tailieunhanh - Báo cáo y học: "Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. | Method Open Access Genome Alteration Print GAP a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays Tatiana Popova Ỷ Elodie Manié Ỷ Dominique Stoppa-Lyonnet n Guillem Rigaill Emmanuel Barillot and Marc Henri Stern Addresses Centre de Recherche Institut Curie 26 rue d Ulm Paris 75248 France. INSERM U830 Institut Curie 26 rue d Ulm Paris 75248 France. Department of Tumor Biology Institut Curie 26 rue d Ulm Paris 75248 France. University Paris Descartes 12 rue de l Ecole de Médecine Paris 75270 France. Translational Research Department Institut Curie 1 avenue Claude Vellefaux Paris 75475 France. MIA 518 AgroParisTech INRA 16 rue Claude Bernard Paris 75231 France. INSERM U900 Institut Curie 26 rue d Ulm Paris 75248 France. Ecole des Mines ParisTech 35 rue Saint Honoré Fontainebleau 77305 France. Correspondence Tatiana Popova. Email Published II November 2009 Genome Biology 2009 10 RI28 doi 86 gb-2009-I0-II-rI 28 The electronic version of this article is the complete one and can be found online at http 2009 I0 II RI28 Received 2 February 2009 Revised 24 September 2009 Accepted I I November 2009 2009 Popova et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism SNP arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data low tumor content and highly rearranged tumor