A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

被引：216

作者：

Stewart, Chip ^{[1
]}

Kural, Deniz ^{[1
]}

Stroemberg, Michael P. ^{[1
]}

Walker, Jerilyn A. ^{[2
]}

Konkel, Miriam K. ^{[2
]}

Stuetz, Adrian M. ^{[3
]}

Urban, Alexander E. ^{[4
]}

Grubert, Fabian ^{[4
]}

Lam, Hugo Y. K. ^{[4
]}

Lee, Wan-Ping ^{[1
]}

Busby, Michele ^{[1
]}

Indap, Amit R. ^{[1
]}

Garrison, Erik ^{[1
]}

Huff, Chad ^{[5
]}

Xing, Jinchuan ^{[5
]}

Snyder, Michael P. ^{[4
]}

Jorde, Lynn B. ^{[5
]}

Batzer, Mark A. ^{[2
]}

Korbel, Jan O. ^{[3
]}

Marth, Gabor T. ^{[1
]}

机构：

[1] Boston Coll, Dept Biol, Chestnut Hill, MA 02167 USA

[2] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA

[3] European Mol Biol Lab, Genome Biol Unit, Heidelberg, Germany

[4] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[5] Univ Utah, Dept Human Genet, Eccles Inst Human Genet, Salt Lake City, UT USA

来源：

PLOS GENETICS | 2011年 / 7卷 / 08期

基金：

美国国家卫生研究院;

关键词：

ANCESTRAL POPULATION SIZES; STRUCTURAL VARIATION; COPY NUMBER; TRANSPOSABLE ELEMENTS; MUTATION-RATE; SVA ELEMENTS; RETROTRANSPOSITION; DELETIONS; DATABASE; RECOMBINATION;

D O I：

10.1371/journal.pgen.1002236

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页数：19

共 75 条

[1]

Abyzov A., 2011, Genome Res

[2]

[Anonymous], 1968, ART COMPUTER PROGRAM

[3]

[Anonymous], 2007, PRINCIPLES POPULATIO

[4] Progress in understanding the biology of the human mutagen LINE-1 [J].

Babushok, Daria V. ;

Kazazian, Haig H., Jr. .

HUMAN MUTATION, 2007, 28 (06) :527-539

[5] Alu repeats and human genomic diversity [J].

Batzer, MA ;

Deininger, PL .

NATURE REVIEWS GENETICS, 2002, 3 (05) :370-379

[6] LINE-1 Retrotransposition Activity in Human Genomes [J].

Beck, Christine R. ;

Collier, Pamela ;

Macfarlane, Catriona ;

Malig, Maika ;

Kidd, Jeffrey M. ;

Eichler, Evan E. ;

Badge, Richard M. ;

Moran, John V. .

CELL, 2010, 141 (07) :1159-U110

[7] LINE dancing in the human genome: transposable elements and disease [J].

Belancio, Victoria P. ;

Deininger, Prescott L. ;

Roy-Engel, Astrid M. .

GENOME MEDICINE, 2009, 1

[8] Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[9] Hot L1s account for the bulk of retrotransposition in the human population [J].

Brouha, B ;

Schustak, J ;

Badge, RM ;

Lutz-Prigget, S ;

Farley, AH ;

Moran, JV ;

Kazazian, HH .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (09) :5280-5285

[10] Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering [J].

Browning, Sharon R. ;

Browning, Brian L. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 81 (05) :1084-1097

← 1 2 3 4 5 6 7 8 →