Journal Article

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

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

in Bioinformatics

Volume 25, issue 3, pages 315-321
Published in print February 2009 | ISSN: 1367-4803
Published online December 2008 | e-ISSN: 1460-2059 | DOI:
Reference alignment of SNP microarray signals for copy number analysis of tumors

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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


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  5608 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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