Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP.

Cancer Res. 2003 Aug 15;63(16):4781-5.. Published: 2003.08.14

Marshall E. Lieberfarb, Ming Lin, Mirna Lechpammer, Cheng Li, David M. Tanenbaum, Phillip G. Febbo, Renee L. Wright, Judy Shim, Philip W. Kantoff, Massimo Loda, Matthew Meyerson and William R. Sellers

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Abstract

Oligonucleotide arrays that detect single nucleotide polymorphisms were used to generate genome-wide loss of heterozygosity (LOH) maps from laser capture microdissected paraffin-embedded samples using as little as 5 ng of DNA. The allele detection rate from such samples was comparable with that obtained with standard amounts of DNA prepared from frozen tissues. A novel informatics platform, dChipSNP, was used to automate the definition of statistically valid regions of LOH, assign LOH genotypes to prostate cancer samples, and organize by hierarchical clustering prostate cancers based on the pattern of LOH. This organizational strategy revealed apparently distinct genetic subsets of prostate cancer.

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Lieberfarb

Supplemental Data

Description Link/Filename
Manuscript Lieberfarb.pdf
Data from Lin et al. 2004 http://biosun1.harvard.edu/complab/dchip/snp
Supplementary Figure 1 Lieberfarb_s1.pdf
Supplementary Table 1 Lieberfarb_s2.pdf
LOH Data LieberfarbSummary LOH data.txt