{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,21]],"date-time":"2025-08-21T16:43:31Z","timestamp":1755794611532},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Current algorithms for estimating DNA copy numbers (CNs) borrow concepts from gene expression analysis methods. However, single nucleotide polymorphism (SNP) arrays have special characteristics that, if taken into account, can improve the overall performance. For example, cross hybridization between alleles occurs in SNP probe pairs. In addition, most of the current CN methods are focused on total CNs, while it has been shown that allele-specific CNs are of paramount importance for some studies. Therefore, we have developed a summarization method that estimates high-quality allele-specific CNs.<\/jats:p>\n               <jats:p>Results: The proposed method estimates the allele-specific DNA CNs for all Affymetrix SNP arrays dealing directly with the cross hybridization between probes within SNP probesets. This algorithm outperforms (or at least it performs as well as) other state-of-the-art algorithms for computing DNA CNs. It better discerns an aberration from a normal state and it also gives more precise allele-specific CNs.<\/jats:p>\n               <jats:p>Availability: The method is available in the open-source R package ACNE, which also includes an add on to the aroma.affymetrix framework (http:\/\/www.aroma-project.org\/).<\/jats:p>\n               <jats:p>Contact: \u00a0arubio@ceit.es<\/jats:p>\n               <jats:p>Supplementaruy information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq300","type":"journal-article","created":{"date-parts":[[2010,6,8]],"date-time":"2010-06-08T01:20:28Z","timestamp":1275960028000},"page":"1827-1833","source":"Crossref","is-referenced-by-count":20,"title":["ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays"],"prefix":"10.1093","volume":"26","author":[{"given":"Maria","family":"Ortiz-Estevez","sequence":"first","affiliation":[{"name":"1 Group of Bioinformatics, CEIT and TECNUN, University of Navarra, San Sebastian, Spain and 2Department of Statistics, University of California, Berkeley, CA, USA"}]},{"given":"Henrik","family":"Bengtsson","sequence":"additional","affiliation":[{"name":"1 Group of Bioinformatics, CEIT and TECNUN, University of Navarra, San Sebastian, Spain and 2Department of Statistics, University of California, Berkeley, CA, USA"}]},{"given":"Angel","family":"Rubio","sequence":"additional","affiliation":[{"name":"1 Group of Bioinformatics, CEIT and TECNUN, University of Navarra, San Sebastian, Spain and 2Department of Statistics, University of California, Berkeley, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,6,6]]},"reference":[{"key":"2023012507595310900_B1","volume-title":"Affymetrix Genotyping Console 3.0 - User Manual.","author":"Affymetrix Inc.","year":"2008"},{"key":"2023012507595310900_B2","author":"Affymetrix Inc.","year":"2009"},{"key":"2023012507595310900_B3","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1038\/nature04226","article-title":"A haplotype map of the human genome","volume":"437","author":"Altshuler","year":"2005","journal-title":"Nature"},{"key":"2023012507595310900_B4","article-title":"aroma.affymetrix: a generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory","volume-title":"Technical Report 745.","author":"Bengtsson","year":"2008"},{"key":"2023012507595310900_B5","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1093\/bioinformatics\/btn016","article-title":"Estimation and assessment of raw copy numbers at the single locus level","volume":"24","author":"Bengtsson","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012507595310900_B6","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1093\/bioinformatics\/btp371","article-title":"A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6","volume":"25","author":"Bengtsson","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012507595310900_B7","doi-asserted-by":"crossref","first-page":"e145","DOI":"10.1093\/nar\/gkn736","article-title":"A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay","volume":"36","author":"Duffy","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012507595310900_B8","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1002\/gcc.20558","article-title":"High-resolution genomic and expression analyses of copy number alterations in breast tumors","volume":"47","author":"Haverty","year":"2008","journal-title":"Genes Chromosomes Cancer"},{"key":"2023012507595310900_B9","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data","volume":"4","author":"Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"2023012507595310900_B10","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1093\/biostatistics\/kxl012","article-title":"PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data","volume":"8","author":"LaFramboise","year":"2007","journal-title":"Biostatistics"},{"key":"2023012507595310900_B11","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1093\/bib\/bbp018","article-title":"Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips","volume":"10","author":"Langdon","year":"2009","journal-title":"Brief. 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