Genome wide identification of recessive cancer genes by combinatorial mutation analysis

PLoS One. 2008;3(10):e3380. doi: 10.1371/journal.pone.0003380. Epub 2008 Oct 10.

Abstract

We devised a novel procedure to identify human cancer genes acting in a recessive manner. Our strategy was to combine the contributions of the different types of genetic alterations to loss of function: amino-acid substitutions, frame-shifts, gene deletions. We studied over 20,000 genes in 3 Gigabases of coding sequences and 700 array comparative genomic hybridizations. Recessive genes were scored according to nucleotide mismatches under positive selective pressure, frame-shifts and genomic deletions in cancer. Four different tests were combined together yielding a cancer recessive p-value for each studied gene. One hundred and fifty four candidate recessive cancer genes (p-value < 1.5 x 10(-7), FDR = 0.39) were identified. Strikingly, the prototypical cancer recessive genes TP53, PTEN and CDKN2A all ranked in the top 0.5% genes. The functions significantly affected by cancer mutations are exactly overlapping those of known cancer genes, with the critical exception for the absence of tyrosine kinases, as expected for a recessive gene-set.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution
  • DNA Mutational Analysis / methods*
  • Databases, Nucleic Acid
  • Expressed Sequence Tags
  • Genes, Neoplasm*
  • Genes, Recessive*
  • Genome*
  • Humans
  • Microarray Analysis
  • Molecular Sequence Data
  • Mutation
  • Neoplasms / genetics*