ICGC Data Access Compliance Office

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This DAC controls 503 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
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 Genome Analyzer IIx Illumina HiSeq 2000	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	None	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	-
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	None	Illumina HiSeq 2000	-
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	None	Illumina HiSeq 2000	68
EGAD00001000735	Here we present the genomes of three secondary angiosarcomas	Illumina HiSeq 2000	7
EGAD00001000738	Extension of angiosarcoma whole genome sequencing study	Illumina HiSeq 2000	4
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	None	Illumina HiSeq 2000	8
EGAD00001001044	None	Ion Torrent PGM	2
EGAD00001001048	Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z	Illumina HiSeq 2000	-
EGAD00001001051	None	Illumina HiSeq 2000	200
EGAD00001001060	None	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
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	150
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	10
EGAD00001001120	Whole Genome Sequencing	Illumina HiSeq 2000 Illumina HiSeq 2500	26
EGAD00001001121	RNA Sequencing	Illumina HiSeq 2000	10
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
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	-
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	-
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	-
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	88
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	-
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	1
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	-
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	-
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	None	Illumina HiSeq 2000	29
EGAD00001001388	Whole-genome bisulfite sequencing (WGBS) on 30 breast cancer cases from the BASIS project.	Illumina HiSeq 2000	-
EGAD00001001394	Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357	Illumina HiSeq 2000	-
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.		-
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.		-
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
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	None	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	-
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
EGAD00001002258	None	Illumina HiSeq 2000	2
EGAD00001002259	None	Illumina HiSeq 2000	37
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	-
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
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	-
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	-
EGAD00001003279	RNA sequencing data for 170 medulloblastoma tumor samples	Illumina HiSeq 2000	171
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		-
EGAD00001003357	Aligned, merged and deduplicated BAM files from HiSeq whole exome sequencing of 106 samples: matched tumour-normal pairs from 53 melanoma patients.		-
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.		-
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
EGAD00001003838	None	Illumina HiSeq 2000	19
EGAD00001003839	None	Illumina HiSeq 2000	26
EGAD00001003840	None	Illumina HiSeq 2000	3
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
EGAD00001003900	None	Illumina HiSeq 2000	83
EGAD00001003901	None	Illumina HiSeq 2000	3
EGAD00001003902	None	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
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
EGAD00001004021	None	Illumina HiSeq 2000	32
EGAD00001004022	None	Illumina HiSeq 2000	10
EGAD00001004023	None	Illumina HiSeq 2000	52
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	-
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	-
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		-
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	-
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	-
EGAD00001004424	Prostate Cancer - RNA-Seq unmapped reads	Illumina HiSeq 2000	148
EGAD00001004430	None	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		-
EGAD00001004478	None	Illumina HiSeq 2500	24
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
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	-
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	-
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.		-
EGAD00001004875	Aligned RNA-seq sequences in this dataset are from the Proteogenomic Landscape of Curable Prostate Cancer study		56
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
EGAD00001005375	None	Illumina HiSeq 2000	73
EGAD00001005376	None	Illumina HiSeq 2000	11
EGAD00001005377	None	Illumina HiSeq 2000	10
EGAD00001005383	None	Illumina HiSeq 2000	20
EGAD00001005384	None	Illumina HiSeq 2000	9
EGAD00001005385	None	Illumina HiSeq 2000	64
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	-
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	-
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	-
EGAD00001005454	Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 103 cases of melanoma Uveal subtype		-
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		-
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.		-
EGAD00001005501	Illumina RNASeq sequencing of tumour samples from 41 cases of melanoma		-
EGAD00001005738	79 RNAseq samples from 56 patients with melanoma who have undergone immune checkpoint blockade immunotherapy.		-
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	-
EGAD00001006003	None	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, Gregson 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	-
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	-
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	48
EGAD00001006439	Illumina RNASeq sequencing of tumour samples from 53 cases of cutaneous melanoma and 61 cases of acral melanoma		-
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
EGAD00001006874	Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. WGS (BAM files) 5 Barrett's samples 5 normal oesophageal samples 5 normal gastric cardia samples 5 normal duodenal samples	Illumina HiSeq 2000 Illumina NovaSeq 6000	10
EGAD00001006882	Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 12 Barrett's samples 12 normal oesophageal samples 11 normal gastric cardia samples	Illumina HiSeq 2000	-
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.		-
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	-
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	-
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	-
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	-
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
EGAD00001009866	whole genome sequencing data	Illumina NovaSeq 6000	512
EGAD00001009867	methyl-seq data 64 cases	Illumina NovaSeq 6000	128
EGAD00001009868	ATAC-seq data 72cases	Illumina HiSeq 2500	144
EGAD00001010003	RNA-seq data. 287 Japanese RCC cases.	Illumina HiSeq 2500	574
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
EGAD00001010184	This dataset includes Illumina EPIC Capture Sequencing Data of 376 samples from 188 men with prostate cancer. Samples were taken from primary tissue obtained at prostatectomy, with matched pathologically assessed non-cancer control material. This DNA methylation data includes donors and samples included in previously published WGS datasets (from CRUK-ICGC batches 1 to 3 [EGAD00001001116] and batches 4 to 6 [EGAD00001003225]; including the majority of donors used in Wedge et al, Nature Genetics 2018 [PMID: 29662167]). The targeted DNA methylation sequencing data in this EGA dataset were generated using the Illumina TruSeq methyl capture method (EPICseq), covering over 3.3 million CpGs in the human genome, representing a total targeted hybridisation capture panel of 107Mbp. According to the EPICseq protocol, DNA samples extracted from prostatectomy tissue samples were enriched for target regions using hybridisation capture, prior to bisulfite conversion, amplification and sequencing in pools of 12 samples (150 single end reads over two Illumina HiSeq4000 lanes). This approach generated DNA methylation profiles from prostate cancer and control samples at base-pair resolution across millions of CpGs in the human genome.	Illumina HiSeq 4000	376
EGAD00001011065	Data supporting: "SMAD4 and KCNQ3 Alterations are Associated with Lymph Node Metastases in Oesophageal Adenocarcinoma" RNAseq (FASTQ files) 6 samples	unspecified	6
EGAD00001011076	Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" RNAseq for 279 samples	Illumina HiSeq 2000 unspecified	-
EGAD00001011095	Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" WGS for 452 samples	HiSeq X Five Illumina HiSeq 2000	-
EGAD00001011187	Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS OACs/BOs/normals)	HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified	63
EGAD00001011188	Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WES OACs/BOs/normals)	unspecified	170
EGAD00001011189	Data supporting: "TBC" Ganguli et al (sWGS for 75 samples)	Illumina HiSeq 2500 Illumina HiSeq 4000	-
EGAD00001011190	Data supporting: "TBC" Ganguli et al (RNA for 394 samples)	Illumina HiSeq 2000 unspecified	49
EGAD00001011191	Data supporting: "TBC" Ganguli et al (WGS for 1298 samples)	HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified	42
EGAD00001011196	Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (WGS for 1397 samples)	HiSeq X Five Illumina HiSeq 2000 Illumina NovaSeq 6000 unspecified	6
EGAD00001011255	Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS BOs/normals)	unspecified	28
EGAD00001011269	Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (RNA for 197 samples)	Illumina HiSeq 2000	-
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	-
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	-
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
EGAD00010001795	Array data for oesophageal and related samples â€“ kno_paper_methyl_release	Illumina	78
EGAD00010001822	Array data for oesophageal and related samples â€“ sj_paper_methyl_tumour_release	Illumina	285
EGAD00010001834	Array data for oesophageal and related samples â€“ sj_paper_methyl_normal_release	Illumina	100
EGAD00010001838	Array data for oesophageal and related samples â€“ 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
EGAD00010002682	Array data for oesophageal and related samples â€“ Ganguli et al (methylation array)	Illumina	327