publication . Preprint . 2019

Origins and long-term patterns of copy-number variation in rhesus macaques

Gregg W.C Thomas; Richard J. Wang; Jelena Nguyen; R. Alan Harris; Muthuswamy Raveendran; Jeffrey Rogers; Matthew W. Hahn;
Open Access English
  • Published: 28 Aug 2019
  • Publisher: Cold Spring Harbor Laboratory
Abstract
<jats:title>Abstract</jats:title><jats:p>Mutations play a key role in the development of disease in an individual and the evolution of traits within species. Recent work in humans and other primates has clarified the origins and patterns of single nucleotide variants, showing that most arise in the father’s germline during spermatogenesis. It remains unknown whether larger mutations, such as deletions and duplications of hundreds or thousands of nucleotides, follow similar patterns. Such mutations lead to copy-number variation (CNV) within and between species, and can have profound effects by deleting or duplicating genes. Here we analyze patterns of CNV mutatio...
53 references, page 1 of 4

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Antaki D, Brandler WM, Sebat J. 2018. Sv2: Accurate structural variation genotyping and de novo mutation detection from whole genomes. Bioinformatics. 34:1774-1777.

Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. 2001. Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res. 11:1005-1017. [OpenAIRE]

Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, Barrera DJ, Lin GN, Malhotra D, Watts AC, et al. 2016. Frequency and complexity of de novo structural mutation in autism. Am J Hum Genet. 98:667-679.

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, et al. 2014. Gibbon genome and the fast karyotype evolution of small apes. Nature. 513:195-201.

Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM. 2015. Speedseq: Ultra-fast personal genome analysis and interpretation. Nat Methods. 12:966-968. [OpenAIRE]

Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. 2006. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 38:75-81.

Crow JF. 2000. The origins, patterns and implications of human spontaneous mutation. Nat Rev Genet. 1:40-47.

Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JR, Sikela JM. 2007. Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res. 17:1266-1277.

Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, Carter NP, Church DM, Felsenfeld A, Guyer M, Lee C, et al. 2007. Completing the map of human genetic variation. Nature. 447:161-165.

Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584. [OpenAIRE]

Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, et al. 2004. Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol. 2:E207. [OpenAIRE]

Gazave E, Darre F, Morcillo-Suarez C, Petit-Marty N, Carreno A, Marigorta UM, Ryder OA, Blancher A, Rocchi M, Bosch E, et al. 2011. Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome Res. 21:1626-1639.

Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, et al. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 316:222-234.

Girard SL, Bourassa CV, Lemieux Perreault LP, Legault MA, Barhdadi A, Ambalavanan A, Brendgen M, Vitaro F, Noreau A, Dionne G, et al. 2016. Paternal age explains a major portion of de novo germline mutation rate variability in healthy individuals. PLoS One. 11:e0164212. [OpenAIRE]

53 references, page 1 of 4
Abstract
<jats:title>Abstract</jats:title><jats:p>Mutations play a key role in the development of disease in an individual and the evolution of traits within species. Recent work in humans and other primates has clarified the origins and patterns of single nucleotide variants, showing that most arise in the father’s germline during spermatogenesis. It remains unknown whether larger mutations, such as deletions and duplications of hundreds or thousands of nucleotides, follow similar patterns. Such mutations lead to copy-number variation (CNV) within and between species, and can have profound effects by deleting or duplicating genes. Here we analyze patterns of CNV mutatio...
53 references, page 1 of 4

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.

Antaki D, Brandler WM, Sebat J. 2018. Sv2: Accurate structural variation genotyping and de novo mutation detection from whole genomes. Bioinformatics. 34:1774-1777.

Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. 2001. Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res. 11:1005-1017. [OpenAIRE]

Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, Barrera DJ, Lin GN, Malhotra D, Watts AC, et al. 2016. Frequency and complexity of de novo structural mutation in autism. Am J Hum Genet. 98:667-679.

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, et al. 2014. Gibbon genome and the fast karyotype evolution of small apes. Nature. 513:195-201.

Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM. 2015. Speedseq: Ultra-fast personal genome analysis and interpretation. Nat Methods. 12:966-968. [OpenAIRE]

Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. 2006. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 38:75-81.

Crow JF. 2000. The origins, patterns and implications of human spontaneous mutation. Nat Rev Genet. 1:40-47.

Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JR, Sikela JM. 2007. Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res. 17:1266-1277.

Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, Carter NP, Church DM, Felsenfeld A, Guyer M, Lee C, et al. 2007. Completing the map of human genetic variation. Nature. 447:161-165.

Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584. [OpenAIRE]

Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, et al. 2004. Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol. 2:E207. [OpenAIRE]

Gazave E, Darre F, Morcillo-Suarez C, Petit-Marty N, Carreno A, Marigorta UM, Ryder OA, Blancher A, Rocchi M, Bosch E, et al. 2011. Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome Res. 21:1626-1639.

Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, et al. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 316:222-234.

Girard SL, Bourassa CV, Lemieux Perreault LP, Legault MA, Barhdadi A, Ambalavanan A, Brendgen M, Vitaro F, Noreau A, Dionne G, et al. 2016. Paternal age explains a major portion of de novo germline mutation rate variability in healthy individuals. PLoS One. 11:e0164212. [OpenAIRE]

53 references, page 1 of 4
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