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Bioinformatics Advance Access originally published online on December 3, 2008
Bioinformatics 2009 25(3):315-321; doi:10.1093/bioinformatics/btn624
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Reference alignment of SNP microarray signals for copy number analysis of tumors

Stan Pounds 1,*, Cheng Cheng 1, Charles Mullighan 2, Susana C. Raimondi 2, Sheila Shurtleff 2 and James R. Downing 2

1Department of Biostatistics and 2Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA

*To whom correspondence should be addressed.


  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{at}stjude.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Trey Ideker

Received on September 16, 2008; revised on November 14, 2008; accepted on November 29, 2008

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