Mapping personal functional data to personal genomes

Marcelo Rivas-Astroza, Dan Xie, Xiaoyi Cao, Sheng Zhong

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Motivation: The sequencing of personal genomes enabled analysis of variation in transcription factor (TF) binding, chromatin structure and gene expression and indicated how they contribute to phenotypic variation. It is hypothesized that using the reference genome for mapping ChIP-seq or RNA-seq reads may introduce errors, especially at polymorphic genomic regions.Results: We developed a Personal Genome Editor (perEditor) that changes the reference human genome (NCBI36/hg18) into an individual genome, taking into account single nucleotide polymorphisms (SNPs), insertions and deletions, copy number variation, and chromosomal rearrangements. perEditor outputs two alleles (maternal, paternal) of the individual genome that is ready for mapping ChIP-seq and RNA-seq reads, and enabling the analyses of allele specific binding, chromatin structure and gene expression.

Original languageEnglish
Article numberbtr578
Pages (from-to)3427-3429
Number of pages3
JournalBioinformatics
Volume27
Issue number24
DOIs
StatePublished - Dec 2011
Externally publishedYes

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