Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies

Human Molecular Genetics
Arthur S LeeCharles Lee

Abstract

Copy number variants (CNVs) are heritable gains and losses of genomic DNA in normal individuals. While copy number variation is widely studied in humans, our knowledge of CNVs in other mammalian species is more limited. We have designed a custom array-based comparative genomic hybridization (aCGH) platform with 385 000 oligonucleotide probes based on the reference genome sequence of the rhesus macaque (Macaca mulatta), the most widely studied non-human primate in biomedical research. We used this platform to identify 123 CNVs among 10 unrelated macaque individuals, with 24% of the CNVs observed in multiple individuals. We found that segmental duplications were significantly enriched at macaque CNV loci. We also observed significant overlap between rhesus macaque and human CNVs, suggesting that certain genomic regions are prone to recurrent CNV formation and instability, even across a total of approximately 50 million years of primate evolution ( approximately 25 million years in each lineage). Furthermore, for eight of the CNVs that were observed in both humans and macaques, previous human studies have reported a relationship between copy number and gene expression or disease susceptibility. Therefore, the rhesus macaque offers...Continue Reading

References

May 15, 1998·Nature·S Kumar, S B Hedges
Aug 12, 1999·Biochemical and Biophysical Research Communications·M MiyamotoT Kamataki
Oct 13, 1999·Mutation Research·T KamatakiK Fujita
Jul 27, 2000·Annals of the New York Academy of Sciences·E M Sellers, R F Tyndale
Sep 16, 2000·Trends in Microbiology·B M NathJ D Boyer
Oct 24, 2001·Trends in Cardiovascular Medicine·R P Shannon
Jan 31, 2002·Trends in Genetics : TIG·Paweł Stankiewicz, James R Lupski
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Aug 10, 2002·Science·Jeffrey A BaileyEvan E Eichler
Sep 13, 2002·Genome Biology·Christopher WorkmanSteen Knudsen
Jun 18, 2003·Clinical Pharmacology and Therapeutics·Michael B SawyerMark J Ratain
Aug 14, 2003·American Journal of Human Genetics·E J HolloxJ C K Barber
Dec 19, 2003·Nucleic Acids Research·Donna KarolchikW James Kent
Mar 9, 2004·Journal of Clinical Microbiology·Sophie JolyJanet M Guthmiller
Jul 15, 2004·PLoS Biology·Andrew FortnaJames M Sikela
Jul 27, 2004·Science·Jonathan SebatMichael Wigler
Aug 3, 2004·Nature Genetics·A John IafrateCharles Lee
Aug 24, 2004·Nature Genetics·Jiangzhen LiWei-Wen Cai
Dec 2, 2004·Proceedings of the National Academy of Sciences of the United States of America·Michael E SteiperTika Y Sukarna
May 3, 2005·Frontiers in Neuroendocrinology·Kim Wallen
May 17, 2005·Nature Genetics·Eray TuzunEvan E Eichler
May 27, 2005·American Journal of Human Genetics·Andrew J SharpEvan E Eichler
Jul 26, 2005·Pharmacogenetics and Genomics·Michael HaberlLeszek Wojnowski
Oct 28, 2005·American Journal of Human Genetics·Michael S JacksonMauro Santibanez-Koref
Dec 6, 2005·Nature Genetics·Donald F ConradJonathan K Pritchard
Dec 6, 2005·Nature Genetics·David A HindsKelly A Frazer
Jan 19, 2006·Nature Reviews. Genetics·Lars FeukStephen W Scherer
Feb 10, 2006·Nature Genetics·Steven A McCarrollUNKNOWN International HapMap Consortium
May 17, 2006·Proceedings of the National Academy of Sciences of the United States of America·George H PerryCharles Lee
Jun 14, 2006·Nature Reviews. Genetics·Jeffrey A Bailey, Evan E Eichler
Jul 1, 2006·Genome Research·Jennifer L FreemanCharles Lee
Jul 11, 2006·American Journal of Human Genetics·Devin P LockeEvan E Eichler
Aug 10, 2006·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Jong ParkJulio Pow-Sang

❮ Previous
Next ❯

Citations

Mar 27, 2007·Immunogenetics·Shelby L O'ConnorDavid H O'Connor
Apr 12, 2008·Breast Cancer Research and Treatment·Charles E WoodJ Mark Cline
May 21, 2013·Trends in Genetics : TIG·Catarina D Campbell, Evan E Eichler
Aug 21, 2013·Trends in Genetics : TIG·Jeffrey A Fawcett, Hideki Innan
Feb 13, 2009·Nature·Tomas Marques-BonetEvan E Eichler
Aug 7, 2013·Nature Communications·Takashi MakinoMasakado Kawata
Sep 20, 2008·Nature Reviews. Genetics·Ajit VarkiEvan E Eichler
Dec 29, 2011·Proceedings of the National Academy of Sciences of the United States of America·Kim H BrownCharles Lee
Jul 17, 2012·Proceedings of the National Academy of Sciences of the United States of America·Rebecca C IskowCharles Lee
Sep 10, 2013·Proceedings of the National Academy of Sciences of the United States of America·Omer GokcumenJan O Korbel
Nov 18, 2009·Zebrafish·Samuel M Peterson, Jennifer L Freeman
Mar 20, 2009·Human Molecular Genetics·Charlotte N HenrichsenAlexandre Reymond
Aug 4, 2009·Human Molecular Genetics·Luz D OrozcoAldons J Lusis
Nov 1, 2013·ILAR Journal·Jeffrey Rogers
Nov 1, 2013·ILAR Journal·Eric J Vallender, Gregory M Miller
Feb 17, 2010·Nucleic Acids Research·Derek A OldridgeFrancesca Demichelis
Jul 2, 2010·Proceedings. Biological Sciences·Daniel R Schrider, Matthew W Hahn
Apr 5, 2012·Cold Spring Harbor Perspectives in Medicine·Amalio Telenti, Welkin E Johnson
Sep 9, 2008·Genome Research·George H PerryRichard Redon
Nov 19, 2008·Genome Research·Wei-Kang ChenCarlos E Alvarez
Mar 10, 2010·Genome Research·George E LiuJohn W Keele
Nov 3, 2010·Genome Research·Ruth A Swanson-WagnerNathan M Springer
Nov 19, 2010·Genome Research·Evelyne ChaignatAlexandre Reymond
Jan 1, 2008·Cytogenetic and Genome Research·G H Perry
Nov 12, 2010·BMC Evolutionary Biology·Zhidong YuanJianming Xie
May 13, 2010·BMC Genomics·João FadistaChristian Bendixen
Jun 8, 2010·BMC Genomics·Xiaofei WangNathaniel Adefope
Nov 19, 2010·BMC Genomics·Luca FontanesiBaldassare Portolano
Feb 28, 2013·BMC Genomics·Francesco CicconardiAlessandro Nardone
Sep 26, 2013·BMC Genomics·Ping YuXing-Hua Wei
Sep 15, 2012·BMC Research Notes·Katie E FowlerDarren K Griffin
Apr 17, 2012·PloS One·Woei Chang LiewLaszlo Orban
May 6, 2010·Clinical Chemistry and Laboratory Medicine : CCLM·Giuseppe CastaldoRossella Tomaiuolo
Mar 4, 2014·Biology of Sex Differences·Zhen-Xia ChenBrian Oliver
Feb 26, 2014·Journal of Applied Genetics·Artur GurgulMonika Bugno-Poniewierska
Sep 29, 2011·Annual Review of Entomology·David W Severson, Susanta K Behura

❮ Previous
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