{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:52:47Z","timestamp":1674820367812},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Somatic amplification of particular genomic regions and selection of cellular lineages with such amplifications drives tumor development. However, pinpointing genes under such selection has been difficult due to the large span of these regions. Our recently-developed method, the amplification distortion test (ADT), identifies specific nucleotide alleles and haplotypes that confer better survival for tumor cells when somatically amplified. In this work, we focus on evaluating ADT's power to detect such causal variants across a variety of tumor dataset scenarios.<\/jats:p>\n               <jats:p>Results: Towards this end, we generated multiple parameter-based, synthetic datasets\u2014derived from real data\u2014that contain somatic copy number aberrations (CNAs) of various lengths and frequencies over germline single nucleotide polymorphisms (SNPs) genome-wide. Gold-standard causal sub-regions were assigned within these CNAs, followed by an assessment of ADT's ability to detect these sub-regions. Results indicate that ADT possesses high sensitivity and specificity in large sample sizes across most parameter cases, including those that more closely reflect existing SNP and CNA cancer data.<\/jats:p>\n               <jats:p>Availability: ADT is implemented in the Java software HADiT and can be downloaded through the SVN repository (via Develop\u2192 Code\u2192SVN Browse) at: http:\/\/sourceforge.net\/projects\/hadit\/.<\/jats:p>\n               <jats:p>Contact: \u00a0ninad.dewal@dbmi.columbia.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp694","type":"journal-article","created":{"date-parts":[[2009,12,24]],"date-time":"2009-12-24T01:52:12Z","timestamp":1261619532000},"page":"518-528","source":"Crossref","is-referenced-by-count":6,"title":["Power to detect selective allelic amplification in genome-wide scans of tumor data"],"prefix":"10.1093","volume":"26","author":[{"given":"Ninad","family":"Dewal","sequence":"first","affiliation":[{"name":"1 Department of Biomedical Informatics, Columbia University, New York, NY 10032, 2 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, 3 Medical and Population Genetics Program, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4 Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106 and 5 Department of Computer Science, Columbia University, New York, NY 10027, USA"}]},{"given":"Matthew L.","family":"Freedman","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, Columbia University, New York, NY 10032, 2 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, 3 Medical and Population Genetics Program, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4 Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106 and 5 Department of Computer Science, Columbia University, New York, NY 10027, USA"},{"name":"1 Department of Biomedical Informatics, Columbia University, New York, NY 10032, 2 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, 3 Medical and Population Genetics Program, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4 Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106 and 5 Department of Computer Science, Columbia University, New York, NY 10027, USA"}]},{"given":"Thomas","family":"LaFramboise","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, Columbia University, New York, NY 10032, 2 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, 3 Medical and Population Genetics Program, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4 Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106 and 5 Department of Computer Science, Columbia University, New York, NY 10027, USA"}]},{"given":"Itsik","family":"Pe'er","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, Columbia University, New York, NY 10032, 2 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, 3 Medical and Population Genetics Program, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4 Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106 and 5 Department of Computer Science, Columbia University, New York, NY 10027, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,12,23]]},"reference":[{"key":"2023012508030275900_B1","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/ng.354","article-title":"Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2","volume":"41","author":"Ahmed","year":"2009","journal-title":"Nat. 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