Landscape of insertion polymorphisms in the human genome

Genome Biology and Evolution
Masahiro OnozawaPeter D Aplan

Abstract

Nucleotide substitutions, small (<50 bp) insertions or deletions (indels), and large (>50 bp) deletions are well-known causes of genetic variation within the human genome. We recently reported a previously unrecognized form of polymorphic insertions, termed templated sequence insertion polymorphism (TSIP), in which the inserted sequence was templated from a distant genomic region, and was inserted in the genome through reverse transcription of an RNA intermediate. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; class 1 TSIPs show target site duplication, polyadenylation, and preference for insertion at a 5'-TTTT/A-3' sequence, suggesting a LINE-1 based insertion mechanism, whereas class 2 TSIPs show features consistent with repair of a DNA double strand break by nonhomologous end joining. To gain a more complete picture of TSIPs throughout the human population, we evaluated whole-genome sequence from 52 individuals, and identified 171 TSIPs. Most individuals had 25-30 TSIPs, and common (present in >20% of individuals) TSIPs were found in individuals throughout the world, whereas rare TSIPs tended to cluster in specific geographic regions. The number of rare TSIPs was great...Continue Reading

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Citations

Jul 9, 2016·Molecular Cell·Jasbeer S KhandujaMo Motamedi
Aug 29, 2017·Nature·Kathrin PieperAntonio Lanzavecchia
Oct 27, 2017·Proceedings of the National Academy of Sciences of the United States of America·Emily A BrownDanika L Bannasch
Dec 3, 2016·Frontiers in Chemistry·Masahiro Onozawa, Peter D Aplan
Sep 10, 2017·Annals of Hematology·José FerrãoPaula Faustino
Aug 15, 2020·Frontiers in Veterinary Science·Peter J Dickinson, Danika L Bannasch

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Datasets Mentioned

BETA
NA19834
NA21732
NA06985
NA20509
NA18555
NA18558
NA18947
HG00732

Methods Mentioned

BETA
PCR
electrophoresis
ubiquitination

Software Mentioned

BLAT
Repeat Masker

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