A genome-wide characterization of copy number variations in native populations of Peninsular Malaysia

• Published in: European Journal of Human Genetics
• Main Author: Fu R.; Mokhtar S.S.; Phipps M.E.; Hoh B.-P.; Xu S.
• Format: Article
• Language: English
• Published: Nature Publishing Group 2018
• Online Access: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042424032&doi=10.1038%2fs41431-018-0120-8&partnerID=40&md5=2e44b83d7f33e369d80d54ef0a39d488

Copy number variations (CNVs) are genomic structural variations that result from the deletion or duplication of large genomic segments. The characterization of CNVs is largely underrepresented, particularly those of indigenous populations, such as the Orang Asli in Peninsular Malaysia. In the present study, we first characterized the genome-wide CNVs of four major native populations from Peninsular Malaysia, including the Malays and three Orang Asli populations; namely, Proto-Malay, Senoi, and Negrito (collectively called PM). We subsequently assessed the distribution of CNVs across the four populations. The resulting global CNV map revealed 3102 CNVs, with an average of more than 100 CNVs per individual. We identified genes harboring CNVs that are highly differentiated between PM and global populations, indicating that these genes are predominantly enriched in immune responses and defense functions, including APOBEC3A-B, beta-defensin genes, and CCL3L1, followed by other biological functions, such as drug and toxin metabolism and responses to radiation, suggesting some attributions between CNV variations and adaptations of the PM groups to the local environmental conditions of tropical rainforests. © 2018 European Society of Human Genetics.