DAC

ICGC Data Access Compliance Office

Dac ID Contact Person Email Access Information
EGAC00001000010 helpdesk Undefined dcc-support [at] icgc [dot] org No additional information is available

DAC description

To access Controlled Access ICGC data at the EGA you must first apply for access on the DACO form. Instructions on this process is available from this web site: http://docs.icgc.org/portal/access/

This DAC controls 339 datasets:

Dataset ID Description Technology Samples
EGAD00001000271 Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood Illumina HiSeq 2000; 10
EGAD00001000133 The landscape of cancer genes and mutational processes in breast cancer Illumina HiSeq 2000, Illumina Genome Analyzer II 199
EGAD00001000306 ICGC prostate cancer whole genome sequencing Illumina HiSeq 2000; 22
EGAD00001000270 DATA_SET_EOP-PCA-LargeAndSmallTumors1 Illumina HiSeq 2000; 18
EGAD00001000063 Triple Negative Breast Cancer sequencing Illumina Genome Analyzer II 6
EGAD00001000023 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer IIx 11
EGAD00010000280 CLL Expression array Affymetrix snp 6.0 4
EGAD00001000044 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer IIx 212
EGAD00010000238 CLL Expression array Affymetrix GeneChip Human Genome U133 plus 2.0 64
EGAD00001000083 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer II;, Illumina Genome Analyzer IIx 61
EGAD00001000102 Myeloproliferative Disorder Sequencing Illumina Genome Analyzer II 6
EGAD00001001693 Fastq files of RNAseq of 182 samples of biliary tract cancer Illumina HiSeq 2000; 182
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
EGAD00001000110 Breast Cancer Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II 179
EGAD00001000131 Genetic landscape of hepatocellular carcinoma Illumina HiSeq 2000 48
EGAD00001000136 CML blast phase rearrangement screen Illumina HiSeq 2000 6
EGAD00001000129 Essential Thrombocythemia Myeloproliferative Disease exome sequencing Illumina HiSeq 2000, Illumina HiSeq 2000; 189
EGAD00001000123 Polycythemia Vera Myeloproliferative Disease exome sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 119
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
EGAD00001000118 Osteosarcoma Exome Sequencing Illumina Genome Analyzer II, Illumina HiSeq 2000; 102
EGAD00001000106 Primary Myelofibrosis Myeloproliferative Disease exome sequencing Illumina Genome Analyzer II, Illumina HiSeq 2000; 67
EGAD00001000045 Somatic mutation of SF3B1 in myelodysplasia with ring sideroblasts and other cancers Illumina Genome Analyzer II, Illumina HiSeq 2000; 33
EGAD00001000117 Myelodysplastic Syndrome Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 152
EGAD00001000096 Pancreatic adenocarcinoma QCMG 20120201 AB SOLiD 4 System 166
EGAD00001000323 Sequencing data for Australian Pancreatic Cancer study submitted 20130102 AB SOLiD 4 System;, Illumina HiSeq 2000; 200
EGAD00001000049 Pancreatic adenocarcinoma QCMG 20110901 AB SOLiD System 3.0, AB SOLiD 4 System 26
EGAD00001000371 Sequencing data for PDAC cell lines generated by QCMG Illumina HiSeq 2000;, Illumina HiSeq 2500; 54
EGAD00001000126 HER2 positive Breast Cancer Illumina HiSeq 2000 101
EGAD00001000107 SCAT osteosarcoma sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II 114
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
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
EGAD00001000278 ICGC MMML-seq Data Freeze November 2012 whole genome sequencing Illumina HiSeq 2000; 12
EGAD00001000281 ICGC MMML-seq Data Freeze November 2012 transcriptome sequencing Illumina HiSeq 2000; 6
EGAD00001000279 ICGC MMML-seq Data Freeze November 2012 whole exome sequencing Illumina Genome Analyzer IIx; 4
EGAD00001000356 ICGC MMML-seq Data Freeze March 2013 transcriptome sequencing Illumina HiSeq 2000; 23
EGAD00001000355 ICGC MMML-seq Data Freeze March 2013 whole genome sequencing Illumina HiSeq 2000; 46
EGAD00001000274 DATA_SET_TRANSCIPTOME_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation Illumina HiSeq 2000; 4
EGAD00001000176 DATA_SET_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 8
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
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
EGAD00001000103 Myeloproliferative Disorder Sequencing Illumina Genome Analyzer II 4
EGAD00001000027 ICGC Germany PedBrain Medulloblastoma Pilot_2_LM Illumina HiSeq 2000, Illumina Genome Analyzer IIx 8
EGAD00010000254 CLL Methylation Arrays Illumina HumanMethylation450 165
EGAD00001000177 Whole Genome Methylation in CLL Illumina Genome Analyzer IIx; 6
EGAD00010000252 CLL Expression Arrays Affymetrix U219 137
EGAD00001000088 ER-, HER2-, PR- breast Cancer genome sequencing Illumina Genome Analyzer II 6
EGAD00001000147 Osteosarcoma Whole Genome Illumina HiSeq 2000, Illumina HiSeq 2000; 108
EGAD00001000328 ICGC PedBrain: RNA sequencing Illumina HiSeq 2000; 28
EGAD00001000122 DATA_SET_ICGC_PedBrainTumor_Medulloblastoma Illumina HiSeq 2000, Illumina Genome Analyzer IIx 206
EGAD00001000327 release_2: ICGC PedBrain: whole genome mate-pair sequencing Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 70
EGAD00001000275 Data set for Whole-genome-Sequencing of adult medulloblastoma Illumina HiSeq 2000; 10
EGAD00001000262 OICR PANCREATIC CANCER DATASET 4
EGAD00001000276 OICR PANCREATIC CANCER DATASET 2 10
EGAD00001000263 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina HiSeq 2000; 18
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
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
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
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
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
EGAD00001000303 ICGC prostate cancer whole genome mate-pair sequencing Illumina Genome Analyzer IIx; 22
EGAD00001000258 Deep RNA sequencing in CLL Illumina Genome Analyzer II; 107
EGAD00001000304 ICGC prostate cancer miRNA sequencing Illumina HiSeq 2000; 8
EGAD00001000305 ICGC prostate cancer RNA sequencing Illumina HiSeq 2000; 12
EGAD00001000616 Pilocytic Astrocytoma ICGC PedBrain whole genome sequencing Illumina HiSeq 2000; 192
EGAD00001000617 Pilocytic Astrocytoma ICGC PedBrain RNA sequencing Illumina HiSeq 2000; 73
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
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
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
EGAD00010000472 CLL Expression Array Affymetrix U219 219
EGAD00001000645 ICGC MMML-seq Data Freeze July 2013 whole genome sequencing 42
EGAD00010000470 CLL Expression Array GPL570 20
EGAD00001000648 ICGC MMML-seq Data Freeze July 2013 transcriptome sequencing 31
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
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: 20x MB59 macroH2A1: 11x H3K36me3: 11x 7
EGAD00001000632 AB SOLiD 4 System; 12
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
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
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
EGAD00010000498 Affymetrix SNP6.0 genotype data for prostate cancer patients Affymetrix_SNP6- 18
EGAD00001000660 Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826 353
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
EGAD00001000650 ICGC MMML-seq Data Freeze July 2013 miRNA sequencing 52
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 HiSeq 2000;, Illumina Genome Analyzer IIx; 90
EGAD00001000272 Genomic Alterations in Gingivo-buccal Cancer: ICGC-India Project_YR01 454 GS FLX Titanium;, Illumina HiSeq 2000; 200
EGAD00001000717 Dataset of CageKid Tumor DNA samples 95
EGAD00001000718 Dataset of CageKid Tumor RNA samples 91
EGAD00001000719 Dataset of CageKid Normal RNA samples 45
EGAD00001000709 Dataset of CageKid Blood DNA samples 95
EGAD00001000720 Dataset of CageKid tumor-normal paired RNA samples 90
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
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
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
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. We found that mutations were already present at high levels in morphologically normal tissue distant from the cancer suggesting clonal expansion. A subgroup of these mutations are present in adjacent cancer. A single nodule of cancer may contain multiple, predominantly genetically independent cancer clones each harbouring distinct ERG fusions. Separate lineages of cancer were in some cases connected by common low frequency mutations. Together our observations support the existence of a genetic field-effect underlying carcinogenesis The presence of a field effect, and of multiple cancer lineages within the same prostate pose serious questions regarding the effectiveness of focal therapy in those with a long life expectancy and imply that predicting future behaviour based on genetic analysis of single tumour sample may be unreliable. 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. Illumina HiSeq 2000; 18
EGAD00001000722 Extension of angiosarcoma whole genome sequencing study Illumina HiSeq 2000; 8
EGAD00001000738 Extension of angiosarcoma whole genome sequencing study Illumina HiSeq 2000; 4
EGAD00001000735 Here we present the genomes of three secondary angiosarcomas Illumina HiSeq 2000; 7
EGAD00001000749 Illumina HiSeq 2000; 12
EGAD00001000758 dataset for BGI bladder cancer project Illumina Genome Analyzer II; 198
EGAD00001000760 dataset for esophageal cancer, 17pairs for whole-genome sequencing and 71pairs for whole-exome sequencing Illumina HiSeq 2000; 176
EGAD00001000704 Illumina HiSeq 2000; 44
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; 400
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
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
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
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
EGAD00001000724 Illumina HiSeq 2000; 68
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
EGAD00010000562 Medulloblastoma DNA methylation Illumina_HumanMethylation450 115
EGAD00001000644 ICGC PedBrain DNA Methylation project Illumina HiSeq 2000; 42
EGAD00001000874 Indel/point mutation of chondrosarcoma 10
EGAD00001000873 Fastq files of 10 samples of condrosarcoma Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 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
EGAD00001000808 RIKEN collection WGS reads for 321 HCC and blood matched samples from 158 donors submitted to ICGC for release 15 Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 321
EGAD00001000809 RIKEN collection WGS reads for 61 liver cancer and matched blood samples from 30 donors displaying biliary phenotype Illumina HiSeq 2000; 61
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
EGAD00001000892 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina HiSeq 2000; 40
EGAD00001000891 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina HiSeq 2000; 62
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
EGAD00010001414 Raw Array data from the PRAD-CA for ICGC DCC Release26 Affymetrix OncoScan FFPE Express 86
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
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
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 HiSeq 2000, Illumina Genome Analyzer II 58
EGAD00001001270 Illumina HiSeq 2000; 196
EGAD00001000158 Subgroup-specific structural variation across 1,000 medulloblastoma genomes 23
EGAD00001001210 Altered translation response to stress by medulloblastoma-associated DDX3X mutations 28
EGAD00001001262 Unaligned bam of 31 samples derived from primary tumor Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 31
EGAD00001001263 Unaligned bam of 31 samples derived from blood Illumina Genome Analyzer IIx; 31
EGAD00001000949 Validations of variants identified by exome sequencing in sequential samples derived after treatment cycle with AZA. Illumina HiSeq 2000; 170
EGAD00001001115 SeqControl Illumina HiSeq 2500; 54
EGAD00001000946 Divergent clonal selection dominates medulloblastoma at recurrence 125
EGAD00001000952 DNA methylation profiling of 8 control samples from adult (4) and fetal brain (4) Illumina HiSeq 2000; 8
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
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
EGAD00010000600 Prostate Adenocarcinomas samples using 450K Illumina450K 80
EGAD00001001035 RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 66
EGAD00001001044 Ion Torrent PGM; 2
EGAD00001001043 Illumina HiSeq 2000; 8
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
EGAD00010000642 CLL Expression Array 144
EGAD00001001024 Fastq files of 52 samples of hepatocellular carcinoma (RCAST, THCC) Illumina HiSeq 2000; 104
EGAD00001000446 Fastq files of 213 samples of hepatocellular carcinoma (NCCRI) Illumina HiSeq 2000; 213
EGAD00001001064 Extension of angiosarcoma whole genome sequencing study Illumina MiSeq; 4
EGAD00001001329 Aligned Sequence (bam format), Duplicates removed 28
EGAD00001001071 Samples from the "100" project that are in the ICGC PanCancer project. Illumina HiSeq 2000; 200
EGAD00001001051 Illumina HiSeq 2000; 200
EGAD00001001094 Raw Fastq files for 124 CPCGene Tumour/Normal Pairs from the 200PG Study Illumina HiSeq 2500;ILLUMINA, Illumina HiSeq 2500; 247
EGAD00001001095 Supporting data for ICGC PACA-CA Release 18 Illumina HiSeq 2000;, Illumina HiSeq 2500; 506
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
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
EGAD00001001060 Illumina HiSeq 2000; 112
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
EGAD00001001116 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina HiSeq 2000; 190
EGAD00001001096 Illumina HiSeq 2000; 419
EGAD00001001351 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000; 2
EGAD00001001349 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000; 4
EGAD00001001353 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000; 2
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. 331
EGAD00001000293 Sequencing data for Australian Ovarian Cancer study submitted 20121116 AB SOLiD 4 System; 72
EGAD00001001423 Illumina HiSeq 2000; 7
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; 238
EGAD00001001394 Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357 Illumina HiSeq 2000; 101
EGAD00001001048 Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z Illumina HiSeq 2000 (ILLUMINA) 86
EGAD00001001466 Whole Genome sequencing. 2 ?g 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. 300
EGAD00001001464 Exome Sequencing. 3 ?g 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. 882
EGAD00001001076 Fastq files of 239 samples of biliary tract cancer Illumina HiSeq 2000; 239
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
EGAD00001001119 Whole Genome Bisulfite Sequencing Illumina HiSeq 2000;, Illumina HiSeq 2500; 26
EGAD00001001121 RNA Sequencing Illumina HiSeq 2000; 26
EGAD00001001120 Whole Genome Sequencing Illumina HiSeq 2000;, Illumina HiSeq 2500; 64
EGAD00001001595 ICGC PACA-CA Release 20 Illumina HiSeq 2000;, Illumina HiSeq 2500; 516
EGAD00001001643 RIKEN collection of WGS read of 59 multi-centric liver cancers or intra-haptatic metastasis and matched blood samples from 19 donors. Illumina HiSeq 2000; 59
EGAD00001001642 RIKEN collection of WGS reads of 530 liver cancer and matched blood samples from 260 donors. Illumina HiSeq 2000; 530
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
EGAD00001001379 Illumina HiSeq 2000; 29
EGAD00001001630 release_2: ICGC PedBrain: whole genome bisulfite sequencing Illumina HiSeq 2000; 108
EGAD00001001624 release_2: ICGC PedBrain: whole exome sequencing and Target-Seq Illumina HiSeq 2000; 188
EGAD00001001621 release_2: ICGC PedBrain: ChIP-Seq Illumina HiSeq 2000; 31
EGAD00001001620 release_2: ICGC PedBrain: RNA sequencing Illumina HiSeq 2000; 45
EGAD00001001625 release_2: ICGC PedBrain: whole genome sequencing Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 209
EGAD00001001891 Whole genome bisulfite sequencing of pedbrain - medulloblastoma Illumina HiSeq 2000; 10
EGAD00001001847 4C-seq data was generated for regions of interest to confirm enhancer-gene promoter interactions Illumina HiSeq 2000; 1
EGAD00010000875 CLL Expression Array Affymetrix U219 1008
EGAD00001001927 Illumina HiSeq 2000; 27
EGAD00001001881 RIKEN collection of WGS reads for 543 liver cancer and matched blood or liver samples from 260 donors. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 543
EGAD00001001880 RIKEN collection of RNA-seq reads for 458 liver cancer samples and matched normal liver from 247 donors. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 458
EGAD00001001899 HDAC and PI3K Antagonists Cooperate to Inhibit Growth of MYC-driven Medulloblastoma 102
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
EGAD00001002683 A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases 22
EGAD00001001956 ICGC Release 21 for PACA-CA from OICR Illumina HiSeq 2000;, Illumina HiSeq 2500; 516
EGAD00001002016 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LICA-FR. 12
EGAD00001001323 A comprehensive characterisation and analysis of human breast cancers through genome-wide approaches through transcriptomics. Illumina HiSeq 2000; 59
EGAD00001001322 A comprehensive characterisation and analysis of human breast cancers through whole-genome sequencing. Illumina HiSeq 2000; 196
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 HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 28
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
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;ILLUMINA 6
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 HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 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
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
EGAD00001001645 Illumina Genome Analyzer II; 28
EGAD00001002002 Pelvic lymph node metastatic samples and matching bloods from prostate cancer patients that had not had androgen deprivation therapy. Collected by Steve Bova. Illumina HiSeq 2000; 20
EGAD00001002126 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PRAD-UK. 116
EGAD00001002120 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ORCA-IN. 26
EGAD00001002123 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MALY-DE. 202
EGAD00001002121 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BTCA-SG. 24
EGAD00001002129 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-EU. 158
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
EGAD00001002157 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MELA-AU. 140
EGAD00001002156 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ESAD-UK. 198
EGAD00001002132 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PACA-AU. 192
EGAD00001002122 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-UK. 90
EGAD00001002119 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LAML-KR. 18
EGAD00001002130 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: CLLE-ES. 194
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
EGAD00001002124 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: EOPC-DE. 113
EGAD00001002153 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PAEN-IT. 74
EGAD00001002125 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BOCA-UK. 148
EGAD00001001844 Whole genome sequencing of 64 HER2-Positive Breast Cancer Illumina HiSeq 2000; 128
EGAD00010000921 samples using Affymetrix CYTOSCANHD CYTOSCANHD 12
EGAD00010000919 samples using Illumina HUMANOMNI1QUAD HUMANOMNI1QUAD 2
EGAD00010000920 samples using Illumina HUMANOMNIEXPRESS HUMANOMNIEXPRESS 50
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
EGAD00001002689 ICGC Oesophageal Adenocarcinoma tissue samples Illumina HiSeq 2000; 10
EGAD00001001960 upcoming publication Illumina HiSeq 2000; 171
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;ILLUMINA, Illumina HiSeq 2500; 100
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; 258
EGAD00001002006 Whole genome sequencing of paediatric glioblastoma in the ICGC PedBrain project Illumina HiSeq 2500; 115
EGAD00001001944 RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project Illumina HiSeq 2500; 42
EGAD00001002662 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LINC-JP. 62
EGAD00001002131 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: RECA-EU. 190
EGAD00001002664 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: CMDI-UK. 98
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;ILLUMINA 9
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
EGAD00001001672 Part of RNA sequencing data of Malignant Lymphoma Study (ICGC) Illumina HiSeq 2000; 56
EGAD00001001632 miRNA seq data of 13 cases (MMML) 13
EGAD00001001673 Part of WGS seq data of Maligant Lymphoma study (ICGC) Illumina HiSeq 2000;, Illumina HiSeq 2500; 112
EGAD00001001619 miRNA seq data of 43 cases out of dataset EGAD00001000650 (MMML) 43
EGAD00001002739 Aligned sequence data from 14 Prostate cancer samples with BRCA2 mutations 49
EGAD00001000723 Relative Spatial Homogeneity of Embryonal Brain Tumors of Childhood 42
EGAD00001002684 Whole genome sequencing of 98 tumour-normal pairs for the PAEN-AU pancreatic neuroendocrine cancer project. 196
EGAD00001002885 Raw sequence data, fastq format Illumina HiSeq 2000;ILLUMINA 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;ILLUMINA 21
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
EGAD00001001100 DCC Project Code: SKCA-BR Skin Adenocarcinoma - BR Brazil Illumina HiSeq 2500;ILLUMINA 200
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;ILLUMINA 86
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 MiSeq;ILLUMINA, Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 164
EGAD00010001079 Affymetrix SNP6.0 array breast cancer data Affymetrix SNP6.0 66
EGAD00001003139 Aligned sequence data for 124 CPCGene Tumour/Normal Pairs from the 200PG Study 262
EGAD00001000141 Triple Negative Breast Cancer Whole Genomes Illumina Genome Analyzer II;, Illumina HiSeq 2000; 243
EGAD00001003163 Whole genome sequencing data of 20 carcinosarcomas. Illumina HiSeq 2000;ILLUMINA 23
EGAD00001003115 Whole genome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer. Illumina HiSeq 2000;ILLUMINA 50
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;ILLUMINA 21
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
EGAD00001003174 There are 116 liver cancer cases in this study and belong to LICA-CN project Illumina HiSeq 2000;ILLUMINA 232
EGAD00001003189 Whole genome sequencing of 8 HER2-Positive Breast Cancer (in complement to EGAD00001001844) Illumina HiSeq 2000;ILLUMINA 16
EGAD00001003162 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PACA-CA. 298
EGAD00010001196 Raw Array data from the CPCGene BRCA study Affymetrix OncoScan FFPE Express 48
EGAD00001003225 ICGC prostate UK study batches 4-6 prostatectomy analysis. Whole genome sequenced normal (blood) and malignant tissue pair of 111 patients. Illumina HiSeq 2000;ILLUMINA 221
EGAD00001003263 ICGC DCC Release 24, PACA-CA Deep KRAS sequencing 82
EGAD00001003227 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: OV-AU. 146
EGAD00001002241 Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - chemo_cohort Illumina HiSeq 2000; 270
EGAD00001003270 ICGC DCC Release 24, PACA-CA Whole Genome sequence merged alignments 95
EGAD00001003264 ICGC DCC Release 24, PACA-CA Exome sequence 190
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;ILLUMINA 52
EGAD00001003292 Illumina HiSeq 2000;ILLUMINA 520
EGAD00001003218 There are 80 Brain cancer cases (160 samples)in this study and belong to GBM-CN project. Illumina HiSeq 2000;ILLUMINA 80
EGAD00001003591 Merged bam files for PACA-CA Whole Genome Sequencing, for DCC release 25 211
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;ILLUMINA 7
EGAD00001003306 Exome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer. Illumina HiSeq 2000;ILLUMINA 50
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 56
EGAD00001003357 Aligned, merged and deduplicated BAM files from HiSeq whole exome sequencing of 106 samples: matched tumour-normal pairs from 53 melanoma patients. 106
EGAD00001003388 Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 366 samples: matched tumour-normal pairs from 183 melanoma patients. 366
EGAD00001003360 Bam files containing mitochondrial alignments, extracted from CPCGene Whole Genome Alignments 432
EGAD00001003361 VCF files containing mitochondrial variant calls using MToolbox 432
EGAD00010001281 SNP array dataset HUMANOMNIEXPRESS 50
EGAD00010001280 Transcriptome array dataset Affymetrix HG_U133_+2 25
EGAD00001003279 RNA sequencing data for 170 medulloblastoma tumor samples Illumina HiSeq 2000;ILLUMINA 171
EGAD00001003127 WGS data of medulloblastoma tumor/control pairs. 482
EGAD00001003128 Exome sequencing data for medulloblastoma tumor/control pairs 35
EGAD00010001301 Medulloblastoma expression profiling Affymetrix expression array 246
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;ILLUMINA 80
EGAD00001001350 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000; 8
EGAD00001001988 Cholangiocarcinoma whole genome sequencing data HiSeq X Ten (ILLUMINA), Illumina HiSeq 2000 (ILLUMINA), Illumina HiSeq 2500 (ILLUMINA) 118
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;ILLUMINA 27
EGAD00001003262 High-coverage WES sequencing of DNA samples from 50 PTCs was performed on the Illumina HiSeq 2500 or 4000 System Illumina HiSeq 2000;ILLUMINA 100
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;ILLUMINA 27
EGAD00001003753 single nucleotide variant calls from somatic sniper, vcf format. input for subclonal reconstruction 20
EGAD00001003754 structural variant calls from Delly, vcf format 37
EGAD00001003752 single nucleotide variant calls from somatic sniper, vcf format 34
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;ILLUMINA 176
EGAD00001003560 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: MALY-DE. 99
EGAD00001003548 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: CLLE-ES. 74
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, Illumina HiSeq 2500;ILLUMINA, unspecified;ILLUMINA 617
EGAD00001003269 High-coverage WGS sequencing of DNA samples from 90pairs GCs was performed on the Illumina HiSeq X Ten System. Illumina HiSeq 2000;ILLUMINA 1332
EGAD00010001323 Medulloblastoma methylation profiling Illumina Infinium HumanMethylation450 BeadChip 911
EGAD00001003592 Merged bam files for PACA-CA Whole Exome Sequencing, for DCC release 25 216
EGAD00001003271 WGS of 23 patients diagnosed with NKTL. The tumor samples were sequenced with Illumina HiSeq 2500 platform and the resulting FASTq files have been uploaded. Illumina HiSeq 2000 (ILLUMINA) 23
EGAD00001003205 160 WES and 25 WGS for HBV related HCC, and 15 WES for ICC belongs LICA-CN Illumina HiSeq 2000;ILLUMINA 402
EGAD00010001218 Raw Array data from the CPCGene 200PG study Affymetrix OncoScan FFPE Express 248
EGAD00001003561 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: MALY-DE. 99
EGAD00001003547 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: LIRI-JP. 130
EGAD00001003559 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: RECA-EU. 100
EGAD00001003558 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: RECA-EU. 100
EGAD00001003549 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: CLLE-ES. 74
EGAD00001003410 ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. 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
EGAD00001003411 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: PACA-AU. 81
EGAD00001003706 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, Illumina HiSeq 2500;ILLUMINA, unspecified;ILLUMINA 616
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. 607
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
EGAD00001003546 ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: LIRI-JP. 130
EGAD00001003580 WGS sequencing for 310 tumor normal pairs from ICGC ESAD-UK project Tumors 50x Normals 30x HiSeq X bam files These samples are all available in ICGC release 26 Illumina HiSeq 2000 (ILLUMINA) 620
EGAD00001003210 Whole genome sequencing data for MMML (cell_line) 8
EGAD00001003208 Whole genome sequencing data for MMML (12 tumor/control pairs) Illumina HiSeq 2000;ILLUMINA 25
EGAD00001003207 Whole genome sequencing data for MMML (28 tumor/control pairs) 56
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
EGAD00001003344 Transcriptome profiling of 25 prostate tumor samples by RNA-Seq Illumina HiSeq 2000;ILLUMINA 25
EGAD00001003276 Whole genome sequencing data for MMML (24 tumor/control pairs), fastq-files Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 49
EGAD00001003274 Whole genome sequencing data for MMML (tumor/control pairs and one cell_line) 315