Literature DB >> 25922366

The impact of human copy number variation on gene expression.

Eric R Gamazon, Barbara E Stranger.   

Abstract

Recent years have witnessed a flurry of important technological and methodological developments in the discovery and analysis of copy number variations (CNVs), which are increasingly enabling the systematic evaluation of their impact on a broad range of phenotypes from molecular-level (intermediate) traits to higher-order clinical phenotypes. Like single nucleotide variants in the human genome, CNVs have been linked to complex traits in humans, including disease and drug response. These recent developments underscore the importance of incorporating complex forms of genetic variation into disease mapping studies and promise to transform our understanding of genome function and the genetic basis of disease. Here we review some of the findings that have emerged from transcriptome studies of CNVs facilitated by the rapid advances in -omics technologies and corresponding methodologies.
© The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Entities:  

Keywords:  GWAS; copy number variation; eQTLs; gene expression; transcriptome

Mesh:

Year:  2015        PMID: 25922366      PMCID: PMC4592354          DOI: 10.1093/bfgp/elv017

Source DB:  PubMed          Journal:  Brief Funct Genomics        ISSN: 2041-2649            Impact factor:   4.241


  57 in total

1.  Structural variation of chromosomes in autism spectrum disorder.

Authors:  Christian R Marshall; Abdul Noor; John B Vincent; Anath C Lionel; Lars Feuk; Jennifer Skaug; Mary Shago; Rainald Moessner; Dalila Pinto; Yan Ren; Bhooma Thiruvahindrapduram; Andreas Fiebig; Stefan Schreiber; Jan Friedman; Cees E J Ketelaars; Yvonne J Vos; Can Ficicioglu; Susan Kirkpatrick; Rob Nicolson; Leon Sloman; Anne Summers; Clare A Gibbons; Ahmad Teebi; David Chitayat; Rosanna Weksberg; Ann Thompson; Cathy Vardy; Vicki Crosbie; Sandra Luscombe; Rebecca Baatjes; Lonnie Zwaigenbaum; Wendy Roberts; Bridget Fernandez; Peter Szatmari; Stephen W Scherer
Journal:  Am J Hum Genet       Date:  2008-01-17       Impact factor: 11.025

2.  Integrated detection and population-genetic analysis of SNPs and copy number variation.

Authors:  Steven A McCarroll; Finny G Kuruvilla; Joshua M Korn; Simon Cawley; James Nemesh; Alec Wysoker; Michael H Shapero; Paul I W de Bakker; Julian B Maller; Andrew Kirby; Amanda L Elliott; Melissa Parkin; Earl Hubbell; Teresa Webster; Rui Mei; James Veitch; Patrick J Collins; Robert Handsaker; Steve Lincoln; Marcia Nizzari; John Blume; Keith W Jones; Rich Rava; Mark J Daly; Stacey B Gabriel; David Altshuler
Journal:  Nat Genet       Date:  2008-09-07       Impact factor: 38.330

3.  Rare chromosomal deletions and duplications increase risk of schizophrenia.

Authors: 
Journal:  Nature       Date:  2008-07-30       Impact factor: 49.962

4.  Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis.

Authors:  Tie-Lin Yang; Xiang-Ding Chen; Yan Guo; Shu-Feng Lei; Jin-Tang Wang; Qi Zhou; Feng Pan; Yuan Chen; Zhi-Xin Zhang; Shan-Shan Dong; Xiang-Hong Xu; Han Yan; Xiaogang Liu; Chuan Qiu; Xue-Zhen Zhu; Teng Chen; Meng Li; Hong Zhang; Liang Zhang; Betty M Drees; James J Hamilton; Christopher J Papasian; Robert R Recker; Xiao-Ping Song; Jing Cheng; Hong-Wen Deng
Journal:  Am J Hum Genet       Date:  2008-11-06       Impact factor: 11.025

5.  Recurrent 16p11.2 microdeletions in autism.

Authors:  Ravinesh A Kumar; Samer KaraMohamed; Jyotsna Sudi; Donald F Conrad; Camille Brune; Judith A Badner; T Conrad Gilliam; Norma J Nowak; Edwin H Cook; William B Dobyns; Susan L Christian
Journal:  Hum Mol Genet       Date:  2007-12-21       Impact factor: 6.150

6.  Chromosome 15q11-13 duplication syndrome brain reveals epigenetic alterations in gene expression not predicted from copy number.

Authors:  A Hogart; K N Leung; N J Wang; D J Wu; J Driscoll; R O Vallero; N C Schanen; J M LaSalle
Journal:  J Med Genet       Date:  2008-10-07       Impact factor: 6.318

7.  Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease.

Authors:  Steven A McCarroll; Alan Huett; Petric Kuballa; Shannon D Chilewski; Aimee Landry; Philippe Goyette; Michael C Zody; Jennifer L Hall; Steven R Brant; Judy H Cho; Richard H Duerr; Mark S Silverberg; Kent D Taylor; John D Rioux; David Altshuler; Mark J Daly; Ramnik J Xavier
Journal:  Nat Genet       Date:  2008-09       Impact factor: 38.330

8.  Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus.

Authors:  Sébastien Jacquemont; Alexandre Reymond; Flore Zufferey; Louise Harewood; Robin G Walters; Zoltán Kutalik; Danielle Martinet; Yiping Shen; Armand Valsesia; Noam D Beckmann; Gudmar Thorleifsson; Marco Belfiore; Sonia Bouquillon; Dominique Campion; Nicole de Leeuw; Bert B A de Vries; Tõnu Esko; Bridget A Fernandez; Fernando Fernández-Aranda; José Manuel Fernández-Real; Mònica Gratacòs; Audrey Guilmatre; Juliane Hoyer; Marjo-Riitta Jarvelin; R Frank Kooy; Ants Kurg; Cédric Le Caignec; Katrin Männik; Orah S Platt; Damien Sanlaville; Mieke M Van Haelst; Sergi Villatoro Gomez; Faida Walha; Bai-Lin Wu; Yongguo Yu; Azzedine Aboura; Marie-Claude Addor; Yves Alembik; Stylianos E Antonarakis; Benoît Arveiler; Magalie Barth; Nathalie Bednarek; Frédérique Béna; Sven Bergmann; Mylène Beri; Laura Bernardini; Bettina Blaumeiser; Dominique Bonneau; Armand Bottani; Odile Boute; Han G Brunner; Dorothée Cailley; Patrick Callier; Jean Chiesa; Jacqueline Chrast; Lachlan Coin; Charles Coutton; Jean-Marie Cuisset; Jean-Christophe Cuvellier; Albert David; Bénédicte de Freminville; Bruno Delobel; Marie-Ange Delrue; Bénédicte Demeer; Dominique Descamps; Gérard Didelot; Klaus Dieterich; Vittoria Disciglio; Martine Doco-Fenzy; Séverine Drunat; Bénédicte Duban-Bedu; Christèle Dubourg; Julia S El-Sayed Moustafa; Paul Elliott; Brigitte H W Faas; Laurence Faivre; Anne Faudet; Florence Fellmann; Alessandra Ferrarini; Richard Fisher; Elisabeth Flori; Lukas Forer; Dominique Gaillard; Marion Gerard; Christian Gieger; Stefania Gimelli; Giorgio Gimelli; Hans J Grabe; Agnès Guichet; Olivier Guillin; Anna-Liisa Hartikainen; Délphine Heron; Loyse Hippolyte; Muriel Holder; Georg Homuth; Bertrand Isidor; Sylvie Jaillard; Zdenek Jaros; Susana Jiménez-Murcia; Géraldine Joly Helas; Philippe Jonveaux; Satu Kaksonen; Boris Keren; Anita Kloss-Brandstätter; Nine V A M Knoers; David A Koolen; Peter M Kroisel; Florian Kronenberg; Audrey Labalme; Emilie Landais; Elisabetta Lapi; Valérie Layet; Solenn Legallic; Bruno Leheup; Barbara Leube; Suzanne Lewis; Josette Lucas; Kay D MacDermot; Pall Magnusson; Christian Marshall; Michèle Mathieu-Dramard; Mark I McCarthy; Thomas Meitinger; Maria Antonietta Mencarelli; Giuseppe Merla; Alexandre Moerman; Vincent Mooser; Fanny Morice-Picard; Mafalda Mucciolo; Matthias Nauck; Ndeye Coumba Ndiaye; Ann Nordgren; Laurent Pasquier; Florence Petit; Rolph Pfundt; Ghislaine Plessis; Evica Rajcan-Separovic; Gian Paolo Ramelli; Anita Rauch; Roberto Ravazzolo; Andre Reis; Alessandra Renieri; Cristobal Richart; Janina S Ried; Claudine Rieubland; Wendy Roberts; Katharina M Roetzer; Caroline Rooryck; Massimiliano Rossi; Evald Saemundsen; Véronique Satre; Claudia Schurmann; Engilbert Sigurdsson; Dimitri J Stavropoulos; Hreinn Stefansson; Carola Tengström; Unnur Thorsteinsdóttir; Francisco J Tinahones; Renaud Touraine; Louis Vallée; Ellen van Binsbergen; Nathalie Van der Aa; Catherine Vincent-Delorme; Sophie Visvikis-Siest; Peter Vollenweider; Henry Völzke; Anneke T Vulto-van Silfhout; Gérard Waeber; Carina Wallgren-Pettersson; Robert M Witwicki; Simon Zwolinksi; Joris Andrieux; Xavier Estivill; James F Gusella; Omar Gustafsson; Andres Metspalu; Stephen W Scherer; Kari Stefansson; Alexandra I F Blakemore; Jacques S Beckmann; Philippe Froguel
Journal:  Nature       Date:  2011-08-31       Impact factor: 49.962

9.  Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

Authors:  Miles Parkes; Jeffrey C Barrett; Natalie J Prescott; Mark Tremelling; Carl A Anderson; Sheila A Fisher; Roland G Roberts; Elaine R Nimmo; Fraser R Cummings; Dianne Soars; Hazel Drummond; Charlie W Lees; Saud A Khawaja; Richard Bagnall; Denis A Burke; Catherine E Todhunter; Tariq Ahmad; Clive M Onnie; Wendy McArdle; David Strachan; Graeme Bethel; Claire Bryan; Cathryn M Lewis; Panos Deloukas; Alastair Forbes; Jeremy Sanderson; Derek P Jewell; Jack Satsangi; John C Mansfield; Lon Cardon; Christopher G Mathew
Journal:  Nat Genet       Date:  2007-06-06       Impact factor: 38.330

10.  Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

Authors:  Roger Horton; Richard Gibson; Penny Coggill; Marcos Miretti; Richard J Allcock; Jeff Almeida; Simon Forbes; James G R Gilbert; Karen Halls; Jennifer L Harrow; Elizabeth Hart; Kevin Howe; David K Jackson; Sophie Palmer; Anne N Roberts; Sarah Sims; C Andrew Stewart; James A Traherne; Steve Trevanion; Laurens Wilming; Jane Rogers; Pieter J de Jong; John F Elliott; Stephen Sawcer; John A Todd; John Trowsdale; Stephan Beck
Journal:  Immunogenetics       Date:  2008-01-10       Impact factor: 2.846

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  44 in total

1.  Integrating CNVs into meta-QTL identified GBP4 as positional candidate for adult cattle stature.

Authors:  Xiu-Kai Cao; Yong-Zhen Huang; Yi-Lei Ma; Jie Cheng; Zhen-Xian Qu; Yun Ma; Yue-Yu Bai; Feng Tian; Feng-Peng Lin; Yu-Lin Ma; Hong Chen
Journal:  Funct Integr Genomics       Date:  2018-05-08       Impact factor: 3.410

Review 2.  De novo vs. inherited copy number variations in multiple sclerosis susceptibility.

Authors:  Kalthoum Tizaoui
Journal:  Cell Mol Immunol       Date:  2018-02-12       Impact factor: 11.530

3.  A Consensus-Based Approach for Harmonizing the OHDSI Common Data Model with HL7 FHIR.

Authors:  Guoqian Jiang; Richard C Kiefer; Deepak K Sharma; Eric Prud'hommeaux; Harold R Solbrig
Journal:  Stud Health Technol Inform       Date:  2017

Review 4.  An evolving view of copy number variants.

Authors:  Stephanie Lauer; David Gresham
Journal:  Curr Genet       Date:  2019-05-10       Impact factor: 3.886

5.  Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact.

Authors:  Xiao Zhang; Yonghui Zhu; Karl A G Kremling; M Cinta Romay; Robert Bukowski; Qi Sun; Shibin Gao; Edward S Buckler; Fei Lu
Journal:  Theor Appl Genet       Date:  2021-10-18       Impact factor: 5.699

6.  Copy Number Analyses Identified a Novel Gene: APOBEC3A Related to Lipid Metabolism in the Pathogenesis of Preeclampsia.

Authors:  Nan Liu; Yu-Na Guo; Xiao-Jin Wang; Jue Ma; Yun-Ting He; Fang Zhang; Hao He; Jin-Liang Xie; Xu Zhuang; Meng Liu; Jian-Hua Sun; Yan Chen; Jian-Hua Lin; Li-Kun Gong; Bing-Shun Wang
Journal:  Front Cardiovasc Med       Date:  2022-05-16

7.  Comprehensive characterization of the rRNA metabolism-related genes in human cancer.

Authors:  Kaisa Cui; Cheng Liu; Xu Li; Qiang Zhang; Youjun Li
Journal:  Oncogene       Date:  2019-09-23       Impact factor: 9.867

8.  Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells.

Authors:  Christopher DeBoever; He Li; David Jakubosky; Paola Benaglio; Joaquin Reyna; Katrina M Olson; Hui Huang; William Biggs; Efren Sandoval; Matteo D'Antonio; Kristen Jepsen; Hiroko Matsui; Angelo Arias; Bing Ren; Naoki Nariai; Erin N Smith; Agnieszka D'Antonio-Chronowska; Emma K Farley; Kelly A Frazer
Journal:  Cell Stem Cell       Date:  2017-04-06       Impact factor: 25.269

9.  Extensive genome-wide duplications in the eastern oyster (Crassostrea virginica).

Authors:  Tejashree H Modak; Robert Literman; Jonathan B Puritz; Kevin M Johnson; Erin M Roberts; Dina Proestou; Ximing Guo; Marta Gomez-Chiarri; Rachel S Schwartz
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2021-04-05       Impact factor: 6.671

Review 10.  Genomics of Adaptations in Ungulates.

Authors:  Vivien J Chebii; Emmanuel A Mpolya; Farai C Muchadeyi; Jean-Baka Domelevo Entfellner
Journal:  Animals (Basel)       Date:  2021-05-29       Impact factor: 2.752

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