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

Ji Qi, Yamao Chen, Gregory P. Copenhaver, Hong Ma

Research output: Contribution to journalArticlepeer-review

37 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)10007-10012
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume111
Issue number27
DOIs
StatePublished - Jul 8 2014

All Science Journal Classification (ASJC) codes

  • General

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