StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	22926521	Schepeler T, Lamy P, Hvidberg V, Laurberg JR, Fristrup N, Reinert T, Bartkova J, Tropia L, Bartek J, Halazonetis TD, Pan CC, Borre M, Dyrskjot L, Orntoft TF	A high resolution genomic portrait of bladder cancer: correlation between genomic aberrations and the DNA damage response	Oncogene	2013 Aug 	8	Bladder cancer	SNP Array	Homo sapiens	B1735	Affymetrix SNP 6.0	chr10:0-62759:0;chr10:135356696-135374737:0;chr10:28819363-135356695:-1;chr10:55106654-82886849:1;chr10:62760-42919144:1;chr10:84041293-84120682:1;chr11:0-188509:0;chr11:134449983-134452384:0;chr11:188510-134449982:-1;chr11:55844245-57208782:1;chr12:0-132349534:0;chr13:0-47869578:0;chr13:47869579-51359596:-1;chr13:51359597-56965032:0;chr13:56965033-64574504:-1;chr13:64574505-114142980:0;chr14:0-18072124:0;chr14:105952894-105989097:0;chr14:105989098-106356482:-1;chr14:106356483-106368585:0;chr14:18072125-105952893:-1;chr14:20981847-22390230:1;chr15:0-18846948:0;chr15:100286565-100338915:0;chr15:18846949-72101389:-1;chr15:62433956-100286564:1;chr15:89058903-100286564:-1;chr16:0-777:0;chr16:29769296-47443493:1;chr16:30536196-69429180:-1;chr16:69429181-69761496:0;chr16:69761497-88815037:-1;chr16:778-29917385:-1;chr16:88815038-88827254:0;chr17:0-526:0;chr17:22359448-78774742:0;chr17:527-22359447:-1;chr18:0-76117153:0;chr19:0-41910:0;chr19:41911-63789667:1;chr19:63789668-63811651:0;chr1:0-247249719:0;chr20:0-9305:0;chr20:62426599-62435964:0;chr20:9306-62426598:1;chr21:0-9965425:0;chr21:42848164-46921386:-1;chr21:46921387-46944323:0;chr21:9965426-46921386:1;chr22:0-14432528:0;chr22:14432529-15566422:-1;chr22:15566423-19174824:0;chr22:19174825-49581322:-1;chr22:49581323-49691432:0;chr2:0-242951149:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-6246866:0;chr5:180722928-180857866:0;chr5:49473152-180722927:-1;chr5:6246867-6629631:-1;chr5:6629632-9415932:0;chr5:9415933-9666220:-1;chr5:9666221-49473151:0;chr6:0-94661:0;chr6:13024644-13042233:-1;chr6:170892932-170899992:0;chr6:32173957-32294274:-1;chr6:32732822-46986613:-1;chr6:36760762-44020003:1;chr6:46986614-56641250:0;chr6:533262-1077236:-1;chr6:56641251-57419168:1;chr6:56900795-60414872:-1;chr6:58249221-61966190:1;chr6:61966190-170892931:-1;chr6:64720033-65084155:1;chr6:94662-36415922:1;chr7:0-52911:0;chr7:158819767-158821424:0;chr7:52912-158819766:1;chr8:0-21254:0;chr8:146268961-146274826:0;chr8:21255-43924583:-1;chr8:37244074-37709713:1;chr8:39600479-39633022:1;chr8:39988202-146268960:1;chr9:0-36430:0;chr9:13340082-16838616:1;chr9:140211217-140273252:0;chr9:26901712-37913961:1;chr9:36431-140211216:-1;chr9:36431-8471745:1;chr9:70136750-70160650:1;chrX:0-154913754:0;chrY:0-57772954:0		LRP1B	Department of Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus N, Denmark	One major challenge in cancer research is to understand the complex interplay between the DNA damage response (DDR), genomic integrity, and tumor development. To address these issues, we analyzed 43 bladder tumor genomes from 22 patients using single nucleotide polymorphism (SNP) arrays, and tissue expression of multiple DDR proteins, including Timeless and its interaction partner Tipin. The SNP profiles confirmed and extended known copy number alterations (CNAs) at high resolution, showed clustering of CNAs at nine common fragile sites, and revealed that most metachronous tumors were clonally related. The occurrence of many novel uniparental disomy regions (UPDs) was of potential functional importance in some tumors because UPDs spanned mutated FGFR3 and PIK3CA alleles, and also homozygous deletion of the CDKN2A tumor suppressor locus. The DDR signaling as evaluated by phospho-epitope-specific antibodies against Ser139-phosphorylated H2A histone family member X (gama-H2AX), ataxia telangiectasia mutated (ATM), and ATM- and Rad3-related (ATR) was commonly activated in tumors with both moderate and high extent of accumulated genomic aberrations, the latter tumors showing a more frequent loss of ATM expression. Strikingly, the tumor genomes exhibiting the most complex alterations were associated with a high Ki67-proliferation index, abundant Timeless but not Tipin expression, aberrant p53 expression, and homozygous CDKN2A deletions. Of clinical relevance, evaluation of a tissue microarray (TMA; n=319) showed that abundant Timeless expression was associated with risk of progression to muscle-invasive disease (P<0.0005; hazard ratio, 2.4; 95% confidence interval, 1.6-3.8) and higher T stage (P<0.05). Univariate analysis confirmed this association (P=0.006) in an independent cohort (n=241) but statistical significance was not reached in a multivariate model. Overall, our results are consistent with DDR activation preceding the accumulation of genomic aberrations. Tumors with extensive genomic rearrangements were associated with inactivation of CDKN2A, excessive proliferation, and robust Timeless expression, the latter also correlating with the risk of disease progression. Moreover, we provide evidence to suggest that UPDs likely contribute to bladder tumorigenesis. 	NCBI 36/hg18				Yes	NA
Research	22926521	Schepeler T, Lamy P, Hvidberg V, Laurberg JR, Fristrup N, Reinert T, Bartkova J, Tropia L, Bartek J, Halazonetis TD, Pan CC, Borre M, Dyrskjot L, Orntoft TF	A high resolution genomic portrait of bladder cancer: correlation between genomic aberrations and the DNA damage response	Oncogene	2013 Aug 	15	Bladder cancer	SNP Array	Homo sapiens	B2120	Affymetrix SNP 6.0	chr10:0-62759:0;chr10:135356696-135374737:0;chr10:28819363-135356695:-1;chr10:42942834-52884342:1;chr10:62760-42919144:1;chr11:0-188509:0;chr11:134449983-134452384:0;chr11:188510-134449982:-1;chr12:0-20703:0;chr12:132288264-132349534:0;chr12:20704-80221556:1;chr12:80221557-89016946:0;chr12:89016947-132288263:1;chr13:0-17924949:0;chr13:103350604-104079457:-1;chr13:104998316-105367736:-1;chr13:114076551-114126500:-1;chr13:114126501-114142980:0;chr13:17924950-114126500:1;chr13:39619501-40139362:-1;chr13:47869579-51359596:-1;chr13:56965033-64574504:-1;chr13:73176342-75200116:-1;chr13:77127934-81311465:-1;chr14:0-18072124:0;chr14:101148001-106356482:1;chr14:106356483-106368585:0;chr14:18072125-105952893:-1;chr14:20981847-22390230:1;chr14:22549488-22646058:1;chr14:32914815-32950451:1;chr14:44643030-44743518:1;chr14:44836032-46201834:1;chr14:55134198-64178550:1;chr14:65958113-67624680:1;chr14:67759880-67992179:1;chr14:70435216-77591627:1;chr15:0-18276341:0;chr15:100286565-100338915:0;chr15:18276342-18839951:-1;chr15:18276342-25501400:1;chr15:18846949-72101389:-1;chr15:26256457-26741881:1;chr15:45744994-51572163:1;chr15:59331351-62058525:1;chr15:62433956-100286564:1;chr15:72391771-78476143:-1;chr15:87323116-87996311:-1;chr15:89058903-100286564:-1;chr16:0-777:0;chr16:10239513-10553903:1;chr16:12926490-16537186:1;chr16:29917386-30536195:0;chr16:30536196-69429180:-1;chr16:69429181-69761496:0;chr16:69761497-88815037:-1;chr16:778-29917385:-1;chr16:88815038-88827254:0;chr16:9717766-9722139:1;chr17:0-21973579:0;chr17:21973580-78643088:1;chr17:27910816-33759421:-1;chr17:41101479-41501468:-1;chr17:45290083-45355051:-1;chr17:74341747-74431623:-1;chr17:76450575-77638327:-1;chr17:78153535-78643088:-1;chr17:78643089-78774742:0;chr18:0-1542:0;chr18:1543-218211:1;chr18:1543-76116029:-1;chr18:67812516-67815816:1;chr18:67943708-68000326:1;chr18:68867536-69174534:1;chr18:69222596-69369586:1;chr18:76116030-76117153:0;chr19:0-41910:0;chr19:41911-28414212:-1;chr19:41911-63789667:1;chr19:63789668-63811651:0;chr1:0-554559:0;chr1:110591317-247191012:1;chr1:247191013-247249719:0;chr1:554560-141577170:-1;chr20:0-9305:0;chr20:62426599-62435964:0;chr20:9306-62426598:1;chr21:0-9965425:0;chr21:42848164-46921386:-1;chr21:46921387-46944323:0;chr21:9965426-20877324:-1;chr21:9965426-46921386:1;chr22:0-15658264:0;chr22:15658265-15734134:-1;chr22:15734135-19174824:0;chr22:19174825-49581322:-1;chr22:31723725-37054519:1;chr22:49581323-49691432:0;chr2:0-2784:0;chr2:242738131-242951149:0;chr2:2785-141043480:1;chr2:2785-242738130:-1;chr3:0-35345:0;chr3:18965512-47731811:1;chr3:35346-18650563:1;chr3:35346-95002438:-1;chr3:95002439-199501827:0;chr4:0-2281:0;chr4:191261906-191273063:0;chr4:2282-191261905:-1;chr5:0-68532:0;chr5:180722928-180857866:0;chr5:49473152-180722927:-1;chr5:68533-49586994:1;chr6:0-94661:0;chr6:170892932-170899992:0;chr6:36415923-36760761:0;chr6:36760762-44020003:1;chr6:44020004-49037968:0;chr6:49037969-49108396:1;chr6:49108397-51068545:0;chr6:51068546-55876400:1;chr6:55876401-56641250:0;chr6:56641251-57419168:1;chr6:57419169-58249220:0;chr6:58249221-61966190:1;chr6:61966190-170892931:-1;chr6:62178982-62299803:1;chr6:64720033-65084155:1;chr6:94662-36415922:1;chr7:0-52911:0;chr7:11158045-11853724:-1;chr7:158819767-158821424:0;chr7:52912-158819766:1;chr7:9047113-10279718:-1;chr8:0-21254:0;chr8:146268961-146274826:0;chr8:21255-43924583:-1;chr8:2129727-2169873:1;chr8:39988202-146268960:1;chr9:0-36430:0;chr9:140211217-140273252:0;chr9:36431-140211216:-1;chrX:0-154913754:0;chrY:0-57772954:0			Department of Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus N, Denmark	One major challenge in cancer research is to understand the complex interplay between the DNA damage response (DDR), genomic integrity, and tumor development. To address these issues, we analyzed 43 bladder tumor genomes from 22 patients using single nucleotide polymorphism (SNP) arrays, and tissue expression of multiple DDR proteins, including Timeless and its interaction partner Tipin. The SNP profiles confirmed and extended known copy number alterations (CNAs) at high resolution, showed clustering of CNAs at nine common fragile sites, and revealed that most metachronous tumors were clonally related. The occurrence of many novel uniparental disomy regions (UPDs) was of potential functional importance in some tumors because UPDs spanned mutated FGFR3 and PIK3CA alleles, and also homozygous deletion of the CDKN2A tumor suppressor locus. The DDR signaling as evaluated by phospho-epitope-specific antibodies against Ser139-phosphorylated H2A histone family member X (gama-H2AX), ataxia telangiectasia mutated (ATM), and ATM- and Rad3-related (ATR) was commonly activated in tumors with both moderate and high extent of accumulated genomic aberrations, the latter tumors showing a more frequent loss of ATM expression. Strikingly, the tumor genomes exhibiting the most complex alterations were associated with a high Ki67-proliferation index, abundant Timeless but not Tipin expression, aberrant p53 expression, and homozygous CDKN2A deletions. Of clinical relevance, evaluation of a tissue microarray (TMA; n=319) showed that abundant Timeless expression was associated with risk of progression to muscle-invasive disease (P<0.0005; hazard ratio, 2.4; 95% confidence interval, 1.6-3.8) and higher T stage (P<0.05). Univariate analysis confirmed this association (P=0.006) in an independent cohort (n=241) but statistical significance was not reached in a multivariate model. Overall, our results are consistent with DDR activation preceding the accumulation of genomic aberrations. Tumors with extensive genomic rearrangements were associated with inactivation of CDKN2A, excessive proliferation, and robust Timeless expression, the latter also correlating with the risk of disease progression. Moreover, we provide evidence to suggest that UPDs likely contribute to bladder tumorigenesis. 	NCBI 36/hg18				Yes	NA