StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	24469795	Morrison CD, Liu P, Woloszynska-Read A, Zhang J, Luo W, Qin M, Bshara W, Conroy JM, Sabatini L, Vedell P, Xiong D, Liu S, Wang J, Shen H, Li Y, Omilian AR, Hill A, Head K, Guru K, Kunnev D, Leach R, Eng KH, Darlak C, Hoeflich C, Veeranki S, Glenn S, You M	Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer	PNAS	2014 Jan	4,5,6	Bladder cancer	Next Generation Sequencing	Homo sapiens	18195	Illumina HiSeq 2000	chr12:15868221-15869407:-1;chr13:25958271-25982948:-1;chr13:47357937-47895151:-1;chr13:50576609-51283899:-1;chr16:89347877-89355605:-1;chr17:15396178-15984150:-1;chr18:8064603-8079939:-1;chr2:141248335-141377828:-1;chr2:141682019-142033558:-1;chr2:141800301-141865698:-1;chr2:166207909-166746319:-1;chr2:212365974-212497679:-1;chr2:55702844-57945495:-1;chr2:76235801-76236576:-1;chr3:60647686-61150861:-1;chr4:143858104-150512751:-1;chr5:24639248-24829428:-1;chr7:51514678-51523200:-1;chr7:78339452-78352430:-1;chr9:13417895-14381409:-1	hs1:189182665-189182665,hs2:4522643-4522643;hs4:123484083-123484083,hs6:24118632-24118632;hs4:123561315-123561315,hs6:24122385-24122385;hs4:124664946-124664946,hs6:10407849-10407849;hs4:125115818-125115818,hs4:169013589-169013589;hs4:128690025-128690025,hs4:128690444-128690444;hs4:143860688-143860688,hs6:10407009-10407009;hs4:145338318-145338318,hs4:151076217-151076217;hs4:169007852-169007852,hs5:40050668-40050668;hs4:169014029-169014029,hs6:20697120-20697120;hs4:185413107-185413107,hs6:50112900-50112900;hs4:185717832-185717832,hs6:49786067-49786067;hs4:185720119-185720119,hs5:41232937-41232937;hs4:185727981-185727981,hs6:49787649-49787649;hs4:185879694-185879694,hs6:10408205-10408205;hs5:14499897-14499897,hs6:10400566-10400566;hs5:14503114-14503114,hs5:24902285-24902285;hs5:14511701-14511701,hs6:24347839-24347839;hs5:24625080-24625080,hs13:50006548-50006548;hs5:25237830-25237830,hs5:40040222-40040222;hs5:29690933-29690933,hs6:49784660-49784660;hs5:37251584-37251584,hs6:10424400-10424400;hs5:37295108-37295108,hs6:49782746-49782746;hs5:40062440-40062440,hs6:20736167-20736167;hs6:24325453-24325453,hs6:49597606-49597606;hs6:37516484-37516484,hs6:37530727-37530727;hs12:63150384-63150384,hs12:63602159-63602159;hs13:25957850-25957850,hs13:25961756-25961756;hs13:25963023-25963023,hs13:25984817-25984817	CDH10;CAB39L	Center for Personalized Medicine and Departments of Pharmacology and Therapeutics, Cancer Genetics, Biostatistics and Bioinformatics, Pathology, Urology, Molecular and Cellular Biology, and Medicine, Roswell Park Cancer Institute, Buffalo, NY 14263.	Using complete genome analysis, we sequenced five bladder tumors accrued from patients with muscle-invasive transitional cell carcinoma of the urinary bladder (TCC-UB) and identified a spectrum of genomic aberrations. In three tumors, complex genotype changes were noted. All three had tumor protein p53 mutations and a relatively large number of single-nucleotide variants (SNVs; average of 11.2 per megabase), structural variants (SVs; average of 46), or both. This group was best characterized by chromothripsis and the presence of subclonal populations of neoplastic cells or intratumoral mutational heterogeneity. Here, we provide evidence that the process of chromothripsis in TCC-UB is mediated by nonhomologous end-joining using kilobase, rather than megabase, fragments of DNA, which we refer to as stitchers, to repair this process. We postulate that a potential unifying theme among tumors with the more complex genotype group is a defective replication-licensing complex. A second group (two bladdertumors) had no chromothripsis, and a simpler genotype, WT tumor protein p53, had relatively few SNVs (average of 5.9 per megabase) and only a single SV. There was no evidence of a subclonal population of neoplastic cells. In this group, we used a preclinical model of bladder carcinoma cell lines to study a unique SV (translocation and amplification) of the gene glutamate receptor ionotropic N-methyl D-aspertate as a potential new therapeutic target in ladder cancer.	NCBI 36/hg18			ERP004006	Yes	CDH10,CAB39L
Research	24469795	Morrison CD, Liu P, Woloszynska-Read A, Zhang J, Luo W, Qin M, Bshara W, Conroy JM, Sabatini L, Vedell P, Xiong D, Liu S, Wang J, Shen H, Li Y, Omilian AR, Hill A, Head K, Guru K, Kunnev D, Leach R, Eng KH, Darlak C, Hoeflich C, Veeranki S, Glenn S, You M	Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer	PNAS	2014 Jan	11,12,17	Bladder cancer	Next Generation Sequencing	Homo sapiens	18698	Illumina HiSeq 2000	chr11:66504877-68461658:-1;chr12:46214421-47093283:-1;chr17:36915522-37804427:-1;chr1:47231278-87529442:-1;chr9:21868718-24184888:-1	hs1:105326347-105326347,hs1:105326669-105326669;hs3:13593328-13593328,hs3:21559260-21559260;hs3:18242480-18242480,hs3:18256751-18256751;hs4:180787743-180787743,hs4:181469774-181469774;hs7:107728025-107728025,hs7:115159186-115159186;hs8:34012822-34012822,hs17:37894488-37894488;hs11:69603563-69603563,hs11:71258963-71258963;hs11:119315586-119315586,hs12:47939157-47939157;hs12:46210326-46210326,hs12:46211370-46211370;hs12:47797901-47797901,hs12:47801447-47801447;hs13:22319164-22319164,hs13:22331301-22331301;hs17:36656397-36656397,hs17:36658640-36658640;hs17:59424176-59424176,hs17:59623009-59623009;hs18:27135323-27135323,hs18:28064691-28064691;hs18:29094661-29094661,hs18:29095531-29095531		Center for Personalized Medicine and Departments of Pharmacology and Therapeutics, Cancer Genetics, Biostatistics and Bioinformatics, Pathology, Urology, Molecular and Cellular Biology, and Medicine, Roswell Park Cancer Institute, Buffalo, NY 14263.	Using complete genome analysis, we sequenced five bladder tumors accrued from patients with muscle-invasive transitional cell carcinoma of the urinary bladder (TCC-UB) and identified a spectrum of genomic aberrations. In three tumors, complex genotype changes were noted. All three had tumor protein p53 mutations and a relatively large number of single-nucleotide variants (SNVs; average of 11.2 per megabase), structural variants (SVs; average of 46), or both. This group was best characterized by chromothripsis and the presence of subclonal populations of neoplastic cells or intratumoral mutational heterogeneity. Here, we provide evidence that the process of chromothripsis in TCC-UB is mediated by nonhomologous end-joining using kilobase, rather than megabase, fragments of DNA, which we refer to as stitchers, to repair this process. We postulate that a potential unifying theme among tumors with the more complex genotype group is a defective replication-licensing complex. A second group (two bladdertumors) had no chromothripsis, and a simpler genotype, WT tumor protein p53, had relatively few SNVs (average of 5.9 per megabase) and only a single SV. There was no evidence of a subclonal population of neoplastic cells. In this group, we used a preclinical model of bladder carcinoma cell lines to study a unique SV (translocation and amplification) of the gene glutamate receptor ionotropic N-methyl D-aspertate as a potential new therapeutic target in ladder cancer.	NCBI 36/hg18				Yes	NA
Research	24469795	Morrison CD, Liu P, Woloszynska-Read A, Zhang J, Luo W, Qin M, Bshara W, Conroy JM, Sabatini L, Vedell P, Xiong D, Liu S, Wang J, Shen H, Li Y, Omilian AR, Hill A, Head K, Guru K, Kunnev D, Leach R, Eng KH, Darlak C, Hoeflich C, Veeranki S, Glenn S, You M	Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer	PNAS	2014 Jan	2,4,5,6,10,18,19	Bladder cancer	Next Generation Sequencing	Homo sapiens	19685	Illumina HiSeq 2000	chr13:21067952-42227057:-1;chr13:46269197-70851443:-1;chr14:102894735-102918992:-1;chr14:41437002-41437905:-1;chr15:89778081-89851425:-1;chr17:47113498-47114554:-1;chr19:14031700-16386190:-1;chr19:14038991-14211307:-1;chr19:18740629-19009858:-1;chr19:28721949-31837160:-1;chr21:27419049-30352374:-1;chr21:27494111-31693492:-1;chr2:142808431-142817549:-1;chr2:194004736-201221178:-1;chr2:62687819-97678586:-1;chr4:19934716-19936610:-1;chr4:81774226-87306782:-1;chr4:87310129-99601329:-1;chr5:142492704-142543234:-1;chr5:31171782-31261268:-1;chr5:33835925-33841123:-1;chr5:61432448-160401023:-1;chr5:62106393-140375046:-1;chr6:20062895-20063651:-1;chr6:49699773-49701405:-1;chr6:62545122-66578795:-1;chr7:120306456-120308862:-1;chr7:44924241-46068829:-1;chr8:140348207-140367209:-1;chr8:141005164-141024666:-1;chr9:89734221-89750048:-1;chrX:24535818-24536939:-1	hs2:74496729-74496729,hs2:88536586-88536586;hs2:84278098-84278098,hs13:74531816-74531816;hs2:177602102-177602102,hs2:180425416-180425416;hs2:177850934-177850934,hs4:134021859-134021859;hs3:2231340-2231340,hs5:163882786-163882786;hs3:2239599-2239599,hs21:31420630-31420630;hs3:2271739-2271739,hs5:163488040-163488040;hs4:80876697-80876697,hs4:90969695-90969695;hs4:88965722-88965722,hs5:159136178-159136178;hs4:90784690-90784690,hs4:111017791-111017791;hs4:98230738-98230738,hs4:98298792-98298792;hs4:110318503-110318503,hs4:115783941-115783941;hs4:114352224-114352224,hs5:53118673-53118673;hs4:117358105-117358105,hs4:118357230-118357230;hs4:137613428-137613428,hs4:139064982-139064982;hs4:179409744-179409744,hs4:183350902-183350902;hs4:190851149-190851149,hs4:190852682-190852682;hs4:190864028-190864028,hs4:190864840-190864840;hs5:29794592-29794592,hs5:39986499-39986499;hs5:44712327-44712327,hs22:44760032-44760032;hs5:159938168-159938168,hs5:159939342-159939342;hs5:163482561-163482561,hs21:30411608-30411608;hs5:163862906-163862906,hs21:31057408-31057408;hs5:163930283-163930283,hs21:14760263-14760263;hs6:38642057-38642057,hs6:123531219-123531219;hs6:95495247-95495247,hs6:95507186-95507186;hs6:123664417-123664417,hs6:168228563-168228563;hs7:39122539-39122539,hs7:43488983-43488983;hs7:51782883-51782883,hs14:49749698-49749698;hs8:54044492-54044492,hs8:54056801-54056801;hs10:14590169-14590169,hs10:17339901-17339901;hs10:14920218-14920218,hs10:19462426-19462426;hs10:20488666-20488666,hs10:82241782-82241782;hs10:77971215-77971215,hs10:77972984-77972984;hs10:81226556-81226556,hs10:81227461-81227461;hs10:82529858-82529858,hs10:82531949-82531949;hs11:6055332-6055332,hs11:30222215-30222215;hs11:39205130-39205130,hs11:46336487-46336487;hs13:25465821-25465821,hs13:25482780-25482780;hs16:33611973-33611973,hs16:33614235-33614235;hs18:24946647-24946647,hs18:24946982-24946982;hs18:26240178-26240178,hs18:57422314-57422314;hs18:34109579-34109579,hs18:58799580-58799580;hs18:57416350-57416350,hs18:58358748-58358748;hs19:17136916-17136916,hs19:17348961-17348961;hs19:46716153-46716153,hs19:50384324-50384324;hs20:44543514-44543514,hs20:44545696-44545696		Center for Personalized Medicine and Departments of Pharmacology and Therapeutics, Cancer Genetics, Biostatistics and Bioinformatics, Pathology, Urology, Molecular and Cellular Biology, and Medicine, Roswell Park Cancer Institute, Buffalo, NY 14263.	Using complete genome analysis, we sequenced five bladder tumors accrued from patients with muscle-invasive transitional cell carcinoma of the urinary bladder (TCC-UB) and identified a spectrum of genomic aberrations. In three tumors, complex genotype changes were noted. All three had tumor protein p53 mutations and a relatively large number of single-nucleotide variants (SNVs; average of 11.2 per megabase), structural variants (SVs; average of 46), or both. This group was best characterized by chromothripsis and the presence of subclonal populations of neoplastic cells or intratumoral mutational heterogeneity. Here, we provide evidence that the process of chromothripsis in TCC-UB is mediated by nonhomologous end-joining using kilobase, rather than megabase, fragments of DNA, which we refer to as stitchers, to repair this process. We postulate that a potential unifying theme among tumors with the more complex genotype group is a defective replication-licensing complex. A second group (two bladdertumors) had no chromothripsis, and a simpler genotype, WT tumor protein p53, had relatively few SNVs (average of 5.9 per megabase) and only a single SV. There was no evidence of a subclonal population of neoplastic cells. In this group, we used a preclinical model of bladder carcinoma cell lines to study a unique SV (translocation and amplification) of the gene glutamate receptor ionotropic N-methyl D-aspertate as a potential new therapeutic target in ladder cancer.	NCBI 36/hg18				Yes	NA