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

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

Research output: Contribution to journalArticle

106 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)4781-4785
Number of pages5
JournalCancer Research
Volume63
Issue number16
StatePublished - Aug 15 2003
Externally publishedYes

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Loss of Heterozygosity
Computational Biology
Prostatic Neoplasms
Lasers
Nucleotides
Alleles
Genome
Informatics
DNA
Oligonucleotide Array Sequence Analysis
Paraffin
Single Nucleotide Polymorphism
Cluster Analysis
Genotype

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

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

In: Cancer Research, Vol. 63, No. 16, 15.08.2003, p. 4781-4785.

Research output: Contribution to journalArticle

Lieberfarb, ME, Lin, M, Lechpammer, M, Li, C, Tanenbaum, DM, Febbo, PG, Wright, RL, Shim, J, Kantoff, PW, Loda, M, Meyerson, M & Sellers, WR 2003, '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 Research, vol. 63, no. 16, pp. 4781-4785.
Lieberfarb, Marshall E. ; Lin, Ming ; Lechpammer, Mirna ; Li, Cheng ; Tanenbaum, David M. ; Febbo, Phillip G. ; Wright, Renée L. ; Shim, Judy ; Kantoff, Philip W. ; Loda, Massimo ; Meyerson, Matthew ; Sellers, William R. / 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. In: Cancer Research. 2003 ; Vol. 63, No. 16. pp. 4781-4785.
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