title: Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits.
abstract: BACKGROUND
  We report here the first genome-wide high-resolution polymorphism resource for non-human primate (NHP) association and linkage studies, constructed for the Caribbean-origin vervet monkey, or African green monkey (Chlorocebus aethiops sabaeus), one of the most widely used NHPs in biomedical research. We generated this resource by whole genome sequencing (WGS) of monkeys from the Vervet Research Colony (VRC), an NIH-supported research resource for which extensive phenotypic data are available.
  
  
  RESULTS
  We identified genome-wide single nucleotide polymorphisms (SNPs) by WGS of 721 members of an extended pedigree from the VRC. From high-depth WGS data we identified more than 4 million polymorphic unequivocal segregating sites; by pruning these SNPs based on heterozygosity, quality control filters, and the degree of linkage disequilibrium (LD) between SNPs, we constructed genome-wide panels suitable for genetic association (about 500,000 SNPs) and linkage analysis (about 150,000 SNPs). To further enhance the utility of these resources for linkage analysis, we used a further pruned subset of the linkage panel to generate multipoint identity by descent matrices.
  
  
  CONCLUSIONS
  The genetic and phenotypic resources now available for the VRC and other Caribbean-origin vervets enable their use for genetic investigation of traits relevant to human diseases.
authors.affiliation: Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.|Present address: 5200 Illumina Way, San Diego, CA, 92122, USA.
authors.forename: Yu S
authors.initials: YS
authors.lastname: Huang
authors.affiliation: Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
authors.forename: Vasily
authors.initials: V
authors.lastname: Ramensky
authors.affiliation: Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
authors.forename: Susan K
authors.initials: SK
authors.lastname: Service
authors.affiliation: Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.|Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
authors.forename: Anna J
authors.initials: AJ
authors.lastname: Jasinska
authors.affiliation: Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
authors.forename: Yoon
authors.initials: Y
authors.lastname: Jung
authors.affiliation: Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
authors.forename: Oi-Wa
authors.initials: OW
authors.lastname: Choi
authors.affiliation: Department of Human Genetics, University of California, Los Angeles, CA, 90095, USA.
authors.forename: Rita M
authors.initials: RM
authors.lastname: Cantor
authors.affiliation: Department of Human Genetics, McGill University, Montreal, Canada.
authors.forename: Nikoleta
authors.initials: N
authors.lastname: Juretic
authors.affiliation: Department of Human Genetics, McGill University, Montreal, Canada.
authors.forename: Jessica
authors.initials: J
authors.lastname: Wasserscheid
authors.affiliation: Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157-1040, USA.
authors.forename: Jay R
authors.initials: JR
authors.lastname: Kaplan
authors.affiliation: Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157-1040, USA.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Jorgensen
authors.affiliation: South Texas Diabetes and Obesity Institute, UTHSCSA/UTRGV, Brownsville, TX, USA.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Dyer
authors.affiliation: Department of Human Genetics, McGill University, Montreal, Canada.
authors.forename: Ken
authors.initials: K
authors.lastname: Dewar
authors.affiliation: South Texas Diabetes and Obesity Institute, UTHSCSA/UTRGV, Brownsville, TX, USA.
authors.forename: John
authors.initials: J
authors.lastname: Blangero
authors.affiliation: The Genome Institute, Washington University School of Medicine, Genome Sequencing Center, St. Louis, MO, 63108, USA.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.affiliation: The Genome Institute, Washington University School of Medicine, Genome Sequencing Center, St. Louis, MO, 63108, USA.
authors.forename: Wesley
authors.initials: W
authors.lastname: Warren
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06001, USA.
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.affiliation: Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA. nfreimer@mednet.ucla.edu.
authors.forename: Nelson B
authors.initials: NB
authors.lastname: Freimer
mesh_terms: D000818:Animals; D002522:Chlorocebus aethiops / Q000235:genetics*; D002874:Chromosome Mapping; D005260:Female; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D018895:Microsatellite Repeats; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017421:Sequence Analysis