"Loss-of-Heterozygosity Analysis of Small-Cell Lung Carcinomas Using Single-Nucleotide Polymorphism Arrays"

Kerstin Lindblad-Toh ^{1, 8}, David M. Tanenbaum ^{2, 3, 4, 8}, Mark J. Daly ¹, Ellen Winchester ¹, Weng-Onn
Lui ⁵, Anuradha Villapakkam ¹, Sasha E. Stanton ², Catharina Larsson ⁵, Thomas J. Hudson ^{1, 6}, Bruce E. Johnson ^{2, 3}, Eric S. Lander ^{1, 7}& Matthew Meyerson ^{2, 4}.

¹ Whitehead Institute/MIT Center for Genome Research, Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA.
² Department of Adult Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
³ Department of Medicine, Harvard Medical School, Boston, MA, USA.
⁴ Department of Pathology, Harvard Medical School, Boston, MA, USA.
⁵ Department of Molecular Medicine, CMM, Karolinska Hospital, Stockholm, S-171 76, Sweden.
⁶ Montreal Genome Centre, McGill University Health Centre, Montreal, Quebec, Canada.
⁷ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

⁸ These two authors ( K.L.-T. and D.M.T.) contributed equally to this work.

Correspondence should be addressed to:
E. S. Lander; e-mail: lander@genome.wi.mit.edu
and M. Meyerson; e-mail: matthew_meyerson@dfci.harvard.edu

Abstract:

Human 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 [1]. Global patterns of LOH can be understood through allelotyping of tumors with polymorphic genetic markers [2]. Simple sequence length polymorphisms (SSLPs, or microsatellites) are reliable genetic markers for studying LOH [3], 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 [4]. 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 [5] 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.

Additional References:

1. "Mated Models of Gene Regulation in Eukaryotes".

2. "Oncogenes as Molecular Targets within Active Chromatin".