Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

• DOI: 10.1093/bioinformatics/btr670
• Publication Date: 2011-12-08T01:24:20Z
• Authors: Valentina Boeva; Tatiana Popova; Kevin Bleakley; Pierre Chiche; Julie Cappo; Gudrun Schleierma...; Isabelle Janoueix...; Olivier Delattre; Emmanuel Barillot
• Keywords: Applications Note; 0303 health sciences; 03 medical and health sciences; DNA Copy Number Variations; Neoplasms; Humans; Loss of Heterozygosity; Polymorphism, Single Nucleotide; Alleles; Software; 3. Good health

Abstract 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 at hand, single-nucleotide polymorphism arrays been considered necessary assess copy number alterations especially loss heterozygosity (LOH). Here, we present the tool Control-FREEC that enables automatic calculation allelic content profiles from NGS data, consequently predicts regions alteration as gains, losses LOH. Taking input aligned reads, constructs B-allele frequency profiles. The are then normalized, segmented analyzed in order assign genotype status (copy content) each region. When a matched normal sample is provided, discriminates somatic germline events. able analyze overdiploid tumor samples contaminated by cells. Low mappability can be excluded analysis using provided tracks. Availability: C++ source code available at: http://bioinfo.curie.fr/projects/freec/ Contact: [e-mail] Supplementary information: Bioinformatics online.