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• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Umea, Sweden.

  Study EGAS00001005842

• Integration of metabolomics, genomics and immune phenotypes reveals the causal roles of metabolites in disease

  Study EGAS00001005348

• Gentoypes_SouthAfrica

  Individuals genotyped on the Illumina Omni2.5. Autosome and X chromosome.

  Dataset EGAD00010002467

• Determining the quality and complexity of NGS data without a reference genome

  Dataset EGAD00001000759

• Biomarker data

  Biomarker data including the time point of sample collection, tumor content and ERBB2 gene expression.

  Dataset EGAD00001009415

• 16S rRNA-Seq of rectal mucus from patients suspected to have colorectal cancer

  Metataxonomic sequencing data targeting the 16S rRNA gene hypervariable regions V3 and V4 on 545 rectal mucus samples from patients suspected to have colorectal cancer and healthy controls.

  Dataset EGAD50000001803

• Two scRNA-seq datasets from control and irradiated organoids.

  Dataset includes two scRNA-seq samples from control and irradiated organoids. Files included in the dataset are Fastq files. Sample libraries produced with Chromium X were sequenced on an Illumina NovaSeq 6000 sequencer.

  Dataset EGAD50000001933

• Locally advanced prostate cancer cohort

  Fastq files from RNA sequencing and BAM files from tNGS of normal and tumor samples from 17 patients from the locally advanced prostate cancer cohort.

  Dataset EGAD50000002380

• WGS data from 20 cholangiocarcinoma cases

  WGS data from biliary tract cancer samples (Holzapfel, et al., J Gastrointest Oncol,14(1):379-389, 2023). The dataset includes tumour and normal BAM files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=20 tumour/normal pairs).

  Dataset EGAD50000002307

• The Dynamic Immune Behavior of Primary and Metastatic Ovarian Carcinoma

  Single-cell RNA-seq data of prospectively collected normal ovarian tissue sample from 1 healthy individual and tumor tissue samples with or without chemotherapy from 19 HGSOC patients.

  Dataset EGAD50000000057

• Whole Exome Data of RFWD3 Fanconi anemia patient

  Dataset contains one sample derived from gDNA of human fibroblasts. Files are in FASTQ format and were generated using the Agilent SureSelect Human All Exon 50Mb Kit and followed by Next Generation Sequencing on a HighSeq2000 instrument (Illumina).

  Dataset EGAD00001003311

• Transcriptome analysis of Tcells from blood, fat and skin

  Tcells were isolated fom Tissues and FACS sorted. In total 50 samples were processed in 5 replicates with the Takara SmartSeq Stranded kit. Single end fastq-files are supplied.

  Dataset EGAD00001007663

• WXS of IgAN-tGBM, IgAN and TBMN

  The dataset consists of 258 bam files by whole exome sequencing. 122 from IgAN-tGBM patients, 64 from IgAN patients and 72 fromTBMN patients.

  Dataset EGAD00001009287

• Dataset for soft_tissue_tumor-RNA

  Rare cancer sequencing data of 243 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008859

• mRNA profiling of CAFs and cancer cells in response to TGF-β and BMP signaling

  TGF-β and BMP signalings are important signaling pathways in the tumor microenvironment during cancer progression. This RNA-sequencing (62 fastq pairs) analysis explored how cancer-associated fibroblasts (CAFs) from human (19TT) and mice (Balbc A/B) respond to TGF-β, BMP2, or Gremlin antibody, as well as how cancer cells (66cl4) respond to Gremlin antibodies.

  Dataset EGAD50000001351

• Targeted capture sequencing to identify MYC, BCL2, and BCL6 rearrangements in non-Hodgkin lymphoma

  Targeted capture sequencing of 364 samples representing a mix of Burkitt lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, and high-grade B-cell lymphomas with MYC and BCL2 or BCL6 rearrangements. Capture space covers 3.5 Mb of the human genome including regions around MYC, BCL2, BCL6, PAX5, and IGH/K/L.

  Dataset EGAD50000000489

• Whole exome sequencing and target gene sequencing of ESCC cases and healthy controls from Henan high-risk region

  In total, 186 FH+ ESCC cases were sequenced using whole-exome sequencing, then 1935 ESCC cases and 1186 geographically-matched healthy controls were sequenced using 7 Mb custom designed Roche SeqCap kit which targeted about 600 genes. The libraries were constructed and then sequenced in Illumina platform.

  Dataset EGAD00001004556

• Whole genome sequencing of HSPCs and pAML

  Whole genome sequencing data (Illumina HiSeq and NovaSeq) of clonal cultures derived from pediatric human bone marrow-derived hematopoietic stem and multipotent progenitor cells (in total 44 samples from 10 donors) and bulk pediatric acute myeloid leukemia blasts (in total 6 samples from 6 patients) to study the mutation accumulation.

  Dataset EGAD00001006338

• Summary statistics of meta-analysis using two genome-wide association study of inflammatory bowel disease in Koreans.

  We combined samples from 1,469 inflammatory bowel disease (IBD) patients consisted of 896 Crohn’s disease (CD) and 573 ulcerative colitis (UC) and 4,041 controls used in our previously published GWAS with 1,726 additional IBD patients (725 CD and 1,001 UC) and 378 additional controls genotyped using the Asian Screening Array (ASA). We uploaded summary statistics of three meta-analyses in text files.

  Dataset EGAD00001006983

• Single-cell RNA-seq of patient-derived organoids across three generations

  Single-cell RNA-seq of first-, second-, and third-generation patient-derived organoids. Obtained using the 10X Genomics single-cell 3' expression solution (v3 chemistry). First- and second-generation PDOs from one patient and first-, second-, and third-generation PDOs from three additional patients.

  Dataset EGAD00001008431

• 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.

  Study EGAS00001005001

• UMCU_Molpheno_Restricted

  This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data obtained from PBMCs derived from blood samples of 34 patients with intellectual disability and/or multiple congenital anomalies and their biological parents (58) included in the University Medical Center Utrecht (The Netherlands).

  Dataset EGAD00001004865

• EGAD00010000807

  Illumina HumanCoreExome genotyping data from the British Society for Surgery of the Hand Genetics of Dupuytren’s Disease consortium (BSSH-GODD consortium) collection

  Dataset EGAD00010000807

• SNP arrays for chemotherapy response project

  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). Illumina SNP arrays (760k markers) were performed using DNA from 49 tumors and associated germline DNA (49x median coverage). Data provided here consist of 98 files.

  Study EGAS00001004519

• Transcriptomic predictors of survival for palbociclib + endocrine therapy vs. capecitabine in aromatase inhibitor-resistant breast cancer from GEICAM/2013-02 PEARL

  We examined transcriptomic tumor features associated with survival from GEICAM/2013-02 PEARL, a phase III trial of palbociclib + ET vs. capecitabine in aromatase inhibitor-resistant HR+/HER2- MBC. PAM50 intrinsic subtype predicted PFS differences between palbociclib + ET and capecitabine, and lower B-cell-associated gene expression predicted longer OS with palbociclib + ET vs. capecitabine. These features may help identify HR+/HER2- tumors resistant to further ET-based treatment with CDK4/6 inhibitors.

  Study EGAS00001008177