StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	8	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0004	Illumina HiSeq 2000	chr10:0-69623992:0;chr10:69623993-90200293:-1;chr10:90200294-135534747:0;chr11:0-135006516:0;chr12:0-38096966:0;chr12:38096967-38924661:-1;chr12:38924662-52370131:0;chr12:52370132-52370409:-1;chr12:52370410-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-10849116:0;chr21:10849117-10944185:-1;chr21:10944186-48129895:0;chr22:0-51304566:0;chr2:0-112307636:0;chr2:112307637-112647111:-1;chr2:112647112-243199373:0;chr3:0-198022430:0;chr4:0-160974802:0;chr4:160974803-161098962:-1;chr4:161098963-191154276:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-159138663:0;chr8:0-5499065:0;chr8:122709151-129674654:0;chr8:129674655-130526331:-1;chr8:130526332-136409771:0;chr8:136409772-137426384:-1;chr8:137426385-146364022:0;chr8:53079435-108692391:-1;chr8:5499066-5628772:-1;chr8:5628773-53079434:0;chr8:87581785-122709150:-1;chr9:0-9170699:0;chr9:9170700-9523598:-1;chr9:9523599-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs1:33183391-33183391,hs1:33260864-33260864;hs1:38432796-38432796,hs6:28863604-28863604;hs1:49491351-49491351,hs1:49494430-49494430;hs1:174962536-174962536,hs1:174928636-174928636;hs2:12369960-12369960,hs2:12372645-12372645;hs2:40555062-40555062,hs2:78686837-78686837;hs2:63900644-63900644,hs2:176179133-176179133;hs2:63900646-63900646,hs2:176179119-176179119;hs2:78685414-78685414,hs2:40555062-40555062;hs2:102379496-102379496,hs2:109355974-109355974;hs2:172448061-172448061,hs2:173637622-173637622;hs2:172448061-172448061,hs2:173637622-173637622;hs2:176179132-176179132,hs2:63900634-63900634;hs2:186672954-186672954,hs2:186654331-186654331;hs3:3834568-3834568,hs3:3820326-3820326;hs3:121013940-121013940,hs3:121014043-121014043;hs3:122200142-122200142,hs3:122200197-122200197;hs4:72714689-72714689,hs22:50158256-50158256;hs4:132283261-132283261,hs4:132297084-132297084;hs4:144317983-144317983,hs4:144317891-144317891;hs5:35305661-35305661,hs10:114205128-114205128;hs7:40850149-40850149,hs7:41846253-41846253;hs7:40850149-40850149,hs7:41846253-41846253;hs8:10022420-10022420,hs8:135029870-135029870;hs8:19817022-19817022,hs8:3489795-3489795;hs8:32797612-32797612,hs8:33003443-33003443;hs8:32797615-32797615,hs8:32801119-32801119;hs8:33003449-33003449,hs8:52593586-52593586;hs8:33003553-33003553,hs8:32801124-32801124;hs8:33565022-33565022,hs8:42751079-42751079;hs8:33802316-33802316,hs8:41389673-41389673;hs8:33802606-33802606,hs8:42740151-42740151;hs8:33938890-33938890,hs8:38383664-38383664;hs8:34363629-34363629,hs8:40439288-40439288;hs8:34738487-34738487,hs8:41349058-41349058;hs8:35152145-35152145,hs8:40457135-40457135;hs8:35425128-35425128,hs8:43030916-43030916;hs8:35425132-35425132,hs8:43030916-43030916;hs8:35518102-35518102,hs8:38726593-38726593;hs8:36018492-36018492,hs8:43491062-43491062;hs8:36092475-36092475,hs8:40439881-40439881;hs8:36905668-36905668,hs8:39138168-39138168;hs8:37962219-37962219,hs8:42650011-42650011;hs8:38383468-38383468,hs8:39137712-39137712;hs8:38406501-38406501,hs8:39434675-39434675;hs8:39005932-39005932,hs8:42750641-42750641;hs8:40456981-40456981,hs8:35518290-35518290;hs8:41690105-41690105,hs8:33940233-33940233;hs8:41981041-41981041,hs8:42053399-42053399;hs8:42717762-42717762,hs8:42590038-42590038;hs8:42820001-42820001,hs8:40131819-40131819;hs8:43030477-43030477,hs8:43098475-43098475;hs8:47009554-47009554,hs8:110862767-110862767;hs8:76083913-76083913,hs8:78682752-78682752;hs8:78220523-78220523,hs8:78124580-78124580;hs8:80126508-80126508,hs8:80039302-80039302;hs8:83233679-83233679,hs8:117921027-117921027;hs8:85916753-85916753,hs8:89436223-89436223;hs8:104500556-104500556,hs8:106574934-106574934;hs8:104715306-104715306,hs8:10039759-10039759;hs8:110321690-110321690,hs8:114907572-114907572;hs8:113323346-113323346,hs8:113333495-113333495;hs8:114367382-114367382,hs8:115137397-115137397;hs8:117072421-117072421,hs8:116982986-116982986;hs8:137590138-137590138,hs8:139591703-139591703;hs10:59924521-59924521,hs10:59929757-59929757;hs10:59929863-59929863,hs10:59934682-59934682;hs10:59930284-59930284,hs10:59928967-59928967;hs10:59930284-59930284,hs10:59928967-59928967;hs10:77810044-77810044,hs10:78522769-78522769;hs10:77810044-77810044,hs10:78522769-78522769;hs10:77810044-77810044,hs10:78522769-78522769;hs10:88402703-88402703,hs10:32507525-32507525;hs12:23542591-23542591,hs14:88593733-88593733;hs12:38953236-38953236,hs12:21529818-21529818;hs17:35499733-35499733,hs17:35617124-35617124;hs19:36686497-36686497,hs10:11230133-11230133;hs20:60521456-60521456,hs20:60520564-60520564;hs23:144263583-144263583,hs23:144472906-144472906	FGFR1;	Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	ADAM32,RNF170;C8orf86,ADAM32;RIMS2,MSRA
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	3	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0059	Illumina HiSeq 2000	chr10:0-127389287:0;chr10:127389288-128439429:-1;chr10:128439430-135534747:0;chr11:0-135006516:0;chr12:0-25872245:0;chr12:25872246-34414441:-1;chr12:34414442-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-21334777:0;chr2:21334778-22001683:-1;chr2:217915725-217993867:-1;chr2:217993868-243199373:0;chr2:22001684-217915724:0;chr3:0-78131967:0;chr3:118877415-80820129:1;chr3:172220462-171989369:1;chr3:172429136-172412681:1;chr3:172476665-82780298:1;chr3:190045000-190048756:-1;chr3:190113509-198022430:0;chr3:78131968-118881483:-1;chr3:83014922-82821204:1;chr3:83114349-190113508:-1;chr4:0-94332899:0;chr4:126686846-127536820:-1;chr4:127536821-140683203:0;chr4:140683204-153459905:-1;chr4:153459906-191154276:0;chr4:94332900-94857806:-1;chr4:94857807-126686845:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-159138663:0;chr8:0-146364022:0;chr9:0-9301697:0;chr9:9301698-9304495:-1;chr9:9304496-9458671:0;chr9:9458672-9684823:-1;chr9:9684824-141213431:0;chrX:0-102271590:0;chrX:102271591-102805328:-1;chrX:102805329-155270560:0;chrY:0-59373566:0	hs1:64103531-64103531,hs1:64023910-64023910;hs1:64850193-64850193,hs10:101600019-101600019;hs1:195973597-195973597,hs1:195973710-195973710;hs1:233962189-233962189,hs1:233963570-233963570;hs2:49854729-49854729,hs2:49864604-49864604;hs2:49862912-49862912,hs2:49872200-49872200;hs2:49865156-49865156,hs2:49865297-49865297;hs2:49865285-49865285,hs2:49872459-49872459;hs2:49867360-49867360,hs2:49860931-49860931;hs2:49872466-49872466,hs2:49865156-49865156;hs2:65859142-65859142,hs2:65858353-65858353;hs2:91937048-91937048,hs12:123873688-123873688;hs3:71415647-71415647,hs3:71413720-71413720;hs3:80971636-80971636,hs3:88407861-88407861;hs3:82817946-82817946,hs3:82828356-82828356;hs3:82830567-82830567,hs3:83015805-83015805;hs3:103627503-103627503,hs3:176341661-176341661;hs3:109924632-109924632,hs3:118615145-118615145;hs3:171997544-171997544,hs3:172384802-172384802;hs3:172072843-172072843,hs3:172238199-172238199;hs3:172235616-172235616,hs3:172438821-172438821;hs3:172385039-172385039,hs3:172433676-172433676;hs3:172475562-172475562,hs3:190530068-190530068;hs3:176538679-176538679,hs3:178048958-178048958;hs3:178952270-178952270,hs3:177916024-177916024;hs4:81239840-81239840,hs8:107752651-107752651;hs5:28652072-28652072,hs14:55618593-55618593;hs5:175733376-175733376,hs18:55381811-55381811;hs6:159046794-159046794,hs6:158969449-158969449;hs7:46595607-46595607,hs7:46595695-46595695;hs8:100916474-100916474,hs8:100895469-100895469;hs10:90368359-90368359,hs10:90368699-90368699;hs10:122628942-122628942,hs18:57150108-57150108;hs12:25660742-25660742,hs12:25130148-25130148;hs12:27023810-27023810,hs12:28180373-28180373;hs12:28103905-28103905,hs12:28211218-28211218;hs12:33211553-33211553,hs12:30979763-30979763;hs13:75213414-75213414,hs14:55618883-55618883;hs13:111852488-111852488,hs13:112019145-112019145;hs14:55618496-55618496,hs14:55618780-55618780;hs14:55618740-55618740,hs6:66526378-66526378;hs14:75581765-75581765,hs14:75581818-75581818;hs15:48101016-48101016,hs15:48101268-48101268;hs17:50197629-50197629,hs12:81391487-81391487;hs17:60807430-60807430,hs17:60807294-60807294;hs19:816668-816668,hs19:816426-816426;hs24:16975482-16975482,hs17:57707528-57707528	BZW1P1;CCT6P4;CLDN16;GCNT1P3;GHSR;NCEH1;SLC31A1P1;TNFSF10;	Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	FNDC3B,NCEH1;FNDC3B,TNFSF10
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	15	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0069	Illumina HiSeq 2000	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-74903578:0;chr15:62553529-88218199:0;chr15:74903579-62553528:1;chr15:81504848-102531392:0;chr15:88218200-81504847:1;chr16:0-6733751:0;chr16:6733752-6746153:-1;chr16:6746154-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-18719933:0;chr4:18719934-18734248:-1;chr4:18734249-191154276:0;chr5:0-17603583:0;chr5:17603377-180915260:0;chr5:17603584-17603376:1;chr6:0-171115067:0;chr7:0-44105123:0;chr7:44105124-55782353:-1;chr7:55782354-159138663:0;chr8:0-52122989:0;chr8:111320246-146364022:0;chr8:52122990-52558645:-1;chr8:52130274-55083438:-1;chr8:55080109-52128202:1;chr8:55083439-75672293:0;chr8:75672294-111320245:-1;chr9:0-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs1:142787688-142787688,hs15:96397373-96397373;hs1:187947763-187947763,hs1:187954812-187954812;hs1:187947874-187947874,hs1:187982378-187982378;hs1:211502242-211502242,hs1:211502184-211502184;hs1:227467579-227467579,hs1:227473100-227473100;hs1:231607793-231607793,hsX:48977124-48977124;hs2:199710953-199710953,hs2:199713112-199713112;hs3:37718635-37718635,hs11:33288559-33288559;hs4:92925961-92925961,hs4:92873309-92873309;hs5:20547860-20547860,hs14:58706090-58706090;hs5:158687077-158687077,hs6:36247111-36247111;hs6:64769003-64769003,hs6:64768847-64768847;hs6:146323409-146323409,hs6:146298596-146298596;hs7:139819169-139819169,hs9:33002774-33002774;hs7:140173603-140173603,hs7:140143717-140143717;hs8:60467589-60467589,hs8:139995367-139995367;hs8:90023956-90023956,hs8:90023845-90023845;hs8:113825306-113825306,hs8:113825791-113825791;hs8:118508994-118508994,hs8:144025317-144025317;hs8:118509173-118509173,hs8:144025398-144025398;hs8:131988002-131988002,hs8:131988363-131988363;hs8:133124731-133124731,hs8:133115405-133115405;hs8:139995354-139995354,hs8:60470377-60470377;hs9:9145661-9145661,hs9:9178310-9178310;hs9:22043338-22043338,hs9:22126816-22126816;hs9:77543231-77543231,hs14:36281163-36281163;hs10:35640895-35640895,hs10:31753837-31753837;hs10:38115409-38115409,hsX:36047768-36047768;hs10:53679561-53679561,hs10:53679308-53679308;hs10:127948245-127948245,hs10:127948104-127948104;hs11:33342098-33342098,hs3:37617555-37617555;hs12:15370630-15370630,hs4:44547855-44547855;hs14:36117834-36117834,hs14:36119384-36119384;hs14:36266813-36266813,hs14:36267359-36267359;hs15:60193482-60193482,hs15:61077249-61077249;hs15:62809305-62809305,hs15:77985573-77985573;hs15:63895421-63895421,hs15:70393108-70393108;hs15:67977261-67977261,hs15:79859530-79859530;hs15:73776062-73776062,hs15:77985774-77985774;hs15:73777897-73777897,hs15:88462273-88462273;hs15:74903299-74903299,hs15:81506142-81506142;hs15:74903835-74903835,hs15:84689610-84689610;hs15:75247135-75247135,hs15:75274351-75274351;hs15:76701227-76701227,hs15:81784703-81784703;hs15:81505406-81505406,hs15:81506956-81506956;hs15:82016551-82016551,hs15:82142753-82142753;hs15:83786247-83786247,hs15:81783495-81783495;hs15:85885730-85885730,hs15:96290030-96290030;hs15:86069395-86069395,hs15:95884178-95884178;hs15:87493382-87493382,hs15:82146848-82146848;hs15:87501351-87501351,hs15:82127312-82127312;hs15:95843285-95843285,hs15:95843736-95843736;hs15:95877591-95877591,hs1:142798913-142798913;hs15:96310320-96310320,hs15:96440775-96440775;hs15:96429613-96429613,hs15:96518482-96518482;hs16:1339821-1339821,hs16:1339966-1339966;hs17:21548442-21548442,hs20:26079438-26079438;hs17:41110532-41110532,hs11:118225545-118225545;hs17:55291966-55291966,hs17:55281492-55281492;hs17:80583762-80583762,hs17:80592511-80592511;hs17:80604418-80604418,hs14:33002460-33002460;hs18:53870184-53870184,hs18:53839900-53839900;hs19:42002896-42002896,hs17:21726667-21726667;hs20:21770031-21770031,hs20:23883452-23883452;hs20:22543146-22543146,hs20:24109800-24109800;hs20:22545819-22545819,hs20:24109799-24109799;hs20:24108704-24108704,hs20:24108764-24108764;hs20:24123371-24123371,hs20:22542678-22542678;hs22:45334390-45334390,hs22:45336237-45336237;hsX:22672575-22672575,hsX:22672930-22672930;hsX:145181974-145181974,hsX:145167812-145167812	AKAP13;BTBD1;HMGN1P26;KLHL25;	Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	C15orf60,LINGO1
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	14	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0131	Illumina HiSeq 2000	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-30736165:0;chr14:30717638-32201370:0;chr14:30736166-30717637:1;chr14:32201371-50990242:-1;chr14:32240974-31010651:1;chr14:32931626-76186652:-1;chr14:37060590-87020375:0;chr14:39493660-32300903:1;chr14:41277629-77774897:0;chr14:46710304-37983249:1;chr14:46710339-107349540:0;chr14:47617843-46350387:1;chr14:50886218-36399382:1;chr14:76186653-76661699:0;chr14:76450454-78505173:0;chr14:76661700-41277628:1;chr14:77585522-78515648:0;chr14:77774898-76450453:1;chr14:78505174-77585521:1;chr14:78515649-37060589:1;chr14:87020376-46710338:1;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-11049112:0;chr17:11049113-11049360:-1;chr17:11049361-43688024:0;chr17:43688025-45520025:-1;chr17:45520026-81195210:0;chr18:0-78077248:0;chr19:0-1062883:0;chr19:1062884-1248605:-1;chr19:1248606-50292185:0;chr19:50292186-50366076:-1;chr19:50366077-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-191154276:0;chr5:0-180915260:0;chr6:0-14745280:0;chr6:14745281-14745698:-1;chr6:14745699-171115067:0;chr7:0-61829245:0;chr7:110601757-110691241:-1;chr7:110691242-159138663:0;chr7:61829246-61829354:-1;chr7:61829355-110601756:0;chr8:0-3583336:0;chr8:3583337-3597576:-1;chr8:3597577-43444523:0;chr8:41138999-146364022:0;chr8:43444524-43448041:-1;chr8:43448042-43536332:0;chr8:43536333-41138998:1;chr9:0-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs1:11954514-11954514,hs21:39050074-39050074;hs1:178716640-178716640,hs1:178716693-178716693;hs2:80222459-80222459,hs2:80222650-80222650;hs2:86640837-86640837,hs2:86640892-86640892;hs2:131969113-131969113,hs6:11809179-11809179;hs2:140049049-140049049,hs2:140049479-140049479;hs2:161931745-161931745,hs2:161931253-161931253;hs3:59999981-59999981,hs3:61096854-61096854;hs3:146002981-146002981,hs3:146003064-146003064;hs3:151146128-151146128,hs18:65405909-65405909;hs3:151146520-151146520,hs18:65405921-65405921;hs4:19521427-19521427,hs4:19522043-19522043;hs4:57279732-57279732,hs4:57279631-57279631;hs4:91192146-91192146,hs4:91169877-91169877;hs4:91222774-91222774,hs4:91171457-91171457;hs4:117913141-117913141,hs4:117919231-117919231;hs4:130170961-130170961,hs14:79739674-79739674;hs4:160534224-160534224,hs4:160453026-160453026;hs4:174788390-174788390,hs4:174789046-174789046;hs5:45664516-45664516,hs2:147020927-147020927;hs5:140563527-140563527,hs5:140573649-140573649;hs6:529086-529086,hs6:528889-528889;hs6:3635254-3635254,hs9:21981015-21981015;hs6:27277783-27277783,hs6:27315562-27315562;hs6:28795495-28795495,hs6:28797390-28797390;hs6:30009588-30009588,hs6:30009687-30009687;hs6:30009588-30009588,hs6:30009687-30009687;hs6:69092656-69092656,hs22:29066425-29066425;hs6:137032520-137032520,hs6:137001570-137001570;hs6:165799869-165799869,hs6:165800027-165800027;hs7:6122062-6122062,hs13:26816255-26816255;hs7:56156974-56156974,hs7:56157331-56157331;hs7:56405153-56405153,hs7:56405505-56405505;hs7:84425628-84425628,hs7:84425682-84425682;hs7:90827334-90827334,hs7:90839050-90839050;hs8:37734921-37734921,hs8:43565999-43565999;hs8:41145404-41145404,hs20:26174848-26174848;hs8:41145407-41145407,hs20:26214817-26214817;hs8:43500445-43500445,hs8:43526143-43526143;hs9:73897323-73897323,hs9:73896989-73896989;hs9:96668254-96668254,hs9:96668330-96668330;hs10:77788790-77788790,hs14:74666901-74666901;hs10:101587566-101587566,hs8:140475594-140475594;hs11:13023333-13023333,hs18:53590744-53590744;hs14:19494321-19494321,hs19:19632149-19632149;hs14:21053497-21053497,hs14:20347986-20347986;hs14:21230084-21230084,hs14:21230288-21230288;hs14:21230253-21230253,hs14:22308469-22308469;hs14:23065372-23065372,hs14:36139860-36139860;hs14:29255148-29255148,hs14:49317840-49317840;hs14:29297657-29297657,hs14:48427020-48427020;hs14:29299826-29299826,hs14:48418411-48418411;hs14:29299914-29299914,hs14:29300177-29300177;hs14:31207400-31207400,hs14:34780066-34780066;hs14:31792425-31792425,hs14:77571384-77571384;hs14:31924403-31924403,hs14:32887898-32887898;hs14:32031755-32031755,hs14:53401721-53401721;hs14:32081588-32081588,hs14:78337991-78337991;hs14:32234403-32234403,hs14:78505185-78505185;hs14:32234554-32234554,hs14:37989959-37989959;hs14:32540107-32540107,hs14:78787608-78787608;hs14:36667226-36667226,hs14:53258916-53258916;hs14:37061176-37061176,hs14:46365854-46365854;hs14:39658225-39658225,hs14:45789061-45789061;hs14:40512548-40512548,hs14:39070240-39070240;hs14:44019855-44019855,hs14:50098927-50098927;hs14:46365654-46365654,hs14:87019882-87019882;hs14:48426422-48426422,hs14:87018854-87018854;hs14:49319884-49319884,hs22:46335540-46335540;hs14:53584736-53584736,hs14:76627967-76627967;hs14:54580071-54580071,hs14:76435482-76435482;hs14:63028197-63028197,hs13:98223904-98223904;hs14:74941307-74941307,hs14:77124207-77124207;hs14:75009783-75009783,hs14:54277712-54277712;hs14:75437756-75437756,hs14:75423484-75423484;hs14:76615806-76615806,hs14:77715188-77715188;hs14:76859227-76859227,hs14:78506179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Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	AKAP6,TTLL5;DDHD1,GPATCH2L;DTD2,AKAP6;HEATR5A,KIAA1737;NUBPL,ADCK1;NUBPL,FERMT2;RP11-176H8.1,AKAP6
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	18	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0154	Illumina HiSeq 2000	chr10:0-135534747:0;chr11:0-62647962:0;chr11:62647963-64550175:-1;chr11:64550176-79066110:0;chr11:68853851-135006516:0;chr11:79066111-68853850:1;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-10268628:0;chr18:10268629-11260768:-1;chr18:11260769-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-15979994:0;chr21:15979995-16139697:-1;chr21:16139698-39214982:0;chr21:39214983-47284002:-1;chr21:47284003-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-191154276:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-159138663:0;chr8:0-109860790:0;chr8:109860791-126920998:-1;chr8:126920999-126934938:0;chr8:126934939-127099671:-1;chr8:127099672-146364022:0;chr9:0-21842702:0;chr9:21842703-22047656:-1;chr9:22047657-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs1:192749594-192749594,hs6:18869815-18869815;hs4:18830687-18830687,hs4:18830763-18830763;hs4:41072750-41072750,hs4:41074456-41074456;hs4:190559871-190559871,hs18:58850148-58850148;hs5:21567041-21567041,hs5:33501106-33501106;hs5:24545507-24545507,hs22:42599855-42599855;hs5:113247176-113247176,hs19:24587974-24587974;hs5:113496069-113496069,hs22:25955548-25955548;hs6:75534095-75534095,hs21:11054315-11054315;hs8:10093410-10093410,hs8:10096202-10096202;hs8:42224568-42224568,hs5:40520773-40520773;hs8:95279094-95279094,hs22:47422451-47422451;hs8:95279591-95279591,hs22:47422075-47422075;hs8:95280341-95280341,hs22:40476239-40476239;hs8:107283500-107283500,hs8:112852147-112852147;hs8:107380443-107380443,hs8:106650799-106650799;hs8:108926849-108926849,hs8:107283570-107283570;hs8:109063583-109063583,hs8:109064538-109064538;hs8:109897015-109897015,hs8:110355271-110355271;hs8:111611664-111611664,hs8:111612482-111612482;hs8:111611664-111611664,hs8:111612482-111612482;hs8:111901730-111901730,hs8:111901818-111901818;hs8:111929739-111929739,hs8:108890548-108890548;hs8:115756851-115756851,hs8:121073502-121073502;hs8:118348670-118348670,hs8:118793307-118793307;hs8:119321539-119321539,hs8:119322723-119322723;hs8:126914696-126914696,hs8:130646395-130646395;hs8:127085791-127085791,hs8:130606405-130606405;hs8:130606060-130606060,hs8:126914532-126914532;hs9:19090081-19090081,hs9:19089825-19089825;hs11:77917875-77917875,hs11:81682531-81682531;hs11:81638858-81638858,hs11:81291300-81291300;hs11:81681062-81681062,hs11:81686570-81686570;hs12:33538777-33538777,hs12:39769603-39769603;hs12:38852808-38852808,hs12:39666732-39666732;hs14:58472424-58472424,hs23:11732036-11732036;hs18:5700895-5700895,hs18:43447835-43447835;hs18:6067752-6067752,hs18:67162206-67162206;hs18:6086302-6086302,hs18:58826878-58826878;hs18:6540031-6540031,hs18:54121994-54121994;hs18:8329567-8329567,hs18:33486002-33486002;hs18:8383800-8383800,hs18:54129354-54129354;hs18:11356902-11356902,hs18:67197176-67197176;hs18:18643142-18643142,hs18:40066128-40066128;hs18:22339305-22339305,hs18:22352839-22352839;hs18:26119477-26119477,hs21:18541134-18541134;hs18:33262431-33262431,hs21:19652837-19652837;hs18:35173973-35173973,hs18:54128946-54128946;hs18:35193393-35193393,hs18:44309448-44309448;hs18:40076857-40076857,hs18:13650258-13650258;hs18:58785908-58785908,hs21:15886805-15886805;hs18:58839106-58839106,hs21:18551324-18551324;hs18:60998180-60998180,hs18:30824859-30824859;hs18:62158707-62158707,hs18:57207252-57207252;hs18:67189037-67189037,hs18:8230489-8230489;hs18:76777013-76777013,hs18:76774346-76774346;hs18:76854054-76854054,hs21:28861248-28861248;hs19:56817730-56817730,hs19:56818508-56818508;hs20:25760369-25760369,hs22:24724822-24724822;hs21:26530221-26530221,hs21:47030004-47030004;hs21:30692690-30692690,hs21:10932393-10932393;hs21:31558887-31558887,hs18:60996277-60996277;hs21:47052950-47052950,hs18:24416200-24416200;hs22:17312856-17312856,hs22:40481905-40481905;hs22:17399026-17399026,hs22:17920312-17920312;hs22:17404618-17404618,hs22:19692098-19692098;hs22:21808336-21808336,hs22:21947710-21947710;hs22:21959775-21959775,hs22:23068182-23068182;hs22:42073403-42073403,hs22:42087567-42087567;hs22:42567363-42567363,hs22:42568119-42568119;hs22:44488406-44488406,hs22:44489267-44489267;hs23:44763368-44763368,hs23:44810110-44810110;hs23:96640614-96640614,hs23:96729973-96729973	GATA6;	Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	DOK6,PTPRM;GALNT1,TMPRSS15;KDSR,CCDC178;L3MBTL4,DOK6
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	2	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0214	Illumina HiSeq 2000	chr10:0-135534747:0;chr11:0-119409357:0;chr11:119409358-121844570:-1;chr11:121844571-135006516:0;chr12:0-127125217:0;chr12:127125218-132439257:-1;chr12:132439258-133851895:0;chr13:0-68241965:0;chr13:68241966-68442104:-1;chr13:68442105-115169878:0;chr14:0-96764158:0;chr14:96764159-99909140:-1;chr14:99909141-107349540:0;chr15:0-53253126:0;chr15:53253127-53501579:-1;chr15:53501580-102531392:0;chr16:0-90354753:0;chr17:0-36478131:0;chr17:36478132-36589895:-1;chr17:36589896-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-208107973:0;chr1:208107974-211175919:-1;chr1:208152650-239097446:-1;chr1:222282392-223680506:-1;chr1:239097447-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-48506967:0;chr22:48506968-49490605:-1;chr22:49490606-51304566:0;chr2:0-1697686:0;chr2:10294062-31552803:-1;chr2:12839903-62521000:0;chr2:14063960-12830974:1;chr2:1697687-62432705:-1;chr2:187572610-214630222:-1;chr2:212020336-230672819:-1;chr2:21435895-38882340:-1;chr2:215089492-215379706:-1;chr2:228249417-187541922:1;chr2:230672820-243199373:0;chr2:31332429-50570836:-1;chr2:31467783-14539980:1;chr2:32256664-32006062:1;chr2:32257480-31925814:1;chr2:32257891-31280645:1;chr2:50379350-50787189:-1;chr2:50379468-187572609:0;chr2:50773133-31325607:1;chr2:50784676-31330005:1;chr2:5841029-5962887:-1;chr2:62432706-62515749:0;chr2:62515750-12839902:1;chr2:62521001-50379467:1;chr3:0-198022430:0;chr4:0-29301965:0;chr4:29301966-29439843:-1;chr4:29439844-191154276:0;chr5:0-98391003:0;chr5:126975307-147852753:-1;chr5:147852754-149690416:0;chr5:149690417-150021960:-1;chr5:150021961-178191019:0;chr5:178191020-178563198:-1;chr5:178563199-180915260:0;chr5:98391004-98622669:-1;chr5:98622670-126975306:0;chr6:0-30780582:0;chr6:30780583-42078753:-1;chr6:42078754-63030194:0;chr6:63030195-63082410:-1;chr6:63082411-91372726:0;chr6:91372727-92099239:-1;chr6:92099240-171115067:0;chr7:0-159138663:0;chr8:0-146364022:0;chr9:0-141213431:0;chrX:0-146317987:0;chrX:146317988-146407684:-1;chrX:146407685-155270560:0;chrY:0-59373566:0	hs1:5717255-5717255,hs1:5784943-5784943;hs1:18433773-18433773,hs17:20748484-20748484;hs1:33858332-33858332,hs4:134852961-134852961;hs1:33858992-33858992,hs1:33859200-33859200;hs1:95598150-95598150,hs1:95922554-95922554;hs1:194764181-194764181,hs3:82867204-82867204;hs1:195403345-195403345,hs3:82854527-82854527;hs1:198481499-198481499,hs1:235656702-235656702;hs1:207995417-207995417,hs1:197009922-197009922;hs1:208108313-208108313,hs1:210988829-210988829;hs1:208158003-208158003,hs1:210991302-210991302;hs2:1473521-1473521,hs2:32257511-32257511;hs2:1677908-1677908,hs2:1718126-1718126;hs2:1678180-1678180,hs2:1923223-1923223;hs2:1687429-1687429,hs2:19671991-19671991;hs2:1690645-1690645,hs2:2355010-2355010;hs2:2220363-2220363,hs2:62447579-62447579;hs2:2220866-2220866,hs2:10416764-10416764;hs2:10275859-10275859,hs2:12897822-12897822;hs2:10404593-10404593,hs2:31291697-31291697;hs2:10404675-10404675,hs2:32589121-32589121;hs2:10423966-10423966,hs2:50385877-50385877;hs2:10431389-10431389,hs2:10580090-10580090;hs2:10555355-10555355,hs2:50509573-50509573;hs2:10557950-10557950,hs2:32277366-32277366;hs2:10558314-10558314,hs2:50382799-50382799;hs2:10558846-10558846,hs2:31810915-31810915;hs2:10575182-10575182,hs2:32274963-32274963;hs2:12830853-12830853,hs2:31450925-31450925;hs2:12839031-12839031,hs2:62095558-62095558;hs2:12843959-12843959,hs2:14277300-14277300;hs2:12875236-12875236,hs2:13673400-13673400;hs2:12880638-12880638,hs2:31941785-31941785;hs2:12927979-12927979,hs2:14540410-14540410;hs2:13043730-13043730,hs2:13678298-13678298;hs2:13049970-13049970,hs2:32277948-32277948;hs2:13054125-13054125,hs2:50381612-50381612;hs2:13054174-13054174,hs2:32105652-32105652;hs2:13059394-13059394,hs2:32003987-32003987;hs2:13064377-13064377,hs2:50719869-50719869;hs2:14273262-14273262,hs2:31997500-31997500;hs2:14273616-14273616,hs2:50879654-50879654;hs2:14275793-14275793,hs2:50815622-50815622;hs2:15314088-15314088,hs2:31520989-31520989;hs2:20753800-20753800,hs2:26136663-26136663;hs2:20760115-20760115,hs2:22217476-22217476;hs2:22226425-22226425,hs2:26130857-26130857;hs2:22227860-22227860,hs2:26140242-26140242;hs2:31279431-31279431,hs2:11991066-11991066;hs2:31281412-31281412,hs2:50350172-50350172;hs2:31291618-31291618,hs2:10424306-10424306;hs2:31325499-31325499,hs2:32576943-32576943;hs2:31329878-31329878,hs2:13678581-13678581;hs2:31455284-31455284,hs2:50773194-50773194;hs2:31520980-31520980,hs2:14545245-14545245;hs2:31521358-31521358,hs2:50884063-50884063;hs2:31552821-31552821,hs2:32576237-32576237;hs2:31553352-31553352,hs2:31289933-31289933;hs2:31806441-31806441,hs2:62474053-62474053;hs2:31809295-31809295,hs2:31956680-31956680;hs2:31810503-31810503,hs2:62519596-62519596;hs2:31934861-31934861,hs2:62218751-62218751;hs2:31996866-31996866,hs2:50350233-50350233;hs2:32082790-32082790,hs2:32288111-32288111;hs2:32106343-32106343,hs2:12928028-12928028;hs2:32256928-32256928,hs2:61997633-61997633;hs2:32287985-32287985,hs2:50510411-50510411;hs2:32294407-32294407,hs2:128897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263,hs20:34954960-34954960;hs22:48428556-48428556,hs22:48428721-48428721;hs23:31455136-31455136,hs23:32385887-32385887;hs23:68764724-68764724,hs2:124651616-124651616;hs23:68766113-68766113,hs23:68866391-68866391;hs23:77580270-77580270,hs23:77800638-77800638;hs23:78199893-78199893,hs23:78200448-78200448;hs23:98103899-98103899,hs23:144304403-144304403;hs23:102744799-102744799,hs23:144291914-144291914;hs23:102825032-102825032,hs23:122165455-122165455;hs23:122143065-122143065,hs23:153199462-153199462;hs23:144247547-144247547,hs23:153723917-153723917;hs23:144247714-144247714,hs23:154466372-154466372;hs23:144260306-144260306,hs23:144242091-144242091;hs23:148148091-148148091,hs23:148147703-148147703;hs23:153212911-153212911,hs23:153709970-153709970	CIR1;HOXD10;HOXD11;HOXD12;HOXD13;HOXD9;SCRN3;	Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	C2orf88,SPAG16;CCT4,NRXN1;DPY30,GALNT14;FAM171B,SPAG16;GALNT14,NRXN1;HPCAL1,NRXN1;ITGAV,TM4SF20;MREG,HIBCH;MYT1L,B3GNT2;NRXN1,GALNT14;SPAG16,VWC2L;SPAST,NRXN1;TPO,DPY30
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	15	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0242	Illumina HiSeq 2000	chr10:0-83677439:0;chr10:83677440-83993433:-1;chr10:83993434-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-24015124:0;chr15:24015125-24019302:-1;chr15:24019303-25234380:0;chr15:25234381-84031593:-1;chr15:25438273-94740245:-1;chr15:28215971-28219152:-1;chr15:94740246-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-105893411:0;chr1:105893412-105893532:-1;chr1:105893533-249250621:0;chr20:0-63025520:0;chr21:0-11121763:0;chr21:11121764-11130259:-1;chr21:11130260-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-42831559:0;chr3:103697747-198022430:0;chr3:103720395-103697746:1;chr3:42831560-66481263:-1;chr3:60425664-60427126:-1;chr3:66481264-103720394:0;chr4:0-137134729:0;chr4:137134730-137138118:-1;chr4:137138119-191154276:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-64245079:0;chr7:107512123-76040784:1;chr7:107676297-159138663:0;chr7:64245080-69414325:-1;chr7:69414326-76038334:0;chr7:76038335-107676296:-1;chr7:76041976-68169942:1;chr7:80850077-81213827:-1;chr8:0-81130493:0;chr8:81130494-81131443:-1;chr8:81131444-146364022:0;chr9:0-7210195:0;chr9:7210196-7210633:-1;chr9:7210634-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs1:117384844-117384844,hs1:117384777-117384777;hs1:120603720-120603720,hs1:120603591-120603591;hs1:149858214-149858214,hs1:149818151-149818151;hs1:218158248-218158248,hs1:218122840-218122840;hs1:246056323-246056323,hs1:246012028-246012028;hs2:11902837-11902837,hs2:11855181-11855181;hs2:60807404-60807404,hs2:60811687-60811687;hs2:60811536-60811536,hs2:60839859-60839859;hs2:101854561-101854561,hs2:101811284-101811284;hs2:174999623-174999623,hs2:174996895-174996895;hs2:181881108-181881108,hs2:181857808-181857808;hs2:193759771-193759771,hs2:193652545-193652545;hs2:195947791-195947791,hs2:195915537-195915537;hs2:204683460-204683460,hs2:204685171-204685171;hs2:208614784-208614784,hs2:208626111-208626111;hs2:208688103-208688103,hs2:208607411-208607411;hs2:234580982-234580982,hs2:234444869-234444869;hs3:47714610-47714610,hs3:47668365-47668365;hs3:81764449-81764449,hs3:81711619-81711619;hs3:88684295-88684295,hs3:88701566-88701566;hs3:88701106-88701106,hs3:88704281-88704281;hs3:106682233-106682233,hs3:106655286-106655286;hs3:110126528-110126528,hs3:110131405-110131405;hs3:110130732-110130732,hs3:110139586-110139586;hs3:116491223-116491223,hs3:116457131-116457131;hs3:116550903-116550903,hs3:116809391-116809391;hs3:170231654-170231654,hs3:170231503-170231503;hs3:174513956-174513956,hs3:174507396-174507396;hs3:175486846-175486846,hs3:175482720-175482720;hs4:18799-18799,hs4:191034022-191034022;hs4:24154925-24154925,hs4:24130380-24130380;hs4:133256150-133256150,hs4:133251378-133251378;hs4:191042352-191042352,hs15:40493080-40493080;hs5:11233276-11233276,hs5:11172452-11172452;hs5:136056618-136056618,hs5:136026092-136026092;hs5:179681482-179681482,hs5:179611720-179611720;hs6:8320580-8320580,hs6:44423199-44423199;hs6:10356405-10356405,hs6:10346713-10346713;hs6:20684219-20684219,hs6:44256981-44256981;hs6:40145563-40145563,hs6:40146918-40146918;hs6:50075469-50075469,hs6:50053681-50053681;hs6:169008548-169008548,hs6:169008460-169008460;hs7:8190915-8190915,hs7:8190862-8190862;hs7:28050835-28050835,hs7:28052410-28052410;hs7:28054629-28054629,hs7:28054869-28054869;hs7:28089326-28089326,hs7:28042996-28042996;hs7:68169139-68169139,hs23:64126024-64126024;hs7:68173671-68173671,hs7:76977289-76977289;hs7:70907446-70907446,hs7:76978056-76978056;hs7:71065850-71065850,hs23:8715825-8715825;hs7:71080181-71080181,hs7:107553891-107553891;hs7:76976273-76976273,hs23:57007690-57007690;hs7:80877376-80877376,hs7:80961799-80961799;hs7:80961995-80961995,hs7:81214376-81214376;hs7:106860301-106860301,hs7:107512583-107512583;hs7:107202170-107202170,hs23:56844976-56844976;hs7:108539773-108539773,hs23:64568051-64568051;hs7:109775375-109775375,hs23:9861435-9861435;hs7:110252583-110252583,hs23:9859576-9859576;hs7:125433572-125433572,hs7:125433888-125433888;hs7:125438029-125438029,hs7:125371388-125371388;hs7:133832518-133832518,hs7:133866002-133866002;hs7:151084996-151084996,hs7:151038374-151038374;hs8:3615089-3615089,hs8:3617067-3617067;hs8:3616934-3616934,hs8:3629563-3629563;hs8:3618478-3618478,hs8:3619453-3619453;hs8:3618693-3618693,hs8:3620311-3620311;hs8:3628698-3628698,hs8:3634307-3634307;hs8:49115924-49115924,hs8:49058935-49058935;hs8:61458505-61458505,hs8:61487845-61487845;hs8:61483122-61483122,hs8:61490494-61490494;hs8:81153027-81153027,hs6:21291589-21291589;hs8:101425725-101425725,hs8:101436386-101436386;hs8:101429035-101429035,hs8:101436069-101436069;hs8:101468965-101468965,hs8:101429357-101429357;hs8:101719225-101719225,hs8:101721361-101721361;hs9:21964433-21964433,hs9:21969775-21969775;hs9:21964438-21964438,hs9:22450624-22450624;hs9:70988414-70988414,hs9:70959068-70959068;hs9:88565290-88565290,hs9:88544343-88544343;hs9:88574650-88574650,hs9:88565808-88565808;hs10:68939011-68939011,hs10:68876425-68876425;hs10:127190418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Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	BTBD1,MEF2A;OTUD7A,SLC28A1
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	14	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0285	Illumina HiSeq 2000	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-22748346:0;chr14:22748347-70039551:-1;chr14:28806200-33253161:-1;chr14:46359233-70177736:-1;chr14:61969520-88787111:-1;chr14:76557977-79122197:-1;chr14:88787112-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-58346598:0;chr2:58346599-58391370:-1;chr2:58391371-243199373:0;chr3:0-60320947:0;chr3:60320948-60590043:-1;chr3:60464067-60587666:-1;chr3:60590044-198022430:0;chr4:0-118436189:0;chr4:118436190-118877701:-1;chr4:118877702-191154276:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-159138663:0;chr8:0-146364022:0;chr9:0-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs1:15028823-15028823,hs11:75631514-75631514;hs1:115389342-115389342,hs1:115389430-115389430;hs1:142674675-142674675,hs4:49220939-49220939;hs2:130822609-130822609,hs2:130823277-130823277;hs2:240217012-240217012,hs17:36169343-36169343;hs3:60665998-60665998,hs3:60668750-60668750;hs3:73630866-73630866,hs3:73630782-73630782;hs6:25361937-25361937,hs6:25462390-25462390;hs6:163814221-163814221,hs8:75184915-75184915;hs7:16963033-16963033,hs7:16848770-16848770;hs7:76144766-76144766,hs7:76648272-76648272;hs7:100875539-100875539,hs12:7032418-7032418;hs8:119222600-119222600,hs12:3072473-3072473;hs8:131734707-131734707,hs13:113037519-113037519;hs8:139754789-139754789,hs8:139754514-139754514;hs10:47621515-47621515,hs10:47683110-47683110;hs11:130835147-130835147,hsX:11732700-11732700;hs11:130835585-130835585,hsX:11731377-11731377;hs12:503368-503368,hs12:506384-506384;hs12:2136299-2136299,hs12:2137198-2137198;hs12:2136302-2136302,hs12:2137072-2137072;hs12:4914054-4914054,hs12:4916494-4916494;hs12:5056660-5056660,hs12:5058136-5058136;hs12:7027858-7027858,hs12:7032386-7032386;hs12:14863361-14863361,hs12:73102548-73102548;hs13:49533344-49533344,hs13:49536625-49536625;hs13:90904631-90904631,hs13:90905841-90905841;hs14:20567119-20567119,hs14:70765261-70765261;hs14:20570529-20570529,hs14:104201816-104201816;hs14:25911556-25911556,hs14:25939492-25939492;hs14:25939239-25939239,hs14:25952440-25952440;hs14:28946711-28946711,hs14:89795007-89795007;hs14:28991980-28991980,hs14:60785597-60785597;hs14:37754429-37754429,hs14:70765870-70765870;hs14:47474391-47474391,hs14:93673586-93673586;hs14:50832570-50832570,hs14:79121478-79121478;hs14:53308020-53308020,hs14:47475441-47475441;hs14:55933286-55933286,hs14:75180469-75180469;hs14:59459822-59459822,hs14:77493487-77493487;hs14:60729531-60729531,hs14:83807231-83807231;hs14:70177409-70177409,hs14:90423041-90423041;hs14:73101069-73101069,hs14:97720809-97720809;hs14:75180523-75180523,hs14:75181867-75181867;hs14:75690551-75690551,hs14:75691743-75691743;hs14:76113998-76113998,hs16:31205301-31205301;hs14:76558319-76558319,hs14:91152317-91152317;hs14:77491801-77491801,hs14:25304825-25304825;hs14:79541771-79541771,hs14:79546183-79546183;hs14:79566785-79566785,hs14:79568348-79568348;hs14:79566820-79566820,hs14:79568791-79568791;hs14:79569115-79569115,hs14:87262838-87262838;hs14:83897092-83897092,hs14:96836537-96836537;hs14:91148147-91148147,hs14:28806596-28806596;hs14:91148148-91148148,hs14:28806715-28806715;hs14:96083512-96083512,hs14:96083457-96083457;hs14:96258975-96258975,hs14:28947810-28947810;hs14:97718173-97718173,hs14:45813125-45813125;hs14:99381415-99381415,hs14:61367574-61367574;hs15:24853619-24853619,hs15:24865097-24865097;hs15:72389131-72389131,hs22:41726727-41726727;hs15:72396048-72396048,hs22:30936193-30936193;hs15:93389841-93389841,hs15:93340422-93340422;hs16:24353297-24353297,hs16:24354566-24354566;hs16:33952705-33952705,hs16:33953695-33953695;hs16:78910362-78910362,hs16:78917807-78917807;hs17:3802553-3802553,hs1:242227150-242227150;hs17:27224031-27224031,hs17:43351838-43351838;hs17:43349269-43349269,hs17:46700561-46700561;hs19:30574825-30574825,hs11:74975891-74975891;hs20:14547529-14547529,hs20:14549049-14549049;hs20:35020897-35020897,hs20:35020993-35020993;hs22:37355133-37355133,hs3:140910140-140910140;hs22:43549345-43549345,hs22:43549653-43549653;hs22:47211171-47211171,hs22:47211234-47211234		Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	CDKL1,NRXN3;IRF2BPL,STXBP6;KIAA0247,TDP1;MDGA2,RP11-371E8.4;MDGA2,UBR7
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	1	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0300	Illumina HiSeq 2000	chr10:0-24861537:0;chr10:24861538-32060125:-1;chr10:31962055-36634117:-1;chr10:36634118-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-23519126:0;chr13:23519127-27784262:-1;chr13:27784263-35147450:0;chr13:35147451-46013185:-1;chr13:35148053-115169878:0;chr13:35555829-33276227:1;chr13:46013186-46067163:0;chr13:46067164-35148052:1;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-16448880:0;chr1:146953171-147013988:-1;chr1:147013989-161043318:0;chr1:161043319-162812008:-1;chr1:162812009-164707019:0;chr1:16448881-16825689:-1;chr1:164707020-223309227:-1;chr1:16825690-43752712:0;chr1:170186635-201274599:-1;chr1:171432473-227249607:-1;chr1:174989280-172994699:1;chr1:180354551-179035249:1;chr1:180634533-234997230:-1;chr1:180634660-249250621:0;chr1:180636656-180634185:1;chr1:180639580-189302029:-1;chr1:229653882-238186131:-1;chr1:238186132-238187955:0;chr1:238187956-180634659:1;chr1:43752713-44196704:-1;chr1:44196705-146953170:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-66252186:0;chr4:66252187-66691404:-1;chr4:66691405-191154276:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-159138663:0;chr8:0-146364022:0;chr9:0-20973150:0;chr9:20973151-32231383:-1;chr9:27384096-28104309:-1;chr9:28386112-32637207:-1;chr9:32637208-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs1:44629872-44629872,hs1:145211144-145211144;hs1:46416637-46416637,hs1:236773470-236773470;hs1:120679380-120679380,hs12:93771899-93771899;hs1:151236474-151236474,hs1:151295285-151295285;hs1:153158652-153158652,hs1:190789771-190789771;hs1:165970033-165970033,hs1:234537355-234537355;hs1:171270695-171270695,hs1:239139224-239139224;hs1:172344237-172344237,hs1:175298952-175298952;hs1:175270747-175270747,hs1:176846371-176846371;hs1:176849248-176849248,hs1:176850451-176850451;hs1:180634124-180634124,hs1:234818350-234818350;hs1:180638958-180638958,hs1:229653506-229653506;hs1:186942630-186942630,hs1:234701944-234701944;hs1:186942893-186942893,hs1:191110727-191110727;hs1:190789608-190789608,hs1:190789758-190789758;hs1:200506286-200506286,hs1:208027250-208027250;hs1:206872695-206872695,hs1:207695080-207695080;hs1:223131595-223131595,hs1:171273271-171273271;hs1:225952133-225952133,hs1:171343521-171343521;hs1:229650108-229650108,hs1:41444007-41444007;hs1:231951031-231951031,hs1:218857562-218857562;hs1:234668836-234668836,hs1:240774472-240774472;hs1:242100869-242100869,hs1:31670934-31670934;hs2:13428696-13428696,hs5:145554181-145554181;hs2:82557847-82557847,hs2:82561311-82561311;hs2:185744146-185744146,hs22:29065829-29065829;hs3:1062579-1062579,hs22:29065775-29065775;hs3:100577155-100577155,hs3:113784681-113784681;hs3:101386193-101386193,hs3:114341392-114341392;hs6:32592405-32592405,hs6:32592536-32592536;hs8:33978043-33978043,hs20:21232971-21232971;hs9:26383599-26383599,hs13:52612486-52612486;hs9:26663709-26663709,hs13:44214501-44214501;hs9:32983897-32983897,hs13:52822182-52822182;hs9:32983998-32983998,hs13:52822178-52822178;hs9:38433266-38433266,hs13:46780225-46780225;hs10:36599399-36599399,hs10:26670112-26670112;hs10:37118755-37118755,hs18:20361720-20361720;hs10:131039151-131039151,hs10:131039421-131039421;hs11:31034639-31034639,hs22:29066114-29066114;hs11:31034640-31034640,hs22:29065466-29065466;hs11:40954283-40954283,hs11:40954390-40954390;hs12:75485425-75485425,hs22:29065435-29065435;hs13:27875958-27875958,hs13:35562754-35562754;hs13:33282781-33282781,hs13:42327476-42327476;hs13:34193537-34193537,hs13:52774139-52774139;hs13:34266700-34266700,hs13:34857815-34857815;hs13:35200485-35200485,hs13:46009631-46009631;hs13:52154612-52154612,hs13:52154409-52154409;hs15:85706213-85706213,hs16:27705000-27705000;hs18:20486904-20486904,hs10:35315815-35315815;hs18:22097962-22097962,hs10:33020151-33020151;hs22:29065904-29065904,hs12:75485444-75485444;hs22:29066066-29066066,hs3:1062570-1062570;hs23:12468357-12468357,hs23:72594491-72594491;hs23:12553888-12553888,hs23:12555125-12555125;hs23:27228798-27228798,hs23:27229315-27229315;hs23:31308303-31308303,hs23:31020428-31020428	ACTA1;ACTBP11;ADAM15;ADAMTSL4;ADAR;AIM2;ANKRD34A;ANKRD35;ANKRD45;ANP32E;ANXA9;APCS;APH1A;APOA1BP;AQP10;ARF1;ARHGEF11;ARHGEF2;ARNT;ASH1L;ATP6V1E1P1;ATP8B2;AXDND1;BANF1P4;BCAN;BGLAP;BNIPL;BOLA1;BTNL10;C1orf110;C1orf138;C1orf145;C1orf148;C1orf189;C1orf35;C1orf43;C1orf51;C1orf54;C1orf56;C1orf61;C1orf85;CA14;CACYBP;CADM3;CAPN2;CCSAP;CCT3;CCT8P1;CD160;CD1A;CD1B;CD1C;CD1D;CD1E;CD5L;CDC42SE1;CENPL;CERS2;CHD1L;CHRNB2;CHTOP;CICP5;CKS1B;CLK2;CNIH4;COX5BP8;CRABP2;CREB3L4;CRP;CRPP1;CRTC2;CTSK;CTSS;CYCSP52;DAP3;DAP3P1;DARC;DARS2;DCST1;DCST2;DEGS1;DENND4B;DPM3;DRD5P2;DUSP5P1;ECM1;EFNA1;EFNA3;EFNA4;EIF4A1P11;ELL2P1;EMBP1;ENAH;ENSA;ETV3;ETV3L;FAM108A2;FAM108A3P;FAM63A;FAM72B;FAM72C;FAM91A2;FAM96AP2;FBXO28;FCER1A;FCGR1A;FCGR1B;FCGR1C;FCRL1;FCRL2;FCRL3;FCRL4;FCRL5;FDPS;FLAD1;FMO5;FTH1P2;GABPB2;GAS5;GBAP1;GJA8;GJC2;GM2AP2;GNRHR2;GON4L;GOT2P2;GPATCH4;GPR52;GPR89A;GPR89B;GPR89C;GUK1;HAPLN2;HAX1;HCN3;HDGF;HFE2;HIST2H2AA3;HIST2H2AA4;HIST2H2AB;HIST2H2AC;HIST2H2BA;HIST2H2BB;HIST2H2BC;HIST2H2BD;HIST2H2BE;HIST2H2BF;HIST2H3A;HIST2H3C;HIST2H3D;HIST2H3DP1;HIST2H3PS2;HIST2H4A;HIST2H4B;HIST3H2A;HIST3H2BA;HIST3H2BB;HIST3H3;HMGB3P6;HMGN1P5;HMGN2P18;HORMAD1;HYDIN2;IBA57;IFI16;IFRG15;IL6R;ILF2;INSRR;INTS3;IQGAP3;ISG20L2;ITGA10;JMJD4;JTB;KCNN3;KIRREL;KLHL20;KRT8P45;KRTCAP2;LAMTOR2;LBR;LENEP;LHX4;LIX1L;LMNA;LRRC71;MCL1;MEF2AP1;MEF2D;MEX3A;MLLT11;MNDA;MRPL24;MRPL55;MRPS14;MRPS21;MRPS21P2;MSTO1;MTMR11;MTX1;MTX1P1;MUC1;NBPF10;NBPF11;NBPF12;NBPF14;NBPF15;NBPF16;NBPF20;NBPF23;NBPF24;NES;NKAIN1P1;NOTCH2NL;NPHS2;NPR1;NTRK1;NUDT17;NUDT4P1;NUF2;NUP210L;NVL;OBSCN;OR10AA1P;OR10J1;OR10J2P;OR10J3;OR10J4;OR10J5;OR10J6P;OR10J7P;OR10J8P;OR10J9P;OR10K1;OR10K2;OR10R1P;OR10R2;OR10R3P;OR10T1P;OR10T2;OR10X1;OR10Z1;OR13Z1P;OR2AQ1P;OR6K1P;OR6K2;OR6K3;OR6K4P;OR6K5P;OR6K6;OR6N1;OR6N2;OR6P1;OR6Y1;OTUD7B;PAQR6;PBXIP1;PDIA3P;PDZK1;PDZK1P1;PDZK1P2;PEAR1;PEX11B;PFN1P12;PFN1P3;PFN1P4;PFN1P5;PFN1P6;PFN1P7;PFN1P8;PHBP11;PIAS3;PKLR;PLEKHO1;PMF1;PMVK;POLR3C;POLR3GL;POU5F1P4;PPIAL4A;PPIAL4C;PPIAL4D;PPIAL4E;PPIAL4F;PRCC;PRDX6;PRKAB2;PRPF3;PRSS38;PRUNE;PTPN2P1;PYGO2;PYHIN1;RAB13;RAB25;RAB4A;RABGAP1L-IT1;RBM8A;RC3H1;RFWD2;RGS4;RGS5;RHBG;RHOU;RIT1;RNA5S1;RNA5S10;RNA5S11;RNA5S12;RNA5S13;RNA5S14;RNA5S15;RNA5S16;RNA5S17;RNA5S2;RNA5S3;RNA5S4;RNA5S5;RNA5S6;RNA5S7;RNA5S8;RNA5S9;RNA5SP18;RNA5SP19;RNA5SP57;RNA5SP58;RNA5SP59;RNA5SP60;RNA5SP62;RNA5SP63;RNA5SP67;RNA5SP68;RNA5SP77;RNF115;RNF187;RPRD2;RPS27;RPS7P2;RRNAD1;RUSC1;RXFP4;S100A1;S100A13;S100A14;S100A16;S100A2;S100A3;S100A4;S100A5;S100A6;SCARNA3;SEC22B;SEMA4A;SERPINC1;SETDB1;SETP10;SF3B4;SH2D2A;SHC1;SHE;SLC25A44;SLC27A3;SLC39A1;SLC50A1;SMG5;SNAP47;SNAPIN;SOAT1;SPHAR;SPRR2A;SPRR2B;SPRR2C;SPRR2E;SPRR2F;SPRR2G;SPTA1;SRGAP2C;SSR2;SV2A;SYT11;TARS2;TDRD10;TDRD5;THBS3;TMEM78;TMEM79;TNFSF18;TNFSF4;TOR1AIP1;TOR3A;TP53BP2;TPM3;TRIM11;TRIM17;TRIM46;TSACC;TTC24;TXNIP;UBAP2L;UBE2D3P3;UBE2Q1;UBQLN4;VDAC1P9;VHLL;VPS45;WDR26;WNT3A;WNT9A;YY1AP1;ZBTB37;ZBTB7B;ZNF678;ZNF847P;	Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	DNM3,TNR;MAPKAPK2,CR1;XPR1,ABCB10
Research	25719666	Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, Johns AL, Miller D, Nones K, Quek K, Quinn MC, Robertson AJ, Fadlullah MZ, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Wani S, Wilson PJ, Markham E, Cloonan N, Anderson MJ, Fink JL, Holmes O, Kazakoff SH, Leonard C, Newell F, Poudel B, Song S, Taylor D, Waddell N, Wood S, Xu Q, Wu J, Pinese M, Cowley MJ, Lee HC, Jones MD, Nagrial AM, Humphris J, Chantrill LA, Chin V, Steinmann AM, Mawson A, Humphrey ES, Colvin EK, Chou A, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Pettitt JA, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Jamieson NB, Graham JS, Niclou SP, Bjerkvig R, Grutzmann R, Aust D, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Falconi M, Zamboni G, Tortora G, Tempero MA; Australian Pancreatic Cancer Genome Initiative, Gill AJ, Eshleman JR, Pilarsky C, Scarpa A, Musgrove EA, Pearson JV, Biankin AV, Grimmond SM	Whole genomes redefine the mutational landscape of pancreatic cancer	Nature	2015 Feb 	18	Pancreatic cancer	Next Generation Sequencing	Homo sapiens	ICGC_0326	Illumina HiSeq 2000	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-128127609:0;chr12:117790616-133851895:0;chr12:128127610-117790615:1;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-79134247:0;chr17:79134248-79214069:-1;chr17:79214070-81195210:0;chr18:0-20697044:0;chr18:20681228-78077248:0;chr18:20697045-21046735:-1;chr18:20719999-22239764:-1;chr18:20732881-21406056:-1;chr18:20887353-25658851:-1;chr18:21414908-30397351:-1;chr18:22243538-30370126:-1;chr18:25632536-33728583:-1;chr18:25653477-35230964:-1;chr18:28401869-38193019:-1;chr18:33735244-20638703:1;chr18:33740209-20733068:1;chr18:38193020-75018808:0;chr18:75018809-20681227:1;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-191154276:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-159138663:0;chr8:0-146364022:0;chr9:0-14072345:0;chr9:14072346-22636514:-1;chr9:20510368-22994820:-1;chr9:22994821-27608641:0;chr9:27608642-34592116:-1;chr9:28008731-28173749:-1;chr9:34592117-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs2:54847169-54847169,hs19:7590836-7590836;hs3:129885829-129885829,hs4:9081729-9081729;hs3:174937457-174937457,hs3:175415198-175415198;hs4:53810-53810,hs18:21427413-21427413;hs4:10631567-10631567,hs11:7236366-7236366;hs4:69555074-69555074,hs17:79050328-79050328;hs4:113035328-113035328,hs4:113035254-113035254;hs4:134782520-134782520,hs4:134782375-134782375;hs5:17900859-17900859,hs11:101256794-101256794;hs5:46164109-46164109,hs5:46164440-46164440;hs5:114990579-114990579,hs5:114990653-114990653;hs6:29332294-29332294,hs6:29332596-29332596;hs7:69907547-69907547,hs7:69964700-69964700;hs7:90260231-90260231,hs13:97252597-97252597;hs9:69006947-69006947,hs9:69007000-69007000;hs9:101897142-101897142,hs9:101898952-101898952;hs11:101903472-101903472,hs5:164468879-164468879;hs12:68339430-68339430,hs12:68341279-68341279;hs12:68340568-68340568,hs12:68339929-68339929;hs12:68343433-68343433,hs12:68343786-68343786;hs12:69758688-69758688,hs12:69759079-69759079;hs12:69758688-69758688,hs12:69759079-69759079;hs12:73647739-73647739,hs12:117789872-117789872;hs12:73745584-73745584,hs12:117799233-117799233;hs12:73746388-73746388,hs12:111332021-111332021;hs12:73921918-73921918,hs12:90846317-90846317;hs12:76686883-76686883,hs12:126699944-126699944;hs12:111332528-111332528,hs12:117809273-117809273;hs12:111333499-111333499,hs12:127774324-127774324;hs12:112964664-112964664,hs15:87156445-87156445;hs12:114200447-114200447,hs12:114201706-114201706;hs12:114987615-114987615,hs12:114988503-114988503;hs12:117755004-117755004,hs12:117755581-117755581;hs12:117790000-117790000,hs12:128128138-128128138;hs12:117790477-117790477,hs12:90845657-90845657;hs12:117790510-117790510,hs12:117790961-117790961;hs12:126553969-126553969,hs12:128290870-128290870;hs12:126780558-126780558,hs15:87005783-87005783;hs17:30313708-30313708,hs17:30298564-30298564;hs17:79047868-79047868,hs17:79213515-79213515;hs17:79131869-79131869,hs17:79131919-79131919;hs17:79196200-79196200,hs17:79202843-79202843;hs17:79197281-79197281,hs4:69554919-69554919;hs17:79205201-79205201,hs17:79240391-79240391;hs17:79240113-79240113,hs17:79242305-79242305;hs17:79241381-79241381,hs17:79211948-79211948;hs18:14184199-14184199,hs18:14184304-14184304;hs18:20675454-20675454,hs4:52076-52076;hs18:20728913-20728913,hs20:2726372-2726372;hs18:20737560-20737560,hs18:21051200-21051200;hs18:20766669-20766669,hs18:30390118-30390118;hs18:20837847-20837847,hs18:38194838-38194838;hs18:20839309-20839309,hs18:29412406-29412406;hs18:20851132-20851132,hs18:20861023-20861023;hs18:20855382-20855382,hs18:33721335-33721335;hs18:20860679-20860679,hs18:33739194-33739194;hs18:20874050-20874050,hs18:37605772-37605772;hs18:21051072-21051072,hs20:2740178-2740178;hs18:21062083-21062083,hs18:35246182-35246182;hs18:21419721-21419721,hs18:29412626-29412626;hs18:21420215-21420215,hs20:2727045-2727045;hs18:22242856-22242856,hs18:29413131-29413131;hs18:22244047-22244047,hs18:75019000-75019000;hs18:22248527-22248527,hs20:2734612-2734612;hs18:22278409-22278409,hs20:15310884-15310884;hs18:24945149-24945149,hs18:20851798-20851798;hs18:25644475-25644475,hs18:29406344-29406344;hs18:29351939-29351939,hs18:30402921-30402921;hs18:29394121-29394121,hs18:35194427-35194427;hs18:29413322-29413322,hs18:74979776-74979776;hs18:29441240-29441240,hs18:20710291-20710291;hs18:30396881-30396881,hs18:20839771-20839771;hs18:33719460-33719460,hs18:75015039-75015039;hs18:33741177-33741177,hs18:33741370-33741370;hs18:38211746-38211746,hs18:75018543-75018543;hs18:38216053-38216053,hs18:29335634-29335634;hs18:74996219-74996219,hs18:22243121-22243121;hs18:75018454-75018454,hs18:33721579-33721579;hs19:6807280-6807280,hs19:6808621-6808621;hs19:7130220-7130220,hs19:7131734-7131734;hs19:58720136-58720136,hs19:58721041-58721041;hs19:58721058-58721058,hs19:58721270-58721270;hs20:20482581-20482581,hs20:23059829-23059829;hs20:23053857-23053857,hs20:23099475-23099475;hs20:23087477-23087477,hs20:23090028-23090028;hs20:29593601-29593601,hs20:29599334-29599334;hs21:16418269-16418269,hs21:17406126-17406126;hs21:16418269-16418269,hs21:17406126-17406126;hs21:27975131-27975131,hs21:26978205-26978205;hs21:41460081-41460081,hs21:41401622-41401622	ARIH2P1;CELF4;FHOD3;TPGS2;	Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia	Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. 	GRCh37/hg19				Yes	CABLES1,LAMA3;CABLES1,TRAPPC8;ELP2,CABLES1;LAMA3,TRAPPC8;TMEM241,CDH2;TMEM241,ELP2;TRAPPC8,GALR1