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• Data Access Committee for IMBA

  Dac EGAC00001001690

• Data Access Committee for data from EGAS00001005174

  Dac EGAC00001002059

• Data Access Committee for data from EGAS00001005395

  Dac EGAC00001002183

• Data Access Committee for PPIL4 Paper

  Dac EGAC00001002301

• Data Access Committee for Massim study

  Dac EGAC00001002522

• Data Access Committee for Institut Curie

  Dac EGAC00001002711

• Data Access Committee for Pediatric Medulloblastoma

  Dac EGAC00001002896

• Institute for Surgical Pathology

  Dac EGAC00001002949

• Data Access Commitee for MNP2

  Dac EGAC00001003033

• DAC for Karolinska Institute REM Lab

  Dac EGAC00001003142

• DAC for Kotsch/Lukassen/Conrad labs

  Dac EGAC00001003464

• Data Access Committee for data from EGAS00001002864

  Dac EGAC00001003487

• Data Access Committee for data from EGAS00001007832

  Dac EGAC00001003500

• Data Access Committee for data from EGAS00001007819

  Dac EGAC00001003501

• Data Access Committee for data from EGAS00001007904

  Dac EGAC00001003512

• Data Access Committee for data from EGAS00001008107

  Dac EGAC00001003568

• UCL Centre for Longitudinal Studies

  Dac EGAC00001001041

• BAP1 Project

  For our BAP1 manuscript

  Dac EGAC50000000006

• EGAD00010000608

  SNP6 data for seminoma samples

  Dataset EGAD00010000608

• Transcriptome - Uveal Melanomas

  Total RNA sequencing on 9 uveal melanomas. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599). Paired-end libraries (2 x 100 bp) were sequenced on a NovaSeq 6000 instrument (Illumina).

  Dataset EGAD50000000763

• WGS of PDO in depleted media

  Whole genome sequencing profiling of 7 PDAC patient-derived organoids (PDO) grown in a culture medium lacking both WNT3A and RSPO1- WGS unmapped reads, sequenced using NovaSeq 6000, 15x coverage 160 million reads per sample.

  Dataset EGAD50000000282

• Single-cell multidimensional profiling of tumor cell heterogeneity in supratentorial ependymomas

  55 Supratentorial Ependymomas patient samples were sequenced scRNA-sequencing using Smart-Seq2 and 10x protocol (51 samples) and 10x Genomics protocol (4 samples) on a NextSeq 550 sequencer (Illumina).

  Dataset EGAD50000002186

• Whole exome genome sequencing data to study "A biobank of patient-derived pediatric brain tumor models"

  Whole exome sequencing data to 30 PDOX models (28 early passages, 3 late passages (1 overlap)), 3 cell lines, and 20 matching human tumors

  Dataset EGAD00001003544

• Independent development of lymphoid and histiocytic malignancies from a shared early precursor

  Whole Exome Sequencing data from the germline of the patient as well as the tumors in bone marrow (T-ALL), Liver (Histiocytic Sarcoma) and ileum (non-Langerhans Cell Histiocytosis).

  Dataset EGAD00001001596

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

  This dataset contains 18 ATACseq reads, in fastq format. Samples were collected from fresh bone marrow and peripheral blood sample from AML patients.

  Dataset EGAD00001006670

• RNA sequencing of PTCL-NOS

  This dataset contains raw .fastq files of a paired-end RNA-seq experiment on 15 PTCL-NOS samples. Samples were prepared with Truseq stranded mRNA library kit.

  Dataset EGAD00001006925

• Medulloblastoma Nanopore whole genome sequencing 3 samples

  ONT (PromethION) sequencing of chromothriptic medulloblastoma. Three samples: blood, primary tumor, and relapse tumor. Includes a fourth low-coverage run that multiplexes blood and primary tumor.

  Dataset EGAD00001009411

• Extensive and differential platinum chemotherapy mutagenesis in livers of children - Whole genome NanoSeq

  Whole genome NanoSeq of a cohort predominantly consisting of paired blood, normal liver and liver tumour from children with liver cancer. The cohort includes platinum-exposed and platinum naïve samples.

  Dataset EGAD00001016142

• MicroRNA Biomarkers for Prediction of Preeclampsia

  Maternal serum was collected between 17-28 weeks gestation. Samples were obtained from the high-risk Placental Study at the University of California, San Diego (n=48) and from the average-risk Proteomic Assessment of Preterm Risk (PAPR) Study at Sera Prognostics (n=164). RNA was extracted from 500 microliter of maternal serum using the miRNeasy Micro kit (Qiagen). NEBNext Small RNAseq Library Preparation Kit was used for library construction.

  Study phs002016

• Whole exome sequencing data for patients with Bosma arhinia microphthalmia syndrome (BAMS).

  The datasets includes 21 samples from 7 families with Bosma arhinia microphthalmia (BAMS). For details of the study please refer to the manuscript "De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development", Nature Genetics 2017. Each sample was exome sequenced and the family ID in sample description refers to the Individual ID in Supplementary figure 2 of the manuscript.

  Study EGAS00001002193

• WGS data for MMML for Study EGAS00001002199

  Whole genome sequencing data for MMML (24 tumor/control pairs), fastq-files

  Dataset EGAD00001003276

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (28 tumor/control pairs)

  Dataset EGAD00001003207

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (12 tumor/control pairs)

  Dataset EGAD00001003208

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (cell_line)

  Dataset EGAD00001003210

• Long-read sequencing for cell-free DNA analysis (human)

  In this study, we compared the two long-read sequencing platforms, namely the single-molecule real-time sequencing by Pacific Biosciences and nanopore sequencing by Oxford Nanopore Technologies, for the analysis of cell-free DNA from plasma. Cell-free DNA from plasma samples of 31 pregnant women at different trimesters, 6 hepatitis B carriers, and 8 patients with hepatocellular carcinoma were sequenced with the two platforms.

  Study EGAS00001006328

• DNA sequencing for human normal endometrial glands

  To elucidate the timing and mechanism of the clonal expansion of somatic mutations in cancer-associated genes in the normal endometrium, we conducted whole-exome and whole-genome sequencing for 56 endometrial glands and matched blood samples from 4 women. By collecting endometrial glands from different parts of the endometrium, we showed that multiple glands with the same somatic mutations occupied substantial areas of the endometrium.

  Study EGAS00001005822

• Paired RNA-Seq of fCAB treated and bisulfite treated VDH01, partly depleted for NSUN3

  Paired RNA-seq of bisulfite treated VDH01 samples control or depleted for NSUN3 (4 replicates each). The samples were prepped with NEBNext Ultra II DNA library prep kit and sequenced on MiSeq. Paired RNA-seq of fCAB treated vdh01 samples control or depleted for NSUN3(4 replicates each). the samples were prepped with NEBNext Ultra II DNA library prep kit and sequenced on MiSeq. Paired RNA-seq of fCAB treated VDH01 samples (3). the samples were prepped with NEBNext Ultra II DNA library prep kit and sequenced on MiSeq. Paired RNA-seq of bisulfite treated VDH01 samples (3). the samples were prepped with NEBNext Ultra II DNA library prep kit and sequenced on MiSeq.

  Dataset EGAD00001008742

• 13 WGS and 8 TCS data of ENKL patients treated with pembrolizumab.

  Whole-genome sequencing (WGS) was performed for 13 pairs of tumor-normal samples from patients diagnosed with NKTL. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 2000 or HiSeq X Ten as 2x101 bp or 2x151 bp, respectively. 8 NKTL FFPE specimens were screened for somatic mutations using deep targeted capture sequencing (TCS). FFPE rolls or slides were extracted using QIAamp DNA FFPE Tissue kit (QIAGEN). The FFPE genomic DNA was treated with NEBNext FFPE DNA Repair Mix and assessed by Quant-it PicoGreen dsDNA Assay Kit (Invitrogen). The library was generated from 10-200 ng DNA with SureSelectXT Low Input Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent Technologies) according to manufacturer’s instructions. RNA based probe was designed with SureDesign (Agilent Technologies) to target-capture 140 genes. Next, the captured libraries were pooled in equimolar concentration and sequenced on Illumina Novaseq 6000 platform with SP or S1 chip. Reads aligning to 40 selected genes were isolated post-alignment for this submission. Prefix used in filenames: T - Tumor samples N - Matched-Normal samples

  Dataset EGAD00001004140

• DAC for achalasia risk consortium (arc)

  Dac EGAC00001000394

• DAC for aflatoxin project Qidong patient samples

  Dac EGAC00001000679

• DAC for the cfSort study (tissue deconvolution)

  Dac EGAC00001003222

• DAC for seminoma genomic data

  Dac EGAC00001000231

• DAC for study WES of pituitary tumors

  Dac EGAC00001000443

• Data Access Committee for Hui Lab

  Dac EGAC00001000454

• INRP - Italian Network for Research on Psychoses

  Dac EGAC00001000576

• DAC for MOMA, Short QT Exome data

  Dac EGAC00001000730

• DAC for Dissecting Tumor Microenvironment with Tumorgrafts

  Dac EGAC00001000809

• Data Access Committee for data from EGAS00001002840

  Dac EGAC00001000834

• DAC for human single nuclei RNAseq of Epilepsy

  Dac EGAC00001000860

• Data Access Committee for the CentralAfricanCMC_Pemberton dataset

  Dac EGAC00001000896

• Laboratory for Neurobiology (VIB-KU Leuven)

  Dac EGAC00001001282

• DAC for HSTCL study. National Cancer Centre Singapore.

  Dac EGAC00001001302

• DAC for MEITL study. National Cancer Centre Singapore.

  Dac EGAC00001001323

• DAC for Phylogenetic reconstruction of breast cancer

  Dac EGAC00001001572

• Center for Technology Licensing at Cornell University

  Dac EGAC00001001587

• Data Access Commitee for single-cell analysis

  Dac EGAC00001001600

• DAC for Stuttgart Breast Cancer Cohort

  Dac EGAC00001001693

• Data Access Committee for data from EGAS00001004619

  Dac EGAC00001001712

• DAC for 16 year brca case report

  Dac EGAC00001001714

• Data Access Committee for data from EGAS00001004666

  Dac EGAC00001001756

• Data Access Committee for data from EGAS00001004455

  Dac EGAC00001001798

• Genentech DAC for IMmotion151

  Dac EGAC00001001813

• Single cell multi-omics (scNOVA) group for AML

  Dac EGAC00001001866

• Data Access Committee for IPF Collaboration

  Dac EGAC00001001878

• Center for Medical Genetics Data Access Commitee

  Dac EGAC00001001892

• DAC for cell free DNA TAPS study

  Dac EGAC00001001903

• Data access committee for lung cancer

  Dac EGAC00001001942

• Data Access Committee for the MPNST project

  Dac EGAC00001001987

• DAC for single cell RNAseq in FL project

  Dac EGAC00001002114

• DAC-for-UniExome-EGA-upload-2021

  Dac EGAC00001002168

• DAC for Germline biallelic mutation

  Dac EGAC00001002423

• DAC for Identification of Germline Monoallelic Mutations

  Dac EGAC00001002461

• DAC for studying human normal breast cells

  Dac EGAC00001002481

• DAC for studying human normal breast cells

  Dac EGAC00001002498

• Annie Huang and the Hospital for Sick Children

  Dac EGAC01000000015

• Data Access Committee for the Berardi group

  Dac EGAC00001003392

• DAC for the study EGASXXX

  Dac EGAC00001002746

• DAC for Castleman. National Cancer Centre Singapore.

  Dac EGAC00001003328

• Data access committee for the HOMOCULTURGEN dataset

  Dac EGAC00001003485

• DAC for the study EGAS00001007247

  Dac EGAC00001003262

• PDiamond. DAC

  DAC for pdiamond project

  Dac EGAC50000000377

• DAC - Institute for Pharmacology and Toxicology

  Dac EGAC00001003385

• DAC_iCope

  DAC for the iCope submission

  Dac EGAC50000000696

• DAC for ALSPAC whole exome sequencing data

  Dac EGAC00001003496

• DAC for NMIBC study - UCLouvain

  Dac EGAC50000000789

• Data Access Committee for data from EGAS00001004454

  Dac EGAC00001002077

• LUMC Department Pediatrics, Laboratory for Pediatric Immunology

  Dac EGAC50000000822

• Data Access Committee for data from EGAS00001006662

  Dac EGAC00001003009

• Data Access Committee for data from EGAS00001005944

  Dac EGAC00001002583

• Tumor educated platelets for BrCA

  Study EGAS00001006821

• RNASeq for BMI GL study

  Study EGAS00001004127

• EGAD00010000606

  SNP6 data for matched normal samples

  Dataset EGAD00010000606

• Genetic analysis in lifestyle-related disease, arteriosclerotic disease, and aging-related diseases.

  Exome sequence analysis was conducted in patients with hypertension (Stage 3). Rare variants in candidate susceptible genes discovered by previous GWASs were prioritised and further analysed for an additional case-control association study.

  Study JGAS000016

• Mitochondrial DNA Mutations at Low-level Heteroplasmy in Chronic Kidney Disease

  To explore for relationship between somatic or heteroplasmic mutations of mtDNA and kidney function, we here performed ultra-deep sequencing based on long-range PCR from DNAs of 78 CKD kidney tissues.

  Study JGAS000611

• CIAO Clinical Trial

  Whole exome and RNA sequencing for samples from CIAO (Checkpoint Inhibitors Assessment in Oropharynx cancer) (NCT03144778) clinical trial testing neoadjuvant anti-PD-L1 durvalumab with or without the anti-CTLA-4 tremelimumab in oropharynx cancer

  Study EGAS50000001174

• Diverse Cellular Composition in Alveolar Rhabdomyosarcoma Revealed by Single Cell RNA Sequencing

  Using single cell RNAseq data to characterize tumor composition and cellular states for Alveolar Rhabdomyosarcoma. We find that that ARMS tumors harbor phenotypically and transcriptionally distinct malignant subpopulations within an immune-influenced microenvironment.

  Study EGAS50000001564

• Single-sell RNA sequencing counts from 7 acute myeloid leukemia patients and 3 healthy donors

  This dataset contains count data (from 10X CellRanger) and metadata from 7 acute myeloid leukemia subjects treated with chemotherapy, as well as data from 3 healthy donors. Additionally, the dataset includes VDJ data for all subjects except for 31_base and the 3 healthy donors (TCRseq not performed).

  Dataset EGAD50000000525

• A_study_of_the_molecular_pathogenesis_of_Splenic_Marginal_Zone_and_Diffuse_Large_B_Cell_Lymphoma

  We will perform exome sequencing on selected cases of splenic marginal zone lymphoma (SMZL) and diffuse large B-cell lymphoma (DLBCL) in order to characterise their genetic makeup and identify biomarkers for prognosis and prediction of treatment response.

  Study EGAS00001000335

• Whole-exome analysis of corticotropin-independent Cushing's syndrome

  We performed WES for 8 cases with corticotropin-independent Cushing’s syndrome, in whom paired tumor and normal DNA was obtained from fresh frozen adenomas and either normal adrenal tissues or peripheral blood, respectively.

  Study EGAS00001000661

• Genetics_and_Networks_of_Congenital_Heart_Defects

  Exome sequencing of families with Congenital Heart Defects of diverse sub-phenotypes. Comprises both parent-offspring trios for sporadic cases and multiplex families. Collaboration with David Brook, University of Nottingham. Funded by the British Heart Foundation.

  Study EGAS00001000762