DAC

ICGC Data Access Compliance Office

Dac ID Contact Person Email Access Information
EGAC00001000010 helpdesk daco [at] icgc-argo [dot] org https://docs.icgc-argo.org/docs/data-access/daco/applying

This DAC controls 487 datasets:

Dataset ID Description Technology Samples
EGAD00001000023 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer IIx 11
EGAD00001000027 ICGC Germany PedBrain Medulloblastoma Pilot_2_LM Illumina Genome Analyzer IIx,Illumina HiSeq 2000 8
EGAD00001000044 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer IIx 212
EGAD00001000045 Somatic mutation of SF3B1 in myelodysplasia with ring sideroblasts and other cancers Illumina Genome Analyzer II,Illumina HiSeq 2000 33
EGAD00001000049 Pancreatic adenocarcinoma QCMG 20110901 AB SOLiD 4 System,AB SOLiD System 3.0 26
EGAD00001000063 Triple Negative Breast Cancer sequencing Illumina Genome Analyzer II 6
EGAD00001000083 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer II,Illumina Genome Analyzer IIx 61
EGAD00001000088 ER-, HER2-, PR- breast Cancer genome sequencing Illumina Genome Analyzer II 6
EGAD00001000096 Pancreatic adenocarcinoma QCMG 20120201 AB SOLiD 4 System 166
EGAD00001000102 Myeloproliferative Disorder Sequencing Illumina Genome Analyzer II 6
EGAD00001000103 Myeloproliferative Disorder Sequencing Illumina Genome Analyzer II 4
EGAD00001000106 Primary Myelofibrosis Myeloproliferative Disease exome sequencing Illumina Genome Analyzer II,Illumina HiSeq 2000 67
EGAD00001000107 SCAT osteosarcoma sequencing Illumina Genome Analyzer II,Illumina HiSeq 2000 114
EGAD00001000110 Breast Cancer Exome Sequencing Illumina Genome Analyzer II,Illumina HiSeq 2000 179
EGAD00001000117 Myelodysplastic Syndrome Exome Sequencing Illumina Genome Analyzer II,Illumina HiSeq 2000 152
EGAD00001000118 Osteosarcoma Exome Sequencing Illumina Genome Analyzer II,Illumina HiSeq 2000 102
EGAD00001000122 DATA_SET_ICGC_PedBrainTumor_Medulloblastoma Illumina Genome Analyzer IIx,Illumina HiSeq 2000 206
EGAD00001000123 Polycythemia Vera Myeloproliferative Disease exome sequencing Illumina Genome Analyzer II,Illumina HiSeq 2000 119
EGAD00001000126 HER2 positive Breast Cancer Illumina HiSeq 2000 101
EGAD00001000129 Essential Thrombocythemia Myeloproliferative Disease exome sequencing Illumina HiSeq 2000 189
EGAD00001000131 Genetic landscape of hepatocellular carcinoma Illumina HiSeq 2000 48
EGAD00001000133 The landscape of cancer genes and mutational processes in breast cancer Illumina Genome Analyzer II,Illumina HiSeq 2000 199
EGAD00001000136 CML blast phase rearrangement screen Illumina HiSeq 2000 6
EGAD00001000138 The expression data for this study can be found here: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1088/and its SNP6 data can be found here:http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1087/ Illumina Genome Analyzer II,Illumina HiSeq 2000 58
EGAD00001000141 Triple Negative Breast Cancer Whole Genomes Illumina Genome Analyzer II,Illumina HiSeq 2000 243
EGAD00001000147 Osteosarcoma Whole Genome Illumina HiSeq 2000 108
EGAD00001000158 Subgroup-specific structural variation across 1,000 medulloblastoma genomes 23
EGAD00001000176 DATA_SET_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation Illumina HiSeq 2000,Illumina Genome Analyzer IIx 8
EGAD00001000177 Whole Genome Methylation in CLL Illumina Genome Analyzer IIx 6
EGAD00001000258 Deep RNA sequencing in CLL Illumina Genome Analyzer II 107
EGAD00001000262 OICR PANCREATIC CANCER DATASET 4
EGAD00001000263 A small subsample of EGAD00001000689. Please do not use. Illumina HiSeq 2000 18
EGAD00001000270 DATA_SET_EOP-PCA-LargeAndSmallTumors1 Illumina HiSeq 2000 18
EGAD00001000271 Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood Illumina HiSeq 2000 10
EGAD00001000272 Genomic Alterations in Gingivo-buccal Cancer: ICGC-India Project_YR01 454 GS FLX Titanium,Illumina HiSeq 2000 200
EGAD00001000274 DATA_SET_TRANSCIPTOME_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation Illumina HiSeq 2000 4
EGAD00001000275 Data set for Whole-genome-Sequencing of adult medulloblastoma Illumina HiSeq 2000 10
EGAD00001000276 OICR PANCREATIC CANCER DATASET 2 10
EGAD00001000278 ICGC MMML-seq Data Freeze November 2012 whole genome sequencing Illumina HiSeq 2000 12
EGAD00001000279 ICGC MMML-seq Data Freeze November 2012 whole exome sequencing Illumina Genome Analyzer IIx 4
EGAD00001000280 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/ Illumina HiSeq 2000 112
EGAD00001000281 ICGC MMML-seq Data Freeze November 2012 transcriptome sequencing Illumina HiSeq 2000 6
EGAD00001000283 Agilent whole exome hybridisation capture was performed on genomic DNA derived from MDS and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to discover the prevalence of our findings using bespoke pulldown methods and sequencing the products from a larger set of patient DNA. Illumina HiSeq 2000 764
EGAD00001000285 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina Genome Analyzer II,Illumina HiSeq 2000 55
EGAD00001000293 Sequencing data for Australian Ovarian Cancer study submitted 20121116 AB SOLiD 4 System 72
EGAD00001000303 ICGC prostate cancer whole genome mate-pair sequencing Illumina Genome Analyzer IIx 22
EGAD00001000304 ICGC prostate cancer miRNA sequencing Illumina HiSeq 2000 8
EGAD00001000305 ICGC prostate cancer RNA sequencing Illumina HiSeq 2000 12
EGAD00001000306 ICGC prostate cancer whole genome sequencing Illumina HiSeq 2000 22
EGAD00001000323 Sequencing data for Australian Pancreatic Cancer study submitted 20130102 AB SOLiD 4 System,Illumina HiSeq 2000 200
EGAD00001000327 release_2: ICGC PedBrain: whole genome mate-pair sequencing Illumina Genome Analyzer IIx,Illumina HiSeq 2000 70
EGAD00001000328 ICGC PedBrain: RNA sequencing Illumina HiSeq 2000 28
EGAD00001000355 ICGC MMML-seq Data Freeze March 2013 whole genome sequencing Illumina HiSeq 2000 46
EGAD00001000356 ICGC MMML-seq Data Freeze March 2013 transcriptome sequencing Illumina HiSeq 2000 23
EGAD00001000358 Chondrosarcoma (CHS) is a heterogeneous collection of malignant bone tumours and is the second most common primary malignancy of bone after osteosarcoma. Recent work has identified frequent, recurrent mutations in IDH1/2 in nearly half of central CHS. However, there has been little systematic genomic analysis of this tumour type and thus the contribution of other genes is unclear. Here we report comprehensive genomic analyses of 49 cases of CHS. We identified hypermutability of the major cartilage collagen COL2A1 with insertions, deletions and rearrangements identified in 37% of cases. The patterns of mutation were consistent with selection for variants likely to impair normal collagen biosynthesis. In addition we identified mutations in IDH1/2 (59%), TP53 (20%), the RB1 pathway (27%) and hedgehog signaling (22%). Illumina HiSeq 2000 17
EGAD00001000368 Genomic libraries (500 bps) will be generated from total genomic DNA derived from Osteosarcoma cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions. Illumina HiSeq 2000 3
EGAD00001000371 Sequencing data for PDAC cell lines generated by QCMG Illumina HiSeq 2000,Illumina HiSeq 2500 54
EGAD00001000385 Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myeloproliferative Disease samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations, insertions, deletions as well as larger structural variants and genomic rearrangements. Illumina HiSeq 2000 108
EGAD00001000386 Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myelodysplastic syndrome patient samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations, insertions, deletions as well as larger structural variants and genomic rearrangements. Illumina HiSeq 2000 83
EGAD00001000387 This study aims to whole genome sequence DNA derived from breast cancer patients who received neo-adjuvany chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved. Illumina HiSeq 2000 35
EGAD00001000390 We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000 101
EGAD00001000446 Fastq files of 213 samples of hepatocellular carcinoma (NCCRI) Illumina HiSeq 2000 213
EGAD00001000616 Pilocytic Astrocytoma ICGC PedBrain whole genome sequencing Illumina HiSeq 2000 192
EGAD00001000617 Pilocytic Astrocytoma ICGC PedBrain RNA sequencing Illumina HiSeq 2000 73
EGAD00001000619 Experiments using targeted pulldown methods will be sequenced to validate findings in the exomes of patients with Myeloproliferative Neoplasms (MPN). Illumina HiSeq 2000 360
EGAD00001000620 A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients. Illumina HiSeq 2000 14
EGAD00001000621 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. This study will aim to validate the findings of the whole genome study by re-sequencing regions of interest using a bespoke pulldown bait. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina MiSeq 18
EGAD00001000625 The main objective of this benchmark is the comparison of the full sequencing pipeline of different ICGC partners, including procedures, methods and performance of library preparation and whole-genome deep-sequencing. A secondary objective will be a follow-up comparison of data analysis pipelines for identification of germline and somatic variants subsequent to the results of the ICGC Somatic Variant Calling Pipeline Benchmark. Illumina HiSeq 2000 2
EGAD00001000632 NA AB SOLiD 4 System 12
EGAD00001000644 ICGC PedBrain DNA Methylation project Illumina HiSeq 2000 42
EGAD00001000645 ICGC MMML-seq Data Freeze July 2013 whole genome sequencing 42
EGAD00001000646 A selection of human cancers harbours somatic driver mutations in genes encoding histones, most notably childhood brain tumours with K27M substitutions of the histone 3.3 gene, H3F3A. We performed whole genome sequencing of the benign cartilage tumour, chondroblastoma, and targeted sequencing of histone 3.3 genes, H3F3A and H3F3B, in seven further skeletal tumour types. We identified an exceptionally high prevalence of novel histone 3.3 driver mutations at glycine 34 and at lysine 36. Histone 3.3 gene mutations were found in 91% in giant cell tumours of bone (48/53), mainly H3F3A G34W variants, and in 92% of chondroblastoma (73/79), predominantly K36M mutations in H3F3B. H3F3B is paralogous to the cancer gene H3F3A. However, H3F3B driver variants have not previously been reported in human cancer. Our observation demonstrate remarkable tumour-specificity of mutations, with respect to which histone 3.3 gene and residue is mutated, indicating that the advantage these mutations confer is tumour dependent. Moreover, tumour-specific mutation of H3F3A and H3F3B suggests, that although both genes encode identical proteins, they are likely non-redundant and employed differentially during skeletal development. Illumina HiSeq 2000 14
EGAD00001000648 ICGC MMML-seq Data Freeze July 2013 transcriptome sequencing 31
EGAD00001000650 ICGC MMML-seq Data Freeze July 2013 miRNA sequencing 52
EGAD00001000653 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. Illumina HiSeq 2000 10
EGAD00001000660 Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826 353
EGAD00001000661 Bespoke validation experiments will be performed on ER+ Breast Cancer cases to confirm the presence of mutations found in whole genome sequencing. Illumina HiSeq 2000 46
EGAD00001000662 We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. This study will use a bespoke bait set to pulldown regions of interest found in whole genome sequencing to validate mutations found. Illumina HiSeq 2000 46
EGAD00001000664 Whole Genome Seq: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009);duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Paired-end RNA sequencing reads were mapped to the hg19 assembly of the human reference genome using BWA.Each ChIP-seq library was sequenced with two complete lanes on the Illumina HiSeq 2500 in the 101-bases paired-end rapid mode and aligned to hg19 using bwa.This resulted in the following coverage values (genome-wide, after deduplication, including all uniquely mapping reads):GBM103 macroH2A1: 17x H3K36me3: 20xMB59 macroH2A1: 11x H3K36me3: 11x 7
EGAD00001000665 Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Sample derived from secondary myelodysplastic syndrome (MDS), arising after treatment for medulloblastoma in an 11-year old female Li-Fraumeni syndrome case (LFS-MB1; Rausch et al., 2012; matching WGS data available under EGAS00001000085). 1
EGAD00001000666 HSC73_clone: Bone marrow mononuclear cells from the healthy 73 years old female were thawed and labeled with Alexa-Fluor 488-conjugated anti-CD34 (581, Biolegend), Alexa-Fluor 700-conjugated anti-CD38 (HIT2, eBioscience), a cocktail of APC-conjugated lineage antibodies consisting of anti-CD4 (RPA-T4), anti-CD8 (RPA-T8), anti-CD11b (ICRF44), anti-CD20 (2H7), anti-CD56 (B159, all BD Biosciences), anti-CD14 (61D3), anti-CD19 (HIB19) and anti-CD235a (HIR2, all eBiocience) and 1 micro-gram/ml propidium iodide (Sigma). Using a BD FACSAria cell sorter, single Lin-CD34+CD38-PI- cells were individually sorted into low-adhesion 96-well tissue culture plates (Corning) containing 100micro-litre of StemSpan Serum-Free Expansion Medium (Stemcell technologies) supplemented with 100ng/ml of human SCF and FLT-3L, 50ng/ml of human TPO, 20ng/ml of human IL-3, IL-6 and G-CSF (all cytokines from Peprotech) and 50U/ml of penicillin and 50μg/ml of streptomycin (Sigma). Cells were incubated at 37 degrees C in a humidified atmosphere with 5% CO2 in air. After 5 days in culture, another 100micro litres of cytokine-containing medium were added. 13 days after seeding, clones B6 and G2 had expanded to approx. 105 cells and were selected for whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) after tagmentation-based library preparation (see Extended Experimental Procedures) for clone B6 and standard library preparation for clone G2. For germline-control ~106 unsorted bone marrow mononuclear cells from the same donor were used for sequencing. An average of 30-fold sequence coverage for each the clones and the matching control were obtained.L4clone: A progenitor cell clone was raised from a peripheral blood sample of the 39 year old healthy female. Frozen peripheral blood mononuclear cells (PBMCs) were isolated from 2 ml heparinised peripheral blood via Ficoll Paque density centrifugation. A methylcellulose assay was performed as described earlier (Weisse et al., 2012). In brief, non-adherent mononuclear cells were incubated in the presence of the recombinant human cytokines IL-3, IL-5 and GM-CSF (R&D systems) over 14 days to induce colony formation. Colonies were detected under an inverted light microscope, and plucked by a pipette when colonies had approximately 10,000 cells/CFU. Each colony was washed three times in PBS and finally frozen as a cell pellet in -80 degrees C. Genomic DNA was isolated using the QIAamp DNA micro kit according to the instructions of the manufacturer (Qiagen, Hilden, Germany). Whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) was performed for colony 4 after tagmentation-based library preparation and resulted in 15-fold sequence coverage for each the colony and the matching whole blood. 5
EGAD00001000677 Genome-wide analysis of H3K27me3 occupancy and DNA methylation in K27M-mutant and H3.3-WT primary pediatric high-grade gliomas (pHGGs) as well as pediatric pHGG cell lines. The study aims to elucidate the connection between K27M-induced H3K27me3 reduction and changes in DNA methylation as well as gene expression. Illumina HiSeq 2000 19
EGAD00001000679 A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients. Illumina HiSeq 2000 107
EGAD00001000689 Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of 3 men. For each of three different prostates, multiple tumour samples (4, 5, and 3 depending on the case) and one normal tissue sample were whole genome sequenced with a matched blood sample using the Illumiuna HiSeq platform. Tumour samples were sequenced to a target depth of 50X and normals and blood to a target depth of 30X. As of September 2020, some of the studies using these data include: Cooper et al, Nature Genetics 2015 (PMID: 25730763) Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007) Illumina HiSeq 2000 18
EGAD00001000697 Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Illumina Genome Analyzer IIx,Illumina HiSeq 2000 90
EGAD00001000698 Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.The whole exome sequencing data of 20 SHH medulloblastomas from phs000504.v1.p1 dataset has been used in our study on SHH medulloblastomas: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000504.v1.p1 4
EGAD00001000699 Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Illumina HiSeq 2000 78
EGAD00001000704 NA Illumina HiSeq 2000 44
EGAD00001000709 Dataset of CageKid Blood DNA samples 95
EGAD00001000717 Dataset of CageKid Tumor DNA samples 95
EGAD00001000718 Dataset of CageKid Tumor RNA samples 91
EGAD00001000719 Dataset of CageKid Normal RNA samples 45
EGAD00001000720 Dataset of CageKid tumor-normal paired RNA samples 90
EGAD00001000721 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. Illumina HiSeq 2000 20
EGAD00001000722 Extension of angiosarcoma whole genome sequencing study Illumina HiSeq 2000 8
EGAD00001000723 Relative Spatial Homogeneity of Embryonal Brain Tumors of Childhood 42
EGAD00001000724 NA Illumina HiSeq 2000 68
EGAD00001000735 Here we present the genomes of three secondary angiosarcomas Illumina HiSeq 2000 7
EGAD00001000737 Whole exome sequencing data from 30 donors (46 tumors and 30 non-tumoral whole exome sequencing, paired-end, HiSeq 2000, Illumina) collected by the Inserm U674, PI Jessica Zucman-Rossi - Institut National du Cancer (INCa), PI Fabien Calvo, France. Illumina HiSeq 2000 76
EGAD00001000738 Extension of angiosarcoma whole genome sequencing study Illumina HiSeq 2000 4
EGAD00001000749 NA Illumina HiSeq 2000 12
EGAD00001000758 dataset for BGI bladder cancer project Illumina Genome Analyzer II 198
EGAD00001000760 dataset for esophageal cancer, 17 pairs for whole-genome sequencing and 71 pairs for whole-exome sequencing Illumina HiSeq 2000 176
EGAD00001000783 Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50 ). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing. Illumina HiSeq 2000,Illumina HiSeq 2500 400
EGAD00001000784 This study aims to target capture sequence regions of interest from DNA derived from breast cancer patients who received neo-adjuvant chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved. Illumina HiSeq 2000 242
EGAD00001000785 We propose to definitively characterise the somatic genetics of a selection of rare bone cancers through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. Illumina HiSeq 2000 33
EGAD00001000808 RIKEN collection WGS reads for 321 HCC and blood matched samples from 158 donors submitted to ICGC for release 15 Illumina Genome Analyzer IIx,Illumina HiSeq 2000 321
EGAD00001000809 RIKEN collection WGS reads for 61 liver cancer and matched blood samples from 30 donors displaying biliary phenotype Illumina HiSeq 2000 61
EGAD00001000810 Dataset for whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors Illumina HiSeq 2000 106
EGAD00001000816 ICGC medulloblastoma whole genome sequencing data, ICGC release 16 44
EGAD00001000818 Quiescent Sox2+ cells drive hierarchical growth and relapse in Sonic hedgehog subgroup medulloblastoma 4
EGAD00001000826 We propose to definitively characterise the somatic genetics of Osteosarcoma cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome and transcriptome sequencing. Illumina HiSeq 2000 10
EGAD00001000842 RIKEN collection WGS reads for 100 HCC and matched blood samples from 50 donors submitted to ICGC for release 16 Illumina HiSeq 2000 100
EGAD00001000873 Fastq files of 10 samples of condrosarcoma Illumina Genome Analyzer IIx,Illumina HiSeq 2000 10
EGAD00001000874 Indel/point mutation of chondrosarcoma 10
EGAD00001000877 Complete WGS and RNA-Seq dataset for Australian ICGC ovarian cancer sequencing project 2014-07-07, representing 93 donors. Sequencing was performed on Illumina HiSeq. Alignment of the lane-level fastq data was performed with bwa (WGS data) and RSEM (transcriptome data). For this dataset lane-level .bam files have been merged and de-duplicated to create a single bam file for each sample type (tumour/normal) for each donor. This dataset supersedes all previous datasets for this study. 2016-08-08 updated with 14 outstanding RNA-seq samples & corresponding RSEM bams 2016-12-07 updated with 7 outstanding RNA-seq controls and corresponding RSEM bams 331
EGAD00001000879 Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing. Illumina HiSeq 2500 335
EGAD00001000891 To characterize the subclonal genomic architecture of androgen-deprived metastatic prostate cancer, we performed whole-genome sequencing (WGS) of 51 tumours from 10 patients to an average sequencing depth of 55x, including multiple metastases from different anatomic sites in each patient and, in five cases, the prostate tumour. Noncancerous DNA from blood or other tissue is used as reference comparison for each patient. The patients are part of PELICAN (Project to ELIminate Lethal Cancer) rapid autopsy study led by G. Steven Bova at Johns Hopkins University (USA) and Tampere University (Finland). As of September 2020, some of the studies using these data include: Gundem et al, Nature 2015 (PMID: 25830880). Additional EGAD00001000891 sample metadata is contained in Supplementary Information in this report.Tubio et al, Science 2014 (PMID: 25082706) Behjati et al, Nature Comm 2015 (PMID: 27615322) Wedge et al, Nature Genetics 2018 (PMID: 29662167)Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)Rodriguez-Martin et al, Nature Genetics 2020 (PMID: 32024998)Woodcock et al, Nature Comm 2020 (In Press) Illumina HiSeq 2000 62
EGAD00001000892 Whole Genome Sequencing Illumina HiSeq data from 20 men with prostate cancer. 20 samples were taken from primary tissue obtained at prostatectomy (target sequencing depth 50X) with matched blood control (target sequencing depth 30X). These were submitted for use in the ICGC Pan-Cancer Analysis of Whole Genomes project. Same raw data submitted in EGAD00001001116. As of September 2020, some of the studies using these data include: Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007) Illumina HiSeq 2000 40
EGAD00001000946 Divergent clonal selection dominates medulloblastoma at recurrence 125
EGAD00001000949 Validations of variants identified by exome sequencing in sequential samples derived after treatment cycle with AZA. Illumina HiSeq 2000 170
EGAD00001000950 Whole genome sequencing data for ependymomas (5 tumor-control pairs). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142). 10
EGAD00001000951 Whole exome sequencing data for ependymomas (42 tumor-control pairs). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142). 84
EGAD00001000952 DNA methylation profiling of 8 control samples from adult (4) and fetal brain (4) Illumina HiSeq 2000 8
EGAD00001000983 65 prostate cancer cases wgs sequencing Illumina HiSeq 2000 10
EGAD00001000988 Validation/deeper sequencing for metastatic prostate cancer samples Illumina HiSeq 2500 94
EGAD00001000989 Validation/deeper sequencing for metastatic prostate cancer samples Illumina HiSeq 2500 26
EGAD00001001004 65 prostate cancer cases wgs sequencing Illumina HiSeq 2000 130
EGAD00001001019 RNA-seq dataset used for the validation of CDK6 cis-regulatory mutation annotated by OncoCis. NB bam files for manuscript A_Proteomic_Chronology_of_Gene_Expression_through_the_Cell_Cycle_in_Human_Myeloid_Leukemia_Cells are now available at the following link:http://www.ebi.ac.uk/ena/data/view/ERP008483 Illumina HiSeq 2000 1
EGAD00001001024 Fastq files of 52 samples of hepatocellular carcinoma(RCAST, THCC) Illumina HiSeq 2000 104
EGAD00001001035 RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors. Illumina Genome Analyzer IIx,Illumina HiSeq 2000 66
EGAD00001001043 NA Illumina HiSeq 2000 8
EGAD00001001044 NA Ion Torrent PGM 2
EGAD00001001048 Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z Illumina HiSeq 2000 0
EGAD00001001051 NA Illumina HiSeq 2000 200
EGAD00001001060 NA Illumina HiSeq 2000 112
EGAD00001001064 Extension of angiosarcoma whole genome sequencing study Illumina MiSeq 4
EGAD00001001071 Samples from the "100" project that are in the ICGC PanCancer project. Illumina HiSeq 2000 10
EGAD00001001076 Fastq files of 239 samples of biliary tract cancer Illumina HiSeq 2000 239
EGAD00001001094 200PG : WGS Raw Sequence (fastq) : Raw WG sequence data (fastq) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672 Illumina HiSeq 2500 247
EGAD00001001095 Supporting data for ICGC PACA-CA Release 18 Illumina HiSeq 2000,Illumina HiSeq 2500 506
EGAD00001001096 NA Illumina HiSeq 2000 419
EGAD00001001100 DCC Project Code: SKCA-BR Skin Adenocarcinoma - BR Brazil AB 5500 Genetic Analyzer,Illumina HiSeq 2500 200
EGAD00001001115 SeqControl Illumina HiSeq 2500 54
EGAD00001001116 Whole Genome Sequencing Illumina HiSeq data from 95 men with prostate cancer. Samples were taken from primary tissue obtained at prostatectomy (target sequencing depth 50X) with matched blood control (target sequencing depth 30X). This data is from batches 1 to 3 and is the bulk of the data used in Wedge et al, Nature Genetics 2018 (PMID: 29662167). As of September 2020, some of the studies using these data include: Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007) Illumina HiSeq 2000 190
EGAD00001001118 Gastric Cancer (GC) is a highly heterogeneous disease. To identify potential clinically actionable therapeutic targets that may inform individualized treatment strategies, we performed whole-exome sequencing on 78 GCs of differing histologies and anatomic locations, as well as whole-genome sequencing on two GC cases, each with 3 primary tumours and 2 matching lymph node metastases. The data showed two distinct GC subtypes with either high-clonality (HiC) or low-clonality (LoC). Illumina HiSeq 2000 168
EGAD00001001119 Whole Genome Bisulfite Sequencing Illumina HiSeq 2000,Illumina HiSeq 2500 26
EGAD00001001121 RNA Sequencing Illumina HiSeq 2000 26
EGAD00001001210 Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress 28
EGAD00001001238 Extension analysis to pursue candidate genes of interest in chordoma Illumina HiSeq 2000 262
EGAD00001001239 Extension analysis to pursue candidate genes of interest in chordoma Illumina HiSeq 2000 262
EGAD00001001262 Unaligned bam of 31 samples derived from primary tumor Illumina Genome Analyzer IIx,Illumina HiSeq 2000 31
EGAD00001001263 Unaligned bam of 31 samples derived from blood Illumina Genome Analyzer IIx,Illumina HiSeq 2000 31
EGAD00001001264 We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000 223
EGAD00001001322 A comprehensive characterisation and analysis of human breast cancers through whole-genome sequencing. Illumina HiSeq 2000 196
EGAD00001001323 A comprehensive characterisation and analysis of human breast cancers through genome-wide approaches through transcriptomics. Illumina HiSeq 2000 59
EGAD00001001329 Aligned Sequence (bam format), Duplicates removed 28
EGAD00001001334 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000 99
EGAD00001001335 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina Genome Analyzer II,Illumina HiSeq 2000 28
EGAD00001001336 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000 6
EGAD00001001337 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000,Illumina HiSeq 2500,Illumina MiSeq 607
EGAD00001001338 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina Genome Analyzer II,Illumina HiSeq 2000 49
EGAD00001001339 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000 76
EGAD00001001340 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000 20
EGAD00001001341 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000 158
EGAD00001001349 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000 4
EGAD00001001350 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000 8
EGAD00001001351 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000 2
EGAD00001001353 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000 2
EGAD00001001379 NA Illumina HiSeq 2000 29
EGAD00001001388 Whole-genome bisulfite sequencing (WGBS) on 30 breast cancer cases from the BASIS project. Illumina HiSeq 2000 30
EGAD00001001394 Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357 Illumina HiSeq 2000 0
EGAD00001001423 NA Illumina HiSeq 2000 7
EGAD00001001441 Despite the established role of the transcription factor MYC in cancer, little is known about the impact of a new class of transcriptional regulators, the long non-coding RNAs (lncRNAs), on the way MYC is able to influence cellular transcriptome. To this aim we have intersected RNA-sequencing data from two MYC-inducible cell lines and from a cohort of 91 mature B-cell lymphomas carrying, or not carrying, genetic variants resulting in MYC over-expression. By this approach, we identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma and regulated in the same direction by MYC in the model cell lines. Among them we focused on a lncRNA that we named MINCR, for MYC-Induced long Non-Coding RNA, showing a strong correlation with MYC expression in MYC-positive lymphomas and also in pancreatic ductal adenocarcinomas. To understand its cellular role we performed RNA interference (RNAi) experiments and found that MINCR knock-down is associated with a reduction in cellular viability, due to an impairment in cell cycle progression. Differential gene expression analysis following RNAi showed a strongly significant enrichment of cell cycle genes among the genes down-regulate following MINCR knock-down. Interestingly these genes are enriched in MYC binding sites in their promoters, suggesting that MINCR acts as a modulator of MYC transcriptional program. Accordingly, following MINCR knock-down, we observed a reduction in the binding of MYC to the promoters of selected cell cycle genes. Finally we provide evidences that down-regulation of AURKA, AURKB and CTD1 may explain the reduction in cellular proliferation observed upon MINCR knock-down. We therefore suggest that MINCR is a newly identified player in the MYC transcriptional network able to control the expression of cell cycle genes. Illumina HiSeq 2000,Illumina HiSeq 2500 49
EGAD00001001443 RNASeq sequencing. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2 × 76 bp. We generated more than 20 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina Inc.) following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files. Illumina Genome Analyzer II 199
EGAD00001001457 All samples from the "100" project Illumina HiSeq 2000 24
EGAD00001001461 CBP has opposing functions during cerebellar development and is a targetable tumor suppressor at late stages of medulloblastoma initiation 30
EGAD00001001464 Exome Sequencing. 3 μg of genomic DNA from each sample were sheared and used for the construction of a paired-end sequencing library as described in the paired-end sequencing sample preparation protocol provided by Illumina41. Enrichment of exonic sequences was then performed for each library using either the Sure Select Human All Exon 50 Mb or All Exon+UTRs v4 kits following the manufacturer’s instructions (Agilent Technologies). Exon-enriched DNA was pulled down by magnetic beads coated with streptavidin (Invitrogen), followed by washing, elution and 18 additional cycles of amplification of the captured library. Enriched libraries were sequenced (2 × 76 bp) in one lane of an Illumina GAIIx sequencer or in two lanes of a HiSeq2000 when using pools of eight samples. 0
EGAD00001001466 Whole Genome sequencing. 2 μg of genomic DNA from each sample was used for the construction of two short-insert paired-end sequencing libraries. Both types of libraries were sequenced in paired-end mode on Illumina GAIIx (2 × 151 bp) using Sequencing kit v4 or Illumina HiSeq2000 (2x101 bp) using TruSeq SBS Kit v3. 0
EGAD00001001595 ICGC PACA-CA Release 20 Illumina HiSeq 2000,Illumina HiSeq 2500 516
EGAD00001001619 miRNA seq data of 43 cases out of dataset EGAD00001000650 (MMML) 43
EGAD00001001620 release_2: ICGC PedBrain: RNA sequencing Illumina HiSeq 2000 45
EGAD00001001621 release_2: ICGC PedBrain: ChIP-Seq Illumina HiSeq 2000 31
EGAD00001001624 release_2: ICGC PedBrain: whole exome sequencing and Target-Seq Illumina HiSeq 2000 188
EGAD00001001625 release_2: ICGC PedBrain: whole genome sequencing Illumina Genome Analyzer IIx,Illumina HiSeq 2000 209
EGAD00001001630 release_2: ICGC PedBrain: whole genome bisulfite sequencing Illumina HiSeq 2000 108
EGAD00001001632 miRNA seq data of 13 cases (MMML) 13
EGAD00001001642 RIKEN collection of WGS reads of 530 liver cancer and matched blood samples from 260 donors. Illumina Genome Analyzer IIx,Illumina HiSeq 2000 530
EGAD00001001643 RIKEN collection of WGS read of 59 multi-centric liver cancers or intra-haptatic metastasis and matched blood samples from 19 donors. Illumina Genome Analyzer IIx,Illumina HiSeq 2000 59
EGAD00001001645 NA Illumina Genome Analyzer II,Illumina HiSeq 2000 28
EGAD00001001672 Part of RNA sequencing data of Malignant Lymphoma Study (ICGC) Illumina HiSeq 2000 56
EGAD00001001673 Part of WGS seq data of Maligant Lymphoma study (ICGC) Illumina HiSeq 2000,Illumina HiSeq 2500 112
EGAD00001001691 Esophageal cancer is one of the most aggressive cancers and the sixth leading cause of cancer death worldwide1. Approximately 70% of the global esophageal cancers occur in China and over 90% histopathological forms of this disease are esophageal squamous cell carcinoma (ESCC)2-3. Currently, there are limited clinical approaches for early diagnosis and treatment for ESCC, resulting in a 10% 5-year survival rate for the patients. Meanwhile, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we show a comprehensive genomic analysis in 158 ESCC cases, as part of the International Cancer Genome Consortium (ICGC) Research Projects (http://icgc.org/icgc/cgp/72/371/1001734). We conducted whole-genome sequencing in 14 ESCC cases and whole-exome sequencing in 90 cases. Illumina HiSeq 2000 208
EGAD00001001693 Fastq files of RNAseq of 182 samples of biliary tract cancer Illumina HiSeq 2000 182
EGAD00001001844 Whole genome sequencing of 64 HER2-Positive Breast Cancer Illumina HiSeq 2000 128
EGAD00001001847 4C-seq data was generated for regions of interest to confirm enhancer-gene promoter interactions Illumina HiSeq 2000 1
EGAD00001001858 Raw fastq files from WGS sequencing of CLL and matching blood normal for the ICGC Techval Benchmark1 study. Sequence data was provided to multiple centers for independent analysis and comparison. Illumina HiSeq 2500 2
EGAD00001001859 Raw fastq files for sequence data generated at 5 sequencing centers from a Medulloblastoma sample and matching blood normal control. Illumina HiSeq 2500 2
EGAD00001001880 RIKEN collection of RNA-seq reads for 458 liver cancer samples and matched normal liver from 247 donors. Illumina Genome Analyzer IIx,Illumina HiSeq 2000 458
EGAD00001001881 RIKEN collection of WGS reads for 269 liver cancer tumors and matched normal blood or liver tissue from 258 donors. In total there are 1864 paired fastq sets sequenced on Illumina HiSeq 2000 or Genome Analyzer II instruments with paired reads of 75–101 bp. Quality control and duplication removal has not been performed. Illumina Genome Analyzer IIx,Illumina HiSeq 2000 528
EGAD00001001891 Whole genome bisulfite sequencing of pedbrain - medulloblastoma Illumina HiSeq 2000 10
EGAD00001001899 HDAC and PI3K Antagonists Cooperate to Inhibit Growth of MYC-driven Medulloblastoma 102
EGAD00001001926 Esophageal Squamous Cell Carcinoma (ESCC) is one of the deadliest cancers worldwide. We performed 71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients. Illumina HiSeq 2000 141
EGAD00001001927 NA Illumina HiSeq 2000 27
EGAD00001001944 RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project Illumina HiSeq 2500 42
EGAD00001001956 ICGC Release 21 for PACA-CA from OICR Illumina HiSeq 2000,Illumina HiSeq 2500 516
EGAD00001001960 upcoming publication Illumina HiSeq 2000 171
EGAD00001001988 Cholangiocarcinoma whole genome sequencing data HiSeq X Ten,Illumina HiSeq 2000,Illumina HiSeq 2500 118
EGAD00001001996 RIKEN collection of WGS reads for 13 multicentric liver cancers or intrahepatic metastasis and matched blood samples for 12 donors. Illumina HiSeq 2000 13
EGAD00001002002 To characterize the subclonal genomic architecture of non-androgen-deprived metastatic prostate cancer, we performed whole-genome sequencing (WGS) of pelvic lymph node metastases and matching noncancerous blood from 10 patients to an average sequencing depth of 55x. The patients are part of PELICAN (Project to ELIminate Lethal Cancer) study led by G. Steven Bova at Johns Hopkins University (USA) and Tampere University (Finland). As of September 2020, study using these data is: Wedge et al, Nature Genetics 2018 (PMID: 29662167) Illumina HiSeq 2000 20
EGAD00001002006 Whole genome sequencing of paediatric glioblastoma in the ICGC PedBrain project Illumina HiSeq 2500 115
EGAD00001002016 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LICA-FR. 12
EGAD00001002119 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LAML-KR. 18
EGAD00001002120 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ORCA-IN. 26
EGAD00001002121 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BTCA-SG. 24
EGAD00001002122 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-UK. 90
EGAD00001002123 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MALY-DE. 202
EGAD00001002124 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: EOPC-DE. 113
EGAD00001002125 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BOCA-UK. 148
EGAD00001002126 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PRAD-UK. 116
EGAD00001002127 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PBCA-DE. 496
EGAD00001002128 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PRAD-CA. 244
EGAD00001002129 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-EU. 158
EGAD00001002130 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: CLLE-ES. 194
EGAD00001002131 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: RECA-EU. 190
EGAD00001002132 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PACA-AU. 192
EGAD00001002153 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PAEN-IT. 74
EGAD00001002154 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PAEN-AU. 98
EGAD00001002155 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LIRI-JP. 524
EGAD00001002156 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ESAD-UK. 198
EGAD00001002157 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MELA-AU. 140
EGAD00001002192 Additional sequencing data for 173 donors in EGAS00001000154, a study of Pancreatic Ductal Adenocarcinoma. WGS libraries were used for high-cellularity cases, WXS sequencing to high depth on low-cellularity cases. HiSeq 2xxx platform was used in all cases. The analysis files associated with this dataset are merged, de-duplicated bams aligned against GRCh37, one tumour and one normal bam per donor. 346
EGAD00001002218 Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 129_cohort EAC whole genomic sequencing data - Publication Secrier & Li et al., 2016, Nature Genetics Illumina HiSeq 2000 10
EGAD00001002241 Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - chemo_cohort Illumina HiSeq 2000 6
EGAD00001002256 Corresponding data set is composed of whole exome sequencing of Korean ER positive breast cancer under 35. This set provides 100 alignment files from normal-tumor paired whole exome sequencing of 50 patients. This is a part of total project data set. Illumina HiSeq 2500 100
EGAD00001002260 Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 129_rnaseq EAC expression data - Publication Secrier & Li et al., 2016, Nature Genetics Illumina HiSeq 2000 15
EGAD00001002662 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LINC-JP. 62
EGAD00001002664 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: CMDI-UK. 98
EGAD00001002669 Part of WGS data for Prostate (ICGC) HiSeq X Ten,Illumina HiSeq 2000 38
EGAD00001002684 Whole genome sequencing of 98 tumour-normal pairs for the PAEN-AU pancreatic neuroendocrine cancer project. 196
EGAD00001002689 ICGC Oesophageal Adenocarcinoma tissue samples Illumina HiSeq 2000 0
EGAD00001002697 Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling. Illumina HiSeq 2000 9
EGAD00001002739 Aligned sequence data from 14 Prostate cancer samples with BRCA2 mutations 49
EGAD00001002740 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing. Illumina HiSeq 2000,Illumina HiSeq 2500,Illumina MiSeq 164
EGAD00001002885 Raw sequence data, fastq format Illumina HiSeq 2000 26
EGAD00001002892 The data contains genome sequencing of clear cell renal cell carcinomas and normal kidney tissues. The samples were collected from patients from different European countries. Illumina HiSeq 1000 21
EGAD00001003092 Using sequencing and gene expression analyses, we identified a subgroup of HCA characterized by fusion of the INHBE and GLI1 genes and activation of sonic hedgehog pathway. Molecular subtypes of HCAs associated with different patients’ risk factors for HCA, disease progression, and pathology features of tumors. This classification system might be used to select treatment strategies for patients with HCA. Related Publication: Molecular Classification of Hepatocellular Adenoma Associates With Risk Factors, Bleeding, and Malignant Transformation Nault, Jean-CharlesLaurent, Christophe et al. Gastroenterology , Volume 152 , Issue 4 , 880 - 894.e6 http://dx.doi.org/10.1053/j.gastro.2016.11.042 Illumina HiSeq 2000 21
EGAD00001003115 Whole genome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer. Illumina HiSeq 2000 50
EGAD00001003125 WGS data of medulloblastoma tumor/control pairs. 224
EGAD00001003127 WGS data of medulloblastoma tumor/control pairs. 482
EGAD00001003128 Exome sequencing data for medulloblastoma tumor/control pairs 35
EGAD00001003132 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: GACA-CN. 84
EGAD00001003133 RRBS data of 86 Ewing patients (French). Illumina HiSeq 2000/2500 (Fastq files available). Sheffield et al. Nat Med. 2017 Jan 30 Illumina HiSeq 2000 86
EGAD00001003139 200PG : WGS Aligned Sequence (fastq) : Aligned WG sequence data (bam) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672 262
EGAD00001003162 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PACA-CA. 298
EGAD00001003163 Whole genome sequencing data of 20 carcinosarcomas. Illumina HiSeq 2000 23
EGAD00001003174 There are 116 liver cancer cases in this study and belong to LICA-CN project Illumina HiSeq 2000 232
EGAD00001003189 Whole genome sequencing of 8 HER2-Positive Breast Cancer (in complement to EGAD00001001844) Illumina HiSeq 2000 16
EGAD00001003190 WGS blood data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 67 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x. Illumina HiSeq 2000 67
EGAD00001003191 WGS cancer data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 78 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 50x. Illumina HiSeq 2000 78
EGAD00001003192 RNA-Seq data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 78 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 75bp paired-end protocol to a minimum mean reads of 50 million. Illumina HiSeq 2000 78
EGAD00001003205 160 WES and 25 WGS for HBV related HCC, and 15 WES for ICC belongs LICA-CN Illumina HiSeq 2000 402
EGAD00001003207 Whole genome sequencing data for MMML (28 tumor/control pairs) 56
EGAD00001003208 Whole genome sequencing data for MMML (12 tumor/control pairs) Illumina HiSeq 2000 25
EGAD00001003210 Whole genome sequencing data for MMML (cell_line) 8
EGAD00001003218 There are 80 Brain cancer cases （160 samples）in this study and belong to GBM-CN project. Illumina HiSeq 2000 80
EGAD00001003223 We collected tumor samples and adjacent nomal mucosae from 5 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing. Illumina HiSeq 2000 10
EGAD00001003224 We collected tumor samples and adjacent nomal mucosae from 17 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing. Illumina HiSeq 2000 34
EGAD00001003225 Whole Genome Sequencing Illumina HiSeq data from 111 men with prostate cancer. Samples were taken from primary tissue obtained at prostatectomy (target sequencing depth 50X) with matched blood control (target sequencing depth 30X). This data is from batches 4 to 6. Illumina HiSeq 2000 221
EGAD00001003227 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: OV-AU. 146
EGAD00001003243 Corresponding data set is composed of RNA sequencing of Korean ER positive breast cancer under 35 years old. This set provides 50 alignment files of 50 tumor samples. This is a part of total project data set. Illumina HiSeq 2500 50
EGAD00001003256 Whole genome sequencing for 131 early onset prostate tumor/control pairs (ICGC) 262
EGAD00001003262 High-coverage WES sequencing of DNA samples from 50 PTCs was performed on the Illumina HiSeq 2500 or 4000 System Illumina HiSeq 2000 100
EGAD00001003263 ICGC DCC Release 24, PACA-CA Deep KRAS sequencing 82
EGAD00001003264 ICGC DCC Release 24, PACA-CA Exome sequence 190
EGAD00001003269 High-coverage WGS sequencing of DNA samples from 90pairs GCs was performed on the Illumina HiSeq X Ten System. Illumina HiSeq 2000 1332
EGAD00001003270 ICGC DCC Release 24, PACA-CA Whole Genome sequence merged alignments 95
EGAD00001003271 WGS of T-cell and NK-cell lymphoma The tumor samples were sequenced with Illumina HiSeq 2500 platform and the resulting FASTq files have been uploaded. Illumina HiSeq 2000 102
EGAD00001003274 Whole genome sequencing data for MMML (tumor/control pairs and one cell_line) 315
EGAD00001003276 Whole genome sequencing data for MMML (24 tumor/control pairs), fastq-files Illumina HiSeq 2000,Illumina HiSeq 2500 49
EGAD00001003279 RNA sequencing data for 170 medulloblastoma tumor samples Illumina HiSeq 2000 171
EGAD00001003281 Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogeneous cellular processes. With a diversity of risk factors including viral infection, carcinogenic exposures and metabolic diseases, liver cancer is an ideal model to study these interactions. Whole genome sequencing of liver tumors identified 10 mutational signatures showing distinct relationships with environmental exposures, replication and transcription. Transcription-coupled damage was specifically associated with the liver-specific signature 16 and alcohol intake. Flood of indels were identified in very highly expressed hepato-specific genes, likely resulting from replication-transcription collisions. Reconstruction of sub-clonal architecture revealed mutational signature evolution during tumor development exemplified by the vanishing of aflatoxin-B1 signature in African migrants. These findings shed new light on the natural history of liver cancers. Illumina HiSeq 2000 52
EGAD00001003283 Whole genome sequencing data for MMML (healthy cell_line) 24
EGAD00001003285 RNA sequencing data for MMML (3 tumor samples and 1 gcbcell) 5
EGAD00001003286 Whole genome sequencing data for MMML (7 tumors and 8 controls) 15
EGAD00001003290 Whole genome sequencing for 12 late onset prostate cancer tumor/control pairs (ICGC) 24
EGAD00001003292 WGS sequencing for cases from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 24 Illumina HiSeq 2000 34
EGAD00001003298 BAM outputs from RSEM (https://deweylab.github.io/RSEM/) analysis of RNASeq sequencing on HiSeq platform of tumour samples from 95 pancreatic adenocarcinoma cases. 96
EGAD00001003304 We collected tumor samples and adjacent nomal mucosae from 46 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing. Complete Genomics 38
EGAD00001003306 Exome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer. Illumina HiSeq 2000 50
EGAD00001003310 There are 66 pairs of LAML cases(complete genomics) in this project which belongs to LAML-CN..The library is constructed by the Completes Genomics protocol. Complete Genomics 66
EGAD00001003317 There are 22 pairs of LAML cases in this project which belongs to LAML-CN.The library is constructed by the Illumina protocol. Illumina HiSeq 2000 63
EGAD00001003336 BAM outputs from RSEM (https://deweylab.github.io/RSEM/) analysis of RNASeq sequencing on HiSeq platform of tumour samples from 29 pancreatic neuroendocrine cases. 29
EGAD00001003339 Whole exome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations This dataset contains all the data available for this study on 2017-05-17. Illumina HiSeq 2000 7
EGAD00001003344 Transcriptome profiling of 25 prostate tumor samples by RNA-Seq Illumina HiSeq 2000 25
EGAD00001003353 BAM outputs from STAR (https://github.com/alexdobin/STAR) analysis of RNASeq sequencing on HiSeq platform of 56 tumour samples from 46 melanoma cases. Gene model = Ensembl version 70 0
EGAD00001003357 Aligned, merged and deduplicated BAM files from HiSeq whole exome sequencing of 106 samples: matched tumour-normal pairs from 53 melanoma patients. 0
EGAD00001003358 The dataset consists of samples from papillary thyroid cancer patients. A total of 181 DNA samples from blood/normal and cancer tissue are subjected to whole exome sequencing using Illumina. The fastq files generated were aligned with reference genome ‘hg19’, duplicates were marked, realignment around indels and quality recalibration were performed to produce good quality variants. The recalibrated “.bam” files are included with this dataset. 189
EGAD00001003360 Bam files containing mitochondrial alignments, extracted from CPCGene Whole Genome Alignments 432
EGAD00001003361 VCF files containing mitochondrial variant calls using MToolbox 432
EGAD00001003388 Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 366 samples: matched tumour-normal pairs from 183 melanoma cases comprising 48 primary melanomas, 15 cell lines, and 120 metastases. Sequencing was performed on the Illumina HiSeq 2000 and Xten platforms at Australian and Korean sequencing centres. Data was aligned to the human genome (GRCh37) using BWA-MEM. 0
EGAD00001003410 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: PACA-AU. 81
EGAD00001003411 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: PACA-AU. 81
EGAD00001003415 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: OV-AU. 93
EGAD00001003416 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: OV-AU. 93
EGAD00001003452 The samples include paired tumor and normal tissues from 205 patients (201 for normal and primary tumor tissues; 4 for normal, primary tumor and liver metastatic tissues). High-coverage WES sequencing or whole genome sequencing of DNA samples were performed on the Illumina HiSeq 2000 system Illumina HiSeq 2000 30
EGAD00001003456 There are 5WGS and 35WES sample pairs from the first affiliated hospital of kunming medical university, which belongs to ICGC projects COCA-CN. Illumina HiSeq 2000 80
EGAD00001003461 H3K27ac ChIP-seq and input genome sequencing was performed in 19 primary prostate tumours classified as intermediate risk. Sequencing of ChIP DNA was performed on an Illumina HiSeq 2000 as either single end 50 bp reads (for 7 samples) or paired end 100 bp reads (for 12 samples). Input DNA from all samples was sequenced using single-end 50 bp reads. The files provided are in fastq format. Illumina HiSeq 2000 38
EGAD00001003546 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: LIRI-JP. 130
EGAD00001003547 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: LIRI-JP. 130
EGAD00001003548 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: CLLE-ES. 74
EGAD00001003549 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: CLLE-ES. 74
EGAD00001003551 The samples include paired tumor and normal tissues from 106 patients . High-coverage WES sequencing or whole genome sequencing of DNA samples were performed on the Illumina HiSeq 2000 system Illumina HiSeq 2000 212
EGAD00001003557 This dataset is belong to 2014 whole genome sequenced AML data which is aligned to human reference(human_g1k_v37.fasta). There are 67 paired CR samples from Chunnam University. All samples has passed QC and recalibration steps while aligning to reference. Illumina HiSeq 2000 134
EGAD00001003558 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: RECA-EU. 100
EGAD00001003559 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: RECA-EU. 100
EGAD00001003560 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: MALY-DE. 99
EGAD00001003561 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: MALY-DE. 99
EGAD00001003580 WGS sequencing for 303 cases (620 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 26 Illumina HiSeq 2000 38
EGAD00001003587 This data is belong to 2015 whole exome sequenced AML data which is aligned to human reference(human_g1k_v37.fasta). There are 40 paired NR samples from Chunnam University. All samples has passed QC and recalibration steps while aligning to reference. HiSeq X Ten 80
EGAD00001003591 Merged bam files for PACA-CA Whole Genome Sequencing, for DCC release 25 211
EGAD00001003592 Merged bam files for PACA-CA Whole Exome Sequencing, for DCC release 25 216
EGAD00001003598 This data is belong to 2017 AML prospective data which is aligned to human reference(human_g1k_v37.fasta). There are 10 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference. HiSeq X Ten 20
EGAD00001003599 This data is belong to 2017 AML genome data which is aligned to human reference(human_g1k_v37.fasta). There are 10 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference. HiSeq X Ten 20
EGAD00001003706 PRAD-CA, DCC Release 26 : This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs Illumina HiSeq 2000,Illumina HiSeq 2500,unspecified 616
EGAD00001003752 single nucleotide variant calls from somatic sniper, vcf format 34
EGAD00001003753 single nucleotide variant calls from somatic sniper, vcf format. input for subclonal reconstruction 20
EGAD00001003754 structural variant calls from Delly, vcf format 37
EGAD00001003755 This dataset provides whole genome sequencing data of normal/tumors pairs from 9 patients with uterine or ovarian carcinosarcoma using the HiSeq 2000 sequencing system. It includes 27 samples (9 normals, 16 uterine tumors and 2 ovarian tumors). Through separate whole genome sequencing of carcinomatous and sarcomatoid components, we analyse and compare the genomic alterations of these components. Illumina HiSeq 2000 27
EGAD00001003756 Prostate Cancer - RNA-Seq unmapped reads Illumina HiSeq 2000 98
EGAD00001003760 There are 88 paired samples from HCC patients including tumors and matched adjacent normal tissues which were sequencing by Illumina HiSeq 2000 platform. Illumina HiSeq 2000 176
EGAD00001003761 This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs Illumina HiSeq 2000,Illumina HiSeq 2500,unspecified 617
EGAD00001003804 Exome fastq files of 98 hepatocellular carcinoma and matched nomral (BCM, HCC-JP) ILLUMINA,Illumina HiSeq 2000 196
EGAD00001003834 This dataset contains whole genome sequencing FASTQ data for 12 cholangiocarcinoma tumor samples, and their matched normal samples. These 12 samples are in addition to 59 samples available in dataset EGAD00001001988, and consist of patients from Thailand, Romania, and Singapore. Paired-end sequencing data was generated by Illumina Hiseq 2000 and 2500, with insert sizes of 170 and 350. Illumina HiSeq 2000,Illumina HiSeq 2500 24
EGAD00001003898 This dataset provides whole genome sequencing data of normal/tumors pairs from 4 patients with uterine or ovarian carcinosarcoma using the HiSeq 2000 sequencing system. It includes 10 samples (4 normals, 4 uterine tumors and 2 ovarian tumors). Through separate whole genome sequencing of carcinomatous and sarcomatoid components, we analyse and compare the genomic alterations of these components. Illumina HiSeq 2000 10
EGAD00001003907 A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases 79
EGAD00001003909 Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls HiSeq X Ten,Illumina HiSeq 2000,Illumina HiSeq 2500,unspecified 610
EGAD00001003912 This data is belong to 2018 AML-ETO patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 12 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference. Illumina HiSeq 2000 24
EGAD00001003925 This data is belong to 2014 AML-WGS patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 10 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference. HiSeq X Ten 20
EGAD00001003927 Merged bam files for PACA-CA Whole Genome Sequencing, for DCC release 27 246
EGAD00001003928 This data is belong to 2016 AML prospective_v1 patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 5 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference. HiSeq X Ten 10
EGAD00001003932 This data is belong to 2014 AML patients' exome data which is aligned to human reference(human_g1k_v37.fasta). There are 51 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference. Illumina HiSeq 2000 102
EGAD00001003945 Bam files for PACA-CA RNA Seq analysis, for DCC release 27 219
EGAD00001003948 Merged bam files for PACA-CA Whole Genome Sequencing, for DCC release 27 39
EGAD00001003950 The dataset consists of samples from papillary thyroid cancer patients. A total of 292 DNA samples from blood/normal and cancer tissue are subjected to whole exome sequencing using Illumina. The fastq files generated were aligned with reference genome ‘hg19’, duplicates were marked, realignment around indels and quality recalibration were performed to produce good quality variants. The recalibrated “.bam” files are included with this dataset.​ 290
EGAD00001003957 Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls Illumina HiSeq 2000,Illumina HiSeq 2500,unspecified 23
EGAD00001003960 This data is belong to 2014 Lung squamous patients' exome data which is aligned to human reference(human_g1k_v37.fasta). There are 104 paired tumor/normal samples from SMC. All samples has passed QC and re-calibration steps while aligning to reference. Illumina HiSeq 2000 208
EGAD00001003972 Fastq files for PACA-CA RNA Seq analysis, for DCC release 27 ILLUMINA,Illumina HiSeq 2500 219
EGAD00001003975 Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls HiSeq X Ten,Illumina HiSeq 2500,unspecified 128
EGAD00001003978 This data is belong to WGS-Lung Cancer patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 30 paired tumor/normal samples from Samsung Hospital. All samples has passed QC and recalibration steps while aligning to reference. Illumina HiSeq 2000 60
EGAD00001003981 This dataset pertains to transcriptome sequencing of paired RNA samples.RNA was isolated from the tumor and adjacent normal tissues of 12 patients (24 samples). We have performed rRNA removal followed by total RNA sequencing in Illumina HiSeq platform.We have uploaded TopHat2 aligned BAM files. Illumina HiSeq 2500 24
EGAD00001003987 This dataset pertains to whole exome sequencing of paired DNA samples of Gingivo-buccal oral cancer patient.DNA was isolated from the tumor and blood tissues of 47 patients (94 samples).We have performed Nextera exome capture and sequenced exome libraries in Illumina HiSeq platform.We have uploaded BWA-ALN aligned BAM files. Illumina HiSeq 2500 94
EGAD00001003993 The present series corresponds to 161 RNA-seq samples from tumors with matched WES or WGS. Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before. ILLUMINA,Illumina HiSeq 2000 161
EGAD00001003994 The present series corresponds to 24 whole genome sequencing (12 Tumoral/Non-tumoral pairs). Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before. Illumina HiSeq 2000 28
EGAD00001004007 Data supporting: "Esophageal adenocarcinoma organoid cultures recapitulate human disease heterogeneity and provide a model for clonality studies and precision therapeutics." Li et al. WGS (BAM files) RNAseq (BAM files) Tumours, organoids, normals Illumina HiSeq 2000 53
EGAD00001004008 This dataset include NPC blood tumor pair sequencing bam file, include 21 pairs, 42 bam files Illumina HiSeq 2000 42
EGAD00001004011 This data is belong to 2015 AML-ETO patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 10 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference. Illumina HiSeq 2000 20
EGAD00001004012 This data is belong to additional 2015 AML-ETO patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 2 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference. Illumina HiSeq 2000 4
EGAD00001004018 The aim of CAGEKID is to carry out comprehensive detection of DNA markers for conventional (clear cell) renal carcinoma. The project includes complete analysis of somatic and constitutional DNA variation, methylation patterns and expression in a large number of constitutional/tumor pairs. CAGEKID is a part of the International Cancer Genome Consortium, ICGC. 708
EGAD00001004027 This data is belong to WES-Lung Cancer patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 36 paired tumor/normal samples from Samsung Hospital. All samples has passed QC and recalibration steps while aligning to reference. Illumina HiSeq 2000 72
EGAD00001004028 WGS sequencing for 63 cases (126 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are earmarked for inclusion in ICGC release 27 (deferred to release 28) Illumina HiSeq 2000 0
EGAD00001004029 WGS sequencing for 43 cases (86 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are earmarked for inclusion in ICGC release 28 Illumina HiSeq 2000 86
EGAD00001004032 Fastq files of whole-genome bisulfite sequence of non-cancerous tissue of HBV-associated hepatocellular carcinoma Illumina Genome Analyzer IIx,Illumina HiSeq 2000 3
EGAD00001004033 Fastq files of whole-genome bisulfite sequence of tumor tissue of HBV-associated hepatocellular carcinoma Illumina Genome Analyzer IIx,Illumina HiSeq 2000 5
EGAD00001004041 As a contribution to the International Cancer Genome Consortium, exome sequencing of 142 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357 Illumina HiSeq 2500 142
EGAD00001004042 As a contribution to the International Cancer Genome Consortium, exome sequencing of 102 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357 Illumina HiSeq 2500 102
EGAD00001004051 fastq of 345 Japanese gastric cancer Illumina HiSeq 2000 345
EGAD00001004061 200PT : WG Aligned Sequence (bam)/ Aligned WG sequence data in this dataset are from CPCGene Tumour/Normal Pairs used in the 200PT Study 404
EGAD00001004072 200PT : SNV vcf files. SNV calls generated using SomaticSniper and PhyloWGS, from the CPCGene 200PT Subclonality study 293
EGAD00001004073 200PT : CNA vcf files. Copy Number Abberation calls generated using TITAN and PhyloWGS, from the CPCGene 200PT Subclonality study 292
EGAD00001004090 This dataset contains the aligned whole genome sequencing data of cell line 380. This cell was established from the peripheral blood of a 15-year-old boy with acute lymphoblastic leukemia at relapse, showing an immature phenotype and carrying an IGH-MYC (t(8;14)) as well as an IGH-BCL2 (t(14;18)) chromosomal translocation. The sequencing was performed on an Illumina X-ten sequencer. HiSeq X Ten 1
EGAD00001004125 Data collected as part of the Normal prostatectomy project analysis. Whole genome sequencing (WGS, targeted at 30X for normal tissue and 50X for tumour tissue) was performed on morphologically normal tissue samples from 30 patients with prostate cancer. In addition, seven prostate tissue samples were sequenced from 7 non-cancer patients: two collected after a cystoprostatectomy and five from samples collected at autopsy. Matched blood controls were included for all patients. An extra five samples were sequenced from the stroma of cell cultured fibroblasts. In addition a few tumour samples obtained at prostatectomy and their blood matched controls are included in this dataset from the main study that are not included elsewhere. Illumina HiSeq 2000 71
EGAD00001004137 WGS sequencing for 409 cases (832 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 28 Illumina HiSeq 2000 0
EGAD00001004141 This study contain the WGS and RNA-seq aligned bam files for this particular inflammatory hepatocellular adenoma sample. Illumina HiSeq 2000,Illumina HiSeq 4000 2
EGAD00001004180 The French ICGC project on liver tumors is coordinated by Pr Jessica Zucman-Rossi and funded by Inca (French Institute for Cancer). The aim of the present project is to identify the catalog of somatic and germline mutations in liver tumors using whole genome (WGS) and whole exome sequencing (WGS), integrated with DNA methylation and RNA sequencing (RNA-seq) data. The present series corresponds to 60 whole exome tumor/normal pairs with matched RNA-seq. Illumina HiSeq 2000,Illumina HiSeq 4000 120
EGAD00001004289 Data supporting: "Low-cost and clinically applicable copy number profiling using repeat DNA." Abujudeh et al. DNA WGS (BAM files) DNA fastSeq (fastq files) Tumours, Barrett's, normals. Illumina HiSeq 2000,Illumina MiSeq 60
EGAD00001004400 SNV calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study 538
EGAD00001004401 SNV calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study 562
EGAD00001004402 SNV calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study 580
EGAD00001004403 CNA calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study 538
EGAD00001004404 CNA calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study 562
EGAD00001004405 CNA calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study 580
EGAD00001004409 Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 134 samples: matched tumour-normal pairs from 67 mucosal melanoma cases 0
EGAD00001004410 DNA extracted from sorted CD19+ tumor cells (16 patients) was used for exome capture with the SureSelect V5 All Exon Kit following the standard protocols. Paired-end sequencing (2 x 100 bp) was performed using HiSeq2000 sequencing instruments. The files are in FASTQ format. Illumina HiSeq 2000 16
EGAD00001004411 DNA extracted from sorted CD3+ cells (16 patients) was used for exome capture with the SureSelect V5 Mb All Exon Kit following the standard protocols. Paired-end sequencing (2 x 100 bp) was performed using HiSeq2000 sequencing instruments.The files are in FASTQ format. Illumina HiSeq 2000 16
EGAD00001004412 RNA-Seq was performed on 12 samples of sorted CD19+ tumor cells. RNA-Seq libraries were prepared using the SureSelect Automated Strand Specific RNA Library Preparation Kit as per manufacturer’s instructions (Agilent technologies) and subjected to paired-end (2 x 100 bp) sequencing on HiSeq2000 (Illumina). The files are in FASTQ format. Illumina HiSeq 2000 12
EGAD00001004417 Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. WGS (BAM files) 379 matched tumour-normal pairs Illumina HiSeq 2000 0
EGAD00001004423 Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. RNAseq (BAM files) 116 tumours Illumina HiSeq 2000 116
EGAD00001004424 Prostate Cancer - RNA-Seq unmapped reads Illumina HiSeq 2000 148
EGAD00001004430 NA Illumina HiSeq 2500 56
EGAD00001004431 SNV calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions 40
EGAD00001004432 SNV calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions 40
EGAD00001004433 SNV calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions 40
EGAD00001004434 SNV calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions 40
EGAD00001004435 Childhood cerebellar tumours mirror conserved fetal transcriptional programs Illumina HiSeq 2000 145
EGAD00001004440 CNA calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions 40
EGAD00001004441 CNA calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions 40
EGAD00001004442 CNA calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions 40
EGAD00001004443 CNA calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions 40
EGAD00001004474 Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 28 samples: matched tumour-normal pairs from 14 melanocytic nevi cases 0
EGAD00001004478 NA Illumina HiSeq 2500 24
EGAD00001004484 Adeno-associated virus (AAV) is a defective mono-stranded DNA virus, endemic in human population (35-80%). Recurrent clonal AAV2 insertions are associated with the pathogenesis of rare human hepatocellular carcinoma (HCC) developed on normal liver. This study aimed to characterize the natural history of AAV infection in the liver and its consequence in tumor development. In silico analyses using viral capture data explored viral variants and new clonal insertions. Clonal AAV insertions were positive selected during HCC development on non-cirrhotic liver challenging the notion of AAV as a non-pathogenic virus. Illumina HiSeq 2000 20
EGAD00001004490 The dataset consists of samples from papillary thyroid cancer patients. A total of 11 DNA samples from blood/normal and cancer tissue are subjected to whole exome sequencing using Illumina. The fastq files generated were aligned with reference genome ‘hg19’, duplicates were marked, realignment around indels and quality recalibration were performed to produce good quality variants. The recalibrated “.bam” files are included with this dataset. 11
EGAD00001004493 Transcriptome of Ewing sarcoma tumors (ICGC project). Fastq files of 57 RNA-seq are available (2x101bp). Illumina HiSeq 2500 57
EGAD00001004555 The aim of our project is to decipher the genomic of advanced hepatocellular carcinoma using whole exome sequencing. To this purpose, we aim to compare genetic landscape of advanced hepatocellular carcinoma with early tumor in order to understand the mechanisms of tumor progression. This work will also help to identify new therapeutic targets potentially useful to treat patients at advanced stage. This dataset contain whole exome sequencing aligned reads for 41 tumor with matched normal samples Illumina HiSeq 2000,Illumina HiSeq 4000 39
EGAD00001004775 Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. WGS (BAM files) 521 samples Illumina HiSeq 2000 0
EGAD00001004776 Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. RNAseq (BAM files) 137 samples Illumina HiSeq 2000 137
EGAD00001004869 Illumina platform sequencing data for matched tumour-normal DNA samples from 77 melanoma patients participating in a study investigating response to immunotherapy. Selected cases also have RNA sequencing of the tumour. 0
EGAD00001004875 Aligned RNA-seq sequences in this dataset are from the Proteogenomic Landscape of Curable Prostate Cancer study 56
EGAD00001004938 Hepatocellular carcinoma (HCC) is a heterogeneous aggressive malignancy with low efficacy of current therapies at advanced stages. We integrated molecular and pharmacological profiling of a large panel of liver cancer cell lines (LCCL) to assess their clinical relevance as HCC preclinical models and identify new effective therapies and biomarkers of response. Here, we performed multi-omic analysis including whole-exome, RNA and microRNA sequencing in a series 34 LCCL. Molecular profiles of LCCL and primary HCC were compared and we searched for molecular features associated with drug response. Our panel of LCCL faithfully recapitulated the most aggressive molecular “proliferation class” of HCC. Illumina HiSeq 2000,Illumina HiSeq 4000 34
EGAD00001004958 Highly recurrent U1 snRNA mutations drive alternative splicing in HH medulloblastoma Illumina HiSeq 2000,Illumina HiSeq 2500 234
EGAD00001004987 This dataset pertains to mitochondrial DNA amplicon sequencing of paired DNA samples from gingivo-buccal oral cancer patients. DNA was isolated from the tumor and blood tissues of 89 patients (178 samples). The sequencing libraries were prepared from whole mitochondrial amplicons using Nextera XT DNA Library Preparation Kit (Illumina) and sequenced in Illumina HiSeq platform. The uploaded BAM files are generated by aligning paired-end reads to the mitochondrial reference sequence (rCRS) using BWA-MEM. Illumina HiSeq 2500,Ion Torrent PGM 178
EGAD00001005283 NA Illumina HiSeq 2000,Illumina HiSeq 4000 30
EGAD00001005284 NA Illumina HiSeq 2000,Illumina HiSeq 4000 22
EGAD00001005308 NA Illumina HiSeq 2000,Illumina HiSeq 4000 112
EGAD00001005388 Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 241 tumour samples Illumina HiSeq 2000 0
EGAD00001005423 Whole Genome sequencing. 1 ug of genomic DNA from each lymph node sample was used for the construction of a TruSeq DNA PCR Free (350) library before sequencing in a Illumina HiSeq X Ten (2 × 151 bp). Mean coverage 30x. HiSeq X Ten 2
EGAD00001005424 Exome Sequencing. 3 ug of genomic DNA from each lymph node sample were sheared and used for the construction of a paired-end sequencing library as described in the paired-end sequencing sample preparation protocol provided by Illumina. Enrichment of exonic sequences was then performed for each library using either the Sure Select Human All Exon 50 Mb or All Exon+UTRs v4 kits following the manufacturer’s instructions (Agilent Technologies). Exon-enriched DNA was pulled down by magnetic beads coated with streptavidin (Invitrogen), followed by washing, elution and 18 additional cycles of amplification of the captured library. Enriched libraries were sequenced in one lane of an Illumina GAIIx sequencer or in two lanes of a HiSeq2000 when using pools of eight samples. unspecified 13
EGAD00001005434 Data supporting: "Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma." Noorani et al. WGS (BAM files) 134 samples for 18 cases Includes primary, lymph-node, distant metastatic, Barrett's and normal samples. Illumina HiSeq 2000 0
EGAD00001005438 Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. scRNAseq (BAM files) 38 Barrett's and normal samples unspecified 0
EGAD00001005454 Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 103 cases of melanoma Uveal subtype 0
EGAD00001005455 Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. Single cell metadata and analysis 38 Barrett's and normals 0
EGAD00001005500 Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 87 cases of melanoma Acral subtype. 63 cases also have RNASeq sequencing from the tumour sample. 0
EGAD00001005501 Illumina RNASeq sequencing of tumour samples from 41 cases of melanoma 0
EGAD00001005738 79 RNAseq samples from 56 patients with melanoma who have undergone immune checkpoint blockade immunotherapy. 0
EGAD00001005915 Data supporting: "Repurposing of KLF5 activates a cell cycle signature during the progression from Barrett’s Oesophagus to Oesophageal Adenocarcinoma." Rogerson et al. RNA-seq data 2 samples Illumina HiSeq 2000 2
EGAD00001006003 NA Illumina HiSeq 2500 144
EGAD00001006032 Previously unpublished WGS reads mapping within the IG loci used in the benchmark of IgCaller. unspecified 176
EGAD00001006033 Data supporting: "Genomic copy number predicts esophageal cancer years before transformation." Killcoyne et al. sWGS data 1000 samples BAM files Illumina HiSeq 2500,Illumina HiSeq 4000 1000
EGAD00001006063 Illumina platform RNA-seq data from 47 Pancreatic neuroendocrine tumour samples 41
EGAD00001006170 Data supporting: "The mutREAD method detects mutational signatures from low quantities of cancer DNA." Perner et al. WGS, sWGS, WES, and reduced representation sequencing data tumour and normal samples BAM files Illumina HiSeq 4000 48
EGAD00001006349 Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. WGS (BAM files) Illumina HiSeq 2000,Illumina NovaSeq 6000 0
EGAD00001006353 Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. RNAseq (BAM files) Illumina HiSeq 2000 0
EGAD00001006373 Data supporting: “Longitudinal tracking of 97 esophageal adenocarcinomas (EAC) using liquid biopsy sampling.” Ococks, Frankell, Masque Soler et al. ctDNA (BAM files) 333 samples NextSeq 500 333
EGAD00001006426 This study contain the WGS and WEX aligned bam files and RNA-seq fastq files for human liver tumors. HiSeq X Five,Illumina HiSeq 2000,Illumina HiSeq 4000,Illumina NovaSeq 6000 183
EGAD00001006439 Illumina RNASeq sequencing of tumour samples from 53 cases of cutaneous melanoma and 61 cases of acral melanoma 0
EGAD00001006738 Data supporting: "Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments" Scott et al. WGS and RNAseq sequencing data Organoid, tumour and normal samples BAM files Illumina HiSeq 2000 7
EGAD00001007055 RNAseq of 55 melanoma tumors that were used as a validation dataset in Garg et al Nat Commun,  2021 Feb 18;12(1):1137. doi: 10.1038/s41467-021-21207-2. 0
EGAD00001007493 Data supporting: "Genomic analysis of response to neoadjuvant chemotherapy in esophageal adenocarcinoma" Izadi et al. WGS for tumour and normal samples. RNAseq for tumour samples. HiSeq X Five,Illumina HiSeq 2000,Illumina NovaSeq 6000 8
EGAD00001007496 Data supporting: "Widespread reorganisation of the regulatory chromatin landscape facilitates resistance to inhibition of oncogenic ERBB2 signalling" Ogden et al. WGS for tumour and normal samples. RNAseq for tumour samples. HiSeq X Five,Illumina HiSeq 2000 0
EGAD00001007762 NA Illumina HiSeq 4000,Illumina MiSeq 82
EGAD00001007785 Data from 496 OCCAMS (Oesophageal Cancer Clinical And Molecular Stratification) cases. WGS BAM files 496x oesophageal adenocarcinoma samples 496x normal samples HiSeq X Five,Illumina HiSeq 2000,Illumina NovaSeq 6000 0
EGAD00001007808 Data supporting "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. WGS (BAM files) 383 oesophageal adenocarcinoma samples 383 normal samples Illumina HiSeq 2000 0
EGAD00001007809 Data supporting: "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. RNAseq (BAM files) 214 oesophageal adenocarcinoma samples Illumina HiSeq 2000 214
EGAD00001007858 NA HiSeq X Five,Illumina HiSeq 4000,Illumina NovaSeq 6000 234
EGAD00001008610 Genomic DNA of 81 cases from Japanese gastric cancer was extracted from tumor and matched normal tissues, and libraries with an insert size of 350–550 bp were prepared. The libraries were sequenced on a HiSeq 2500 instrument (Illumina) with paired-end reads of 101 bp. The read data are stored as FASTQ formatted files. Illumina HiSeq 2500 161
EGAD00001008798 Illumina platform whole genome sequencing data for matched tumour-normal DNA samples from 570 melanoma patients 1139
EGAD00001008837 Illumina RNASeq sequencing of tumour samples from 230 cases of melanoma 230
EGAD00001010074 Data supporting: “Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.” Nowicki-Osuch, Zhuang et al. scRNAseq (FASTQ files) 59 samples unspecified 16
EGAD00010000238 CLL Expression array Affymetrix GeneChip Human Genome U133 plus 2.0 64
EGAD00010000252 CLL Expression Arrays Affymetrix U219 137
EGAD00010000254 CLL Methylation Arrays Illumina HumanMethylation450 165
EGAD00010000280 CLL Expression array Affymetrix snp 6.0 4
EGAD00010000377 DNA methylation analysis of 6 primary lymphoma samples HumanMethylation450k Bead Chip - Genome Studio 6
EGAD00010000379 DNA methylation analysis of 2 peripheral blood samples HumanMethylation450k Bead Chip - Genome Studio 2
EGAD00010000427 DNA methylation analysis of 4 peripheral blood samples HumanMethylation450k Bead Chip - Genome Studio 4
EGAD00010000429 DNA methylation analysis of 4 primary lymphoma samples HumanMethylation450k Bead Chip - Genome Studio 4
EGAD00010000470 CLL Expression Array GPL570 20
EGAD00010000472 CLL Expression Array Affymetrix U219 219
EGAD00010000498 Affymetrix SNP6.0 genotype data for prostate cancer patients Affymetrix_SNP6- 18
EGAD00010000562 Medulloblastoma DNA methylation Illumina_HumanMethylation450 115
EGAD00010000600 Prostate Adenocarcinomas samples using 450K Illumina450K 80
EGAD00010000642 CLL Expression Array 1
EGAD00010000875 CLL Expression Array Affymetrix U219 0
EGAD00010000915 Affymetrix SNP6.0 breast cancer genome sequencing data Affymetrix SNP6.0 344
EGAD00010000916 BASIS breast cancer DNA methylation Illumina 450k Illumina 450k 457
EGAD00010000917 399 tumors profiled using Agilent miRNA microarrays (Product Number G4872A, design ID 046064). The arrays are based on miRBase release 19.0 and 2006 human miRNAs are represented. 150 ng total RNA was used as input. Agilent miRNA microarrays 399
EGAD00010000919 samples using Illumina HUMANOMNI1QUAD HUMANOMNI1QUAD 2
EGAD00010000920 samples using Illumina HUMANOMNIEXPRESS HUMANOMNIEXPRESS 50
EGAD00010000921 samples using Affymetrix CYTOSCANHD CYTOSCANHD 12
EGAD00010001079 Affymetrix SNP6.0 array breast cancer data Affymetrix SNP6.0 66
EGAD00010001196 Raw Array data from the CPCGene BRCA study Affymetrix OncoScan FFPE Express 48
EGAD00010001218 Raw Array data from the CPCGene 200PG study Affymetrix OncoScan FFPE Express 502
EGAD00010001280 Transcriptome array dataset Affymetrix HG_U133_+2 25
EGAD00010001281 SNP array dataset HUMANOMNIEXPRESS 50
EGAD00010001301 Medulloblastoma expression profiling Affymetrix expression array 246
EGAD00010001323 Medulloblastoma methylation profiling Illumina Infinium HumanMethylation450 BeadChip 911
EGAD00010001414 Raw Array data from the PRAD-CA for ICGC DCC Release26 Affymetrix OncoScan FFPE Express 0
EGAD00010001506 Methylation array dataset Illumina 450k 38
EGAD00010001513 Copy Number Variation as determined on Illumia Omin Arrays Illumina Beadchip 122
EGAD00010001519 Raw Array data from the PRAD-CA for ICGC DCC Release27 Affymetrix OncoScan FFPE Express 110
EGAD00010001703 RNAseq reads were aligned with STAR 2.5.3a and gene expression was quantified with RSEM 1.3.0 144
EGAD00010001822 Array data for oesophageal and related samples – sj_paper_methyl_tumour_release Illumina 285
EGAD00010001834 Array data for oesophageal and related samples – sj_paper_methyl_normal_release Illumina 100
EGAD00010001838 Array data for oesophageal and related samples – sj_paper_methyl_barretts_release Illumina 150
EGAD00010001850 Epigenome wide DNA methylation assay of OSCC-GB using Illumina methylation array Illumina Infinium 450K BeadChip Array; Illumina Infinium EPIC Beadchip Array 174
EGAD00010001972 Array data for oesophageal and related samples - aks_paper_methyl_barretts_release Illumina 107