A comprehensive map of mobile element insertion polymorphisms in humans.

PLoS Genetics. 2011;7(8):e1002236 DOI 10.1371/journal.pgen.1002236

 

Journal Homepage

Journal Title: PLoS Genetics

ISSN: 1553-7390 (Print); 1553-7404 (Online)

Publisher: Public Library of Science (PLoS)

LCC Subject Category: Science: Biology (General): Genetics

Country of publisher: United States

Language of fulltext: English

Full-text formats available: PDF, HTML, XML

 

AUTHORS

Chip Stewart
Deniz Kural
Michael P Strömberg
Jerilyn A Walker
Miriam K Konkel
Adrian M Stütz
Alexander E Urban
Fabian Grubert
Hugo Y K Lam
Wan-Ping Lee
Michele Busby
Amit R Indap
Erik Garrison
Chad Huff
Jinchuan Xing
Michael P Snyder
Lynn B Jorde
Mark A Batzer
Jan O Korbel
Gabor T Marth
1000 Genomes Project

EDITORIAL INFORMATION

Peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 26 weeks

 

Abstract | Full Text

As a consequence of the accumulation of insertion events over evolutionary time, mobile elements now comprise nearly half of the human genome. The Alu, L1, and SVA mobile element families are still duplicating, generating variation between individual genomes. Mobile element insertions (MEI) have been identified as causes for genetic diseases, including hemophilia, neurofibromatosis, and various cancers. Here we present a comprehensive map of 7,380 MEI polymorphisms from the 1000 Genomes Project whole-genome sequencing data of 185 samples in three major populations detected with two detection methods. This catalog enables us to systematically study mutation rates, population segregation, genomic distribution, and functional properties of MEI polymorphisms and to compare MEI to SNP variation from the same individuals. Population allele frequencies of MEI and SNPs are described, broadly, by the same neutral ancestral processes despite vastly different mutation mechanisms and rates, except in coding regions where MEI are virtually absent, presumably due to strong negative selection. A direct comparison of MEI and SNP diversity levels suggests a differential mobile element insertion rate among populations.