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- Title
Reference alignment of SNP microarray signals for copy number analysis of tumors.
- Authors
Stan Pounds; Cheng Cheng; Charles Mullighan; Susana C. Raimondi; Sheila Shurtleff; James R. Downing
- Abstract
A new procedure to align single nucleotide polymorphism (SNP) microarray signals for copy number analysis is proposed. For each individual array, this reference alignment procedure (RAP) uses a set of selected markers as internal references to direct the signal alignment. RAP aligns the signals so that each array has a similar signal distribution among its reference markers. An accompanying reference selection algorithm (RSA) uses genotype calls and initial signal intensities to choose two-copy markers as the internal references for each array. After RSA and RAP are applied, each array has a similar distribution of signals of two-copy markers so that across-array signal comparisons are biologically meaningful. An upper bound for a statistical metric of signal misalignment is derived and provides a theoretical basis to choose RSA-RAP over other alignment procedures for copy number analysis of cancers. In our study of acute lymphoblastic leukemia, RSA-RAP gives copy number analysis results that show substantially better concordance with cytogenetics than do two other alignment procedures. Availability: Documented R code is freely available from www.stjuderesearch.org/depts/biostats/refnorm. Contact: stanley.pounds@stjude.org Supplementary information: Supplementary data are available at Bioinformatics online.
- Publication
Bioinformatics, 2009, Vol 25, Issue 3, p315
- ISSN
1367-4803
- Publication type
Academic Journal
- DOI
10.1093/bioinformatics/btn624