title: A comprehensive map of mobile element insertion polymorphisms in humans.
abstract: 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.
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA.
authors.forename: Chip
authors.initials: C
authors.lastname: Stewart
authors.forename: Deniz
authors.initials: D
authors.lastname: Kural
authors.forename: Michael P
authors.initials: MP
authors.lastname: Strömberg
authors.forename: Jerilyn A
authors.initials: JA
authors.lastname: Walker
authors.forename: Miriam K
authors.initials: MK
authors.lastname: Konkel
authors.forename: Adrian M
authors.initials: AM
authors.lastname: Stütz
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Urban
authors.forename: Fabian
authors.initials: F
authors.lastname: Grubert
authors.forename: Hugo Y K
authors.initials: HY
authors.lastname: Lam
authors.forename: Wan-Ping
authors.initials: WP
authors.lastname: Lee
authors.forename: Michele
authors.initials: M
authors.lastname: Busby
authors.forename: Amit R
authors.initials: AR
authors.lastname: Indap
authors.forename: Erik
authors.initials: E
authors.lastname: Garrison
authors.forename: Chad
authors.initials: C
authors.lastname: Huff
authors.forename: Jinchuan
authors.initials: J
authors.lastname: Xing
authors.forename: Michael P
authors.initials: MP
authors.lastname: Snyder
authors.forename: Lynn B
authors.initials: LB
authors.lastname: Jorde
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
authors.forename: Jan O
authors.initials: JO
authors.lastname: Korbel
authors.forename: Gabor T
authors.initials: GT
authors.lastname: Marth
mesh_terms: D004251:DNA Transposable Elements; D005787:Gene Frequency; D015894:Genome, Human; D005838:Genotype; D006579:Heterozygote; D006801:Humans; D016254:Mutagenesis, Insertional; D059645:Mutation Rate; D020641:Polymorphism, Single Nucleotide
chemical_list: D004251:DNA Transposable Elements