CoV-2 infections. Sequences uploaded as part of this study include samples with rhinovirus, human coronavirus NL63, and 8 samples as part of the January 2017 screen for undiagnosed respiratory viral infections.

  Study phs002442

• RNAseq Transcriptomic Analyses of European Ancestry Samples in MGS Dataset

  Schizophrenia is a common and severe psychotic disorder. While some common SNPs and rare copy number variants have been identified as being significantly associated with disease risk, the biological mechanisms remain undefined. To identify gene expression abnormalities in schizophrenia, we generated whole-genome gene expression profiles using RNAseq on lymphoblastoid cell lines from schizophrenia cases and controls of European ancestry. Subsets of these data have been used in three studies: (1) gene expression outliers (extreme tails of the distribution of transcript expression values) in 634 cases and 713 controls (PMID: 26022996); (2) baseline differential gene expression by affection status in 529 cases and 660 controls (PMID: 28418402); and (3) baseline versus dopamine stimulated differential gene expression by affection status in 514 cases and 690 controls (PMID: 30115913). Various classes of classes were enriched in the differentially expressed genes, especially brain expressed genes and genes related to immune processes.

  Study phs001932

• Emory University African American Vaginal, Oral, and Gut Microbiome in Pregnancy Cohort Study

  The Emory University African American Microbiome in Pregnancy Cohort Study prospectively enrolls African American women between 18-40 years of age without chronic medical conditions into a longitudinal follow-up study that involves completing microbiome sampling and data collection at two time points in pregnancy (8-14 weeks gestation and 24-30 weeks gestation). The study is investigating the role of the oral, vaginal, and gut microbiome on preterm birth and other pregnancy outcomes as well as biobehavioral factors that shape the microbiome among this socio-demographically diverse group of women. Microbiome sampling involves the oral, vaginal, and gut sites. Biobehavioral factors that are being explored for their association with microbiome composition at the three body sites include measures of sociodemographic status as well as diet and nutrition, infectious and stress exposures.

  Study phs001865

• Somatic L1 Retrotransposition in Colorectal Tumors

  The purpose of this study is to ascertain the locations of somatic LINE-1 retrotransposition events in human colon tumor samples by pooling multiple tumor samples from different patients and performing a targeted resequencing assay (Ewing and Kazazian, Genome Research 2010) to sequence the 3' flanking regions of all insertions in the pooled sample. The result is compared to the result of applying the same method to pooled normal samples from the same patients as were used in the pooled tumor sample and selecting sites that show an insertion in the tumor but not in the normaltissue and do not correspond to any known non-reference LINE-1 insertion allele. The selected sites are then validated by site-specific PCR and capillary sequencing to confirm that they represent LINE-1 insertions and to obtain breakpoint sequences.

  Study phs000536

• Natural History of and Genetic Modifiers in Spinocerebellar Ataxias

  Spinocerebellar ataxias (SCA) are genetic neurological diseases that cause imbalance, poor coordination, and speech difficulties. There are different kinds of SCA and this study will focus on types 1, 2, 3, and 6 (SCA 1, SCA 2, SCA 3, also known as Machado-Joseph disease and SCA 6). The diseases are rare, slowly progressive, cause increasingly severe neurological difficulties and are variable across and within genotypes. The purpose of this research study is to bring together a group of experts in the field of SCA for the purpose of learning more about the disease. The research questions are: How does the disease progress over time? What are the best ways to measure disease progression? Do some genes, other than the gene that is abnormal in the SCA disease, have any effect on the way the disease behaves?

  Study phs001332

• MP2PRT: Identification of Genetic Changes Associated with Relapse and/or Adaptive Resistance in Patients Registered as Favorable Histology Wilms Tumor on AREN03B2

  The Molecular Profiling to Predict Response to Treatment (MP2PRT) program is part of the NCI's Cancer Moonshot Initiative. The aim of this program is the retrospective characterization and analysis of biospecimens collected from completed NCI-sponsored trials of the National Clinical Trials Network and the NCI Community Oncology Research Program. This study, titled "Identification of Genetic Changes Associated with Relapse and/or Adaptive Resistance in Patients Registered as Favorable Histology Wilms Tumor on AREN03B2", performs genomic characterization (WGS 30X, Total RNAseq, miRNAseq) on a discovery set of 70 trio cases (normal tissue, tumor tissue at time of diagnosis, tumor tissue at time of relapse) from patients who relapsed with Favorable Histology Wilms Tumor. Prioritized findings from the discovery set will be validated using Targeted Sequencing in an independent validation set of 47 relapse samples.

  Study phs001965

• Gabriella Miller Kids First Pediatric Research Program in Genetics at the Intersection of Childhood Cancer and Birth Defects

  The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). All of the WGS and phenotypic data from this study are accessible through dbGaP and kidsfirstdrc.org, where other Kids First datasets can also be accessed. Birth defects and childhood cancer share biological pathways that are important for cell growth and division. We propose that sequencing pediatric patients suffering both conditions will allow us to discover the underlying genes and in turn advance our understanding of the causes of these devastating diseases.

  Study phs001846

• Childhood Cancer Data Initiative (CCDI): OncoKids - NGS Panel for Pediatric Malignancies

  This study aimed to systematically collect clinical, registry and genomic data on pediatric cancer patients, and to contribute to the CCDI Pediatric Data Ecosystem. Clinical, treatment and outcome data on 1,039 pediatric cancer patients whose molecular profile was characterized on OncoKids gene panel at Children's Hospital Los Angeles was abstracted and harmonized for submission to the NCI’s Cancer Data Service. The OncoKids panel was designed to detect DNA mutations and amplification in almost 200 oncogenes and tumor suppressor genes, a limited number of pharmacogenomic targets and 1,700 disease-associated gene fusions at the RNA level. The panel encompasses the vast majority of FDA’s relevant pediatric molecular target list, as well as additional genes associated with ultra-rare pediatric tumors. The final data elements included DNA/RNA sequence data, OncoKids test results, clinical data on demographics, diagnosis, comorbidity and adverse events and treatment data.

  Study phs002518

• African American Breast Cancer GWAS

  The GWAS includes African American participants from 9 epidemiological studies of breast cancer, comprising a total of 3,153 cases and 2,831 controls (cases/controls: The Multiethnic Cohort Study (MEC), 734/1,003; The Los Angeles component of The Women's Contraceptive and Reproductive Experiences (CARE) Study, 380/224; The Women's Circle of Health Study (WCHS), 272/240; The San Francisco Bay Area Breast Cancer Study (SFBCS), 172/231; The Northern California Breast Cancer Family Registry (NC-BCFR), 440/53;The Carolina Breast Cancer Study (CBCS), 656/608; The Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Cohort, 64/133; The Nashville Breast Health Study (NBHS), 310/186; and, The Wake Forest University Breast Cancer Study (WFBC), 125/153). Quality control of the GWAS data and additional details can be found in Chen et al. Hum Genet. 2013 (PMID: 22923054)

  Study phs000851

• OncoArray: Oral and Pharynx Cancer

  Genetic factors play an important role in susceptibility to head and neck cancer and could also explain differences in response to treatment and outcome. The goal of this project is to investigate genetic variation involved in oral and oropharyngeal cancer susceptibility by performing the largest GWAS on these diseases, using a novel genotyping tool specifically designed for cancer studies by the OncoArray Network. This project encompasses data from approximately 6000 oral and pharynx cancer cases and 4000 controls derived from 12 epidemiological studies most of case-control design. The genotyping was centralized at the Center for Inherited Disease Research (CIDR), and the epidemiological data harmonization and analysis were completed at the International Agency for Research on Cancer (IARC). This study was supported by National Institute of Dental and Craniofacial Research (NIDCR) with direct funding to CIDR.

  Study phs001202

• Center for Common Disease Genomics (CCDG) - Cardiovascular: Cleveland Clinic Cohort

  The National Human Genome Research Institute (NHGRI) has funded the Centers for Common Disease Genomics (CCDG), a collaborative large-scale genome sequencing effort to comprehensively identify rare risk and protective variants contributing to common disease phenotypes and to better understand the general principles of genomic architecture underlying common, complex inherited diseases. This study contains variant calls derived from the whole genome sequence data of an early-onset coronary artery disease case-control cohort collected by the Cleveland Clinic. Case status was assigned based on the presence of myocardial infarction, coronary artery stenosis greater than 70% in at least one coronary artery, and/or revascularization (coronary angioplasty with or without stent placement or coronary artery bypass grafting) at an early age. For these samples, "early age" is defined as men 60 years of age or younger and women 70 years of age or younger.

  Study phs001871