{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T02:56:35Z","timestamp":1781837795952,"version":"3.54.5"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1762,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: More and more cancer studies use next-generation sequencing (NGS) data to detect various types of genomic variation. However, even when researchers have such data at hand, single-nucleotide polymorphism arrays have been considered necessary to assess copy number alterations and especially loss of heterozygosity (LOH). Here, we present the tool Control-FREEC that enables automatic calculation of copy number and allelic content profiles from NGS data, and consequently predicts regions of genomic alteration such as gains, losses and LOH. Taking as input aligned reads, Control-FREEC constructs copy number and B-allele frequency profiles. The profiles are then normalized, segmented and analyzed in order to assign genotype status (copy number and allelic content) to each genomic region. When a matched normal sample is provided, Control-FREEC discriminates somatic from germline events. Control-FREEC is able to analyze overdiploid tumor samples and samples contaminated by normal cells. Low mappability regions can be excluded from the analysis using provided mappability tracks.<\/jats:p>\n               <jats:p>Availability: C++ source code is available at: http:\/\/bioinfo.curie.fr\/projects\/freec\/<\/jats:p>\n               <jats:p>Contact: \u00a0freec@curie.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr670","type":"journal-article","created":{"date-parts":[[2011,12,8]],"date-time":"2011-12-08T01:24:20Z","timestamp":1323307460000},"page":"423-425","source":"Crossref","is-referenced-by-count":929,"title":["Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data"],"prefix":"10.1093","volume":"28","author":[{"given":"Valentina","family":"Boeva","sequence":"first","affiliation":[{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatiana","family":"Popova","sequence":"additional","affiliation":[{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Bleakley","sequence":"additional","affiliation":[{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"Chiche","sequence":"additional","affiliation":[{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Cappo","sequence":"additional","affiliation":[{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gudrun","family":"Schleiermacher","sequence":"additional","affiliation":[{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Janoueix-Lerosey","sequence":"additional","affiliation":[{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Delattre","sequence":"additional","affiliation":[{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel","family":"Barillot","sequence":"additional","affiliation":[{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"},{"name":"1 Institut Curie, 2INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris 75248, 3Mines ParisTech, Fontainebleau 77300, 4INSERM, U830, Genetics and Biology of Cancers, Paris 75248 and 5INRIA Saclay, Orsay 91893, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,12,6]]},"reference":[{"key":"2023012512165533600_B1","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/bioinformatics\/btq635","article-title":"Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization","volume":"27","author":"Boeva","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512165533600_B2","doi-asserted-by":"crossref","first-page":"4323","DOI":"10.1073\/pnas.0910684107","article-title":"High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset","volume":"107","author":"Caren","year":"2010","journal-title":"Proc. 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