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Small Insertions Are More Deleterious than Small Deletions in Human Genomes
Author(s) -
Huang Shengfeng,
Li Jie,
Xu Anlong,
Huang Guangrui,
You Leiming
Publication year - 2013
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.22435
Subject(s) - indel , biology , genome , genetics , indel mutation , human genome , 1000 genomes project , natural selection , selection (genetic algorithm) , negative selection , population , single nucleotide polymorphism , computational biology , gene , genotype , demography , artificial intelligence , sociology , computer science
Although lines of evidence suggest that small insertions and deletions differ in their mechanisms of formation, there remains the debate on whether natural selection acts differently on the two indel types. Currently available personal genomes and the 1000 G enomes P roject permit population level and genome scale comparison of the selection regimes on the two indel types. We first developed a statistical model to evaluate the indel frequency biases of the 1000 G enomes P roject phase 1 data. We then identified four independent lines of evidence demonstrating that human small (1–4 bp) insertions are on average more deleterious than deletions. This genome‐wide selection pattern is not affected by methodology, demography, and regional differences including indel density, introns versus exons, repeats versus nonrepeats, recombination rates, and the timing of DNA replication. This selection pattern has a profound effect on indel frequency spectra, deletional bias, and local single‐nucleotide mutation rates. Finally, we observed that small insertions appear to be more actively implicated in shaping fast‐evolving genomic sequences (or nonconserved regions).