{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T01:27:08Z","timestamp":1779240428914,"version":"3.51.4"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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.<\/jats:p><jats:p>Availability: Documented R code is freely available from www.stjuderesearch.org\/depts\/biostats\/refnorm.<\/jats:p><jats:p>Contact: \u00a0stanley.pounds@stjude.org<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn624","type":"journal-article","created":{"date-parts":[[2008,12,4]],"date-time":"2008-12-04T01:47:06Z","timestamp":1228355226000},"page":"315-321","source":"Crossref","is-referenced-by-count":50,"title":["Reference alignment of SNP microarray signals for copy number analysis of tumors"],"prefix":"10.1093","volume":"25","author":[{"given":"Stan","family":"Pounds","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng","family":"Cheng","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles","family":"Mullighan","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susana C.","family":"Raimondi","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sheila","family":"Shurtleff","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James R.","family":"Downing","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and 2Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,12,3]]},"reference":[{"key":"2023013110014746900_B1","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array based on variance and bias","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013110014746900_B2","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1038\/nature05690","article-title":"Genes regulating B cell development are mutated in acute lymphoid leukaemia","volume":"446","author":"Mullighan","year":"2007","journal-title":"Nature"},{"key":"2023013110014746900_B3","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/gb-2001-2-8-research0032","article-title":"Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application","volume":"2","author":"Li","year":"2001","journal-title":"Genome Biol."},{"key":"2023013110014746900_B4","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1089\/cmb.2005.12.482","article-title":"Statistical development and evaluation of gene expression data filters","volume":"12","author":"Pounds","year":"2005","journal-title":"J. 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