A Preliminary Study of Copy Number Variation in Tibetans

Abstract

Genetic features of Tibetans have been broadly investigated, but the properties of copy number variation (CNV) have not been well examined. To get a preliminary view of CNV in Tibetans, we scanned 29 Tibetan genomes with the Illumina Human-1 M high-resolution genotyping microarray and identified 139 putative copy number variable regions (CNVRs), consisting of 70 deletions, 61 duplications, and 8 multi-allelic loci. Thirty-four of the 139 CNVRs showed differential allele frequencies versus other East-Asian populations, with P values <0.0001. These results indicated a distinct pattern of CNVR allele frequency distribution in Tibetans. The Tibetan CNVRs are enriched for genes in the disease class of human reproduction (such as genes from the DAZ, BPY2, CDY, and HLA-DQ and -DR gene clusters) and biological process categories of “response to DNA damage stimulus” and “DNA repair” (such as RAD51, RAD52, and MRE11A). These genes are related to the adaptive traits of high infant birth weight and darker skin tone of Tibetans, and may be attributed to recent local adaptation. Our results provide a different view of genetic diversity in Tibetans and new insights into their high-altitude adaptation.

Novel Population Specific Autosomal Copy Number Variation and Its Functional Analysis amongst Negritos from Peninsular Malaysia

“…Overall size of the CNV observed also corresponded well. Approximately 58% of the CNVs found in Negrito were <30 kb, in line with reports by Yim et al [27] on the Korean genomes and Ku et al [32]; but was relatively higher than the reported by Zhang et al [30] and McElroy et al [33]. The average number of CNVs detected in the HapMap3 dataset (average CNV call per genome  = 102.2) (data not shown) and the Chinese populations (average CNV call per genome  = 140.9) [29] were much higher.…”

Identification of Independent Primary Tumors and Intrapulmonary Metastases Using DNA Rearrangements in Non–Small-Cell Lung Cancer

“…A study on the genomes of 385 healthy African American and 435 healthy white patients predicted averages of 3.5 and 4.8 CNV per genome, respectively. 35 In these and other germline CNV studies, [36][37] the majority of events arise from smaller intrachromosomal events spanning less than 30 kb. Through our extensive MP sequencing data of more than 500 tumors, we have been able to assemble a robust database of common germline variations to efficiently filter out the majority of polymorphic germline events.…”

Ladakh, India: the land of high passes and genetic heterogeneity reveals a confluence of migrations

“…Of all the populations examined in this study (see Supplementary Table S1 for articles [24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] citing the reference populations), Ladakh, Southern Iran and Pakistan, exhibit the highest Y-chromosome diversity. Interesting, these three populations lie in a region of genetic confluence geographically located in west-central Asia.…”