A comparison of DNA copy number profiling platforms

Cancer Res. 2007 Nov 1;67(21):10173-80. doi: 10.1158/0008-5472.CAN-07-2102. Epub 2007 Oct 29.

Abstract

The accurate mapping of recurring DNA copy number aberrations (CNAs), a hallmark feature of the cancer genome, has facilitated the discovery of tumor suppressor genes and oncogenes. Microarray-based assays designed to detect these chromosomal copy number alterations on a genome-wide and high-resolution scale have emerged as a cornerstone technology in the genomic era. The diversity of commercially available platforms prompted a systematic comparison of five copy number profiling assays for their ability to detect 2-fold copy number gain and loss (4n or 1n, respectively) as well as focal high-amplitude CNAs. Here, using a collection of established human melanoma cell lines, we defined the reproducibility, absolute signals, signal to noise, and false-positive and false-negative rates for each of the five assays against ground truth defined by spectral karyotyping, in addition to comparing the concordance of CNA detection by two high-resolution Agilent and Affymetrix microarray platforms. Our analyses concluded that the Agilent's 60-mer oligonucleotide microarray with probe design optimized for genomic hybridization offers the highest sensitivity and specificity (area under receiver operator characteristic curve >0.99), whereas Affymetrix's single nucleotide polymorphism microarray seems to offer better detection of CNAs in gene-poor regions. Availability of these comparison results should guide study design decisions and facilitate further computational development.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Cell Line, Tumor
  • Gene Dosage*
  • Gene Expression Profiling*
  • Humans
  • Melanoma / genetics*
  • Oligonucleotide Array Sequence Analysis
  • Reproducibility of Results
  • Sensitivity and Specificity