Identification of transposable element-mediated deletions in 27 Korean individuals based on whole genome sequencing data
- 179 Downloads
The human genome has various genomic structural variations such as insertion/deletions between human individuals. These structural variations have led to genomic fluidity and rearrangements in individuals and populations. To investigate Korean-specific structural genomic variations, we performed next generation sequencing with 30× mean coverage from 27 Korean individuals using illumina-HiSeq 2000 platform. We collected a total of 119 deletion loci as transposable element-mediated Korean-specific deletion (KSD) candidates. Of the 119 loci, 35 were filtered out due to computational overlapping regions. A total of 78 loci were validated by PCR amplification with 27 Korean individuals and 80 human individuals from four different populations. We confirmed deletion breakpoints of the 78 loci using Sanger sequencing. We also investigated different deletion mechanisms based on sequencing alignment analysis. We found at least one KSD locus in 80 human individual panel. It has not been previously reported in human genomes. Here, for the first time, we report transposable element-mediated KSD study based on whole genome sequencing data of 27 Korean.
KeywordsNext generation sequencing Korean specific deletion Korean genome Transposable element
Compliance with ethical standards
Conflict of interest
The authors declare that there is no conflict of interests exists in this paper.
Written informed consent was obtained from all participants, and this research was approved by the institutional review boards of TheragenEtex Bio Institute.
- Riveira-Munoz E, He SM, Escaramis G, Stuart PE, Huffmeier U, Lee C, Kirby B, Oka A, Giardina E, Liao W et al (2011) Meta-analysis confirms the LCE3C_LCE3B deletion as a risk factor for psoriasis in several ethnic groups and finds interaction with HLA-Cw6. J Invest Dermatol 131:1105–1109PubMedCentralCrossRefPubMedGoogle Scholar