Scientific Publications

Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays

Publication TypeJournal Article
AuthorsLindblad-Toh, K., Tanenbaum D. M., Daly M. J., Winchester E., Lui W. O., Villapakkam A., Stanton S. E., Larsson C., Hudson T. J., Johnson B. E., Lander E. S., and Meyerson M.
AbstractHuman cancers arise by a combination of discrete mutations and chromosomal alterations. Loss of heterozygosity (LOH) of chromosomal regions bearing mutated tumor suppressor genes is a key event in the evolution of epithelial and mesenchymal tumors. Global patterns of LOH can be understood through allelotyping of tumors with polymorphic genetic markers. Simple sequence length polymorphisms (SSLPs, or microsatellites) are reliable genetic markers for studying LOH, but only a modest number of SSLPs are used in LOH studies because the genotyping procedure is rather tedious. Here, we report the use of a highly parallel approach to genotype large numbers of single-nucleotide polymorphisms (SNPs) for LOH, in which samples are genotyped for nearly 1,500 loci by performing 24 polymerase chain reactions (PCR), pooling the resulting amplification products and hybridizing the mixture to a high-density oligonucleotide array. We characterize the results of LOH analyses on human small-cell lung cancer (SCLC) and control DNA samples by hybridization. We show that the patterns of LOH are consistent with those obtained by analysis with both SSLPs and comparative genomic hybridization (CGH), whereas amplifications rarely are detected by the SNP array. The results validate the use of SNP array hybridization for tumor studies.
Year of Publication2000
JournalNature Biotechnology
Volume18
Issue9
Pages1001 - 5
Date Published (YYYY/MM/DD)2000/09//
ISBN Number1087-0156
KeywordsAlleles, Cancer, Carcinoma, Chromosomes, G, Genotype, Heterozygote, Human, Humans, Loss of Heterozygosity, Lung Neoplasms, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Pair 20, Pair 3, Ploidies, Polymorphism, Small Cell