Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the affymetrix 10K SNP mapping array

• Published in: Human genetics Vol. 115; no. 4; pp. 327 - 330
• Main Authors: XIAOFENG ZHOU, MOK, Samuel C, ZUGEN CHEN, YANG LI, WONG, David T. W
• Format: Journal Article
• Language: English
• Published: Heidelberg Springer 01.09.2004; Berlin Springer Nature B.V; New York, NY
• Subjects: Biological and medical sciences; Carcinoma, Squamous Cell - genetics; Cell Line; Chromosome Aberrations; Classical genetics, quantitative genetics, hybrids; Feasibility Studies; Fundamental and applied biological sciences. Psychology; Gene Dosage; Genetic Markers - genetics; Genetics of eukaryotes. Biological and molecular evolution; Human; Humans; Loss of Heterozygosity; Methods, theories and miscellaneous; Models, Genetic; Polymorphism, Single Nucleotide; Genetic mapping; Premalignant lesion; Copy number; Analysis; Loss of heterozygosity; Genetics; Single nucleotide polymorphism
• ISSN: 0340-6717; 1432-1203
• DOI: 10.1007/s00439-004-1163-1

Like most human cancers, oral squamous cell carcinoma (SCC) is characterized by genetic instabilities. In this study, a single platform (Affymetrix 10K SNP mapping array) was used to generate both loss of heterozygosity (LOH) and DNA copy number abnormality (CNA) read-outs for precise and high-resolution genetic alteration profiles. As a proof of principle, we performed this concordant analysis on a panel of deletion and trisomy cell lines with known chromosomal alterations and the precise LOH and CNA regions were detected as expected. Using a previously described oral SCC progression model system, we identified a set of genomic regions that may be associated with the malignancy progression, including chromosome regions 3pter-3p35.3, 3p14.1-3p13, 11p, 11q14.3-11q22.2, and 11q13.5-11q14.1. These data show that it is feasible to utilize high-density SNP arrays to generate concordant LOH and CNA profiles at high resolution.