Novel and low allele frequency variants observed in the exomes of Southern Han Chinese

作者：Ou, Minglin; Sui, Weiguo; Yang, Ming; Xiang, Zhen; Tang, Donge; Lin, Hua; Zhang, Yue; Chen, Jiejing; Zhu, Peng; Xue, Wen; Dai, Chengfu^*; Dai, Yong^*

来源：International Journal of Clinical and Experimental Medicine, 2017, 10(11): 15294-+.

• Southern Han Chinese
• DNA variant
• exome
• SNPs
• InDels

Precision medicine is growing recognized by clinicians, and well understanding of personal genomics is important for precision medicine in clinical practice. However, human DNA genetic variants in different regions still need to be emulated today. Here, we performed variant analysis of similar to 30,000 genes that affect the protein coding portion in Southern Han Chinese by whole exome sequencing. The sequencing data was aligned to the human reference genome and filtered by NCBI dbSNP database, the novel variants that were absent in the HapMap and dpSNP database were further annotated by 1000 Genomes (1 KG) and Exome Aggregation Consortium (ExAC). We identified 11,081 novel variants that were absent in the HapMap and dpSNP database, including 7,748 uncommon variants that were novel or with a low frequency in 1 KG and ExAC in eight individuals from south of China. The uncommon variants were scattered across the exomes in the different chromosomes. There were 494 uncommon variants, including 389 SNPs and 105 InDels observed in 3 individuals at least, of which 20 SNPs and 22 InDels were observed in three-quarters individuals. Function analysis indicated that the majority of observed uncommon variants in this study appeared to be functionally neutral in the Southern Han Chinese. In summary, we discover a great number of novel and low allele frequency DNA variants recurring in the exomes of Southern Han Chinese, which may be valuable for variant filtering in whole exome sequencing, improving the current human reference genome and precision medicine in the future.

• 出版日期2017
• 单位中国人民解放军第一八一医院; 暨南大学