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PMID: 24958856 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 111 ·No. 27 ·2014-07-08 ·Pages 10007-12

Qi J, Chen Y, Copenhaver GP, Ma H

Abstract

DNA polymorphisms are important markers in genetic analyses and are increasingly detected by using genome resequencing. However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. Here, we describe an analysis strategy that minimizes false positives in allelic detection and present analyses of recently published resequencing data from Arabidopsis meiotic products and individual humans. Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences.

Keywords
genotyping high-throughput sequencing insertions–deletions structural variation
MeSH Terms
Alleles Arabidopsis/genetics Base Sequence DNA, Plant/genetics Genome, Plant Humans Meiosis/genetics Molecular Sequence Data Polymorphism, Single Nucleotide Recombination, Genetic
Chemicals
DNA, Plant
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Qi Ji
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, andMinistry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Sciences, Fudan University, Shanghai 200433, China;
Chen Yamao
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, andMinistry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Sciences, Fudan University, Shanghai 200433, China;
Copenhaver Gregory P
Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599-3280;Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599-3280; and.
Ma Hong
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, andMinistry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Sciences, Fudan University, Shanghai 200433, China;Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China [email protected].
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
1091-6490
DOI
10.1073/pnas.1321897111
Email
[email protected]
Published
2014-07-08
Epub
2014-00-23
Pages
10007-12
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC4103349
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.1321897111 PMC Full Text View journal details
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