A Comparison of DNA Copy Number Profiling Platforms
2007; American Association for Cancer Research; Volume: 67; Issue: 21 Linguagem: Inglês
10.1158/0008-5472.can-07-2102
ISSN1538-7445
AutoresJoel Greshock, Bin Feng, Cristina Nogueira, Elena Ivanova, Ilana Perna, Katherine L. Nathanson, Alexei Protopopov, Barbara Weber, Lynda Chin,
Tópico(s)Chromosomal and Genetic Variations
ResumoAbstract 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. [Cancer Res 2007;67(21):10173–80]
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