title: Species specific exome probes reveal new insights in positively selected genes in nonhuman primates.
abstract: Nonhuman primates (NHP) are important biomedical animal models for the study of human disease. Of these, the most widely used models in biomedical research currently are from the genus Macaca. However, evolutionary genetic divergence between human and NHP species makes human-based probes inefficient for the capture of genomic regions of NHP for sequencing and study. Here we introduce a new method to resequence the exome of NHP species by a designed capture approach specifically targeted to the NHP, and demonstrate its superior performance on four NHP species or subspecies. Detailed investigation on biomedically relevant genes demonstrated superior capture by the new approach. We identified 28 genes that appeared to be pseudogenized and inactivated in macaque. Finally, we identified 187 genes showing strong evidence for positive selection across all branches of the primate phylogeny including many novel findings.
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong 518083, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Su
authors.affiliation: Shool of bioscience &bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Translational Medicine Research Centre, Merck Research Laboratories, MSD, 8 Biomedical Grove, Neuros #04-01, Singapore 138665, Singapore.
authors.forename: Chanchal
authors.initials: C
authors.lastname: Kumar
authors.affiliation: Merck Research Laboratories, Merck &Co. Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA.
authors.forename: Cliona
authors.initials: C
authors.lastname: Molony
authors.affiliation: Informatics IT, MSD R&D (China) Co., Ltd., Beijing, China.
authors.forename: Hongchao
authors.initials: H
authors.lastname: Lu
authors.affiliation: Informatics IT, MSD R&D (China) Co., Ltd., Beijing, China.|Informatics IT, Merck &Co., Inc., Boston, MA, USA.
authors.forename: Ronghua
authors.initials: R
authors.lastname: Chen
authors.affiliation: Merck Research Laboratories, Merck &Co. Inc., 770 Sumneytown Pike, WP53B-120 West Point, PA 19486, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Stone
authors.affiliation: Shool of bioscience &bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Ling
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong 518083, China.|Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark.
authors.forename: Xiao
authors.initials: X
authors.lastname: Liu