Literature DB >> 22483647

Exploring the role of copy number variants in human adaptation.

Rebecca C Iskow1, Omer Gokcumen, Charles Lee.   

Abstract

Over the past decade, the ubiquity of copy number variants (CNVs, the gain or loss of genomic material) in the genomes of healthy humans has become apparent. Although some of these variants are associated with disorders, a handful of studies documented an adaptive advantage conferred by CNVs. In this review, we propose that CNVs are substrates for human evolution and adaptation. We discuss the possible mechanisms and evolutionary processes in which CNVs are selected, outline the current challenges in identifying these loci, and highlight that copy number variable regions allow for the creation of novel genes that may diversify the repertoire of such genes in response to rapidly changing environments. We expect that many more adaptive CNVs will be discovered in the coming years, and we believe that these new findings will contribute to our understanding of human-specific phenotypes.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22483647      PMCID: PMC3533238          DOI: 10.1016/j.tig.2012.03.002

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  109 in total

1.  High-resolution human genome structure by single-molecule analysis.

Authors:  Brian Teague; Michael S Waterman; Steven Goldstein; Konstantinos Potamousis; Shiguo Zhou; Susan Reslewic; Deepayan Sarkar; Anton Valouev; Christopher Churas; Jeffrey M Kidd; Scott Kohn; Rodney Runnheim; Casey Lamers; Dan Forrest; Michael A Newton; Evan E Eichler; Marijo Kent-First; Urvashi Surti; Miron Livny; David C Schwartz
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-01       Impact factor: 11.205

2.  Identification of copy number variation hotspots in human populations.

Authors:  Wenqing Fu; Feng Zhang; Yi Wang; Xun Gu; Li Jin
Journal:  Am J Hum Genet       Date:  2010-10-08       Impact factor: 11.025

Review 3.  The evolution of gene duplications: classifying and distinguishing between models.

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Journal:  Nat Rev Genet       Date:  2010-01-06       Impact factor: 53.242

4.  A composite of multiple signals distinguishes causal variants in regions of positive selection.

Authors:  Sharon R Grossman; Ilya Shlyakhter; Ilya Shylakhter; Elinor K Karlsson; Elizabeth H Byrne; Shannon Morales; Gabriel Frieden; Elizabeth Hostetter; Elaine Angelino; Manuel Garber; Or Zuk; Eric S Lander; Stephen F Schaffner; Pardis C Sabeti
Journal:  Science       Date:  2010-01-07       Impact factor: 47.728

5.  Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.

Authors:  Hansoo Park; Jong-Il Kim; Young Seok Ju; Omer Gokcumen; Ryan E Mills; Sheehyun Kim; Seungbok Lee; Dongwhan Suh; Dongwan Hong; Hyunseok Peter Kang; Yun Joo Yoo; Jong-Yeon Shin; Hyun-Jin Kim; Maryam Yavartanoo; Young Wha Chang; Jung-Sook Ha; Wilson Chong; Ga-Ram Hwang; Katayoon Darvishi; Hyeran Kim; Song Ju Yang; Kap-Seok Yang; Hyungtae Kim; Matthew E Hurles; Stephen W Scherer; Nigel P Carter; Chris Tyler-Smith; Charles Lee; Jeong-Sun Seo
Journal:  Nat Genet       Date:  2010-04-04       Impact factor: 38.330

6.  Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.

Authors:  Nick Craddock; Matthew E Hurles; Niall Cardin; Richard D Pearson; Vincent Plagnol; Samuel Robson; Damjan Vukcevic; Chris Barnes; Donald F Conrad; Eleni Giannoulatou; Chris Holmes; Jonathan L Marchini; Kathy Stirrups; Martin D Tobin; Louise V Wain; Chris Yau; Jan Aerts; Tariq Ahmad; T Daniel Andrews; Hazel Arbury; Anthony Attwood; Adam Auton; Stephen G Ball; Anthony J Balmforth; Jeffrey C Barrett; Inês Barroso; Anne Barton; Amanda J Bennett; Sanjeev Bhaskar; Katarzyna Blaszczyk; John Bowes; Oliver J Brand; Peter S Braund; Francesca Bredin; Gerome Breen; Morris J Brown; Ian N Bruce; Jaswinder Bull; Oliver S Burren; John Burton; Jake Byrnes; Sian Caesar; Chris M Clee; Alison J Coffey; John M C Connell; Jason D Cooper; Anna F Dominiczak; Kate Downes; Hazel E Drummond; Darshna Dudakia; Andrew Dunham; Bernadette Ebbs; Diana Eccles; Sarah Edkins; Cathryn Edwards; Anna Elliot; Paul Emery; David M Evans; Gareth Evans; Steve Eyre; Anne Farmer; I Nicol Ferrier; Lars Feuk; Tomas Fitzgerald; Edward Flynn; Alistair Forbes; Liz Forty; Jayne A Franklyn; Rachel M Freathy; Polly Gibbs; Paul Gilbert; Omer Gokumen; Katherine Gordon-Smith; Emma Gray; Elaine Green; Chris J Groves; Detelina Grozeva; Rhian Gwilliam; Anita Hall; Naomi Hammond; Matt Hardy; Pile Harrison; Neelam Hassanali; Husam Hebaishi; Sarah Hines; Anne Hinks; Graham A Hitman; Lynne Hocking; Eleanor Howard; Philip Howard; Joanna M M Howson; Debbie Hughes; Sarah Hunt; John D Isaacs; Mahim Jain; Derek P Jewell; Toby Johnson; Jennifer D Jolley; Ian R Jones; Lisa A Jones; George Kirov; Cordelia F Langford; Hana Lango-Allen; G Mark Lathrop; James Lee; Kate L Lee; Charlie Lees; Kevin Lewis; Cecilia M Lindgren; Meeta Maisuria-Armer; Julian Maller; John Mansfield; Paul Martin; Dunecan C O Massey; Wendy L McArdle; Peter McGuffin; Kirsten E McLay; Alex Mentzer; Michael L Mimmack; Ann E Morgan; Andrew P Morris; Craig Mowat; Simon Myers; William Newman; Elaine R Nimmo; Michael C O'Donovan; Abiodun Onipinla; Ifejinelo Onyiah; Nigel R Ovington; Michael J Owen; Kimmo Palin; Kirstie Parnell; David Pernet; John R B Perry; Anne Phillips; Dalila Pinto; Natalie J Prescott; Inga Prokopenko; Michael A Quail; Suzanne Rafelt; Nigel W Rayner; Richard Redon; David M Reid; Susan M Ring; Neil Robertson; Ellie Russell; David St Clair; Jennifer G Sambrook; Jeremy D Sanderson; Helen Schuilenburg; Carol E Scott; Richard Scott; Sheila Seal; Sue Shaw-Hawkins; Beverley M Shields; Matthew J Simmonds; Debbie J Smyth; Elilan Somaskantharajah; Katarina Spanova; Sophia Steer; Jonathan Stephens; Helen E Stevens; Millicent A Stone; Zhan Su; Deborah P M Symmons; John R Thompson; Wendy Thomson; Mary E Travers; Clare Turnbull; Armand Valsesia; Mark Walker; Neil M Walker; Chris Wallace; Margaret Warren-Perry; Nicholas A Watkins; John Webster; Michael N Weedon; Anthony G Wilson; Matthew Woodburn; B Paul Wordsworth; Allan H Young; Eleftheria Zeggini; Nigel P Carter; Timothy M Frayling; Charles Lee; Gil McVean; Patricia B Munroe; Aarno Palotie; Stephen J Sawcer; Stephen W Scherer; David P Strachan; Chris Tyler-Smith; Matthew A Brown; Paul R Burton; Mark J Caulfield; Alastair Compston; Martin Farrall; Stephen C L Gough; Alistair S Hall; Andrew T Hattersley; Adrian V S Hill; Christopher G Mathew; Marcus Pembrey; Jack Satsangi; Michael R Stratton; Jane Worthington; Panos Deloukas; Audrey Duncanson; Dominic P Kwiatkowski; Mark I McCarthy; Willem Ouwehand; Miles Parkes; Nazneen Rahman; John A Todd; Nilesh J Samani; Peter Donnelly
Journal:  Nature       Date:  2010-04-01       Impact factor: 49.962

7.  Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease.

Authors:  Steven A McCarroll; James E Bradner; Hannu Turpeinen; Liisa Volin; Paul J Martin; Shannon D Chilewski; Joseph H Antin; Stephanie J Lee; Tapani Ruutu; Barry Storer; Edus H Warren; Bo Zhang; Lue Ping Zhao; David Ginsburg; Robert J Soiffer; Jukka Partanen; John A Hansen; Jerome Ritz; Aarno Palotie; David Altshuler
Journal:  Nat Genet       Date:  2009-12       Impact factor: 38.330

8.  Origins and functional impact of copy number variation in the human genome.

Authors:  Donald F Conrad; Dalila Pinto; Richard Redon; Lars Feuk; Omer Gokcumen; Yujun Zhang; Jan Aerts; T Daniel Andrews; Chris Barnes; Peter Campbell; Tomas Fitzgerald; Min Hu; Chun Hwa Ihm; Kati Kristiansson; Daniel G Macarthur; Jeffrey R Macdonald; Ifejinelo Onyiah; Andy Wing Chun Pang; Sam Robson; Kathy Stirrups; Armand Valsesia; Klaudia Walter; John Wei; Chris Tyler-Smith; Nigel P Carter; Charles Lee; Stephen W Scherer; Matthew E Hurles
Journal:  Nature       Date:  2009-10-07       Impact factor: 49.962

9.  Mechanisms of copy number variation and hybrid gene formation in the KIR immune gene complex.

Authors:  James A Traherne; Maureen Martin; Rosemary Ward; Maki Ohashi; Fawnda Pellett; Dafna Gladman; Derek Middleton; Mary Carrington; John Trowsdale
Journal:  Hum Mol Genet       Date:  2009-12-03       Impact factor: 6.150

10.  Large, rare chromosomal deletions associated with severe early-onset obesity.

Authors:  Elena G Bochukova; Ni Huang; Julia Keogh; Elana Henning; Carolin Purmann; Kasia Blaszczyk; Sadia Saeed; Julian Hamilton-Shield; Jill Clayton-Smith; Stephen O'Rahilly; Matthew E Hurles; I Sadaf Farooqi
Journal:  Nature       Date:  2009-12-06       Impact factor: 49.962

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  61 in total

Review 1.  Adaptive potential of genomic structural variation in human and mammalian evolution.

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Journal:  Brief Funct Genomics       Date:  2015-05-23       Impact factor: 4.241

Review 2.  A copy number variation map of the human genome.

Authors:  Mehdi Zarrei; Jeffrey R MacDonald; Daniele Merico; Stephen W Scherer
Journal:  Nat Rev Genet       Date:  2015-02-03       Impact factor: 53.242

3.  Copy Number Variations in Tilapia Genomes.

Authors:  Bi Jun Li; Hong Lian Li; Zining Meng; Yong Zhang; Haoran Lin; Gen Hua Yue; Jun Hong Xia
Journal:  Mar Biotechnol (NY)       Date:  2017-02-06       Impact factor: 3.619

4.  Global patterns of apparent copy number variation in birds revealed by cross-species comparative genomic hybridization.

Authors:  Benjamin M Skinner; Abdullah Al Mutery; Deborah Smith; Martin Völker; Nilofour Hojjat; Sannaa Raja; Steven Trim; Peter Houde; William J Boecklen; Darren K Griffin
Journal:  Chromosome Res       Date:  2014-04       Impact factor: 5.239

5.  Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift.

Authors:  David C Rinker; Natalya K Specian; Shu Zhao; John G Gibbons
Journal:  Proc Natl Acad Sci U S A       Date:  2019-06-17       Impact factor: 11.205

6.  Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus.

Authors:  Jakob B Butler; Jules S Freeman; Brad M Potts; René E Vaillancourt; Dario Grattapaglia; Orzenil B Silva-Junior; Blake A Simmons; Adam L Healey; Jeremy Schmutz; Kerrie W Barry; David J Lee; Robert J Henry; Graham J King; Abdul Baten; Mervyn Shepherd
Journal:  Heredity (Edinb)       Date:  2018-03-10       Impact factor: 3.821

7.  Detecting highly differentiated copy-number variants from pooled population sequencing.

Authors:  Daniel R Schrider; David J Begun; Matthew W Hahn
Journal:  Pac Symp Biocomput       Date:  2013

8.  Asymmetric functional divergence of young, dispersed gene duplicates in Arabidopsis thaliana.

Authors:  Sarah M Owens; Nicholas A Harberson; Richard C Moore
Journal:  J Mol Evol       Date:  2013-01-24       Impact factor: 2.395

Review 9.  New genes contribute to genetic and phenotypic novelties in human evolution.

Authors:  Yong E Zhang; Manyuan Long
Journal:  Curr Opin Genet Dev       Date:  2014-09-16       Impact factor: 5.578

10.  Adaptation of the osmotolerant yeast Zygosaccharomyces rouxii to an osmotic environment through copy number amplification of FLO11D.

Authors:  Jun Watanabe; Kenji Uehara; Yoshinobu Mogi
Journal:  Genetics       Date:  2013-07-26       Impact factor: 4.562

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