ICGC PanCancer Analysis of Whole Genomes

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

37 Datasets 22 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Samples
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
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
EGAD00001003132	ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: GACA-CN.	84
EGAD00001003162	ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PACA-CA.	298
EGAD00001003227	ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: OV-AU.	146
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
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
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

Publications	Citations
Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers. Guo YA, Chang MM, Huang W, Ooi WF, Xing M, Tan P, Skanderup AJ. Nat Commun 9: 2018 1520	81
Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, Sungalee S, Russell RB, Russell RB, Bausinger J, Kretzmer H, Ammerpohl O, Bergmann AK, Binder H, Borkhardt A, Brors B, Claviez A, Doose G, Feuerbach L, Haake A, Hansmann ML, Hoell J, Hummel M, Korbel JO, Lawerenz C, Lenze D, Radlwimmer B, Richter J, Rosenstiel P, Rosenwald A, Schilhabel MB, Stein H, Stilgenbauer S, Stadler PF, Szczepanowski M, Weniger MA, Zapatka M, Eils R, Lichter P, Loeffler M, Möller P, Trümper L, Klapper W, ICGC MMML-Seq Consortium, Hoffmann S, Küppers R, Burkhardt B, Schlesner M, Siebert R. Nat Commun 10: 2019 1459	66
Pan-cancer analysis of whole genomes. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Nature 578: 2020 82-93	1306
A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies. Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G, Momen SE, Georgakopoulos-Soares I, Dias JML, Young J, Memari Y, Davies H, Nik-Zainal S. Nat Cancer 1: 2020 249-263	125
Timing the initiation of multiple myeloma. Rustad EH, Yellapantula V, Leongamornlert D, Bolli N, Ledergor G, Nadeu F, Angelopoulos N, Dawson KJ, Mitchell TJ, Osborne RJ, Ziccheddu B, Carniti C, Montefusco V, Corradini P, Anderson KC, Moreau P, Papaemmanuil E, Alexandrov LB, Puente XS, Campo E, Siebert R, Avet-Loiseau H, Landgren O, Munshi N, Campbell PJ, Maura F. Nat Commun 11: 2020 1917	78
Accurate and efficient detection of gene fusions from RNA sequencing data. Uhrig S, Ellermann J, Walther T, Burkhardt P, Fröhlich M, Hutter B, Toprak UH, Neumann O, Stenzinger A, Scholl C, Fröhling S, Brors B. Genome Res 31: 2021 448-460	165
Alternative lengthening of telomeres is not synonymous with mutations in ATRX/DAXX. de Nonneville A, Reddel RR. Nat Commun 12: 2021 1552	24
Structural Variants at the <i>BRCA1/2</i> Loci are a Common Source of Homologous Repair Deficiency in High-grade Serous Ovarian Carcinoma. Ewing A, Meynert A, Churchman M, Grimes GR, Hollis RL, Herrington CS, Rye T, Bartos C, Croy I, Ferguson M, Lennie M, McGoldrick T, McPhail N, Siddiqui N, Dowson S, Glasspool R, Mackean M, Nussey F, McDade B, Ennis D, McMahon L, Matakidou A, Dougherty B, March R, Barrett JC, McNeish IA, Scottish Genomes Partnership, Biankin AV, Roxburgh P, Gourley C, Semple CA. Clin Cancer Res 27: 2021 3201-3214	17
dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India. Pradhan S, Das S, Singh AK, Das C, Basu A, Majumder PP, Biswas NK. Database (Oxford) 2021: 2021 baab034	2
Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma. Jain MD, Ziccheddu B, Coughlin CA, Faramand R, Griswold AJ, Reid KM, Menges M, Zhang Y, Cen L, Wang X, Hussaini M, Landgren O, Davila ML, Schatz JH, Locke FL, Maura F. Blood 140: 2022 491-503	29
The genomic and transcriptional landscape of primary central nervous system lymphoma. Radke J, Ishaque N, Koll R, Gu Z, Schumann E, Sieverling L, Uhrig S, Hübschmann D, Toprak UH, López C, Hostench XP, Borgoni S, Juraeva D, Pritsch F, Paramasivam N, Balasubramanian GP, Schlesner M, Sahay S, Weniger M, Pehl D, Radbruch H, Osterloh A, Korfel A, Misch M, Onken J, Faust K, Vajkoczy P, Moskopp D, Wang Y, Jödicke A, Trümper L, Anagnostopoulos I, Lenze D, Küppers R, Hummel M, Schmitt CA, Wiestler OD, Wolf S, Unterberg A, Eils R, Herold-Mende C, Brors B, ICGC MMML-Seq Consortium, Siebert R, Wiemann S, Heppner FL. Nat Commun 13: 2022 2558	38
A pan-cancer compendium of chromosomal instability. Drews RM, Hernando B, Tarabichi M, Haase K, Lesluyes T, Smith PS, Morrill Gavarró L, Couturier DL, Liu L, Schneider M, Brenton JD, Van Loo P, Macintyre G, Markowetz F. Nature 606: 2022 976-983	100
Substitution mutational signatures in whole-genome-sequenced cancers in the UK population. Degasperi A, Zou X, Amarante TD, Martinez-Martinez A, Koh GCC, Dias JML, Heskin L, Chmelova L, Rinaldi G, Wang VYW, Nanda AS, Bernstein A, Momen SE, Young J, Perez-Gil D, Memari Y, Badja C, Shooter S, Czarnecki J, Brown MA, Davies HR, Genomics England Research Consortium, Nik-Zainal S. Science 376: 2022 science.abl9283	90
<i>BTG1</i> mutation yields supercompetitive B cells primed for malignant transformation. Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B, Tsialta I, Doane AS, Geng H, Rehman MH, Melnick J, Morgan W, Nguyen DTT, Elemento O, Kharas MG, Jaffrey SR, Scott DW, Khelashvili G, Meyer-Hermann M, Victora GD, Melnick A. Science 379: 2023 eabj7412	11
Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells. Maura F, Ziccheddu B, Xiang JZ, Bhinder B, Rosiene J, Abascal F, Maclachlan KH, Eng KW, Uppal M, He F, Zhang W, Gao Q, Yellapantula VD, Trujillo-Alonso V, Park SI, Oberley MJ, Ruckdeschel E, Lim MS, Wertheim GB, Barth MJ, Horton TM, Derkach A, Kovach AE, Forlenza CJ, Zhang Y, Landgren O, Moskowitz CH, Cesarman E, Imielinski M, Elemento O, Roshal M, Giulino-Roth L. Blood Cancer Discov 4: 2023 208-227	11
Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns. Sørensen SG, Shrikhande A, Poulsgaard GA, Christensen MH, Bertl J, Laursen BE, Hoffmann ER, Pedersen JS. Elife 12: 2023 e81224	1
Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus. Luebeck J, Ng AWT, Galipeau PC, Li X, Sanchez CA, Katz-Summercorn AC, Kim H, Jammula S, He Y, Lippman SM, Verhaak RGW, Maley CC, Alexandrov LB, Reid BJ, Fitzgerald RC, Paulson TG, Chang HY, Wu S, Bafna V, Mischel PS. Nature 616: 2023 798-805	35
Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers. Setton J, Hadi K, Choo ZN, Kuchin KS, Tian H, Da Cruz Paula A, Rosiene J, Selenica P, Behr J, Yao X, Deshpande A, Sigouros M, Manohar J, Nauseef JT, Mosquera JM, Elemento O, Weigelt B, Riaz N, Reis-Filho JS, Powell SN, Imieliński M. Nature 621: 2023 129-137	2
Sequence dependencies and mutation rates of localized mutational processes in cancer. Poulsgaard GA, Sørensen SG, Juul RI, Nielsen MM, Pedersen JS. Genome Med 15: 2023 63	2
The m<sup>6</sup>A-related gene signature stratifies poor prognosis patients and characterizes immunosuppressive microenvironment in hepatocellular carcinoma. Ma E, Li J, Shen C, Gu Y, Zhang X, Li L, Zhao J, Wang Z. Front Immunol 14: 2023 1227593	1
Most large structural variants in cancer genomes can be detected without long reads. Choo ZN, Behr JM, Deshpande A, Hadi K, Yao X, Tian H, Takai K, Zakusilo G, Rosiene J, Da Cruz Paula A, Weigelt B, Setton J, Riaz N, Powell SN, Busam K, Shoushtari AN, Ariyan C, Reis-Filho J, de Lange T, Imieliński M. Nat Genet 55: 2023 2139-2148	8
A deep-learning-based genomic status estimating framework for homologous recombination deficiency detection from low-pass whole genome sequencing. Liu Y, Bi X, Leng Y, Chen D, Wang J, Ma Y, Zhang MZ, Han BW, Li Y. Heliyon 10: 2024 e26121	0