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• DLBCL NGS Genomic Datasets of non-China cohort from Phoenix Clinical Trial

  Study biopsies (n=773; 189 cases as China cohort and 584 cases as non-China cohort) underwent whole exome sequencing or targeted gene panel DNA sequencing and RNA sequencing, allowing the identification of somatic mutations. Tumors were assigned to DLBCL genetic subtypes as the MCD (n=110), BN2 (n=47) or N1 (n=28) using the LymphGen algorithm based on their somatically mutated genes. In younger patients (age≤60), ibrutinib plus R-CHOP was associated with a 100% event free survival (EFS) at 3-years in the MCD and N1 groups, whereas R-CHOP alone was associated with a 3-year EFS of 42.9% (p=0.01) and 50% (p=0.016) in the MCD and N1 groups, respectively. This analysis showed a benefit of ibrutinib with R-CHOP chemotherapy in particular genetic subtypes, providing mechanistic support for its survival benefit in younger patients with non-GCB DLBCL. The EGA collects RNA-Seq and NuGene targeted sequencing datasets of 584 cases for non-China cohort.

  Study EGAS00001005554

• Targeted Myeloid DNA-Panelsequencing, DKFZ

  Targeted myeloid DNA-Panelsequencing from purified bone marrow blasts of 104 treatment naive AML patients from the discovery cohort. For more details, we refere to Jayavelu, Wolf, Buettner et al. Libraries were prepared from 40 ng DNA using the QIASeq Human Myeloid Neoplasms Panel (Qiagen) according to the manufacturer’s protocol. Samples were tagged with the QIAseq 96-Unique Dual Index Set A for Illumina platforms (Qiagen) to yield unique combinations of i5 and i7 barcodes for each sample. Sample fragment size distribution and concentration was estimated using the Agilent High Sensitivity DNA kit on a 2100 Bioanalyzer (Agilent). Samples were pooled in an equimolar fashion, denatured, and diluted to 1.5 pM according to Illumina’s recommendations. The diluted library was sequenced on a NextSeq 500 benchtop sequencer (Illumina) using NextSeq High Output cartridges. Demultiplexing was performed using the BaseSpace cloud platform (Illumina).

  Dataset EGAD00001008501

• NEOPREDICT-Lung: longitudinal whole exome sequencing of non-small cell lung cancers under immunotherapy

  In 43 patients pretreatment tumor biopsies, resected tumors and normal tissue of sufficient quality and quantity were obtained to longitudinally explore the mutational profiles of a comprehensive set of cancer-related genes. For tumor samples, one to four FFPE sections (10 µm thickness, number depending on sample size) were lysed for genomic DNA isolation. Isolation was performed semi-automatically on the Maxwell purification system (Maxwell RSC DNA FFPE Kit, AS1450, Promega) as specified by the manufacturer. DNA was eluted in 50 µl RNase-free water and quantified fluorescently for library preparation using a Qubit 2.0 fluorometer (Life Technology) with its appertaining DNA broad-range assay. Corresponding normal DNA was isolated from blood or PBMCs using routinely available QIAGEN technology. DNA was stored at -20°C before use. Whole-exome sequencing (WES) was performed using the Twist Human Core + RefSeq + Mitochondrial Panel (Twist Bioscience), and 2 x 100 bp fragment sizes were sequenced using a NovaSeq6000 (Illumina). Demultiplexing of sequenced reads was achieved using bcl2fastq (version 2.2).

  Dataset EGAD00001015362

• Multiethnic Cohort Adiposity Phenotype Study (MEC-APS)

  A total of 1,861 healthy men and postmenopausal women aged 60-77 years with body mass indexes (BMIs) of 17.1-46.2 kg/m2 were enrolled into the study. Stratified sampling was conducted based on sex, race/ethnicity, and six BMI categories (18.5-21.9, 22-24.9, 25-26.9, 27-29.9, 30-34.9, and 35-40 kg/m2) to balance the sample size across the wide range of BMI and optimize adjustment for total adiposity in populations with different BMI distributions. Study participants underwent body composition assessment, in person interview, blood collection, and completed a self-administered questionnaire. A genome-wide association study of obesity phenotypes was conducted among five racial/ethnic groups of the Multiethnic Cohort Study.

  Study phs001689

• Whole Exome Sequencing Analysis of Carfilzomib-Related Cardiotoxicity in Multiple Myeloma Patients

  This study investigated the contribution of germline genetic variants in protein-coding genes in carfilzomib-related cardiovascular adverse events among patients with multiple myeloma using whole-exome sequencing (WES) analysis. We analyzed 247 patients with multiple myeloma who had been treated with carfilzomib at the Moffitt Cancer Center. We identified a missense mutation in the TMSB10/TRABD2A locus that appeared to be associated with a higher risk for cardiovascular adverse events in these patients. In this submission, we will provide all the genotype data along with the phenotype data of whether or not a patient developed cardiovascular adverse events after carfilzomib treatment and all the covariates used in this analysis.

  Study phs003308

• Genetics of Congenital Anomalies of the Kidney and Urinary Tract

  The Genetics of Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) contributes data from unrelated individuals who were recruited at the Columbia University Medical Center (New York, USA), the Polish Registry of Congenital Malformations (Poland), the Universities of Parma, Bari, and Brescia, and the Gaslini Institute (Italy), the University of Skopje (Macedonia), and VUMC of Amsterdam (Netherlands). These individuals consented to share their data for scientific discovery. The purpose of the study is to investigate the genetic architecture of CAKUT.  Additionally, part of the data in this study was generated from 418 DNA samples from the Randomized Intervention for Children with Vesicoureteral Reflux (RIVUR) study, and supplied by the NIDDK Central Repository. The RIVUR study was conducted by the RIVUR study investigators, and supported by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). The Genetics of CAKUT study was not conducted in collaboration with investigators of the RIVUR study and does not necessarily reflect the opinions or views of the RIVUR study, the NIDDK Central Repository, or the NIDDK. Genomic DNA samples were genotyped on Illumina Multi-Ethnic Global Arrays.

  Study phs001749

• Defining and Overcoming Intrinsic T Cell Dysfunction to Enable Pediatric Immunotherapy

  T-cells from 71 children and young adults with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy were analyzed. These T-cells represent the pre-manufacture T-cells that were subsequently used for CAR T manufacture. Bulk RNA-Seq was performed on sorted T-cell subsets for all patients, in addition to CITE-Seq and single-cell ATAC-Seq on a subset of 6 patients. The primary clinical outcome was duration of B-cell aplasia, a surrogate measure of functional CAR T-cell persistence. From these data, molecular signatures associated with long and short-term CAR T-cell persistence were identified. This data submission includes bulk RNA-Seq, CITE-Seq, and single-cell ATAC-Seq data from this study.

  Study phs002323

• CMMRD tumors sequencing data

  Whole exome sequencing data from the tumors of individuals with constitutional mismatch repair deficiency. These are 16 tumors from the bigger study of 41 tumors in total (from 17 individuals in total).

  Dataset EGAD50000000113

• VIKING Health Study - Shetland 30X WGS

  30x whole genome sequencing of samples from the VIKING Health Study - Shetland. 500 DNA samples were sequenced using the Illumina HiSeq X system. FASTQ files are deposited

  Dataset EGAD00001005378

• Human tumour bulk RNA-seq

  We profiled 18 high-grade gliomas patient tumor samples by bulk RNA-seq. The raw fastqs are provided.

  Dataset EGAD00001006098

• Epigenomic profile of diverse cancer

  The samples are from patients of multiple cancer types. The library preparation protocol was developed by the laboratory. The DNA libraries were then sequenced with 150bp paired-end reads.

  Dataset EGAD00001006124

• ATAC Analysis of Treg and Tfh cells

  Treg and Tfh cells (8 Samples)from the same donors was subject to ATAC-seq processing. Paired end fastq-files are supplied.

  Dataset EGAD00001007660

• APL nanopore sequencing data

  APL nanopore sequencing data are deposited into 2 data formats: 1. CRAM files 2. h5 files

  Dataset EGAD00001008146

• Transcriptome Profiling of human AT2 cells in COPD

  RNA-seq of FACS sorted AT2 cells from ex-smokers with (n=6) and without (n=3) COPD at different disease stages. Fastq files are provided.

  Dataset EGAD00001011115

• Methylation Profiling of human AT2 cells in COPD

  WGBS of FACS sorted AT2 cells from ex-smokers with (n=6) and without (n=3) COPD at different disease stages. Fastq files are provided.

  Dataset EGAD00001011116

• Homologous recombination deficient breast cancers

  Exome sequencing data from homologous recombination deficient primary breast cancers as assessed by the functional RAD51 based HR test. There are 12 tumour samples, of which 10 also have matching normal.

  Dataset EGAD00001003929

• Fragmentomics analyses of urinary cell-free DNA permit multi-urologic cancer detection and reduction in tissue biopsies for prostate cancer

  This study demonstrated the close association between urinary cell-free DNA (cfDNA) methylation status and the fragmentation patterns in healthy controls and patients with various diseases. Fragmentomics-based methylation analysis (FRAGMA) enables accurate estimation of methylation levels in urinary cfDNA, which is proved by paired bisulfite sequencing and non-bisulfite sequencing data. FRAGMA showed high accuracy in deducing tissue-of-origin of urinary cfDNA in transplantation patients and pregnant women. Moreover, FRAGMA showed great potential in the detection and classification of multiple cancers from the urinary system, including bladder, kidney, and prostate cancer. This study demonstrated that FRAGMA could be applied to improve current diagnostic strategies based on urine samples.

  Study EGAS50000001431

• McQuillin_Global_London_SCZ_Bipolar_WES

  "McQuillin_Global_London_SCZ_Bipolar_WES. This research project was a collaboration between University College London, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 1,623 Schizophrenia and Bipolar case/control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. For EGA Study ID: 1128"

  Dac EGAC50000000311

• Sequencing data for CLL patients

  Single-cell RNA-sequencing and other genome-wide approaches were applied to a cohort of CLL patients receiving Venetoclax treatment to study mechanisms of resistance.

  Study EGAS00001005815

• FACS-based purification and paired-end RNA sequencing

  We performed a prospective investigation in Sézary syndrome by the application of a standardized multiparameter flow cytometry, FACS-cell sorting, and RNA-sequencing for an in-depth immunophenotypic and transcriptional profiling of Sézary cells.

  Dataset EGAD00001007687

• Exome sequencing files for "A single mutant clone populates the pancreatic ductal system to generate coexisting neoplastic lesions"

  Files from whole exome sequencing of eight tumors from eight pancreatic cancer patients along with matched PanIN precursor lesion(s) and a matched normal tissue.

  Dataset EGAD00001004044

• BRIDGE SPEED April 2016

  Whole genome sequencing CRAM files for four samples from the BRIDGE Consortium (SPEED project) with pathogenic variants in a gene associated with a movement disorder.

  Dataset EGAD00001002070

• Cell Type-Specific and Disease-Associated eQTL in the Human Lung

  This study was conducted to investigate the genetic control of gene expression in a cell-type and context-specific manner in the human lung. We performed single-cell RNA-sequencing (scRNA-seq) of lung tissue from 66 Interstitial Lung Disease (ILD) cases and 48 unaffected donors. Employing a pseudo-bulk approach, we mapped expression quantitative trait loci (eQTL) across 38 cell types. The scRNA-seq data presented here include previously published (PMID 34262047) and unpublished samples. ILD tissue samples were obtained from lungs removed at the time of lung transplantation at either Vanderbilt University Medical Center (VUMC) or the Norton Thoracic Institute (NTI). Control tissue samples were obtained from lungs declined for organ donation either at the Donor Network of Arizona (DNA) or VUMC. The self-reported ethnicities of donors were 66.7% European, 9.6% African American, 17.5% not available (N/A), and 6.1% other. The smoking history includes 46.5% ever smoker, 29.8% never smoker, 23.7% N/A. For genotyping, flash-frozen tissue in DNA/RNA shield was homogenized via a bullet blender. Genomic DNA was extracted using Zymo Quick DNA/RNA microprep plus kit. Library preparation and low-pass Whole Genome Sequencing (WGS) were carried out at TGen or by Gencove Inc. At TGen, libraries were prepared using PCR-free Watchmaker kits (Watchmaker Genomics) with 200 ng input. Genomes were sequenced on NovaSeq at low coverage (typically 0.4–1x). The resulting sequence data were processed and imputed using Gencove's imputation platform.

  Study phs003521

• KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population

  The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. KIR gene gene copy number variation associates with the outcome of transplantations and susceptibility to immune-mediated diseases. Here we describe a stand-alone and freely available gene content imputation for 12 KIR genes. The models were trained using 818 Finnish biobank samples genotyped for 5774 KIR-region SNPs and analysed for KIR gene content with targeted sequencing.

  Study EGAS00001005457

• Data access committee for study - The subclonal architecture of metastatic breast cancer: Results from a prospective community-based rapid autopsy program "CASCADE".

  Dac EGAC00001000574