title: 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.
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.
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.
authors.forename: Marshall E
authors.initials: ME
authors.lastname: Lieberfarb
authors.forename: Ming
authors.initials: M
authors.lastname: Lin
authors.forename: Mirna
authors.initials: M
authors.lastname: Lechpammer
authors.forename: Cheng
authors.initials: C
authors.lastname: Li
authors.forename: David M
authors.initials: DM
authors.lastname: Tanenbaum
authors.forename: Phillip G
authors.initials: PG
authors.lastname: Febbo
authors.forename: Renée L
authors.initials: RL
authors.lastname: Wright
authors.forename: Judy
authors.initials: J
authors.lastname: Shim
authors.forename: Philip W
authors.initials: PW
authors.lastname: Kantoff
authors.forename: Massimo
authors.initials: M
authors.lastname: Loda
authors.forename: Matthew
authors.initials: M
authors.lastname: Meyerson
authors.forename: William R
authors.initials: WR
authors.lastname: Sellers
mesh_terms: 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*
chemical_list: D004273:DNA, Neoplasm