Identification of gains and losses of DNA sequences in primary bladder cancer by comparative genomic hybridization

Kallioniemi, Anne; Kallioniemi, Olli-P.; Citro, Gil; Sauter, Guido; DeVries, Sandy; Kerschmann, Russell; Caroll, Peter R.; Waldman, F.

doi:10.1002/gcc.2870120309

Cited by 196 publications

(139 citation statements)

References 14 publications

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“…20,21 DNA copy number changes involving 16p and 19 were excluded from the analysis unless they represented a high-level amplification. 22,23 All results were confirmed using a 99% confidence interval with 1% error probability. Briefly, intraexperimental standard deviations for all positions in the CGH ratio profiles were calculated from the variation of the ratio values of all homologous chromosomes within the experiment.…”

Section: Digital Image Analysismentioning

confidence: 63%

Recurrent DNA copy number changes revealed by comparative genomic hybridization in primary Merkel cell carcinomas

et al. 2004

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Comparative genomic hybridization (CGH) was used to search for gains, high-level amplifications and losses of DNA sequences along all chromosome arms in 19 primary Merkel cell carcinomas (MCC). Extensive genetic aberrations, with a mean value of 5.571.1 changes per tumor were detected in 13 out of the 19 samples analyzed. Our CGH results reveal several new and other previously known chromosomal regions that are involved in the pathogenesis of MCC. The majority of the alterations were gains of whole chromosomes or whole chromosome arms. Compared to losses, the frequency of DNA copy number gains was two-fold. DNA sequence copy number gains were most common in chromosomes 6 (42%), 1 (37%), and 5 (32%). The most frequent minimal common regions of gains were 6pterqter (42%), 1q11q31 (32%), and 5p (32%). No recurrent high-level amplifications were observed. High-level amplifications of small chromosomal regions were found in four samples out of the 19 tumors analyzed (21%). Amplifications affected 1q22q24 (5%), 4p (5%), and 5p (5%). Losses most frequently affected chromosomes 13 (21%) and 4 (16%). Minimal common regions with the most frequent losses were 13q13q31 (21%), 4q (16%), and 16q (11%). No significant statistical correlation between genomic aberrations and clinicopathological factors was revealed, despite the fact that there was an obvious tendency towards it. Primary MCC expressing DNA alterations were predominantly distinguished in large tumors, and risk of metastatic dissemination was three-fold compared to tumors with no DNA alterations.

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Section: Digital Image Analysismentioning

confidence: 63%

Recurrent DNA copy number changes revealed by comparative genomic hybridization in primary Merkel cell carcinomas

et al. 2004

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“…The signi®cant association between gene ampli®cations and advanced tumor stage and high tumor grade was expected. Previous studies by us and others had repeatedly shown that invasively growing cancers (stage pT1 ± 4) are genetically less stable than non-invasive (pTa) tumors and that all types of chromosomal rearrangements are markedly more frequent in pT1-4 than in pTa tumors (Kallioniemi et al, 1995;Richter et al, 1997Richter et al, , 1999Simon et al, 1998Simon et al, , 2000Voorter et al, 1995;Zhao et al, 1999). Interestingly, an association was found between CDK4 ampli®cation and tumor survival in all tumors and also in the subgroup of pT2 ± 4 cancers.…”

Section: Discussionmentioning

confidence: 97%

Amplification pattern of 12q13-q15 genes (MDM2, CDK4, GLI) in urinary bladder cancer

et al. 2002

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The chromosomal region 12q13-q15 is recurrently ampli®ed in bladder cancer. Putative target genes located in this region include MDM2, CDK4, and GLI. To evaluate the involvement of these genes in bladder cancer, we screened a tissue microarray (TMA) containing 2317 samples by¯uorescence in situ hybridization (FISH). Ampli®cation was found for MDM2 in 5.1%, for CDK4 in 1.1%, and for GLI in 0.4% of interpretable tumors. Among tumors having ampli®cation of at least one of these 12q13-q15 genes, 76.6% had ampli®cation of MDM2 alone and 6.4% had ampli®cation of CDK4 alone. Coampli®cations were seen of MDM2 and CDK4 in 10.6%, and of CDK4 and GLI in 6.4%. Neither coampli®cations of all three genes nor isolated GLI ampli®cations were found. These data suggest a prominent role of MDM2 as a 12q13-q15 ampli®cation target in bladder cancer. However, independent CDK4 ampli®cations do also occur suggesting either two nonoverlapping ampli®cation sites or else a minimal overlapping region between MDM2 and CDK4 perhaps containing another yet unknown oncogene. The frequency of ampli®cation increased signi®cantly from stage pTa to pT1-4 (P50.04) and from low to high grade (P50.005). These data are consistent with a high level of genetic instability in invasively growing and highgrade bladder tumors.

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“…This aberration is common among different tumour types and has been detected by CGH for example in diffuse large B-cell lymphoma, breast cancer and bladder cancer Kallioniemi et al, 1995;Ried et al, 1995;Monni et al, 1996). According to the Genome Data Base, chromosome lq carries several proto-oncogenes, which highlights the probability that imbalances at chromosome lq may be critical for oncogene dosage in certain neoplasias.…”

Section: Discussionmentioning

confidence: 98%

Recurrent DNA copy number changes in 1q, 4q, 6q, 9p, 13q, 14q and 22q detected by comparative genomic hybridization in malignant mesothelioma

Björkqvist

Tammilehto²,

Anttila³

et al. 1997

Br J Cancer

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Summary Comparative genomic hybridization (CGH) analyses were performed on 27 human pleural mesothelioma tumour specimens, consisting of 18 frozen tumours and nine paraffin-embedded tumours, to screen for gains and losses of DNA sequences. Copy number changes were detected in 15 of the 27 specimens with a range from one to eight per specimen. On average, more losses than gains of genetic material were observed. The loss of DNA sequences occurred most commonly in the short arm of chromosome 9 (p21-pter), in 60% of the abnormal specimens. Other losses among the abnormal specimens were frequently detected in the long arms of chromosomes 4 (q31 .1-qter, 20%), 6 (q22-q24, 33%), 13 (33%), 14 (q24-qter, 33%) and 22 (q13, 20%). A gain in DNA sequences was found in the long arm of chromosome 1 (cen-qter) in 33% of the abnormal specimens. Our analysis is the first genome-wide screening for gains and losses of DNA sequences using comparative genomic hybridization in malignant pleural mesothelioma tumours. The recurrent DNA sequence changes detected in this study suggest that the corresponding chromosomal areas most probably contain genes important for the initiation and progression of mesothelioma.

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Identification of gains and losses of DNA sequences in primary bladder cancer by comparative genomic hybridization

Cited by 196 publications

References 14 publications

Recurrent DNA copy number changes revealed by comparative genomic hybridization in primary Merkel cell carcinomas

Recurrent DNA copy number changes revealed by comparative genomic hybridization in primary Merkel cell carcinomas

Amplification pattern of 12q13-q15 genes (MDM2, CDK4, GLI) in urinary bladder cancer

Recurrent DNA copy number changes in 1q, 4q, 6q, 9p, 13q, 14q and 22q detected by comparative genomic hybridization in malignant mesothelioma

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