A computational strategy to adjust for copy number in tumor Hi-C data

作者：Wu, Hua-Jun; Michor, Franziska^*

来源：Bioinformatics, 2016, 32(24): 3695-3701.

DOI：10.1093/bioinformatics/btw540

• CHROMATIN
• ORGANIZATION
• ARCHITECTURE
• CHROMOSOME
• PRINCIPLES
• DOMAINS
• BIASES
• SUITE
• MAP

Motivation: The Hi-C technology was designed to decode the three-dimensional conformation of the genome. Despite progress towards more and more accurate contact maps, several systematic biases have been demonstrated to affect the resulting data matrix. Here we report a new source of bias that can arise in tumor Hi-C data, which is related to the copy number of genomic DNA. To address this bias, we designed a chromosome-adjusted iterative correction method called caICB. Our caICB correction method leads to significant improvements when compared with the original iterative correction in terms of eliminating copy number bias. @@@ Availability and Implementation: The method is available at https://bitbucket.org/mthjwu/hicapp. @@@ Contact: [e-mail] @@@ Supplementary information: Supplementary data are available at Bioinformatics online.

• 出版日期2016-12-15