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• Deep sequencing of the gut microbiome from donors of the Milieu Intérieur cohort

  This dataset includes 1,359 paired-end shotgun metagenomics samples from 946 healthy donors of the Milieu Intérieur cohort. 413 of the donors provided two samples (V1 and V2).

  Dataset EGAD00001006554

• Genome-Wide Scan for Genetic Variants Associated with Early-Onset Prostate Cancer

  This is a genome-wide association scan of 931 early-onset prostate cancer cases of European ancestry. The samples were selected from prostate cancer studies at the University of Michigan. Controls were previously genotyped individuals selected from the Cancer Genetics Markers of Susceptibility (CGEMS) and Illumina's iControlDB database.

  Study phs001185

• Whole exome and ChIP sequencing of external auditory canal squamous cell carcinoma (EACSCC)

  We performed whole exome sequencing of the primary tumor tissues, peripheral blood mononuclear cells from an EACSCC patient as well as the cell line established from the primary tumor tissues. We performed ChIP sequencing of primary tumor tissues and noncancerous ear skin tissues from EACSCC patients as well.

  Study JGAS000645

• Paroxysmal_Neurological_Disorders_2

  We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.

  Study EGAS00001000190

• Paroxysmal_neurological_Disorders

  We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.

  Study EGAS00001000386

• Paroxysmal neurological disorders

  We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.

  Study EGAS00001000048

• Whole-genome sequencing of Tibetans from China

  Whole-genome sequencing of 27 Tibetan individuals from China using the Illumina-B HiSeq X platform. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.

  Study EGAS00001003500

• Exome sequencing of 317 rainforest hunter-gatherers and neighbouring farmers from Central Africa

  Exome sequencing of 317 rainforest hunter-gatherers (RHG) and neighbouring farmers (AGR) from Central Africa was performed based on the Nextera Rapid Capture Expanded Exome Kit (62-Mb content) with the Illumina HiSeq 2500. The population sample includes the Baka of south-eastern Cameroon and northern Gabon (wRHG), the Bantu-speaking Nzebi and Bapunu sedentary agriculturalists of Gabon (wAGR), and the BaTwa (eRHG) and BaKiga (eAGR) from Uganda. After QC filters, exomes of 300 unrelated individuals were obtained at high coverage (mean depth 68x), including 406,270 variants.

  Dataset EGAD00001004569

• Hi-C analysis of metastatic prostate tumors

  DNA strands have a complex and highly structured three-dimensional shape within the nucleus that has profound but poorly characterized impacts on transcriptional activity. Herein, we performed the first integrated deep Hi-C sequencing on 80 metastatic castration-resistant prostate cancer biopsy samples from the West Coast Dream Team consortium.

  Study EGAS00001006604

• Hi-C analysis of metastatic prostate tumors - Part 2

  DNA strands have a complex and highly structured three-dimensional shape within the nucleus that has profound but poorly characterized impacts on transcriptional activity. Herein, we performed the first integrated deep Hi-C sequencing on 80 metastatic castration-resistant prostate cancer biopsy samples from the West Coast Dream Team consortium.

  Study EGAS00001006612

• Whole-genome sequencing of Himalayan populations

  Whole-genome sequencing of 60 individuals from 15 Himalayan populations using the Illumina-B HiSeq X platform. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.

  Study EGAS00001007269

• MeDALL epigenetics study

  MeDALL- (Mechanisms of the Development of ALLergy) is a collaborative project supported by the European Union under the Health Cooperation Work Programme of the 7th Framework programme (grant agreement number 261357).MeDALL epigenetics study includes illumina 450k methylation measurements from 4 cohorts: Infancia y Medio Ambiente (INMA), Etudes des Déterminants pré et postnatals précoces du développement et de la santé de l’ENfant (EDEN), Children’s Allergy Environment Stockholm Epidemiology study(BAMSE), and Prevention and Incidence of Asthma and Mite Allergy (PIAMA)

  Study EGAS00001002169

• Solve-RD_EuroNMD_cohort-1_DF1+2_V1

  Solve-RD data submitted to the ERN-EuroNMD cohort for re-analysis (Data freeze 1+2) v1

  Dataset EGAD00001009768

• Identification of biomarkers for prediction of efficacy of microtubule inhibitors and antifolates in non-small cell lung cancer

  Identification of predictive markers based on transcriptome modules for microtubule inhibitors of lung adenocarcinoma patients

  Study JGAS000267

• RNA-seq data for Heterogeneity of IKZF1 genomic alterations and risk of relapse in childhood BALL

  RNA-seq data for 14 samples with B-cell acute lymphoblastic leukemia

  Dataset EGAD50000000151

• Genomic Alterations in Gingivo-buccal Cancer: ICGC-India Project_YR02

  Dataset EGAD00001001060

• Biological and Therapeutic Implications of a Unique Subtype of NPM1 Mutated AML (RNAseq Data)

  This dataset contains 91 RNAseq paired reads, in fastq format. Samples were collected from fresh bone marrow and peripheral blood sample from AML patients.

  Dataset EGAD00001006669

• Transcriptome profiling of desmoplastic small round cell tumors (DSRCTs)

  RNA sequencing of frozen resected specimens of desmoplastic small round cell tumors (DSRCTs). Four patients have specimens from multiple tissue sites included in this dataset.

  Dataset EGAD00001006388

• Dataset-linking-WGS-and-WES-files-from-EGAS00001004276-via-README-for-new-study-EGAS00001005327

  This dataset contains 538 Tumor and Control WGS and WES files for samples already submitted and published in study EGAS00001004276

  Dataset EGAD00001007817

• Aggressive genomic features in clinically indolent primary HHV8-negative effusion-based lymphoma

  Genomic profiling of effusion-based fluid samples from 8 HHV8-negative effusion-based lymphoma patients.

  Dataset EGAD00001008364

• Chromatin profiling using Cut&Run technique of hepatoblastoma organoids

  CUT&RUN LoV-U profiling of b-catenin, LEF1 and TCF7L2 binding in biological replicates (Replicate A, Replicate B) of hepatoblastoma organoids: 10F, 13F, 13E, 17E, 22E and 135F.

  Dataset EGAD50000001749

• scRNAseq and scTCRseq of three tumor lesions derived from one patient receiving adoptive TIL therapy

  scRNA sequencing and scTCR sequencing on three tumor lesions derived from one patient receiving adoptive tumor-infiltrating lymphocyte (TIL) therapy. Expanded metastasis was used for TIL expansion and yielded the TIL product which also was used for scTCR sequencing. 10 weeks after transfer of the TIL product the regressing metastasis was resected. After the patient progressed the progressing metastasis was removed (61 weeks).

  Dataset EGAD50000000406

• Raw sequencing data for donor and patient fecal samples

  Microbiome analysis was performed on the patient samples collected pre-FMT and on days after FMT, and on samples collected from the FMT donor. Genomic bacterial DNA was extracted from fecal samples using the QIAamp DNA Stool kit (Qiagen, Hilden, Germany), with the addition of a bead-beating lysis step. Genomic 16S ribosomal-RNA V4 variable regions were amplified and sequenced on the Illumina MiSeq platform.

  Dataset EGAD00001004371

• Development and Validation of Patient-Derived Xenografts from Fibrolamellar Carcinoma Human Tissue

  We developed and validated Patient-Derived Xenografts (PDX) of Fibrolamellar Carcinoma human tissue from surgical resections. Human tissues from primary liver tumor, recurrent liver, and liver metastases were implanted into NOD-SCID-Gamma (NSG) mice (Jackson laboratories) and monitored for tumor growth. Some of the original tissues were frozen for further analysis including RNA sequencing. Tumors that grew were then harvested and passaged into additional mice. Some tumor tissues from the PDX samples were frozen for RNA-Seq analysis. The PDX was validated by histologic, transcriptomic and proteomic analysis. The RNA-Seq analysis was performed on original tissue samples including primary liver tumor, recurrent liver, liver metastases, normal liver, and the derived PDX.

  Study phs002435

• Sequencing data of tumor tissue obtained from GANNET53 study patients

  The GANNET53 clinical trial evaulated novel treatment options for ovarian cancer patients with platinum-resistant relapse. Archival fresh-frozen paraffin embedded tissue was available from 131 of the 133 enrolled patients. NGS sequencing aimed at assessing the mutational spectrum of key ovarian cancer genes (with a focus on TP53), and their relevance for therapy resistance. From available FFPE samples, DNA was extracted and NGS sequenced using the SureSeq™ Ovarian Cancer Panel and the NGS Library Preparation kit covering all exons of 7 key ovarian cancer genes BRCA1, BRCA2,TP53, PTEN, ATM, ATR, NF1 for single nucleotide variants (SNV) and indels. Finally, sequence data from 118 individual FFPE tumor tissue samples were generated.

  Study EGAS50000000935