Paper Info
Title
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data.
Abstract
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. Availability: C++ source code is available at: http://bioinfo.curie.fr/projects/freec/
Year
DOI
Venue
2012
10.1093/bioinformatics/btr670
BIOINFORMATICS
Keywords
Field
DocType
alleles,loss of heterozygosity
Genotype,Allele,Biology,Loss of heterozygosity,Polymorphism (computer science),Bioinformatics,Genetics,Copy number analysis
Journal
Volume
Issue
ISSN
28
3
1367-4803
Citations 
PageRank 
References 
28
2.38
3
Authors
9
Name
Order
Citations
PageRank
Valentina Boeva117214.86
Tatiana Popova2322.85
Bleakley, Kevin328516.82
Pierre Chiche4282.38
Julie Cappo5433.41
Gudrun Schleiermacher6454.59
Isabelle Janoueix-Lerosey712010.88
Olivier Delattre812710.75
Emmanuel Barillot9950165.00