Genomic Imbalances in 5918 Malignant Epithelial Tumors: an Explorative Meta-analysis of Chromosomal CGH Data

Overview

Journal BMC Cancer

Publisher Biomed Central

Specialty Oncology

Date 2007 Dec 20

PMID 18088415

Citations 76

Authors

Michael Baudis

Affiliations

Soon will be listed here.

Abstract

Background: Chromosomal abnormalities have been associated with most human malignancies, with gains and losses on some genomic regions associated with particular entities.

Methods: Of the 15429 cases collected for the Progenetix molecular-cytogenetic database, 5918 malignant epithelial neoplasias analyzed by chromosomal Comparative Genomic Hybridization (CGH) were selected for further evaluation. For the 22 clinico-pathological entities with more than 50 cases, summary profiles for genomic imbalances were generated from case specific data and analyzed.

Results: With large variation in overall genomic instability, recurring genomic gains and losses were prominent. Most entities showed frequent gains involving 8q2, while gains on 20q, 1q, 3q, 5p, 7q and 17q were frequent in different entities. Loss "hot spots" included 3p, 4q, 13q, 17p and 18q among others. Related average imbalance patterns were found for clinically distinct entities, e.g. hepatocellular carcinomas (ca.) and ductal breast ca., as well as for histologically related entities (squamous cell ca. of different sites).

Conclusion: Although considerable case-by-case variation of genomic profiles can be found by CGH in epithelial malignancies, a limited set of variously combined chromosomal imbalances may be typical for carcinogenesis. Focus on the respective regions should aid in target gene detection and pathway deduction.

Citing Articles

Copy number variation heterogeneity reveals biological inconsistency in hierarchical cancer classifications.

Yang Z, Carrio-Cordo P, Baudis M Mol Cytogenet. 2024; 17(1):26.

PMID: 39506842 PMC: 11542350. DOI: 10.1186/s13039-024-00692-2.

Selection forces underlying aneuploidy patterns in cancer.

Klockner T, Campbell C Mol Cell Oncol. 2024; 11(1):2369388.

PMID: 38919375 PMC: 11197905. DOI: 10.1080/23723556.2024.2369388.

Exploring the prognostic significance of arm-level copy number alterations in triple-negative breast cancer.

Dore S, Ali M, Sorin M, McDowell S, Desharnais L, Breton V Oncogene. 2024; 43(26):2015-2024.

PMID: 38744952 PMC: 11196216. DOI: 10.1038/s41388-024-03051-y.

Advancements in minimal residual disease detection: a practical approach using single-cell droplet PCR for comprehensive monitoring in hematological malignancy.

Uchiyama S, Fukushima K, Katagiri S, Tsuchiya J, Kubo T, Chi S Ther Adv Hematol. 2024; 15:20406207241245510.

PMID: 38628436 PMC: 11020714. DOI: 10.1177/20406207241245510.

Data-driven information extraction and enrichment of molecular profiling data for cancer cell lines.

Smith E, Paloots R, Giagkos D, Baudis M, Stockinger K Bioinform Adv. 2024; 4(1):vbae045.

PMID: 38560553 PMC: 10978572. DOI: 10.1093/bioadv/vbae045.

References

Baudis M . Online database and bioinformatics toolbox to support data mining in cancer cytogenetics. Biotechniques. 2006; 40(3):269-70, 272. DOI: 10.2144/000112102. View

Osterberg L, Akeson M, Levan K, Partheen K, Zetterqvist B, Brannstrom M . Genetic alterations of serous borderline tumors of the ovary compared to stage I serous ovarian carcinomas. Cancer Genet Cytogenet. 2006; 167(2):103-8. DOI: 10.1016/j.cancergencyto.2006.01.009. View

Burnworth B, Popp S, Stark H, Steinkraus V, Brocker E, Hartschuh W . Gain of 11q/cyclin D1 overexpression is an essential early step in skin cancer development and causes abnormal tissue organization and differentiation. Oncogene. 2006; 25(32):4399-412. DOI: 10.1038/sj.onc.1209474. View

Aubele M, Auer G, Braselmann H, Nahrig J, Zitzelsberger H, Quintanilla-Martinez L . Chromosomal imbalances are associated with metastasis-free survival in breast cancer patients. Anal Cell Pathol. 2002; 24(2-3):77-87. PMC: 4618589. DOI: 10.1155/2002/820269. View

Perry A, Nobori T, Ru N, Anderl K, Borell T, Mohapatra G . Detection of p16 gene deletions in gliomas: a comparison of fluorescence in situ hybridization (FISH) versus quantitative PCR. J Neuropathol Exp Neurol. 1997; 56(9):999-1008. DOI: 10.1097/00005072-199709000-00005. View

Speicher M, Schoell B, Du Manoir S, Schrock E, Ried T, Cremer T . Specific loss of chromosomes 1, 2, 6, 10, 13, 17, and 21 in chromophobe renal cell carcinomas revealed by comparative genomic hybridization. Am J Pathol. 1994; 145(2):356-64. PMC: 1887405. View

Ghadimi B, Grade M, Liersch T, Langer C, Siemer A, Fuzesi L . Gain of chromosome 8q23-24 is a predictive marker for lymph node positivity in colorectal cancer. Clin Cancer Res. 2003; 9(5):1808-14. View

Terracciano L, Tornillo L . Cytogenetic alterations in liver cell tumors as detected by comparative genomic hybridization. Pathologica. 2003; 95(2):71-82. View

Lichter P, Cremer T, Borden J, Manuelidis L, Ward D . Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet. 1988; 80(3):224-34. DOI: 10.1007/BF01790090. View

10.

Liu J, Mohammed J, Carter J, Ranka S, Kahveci T, Baudis M . Distance-based clustering of CGH data. Bioinformatics. 2006; 22(16):1971-8. DOI: 10.1093/bioinformatics/btl185. View

11.

Vogelstein B, Kinzler K . The multistep nature of cancer. Trends Genet. 1993; 9(4):138-41. DOI: 10.1016/0168-9525(93)90209-z. View

12.

Gebhart E . Genomic imbalances in human leukemia and lymphoma detected by comparative genomic hybridization (Review). Int J Oncol. 2005; 27(3):593-606. View

13.

Vos C, ter Haar N, Rosenberg C, Peterse J, Cleton-Jansen A, Cornelisse C . Genetic alterations on chromosome 16 and 17 are important features of ductal carcinoma in situ of the breast and are associated with histologic type. Br J Cancer. 1999; 81(8):1410-8. PMC: 2362977. DOI: 10.1038/sj.bjc.6693372. View

14.

Li X, Wang E, Zhao Y, Ren J, Jin P, Yao K . Chromosomal imbalances in nasopharyngeal carcinoma: a meta-analysis of comparative genomic hybridization results. J Transl Med. 2006; 4:4. PMC: 1403800. DOI: 10.1186/1479-5876-4-4. View

15.

Bryndorf T, Kirchhoff M, Larsen J, Andreasson B, Bjerregaard B, Westh H . The most common chromosome aberration detected by high-resolution comparative genomic hybridization in vulvar intraepithelial neoplasia is not seen in vulvar squamous cell carcinoma. Cytogenet Genome Res. 2004; 106(1):43-8. DOI: 10.1159/000078559. View

16.

Ribeiro F, Jeronimo C, Henrique R, Fonseca D, Oliveira J, Lothe R . 8q gain is an independent predictor of poor survival in diagnostic needle biopsies from prostate cancer suspects. Clin Cancer Res. 2006; 12(13):3961-70. DOI: 10.1158/1078-0432.CCR-05-1977. View

17.

Penzel R, Hoegel J, Schmitz W, Blaeker H, Morresi-Hauf A, Aulmann S . Clusters of chromosomal imbalances in thymic epithelial tumours are associated with the WHO classification and the staging system according to Masaoka. Int J Cancer. 2003; 105(4):494-8. DOI: 10.1002/ijc.11101. View

18.

Schwaenen C, Nessling M, Wessendorf S, Salvi T, Wrobel G, Radlwimmer B . Automated array-based genomic profiling in chronic lymphocytic leukemia: development of a clinical tool and discovery of recurrent genomic alterations. Proc Natl Acad Sci U S A. 2004; 101(4):1039-44. PMC: 327147. DOI: 10.1073/pnas.0304717101. View

19.

Rowley J . Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature. 1973; 243(5405):290-3. DOI: 10.1038/243290a0. View

20.

Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T . Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer. 1997; 20(4):399-407. View