Mapping personal functional data to personal genomes.
Open accessAbstract
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. Availability perEditor is available at http://biocomp.bioen.uiuc.edu/perEditor. Contact szhong@illinois.edu.
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Current approaches to allele-specific expression discard allelic multireads that map to both parents and fail to account for reads that are simultaneously genomic and allelic multireads.
“These methods discard allelic multireads that map to both parents and fail to account for reads that are simultaneously genomic and allelic multireads.”
From RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations (2014) · cites this paper as Rivas-Astroza et al. 2011
Aligning sequence reads to both parental genomes can eliminate the systematic bias in relative allele-specific expression favoring the reference allele.
“two alternative strategies for aligning reads have been shown to eliminate the systematic bias in measures of relative ASE favoring the reference allele”
From Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome (2013) · cites this paper as [19]
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Stevenson, K. R., Coolon, J. D., & Wittkopp, P. J. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-536 · Cited by 140 · see citing works
Munger, S. C., Raghupathy, N., Choi, K., Simons, A. K., Gatti, D. M., Hinerfeld, D. A., Svenson, K. L., Keller, M. P., Attie, A. D., Hibbs, M. A., et al. (2014) · Genetics · doi:10.1534/genetics.114.165886 · Cited by 85 · see citing works
- Authors
- Rivas-Astroza, M., Xie, D., Cao, X., & Zhong, S.
- Affiliations
- 1 Department of Bioengineering and 2Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- University of Illinois Urbana-Champaign (US)
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-10-17
- Volume
- 27
- Issue
- 24
- Pages
- 3427-3429
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3232370
- OpenAlex
- W2154442667
- Cited by
- 9
- References
- 0
- Citations by year
- 2024: 1 · 2022: 1 · 2019: 1 · 2016: 1 · 2015: 1 · 2014: 2 · 2013: 2
- FWCI
- 0.52
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health (DP2OD007417)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- personal genome, reference genome mapping, ChIP-seq, RNA-seq, single nucleotide polymorphisms, copy number variation, chromosomal rearrangements, indels, allele-specific binding, chromatin structure, gene expression
- MeSH terms
- Humans, Individuality, Polymorphism, Genetic, Genome, Human, Sequence Analysis, DNA, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Genomics, DNA Copy Number Variations
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