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.
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.
Lieberfarb
Marshall E
ME
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.
Lin
Ming
M
Lechpammer
Mirna
M
Li
Cheng
C
Tanenbaum
David M
DM
Febbo
Phillip G
PG
Wright
Renée L
RL
Shim
Judy
J
Kantoff
Philip W
PW
Loda
Massimo
M
Meyerson
Matthew
M
Sellers
William R
WR
D000483:Alleles; D019295:Computational Biology; D004273:DNA, Neoplasm / Q000032:analysis; D006801:Humans; D019656:Loss of Heterozygosity; D008297:Male; D020641:Polymorphism, Single Nucleotide; D011471:Prostatic Neoplasms / Q000235:genetics*
D004273:DNA, Neoplasm