Genome-wide analysis of genetic alterations in testicular primary seminoma using high resolution single nucleotide polymorphism arrays

Cynthia LeBron, Prodipto Pal, Mariana Brait, Santanu Dasgupta, Rafael Guerrero-Preston, Leendert H J Looijenga, Jeanne Kowalski, George Netto, Mohammad O Hoque

Research output: Contribution to journalArticlepeer-review

24 Citations (Scopus)

Abstract

Testicular germ cell tumors (TGCT) represent the most common malignancy among young males. To our knowledge no comprehensive Copy Number Variation (CNVs) studies of TGCT using high-resolution Single Nucleotide Polymorphism (SNP) array have been performed. By a genome-wide analysis of CNV and loss of heterozygosity (LOH) in 25 primary seminomas, we confirmed several previously reported genomic alterations and discovered eight novel genomic alterations including amplifications and homozygous deletions. Moreover, a comparison of genomic alterations of early and late stage seminoma identified CNVs that correlate with progression, which included deletions in chromosomes 4q, 5p, 9q, 13q and 20p and amplifications in chromosomes 9q and 13q. We compared previously perform Affymetrix expression analysis in a subset of samples and found robust correlation between expression and genomic alterations. Furthermore, high correlations (40-75%) were observed between CNV by SNP analysis and quantitative PCR. Our findings may lead to better understanding of TGTC's pathogenesis.

Original languageEnglish
Pages (from-to)341-9
Number of pages9
JournalGenomics
Volume97
Issue number6
DOIs
Publication statusPublished - Jun 2011
Externally publishedYes

Keywords

  • Adult
  • Chromosomes, Human/genetics
  • DNA Copy Number Variations
  • Gene Amplification
  • Genes, Neoplasm
  • Genome-Wide Association Study
  • Humans
  • Loss of Heterozygosity
  • Male
  • Middle Aged
  • Oligonucleotide Array Sequence Analysis
  • Polymorphism, Single Nucleotide
  • Seminoma/genetics
  • Sequence Analysis, DNA/methods
  • Sequence Deletion
  • Testicular Neoplasms/genetics

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