{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T09:10:16Z","timestamp":1738919416247,"version":"3.37.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: DNA copy number aberration\u2014both inherited and sporadic\u2014is a significant contributor to a variety of human diseases. Copy number characterization is therefore an area of intense research. Probe hybridization-based arrays are important tools used to measure copy number in a high-throughput manner.<\/jats:p><jats:p>Results: In this article, we present a simple but powerful nonparametric rank-based approach to detect deletions and gains from raw array copy number measurements. We use three different rank-based statistics to detect three separate molecular phenomena\u2014somatic lesions, germline deletions and germline gains. The approach is robust and rigorously grounded in statistical theory, thereby enabling the meaningful assignment of statistical significance to each putative aberration. We demonstrate the flexibility of our approach by applying it to data from three different array platforms. We show that our method compares favorably with established approaches by applying it to published well-characterized samples. Power simulations demonstrate exquisite sensitivity for array data of reasonable quality.<\/jats:p><jats:p>Conclusions: Our flexible rank-based framework is suitable for multiple platforms including single nucleotide polymorphism arrays and array comparative genomic hybridization, and can reliably detect gains or losses of genomic DNA, whether inherited, de novo, or somatic.<\/jats:p><jats:p>Availability: An R package RankCopy containing the methods described here, and is freely available from the author's web site (http:\/\/mendel.gene.cwru.edu\/laframboiselab\/).<\/jats:p><jats:p>Contact: \u00a0Thomas.LaFramboise@case.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp063","type":"journal-article","created":{"date-parts":[[2009,1,29]],"date-time":"2009-01-29T01:31:13Z","timestamp":1233192673000},"page":"722-728","source":"Crossref","is-referenced-by-count":6,"title":["A flexible rank-based framework for detecting copy number aberrations from array data"],"prefix":"10.1093","volume":"25","author":[{"given":"Thomas","family":"LaFramboise","sequence":"first","affiliation":[{"name":"1 Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, 2Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, 3The Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA, 4Max Planck Institute for Neurological Research with Klaus-Joachim-Z\u00fclch Laboratories of the Max Planck Society and 5The Medical Faculty of the University of K\u00f6ln, K\u00f6ln, Germany"},{"name":"1 Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, 2Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, 3The Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA, 4Max Planck Institute for Neurological Research with Klaus-Joachim-Z\u00fclch Laboratories of the Max Planck Society and 5The Medical Faculty of the University of K\u00f6ln, K\u00f6ln, Germany"}]},{"given":"Wendy","family":"Winckler","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, 2Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, 3The Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA, 4Max Planck Institute for Neurological Research with Klaus-Joachim-Z\u00fclch Laboratories of the Max Planck Society and 5The Medical Faculty of the University of K\u00f6ln, K\u00f6ln, Germany"}]},{"given":"Roman K.","family":"Thomas","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, 2Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, 3The Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA, 4Max Planck Institute for Neurological Research with Klaus-Joachim-Z\u00fclch Laboratories of the Max Planck Society and 5The Medical Faculty of the University of K\u00f6ln, K\u00f6ln, Germany"},{"name":"1 Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, 2Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, 3The Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA, 4Max Planck Institute for Neurological Research with Klaus-Joachim-Z\u00fclch Laboratories of the Max Planck Society and 5The Medical Faculty of the University of K\u00f6ln, K\u00f6ln, Germany"}]}],"member":"286","published-online":{"date-parts":[[2009,1,28]]},"reference":[{"article-title":"GeneChip human mapping 500K set data sheet.","year":"2006","author":"Affymetrix","key":"2023051209025133000_B1"},{"key":"2023051209025133000_B2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate \u2013 a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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