Application of oligonucleotides arrays for coincident comparative genomic hybridization, ploidy status and loss of heterozygosity studies in human cancers

John K. Cowell, Ken C. Lo

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Scopus citations

Abstract

Many oligonucleotide arrays comprise of spotted short oligonucleotides from throughout the genome under study. Hybridization of tumor DNA samples to these arrays will provide copy number estimates at each reference point with varying degrees of accuracy. In addition to copy number changes, however, tumors often undergo loss of heterozygosity for specific regions of the genome without copy number changes and these genetic changes can only be identified using arrays that identify polymorphic alleles at each reference point. In addition, because the hybridization intensity can be measured at each of the allelic variants, allelic ratios can be established which give indications of ploidy status in the tumor which is not generally possible using most other oligonucleotide array designs. The only arrays currently available that simultaneously report copy number, ploidy, and loss of heterozygosity are the Affymetrix SNP mapping arrays. In this review, the features of the SNP mapping arrays are described and computational tools explored which allow the maximum genetic information to be extracted from the experiment. Although the methodologies to generate the SNP data are now well established, approaches to interpret the data are only just being developed. From our experience using these arrays, we provide insights into how to evaluate the SNP data to report copy number changes, loss of heterozygosity, and ploidy in the same tumor samples using a single array.

Original languageEnglish (US)
Title of host publicationMicroarray Analysis of the Physical Genome
Subtitle of host publicationMethods and Protocols
EditorsJonathan Pollack
Pages47-65
Number of pages19
DOIs
StatePublished - Dec 1 2009

Publication series

NameMethods in Molecular Biology
Volume556
ISSN (Print)1064-3745

Keywords

  • CGH visualization tools
  • SNP mapping arrays
  • allelic ratios
  • comparative genome hybridization
  • loss of heterozygosity
  • oligonucleotide arrays

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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