title: Strategies for complete mitochondrial genome sequencing on Ion Torrent PGM™ platform in forensic sciences.
abstract: Next generation sequencing (NGS) is a time saving and cost-efficient method to detect the complete mitochondrial genome (mtGenome) compared to Sanger sequencing. In this study we focused on developing strategies for mtGenome sequencing on the Ion Torrent PGM™ platform and NGS data analysis. With our experience, 4, 15 and 30 samples could be loaded onto Ion 314™, Ion 316™ and Ion 318™ chips respectively at a pooling concentration of 26pM, achieving to sufficient average coverage of ≥1500 × and well strand balance of 1.05. Data processing software is essential to NGS mega data analysis. The in-house Perl scripts were developed for primary data analysis to screen out uncertain positions and samples from variant call format (VCF) reports and for pedigree study to perform pairwise comparisons. The Integrative Genomic Viewer (IGV) and the NextGENe software were introduced to secondary data analysis. The mthap and EMMA were employed for haplogroup assignment. The dataset was reviewed and approved by the EMPOP as the final version, which showed 2.66% error rate generated from the Torrent Variant Caller (TVC). Across the mtGenome, 4022 variants were found at 725 nucleotide positions, where ratio of transitions to transversions was estimated at 20.89:1 and 22.18% of variants was concentrated at hypervariable segments I and II (HVS-I and HVS-II). Totally, 107 complete mtGenome haplotypes were observed from 107 Northern Chinese Han and assigned to 88 haplogroups. The random match probability (RMP) of complete mtGenome was calculated as 0.009345794, decreasing 26.19% by comparison to that of HVS-I only, and the haplotype diversity (HD) was evaluated as 1, increasing 0.33% by comparison to that of HVS-I only. Principal component analysis (PCA) showed that our population was clustered to East and Southeast Asians. The strategies in this study are suitable for complete mtGenome sequencing on Ion Torrent PGM™ platform and Northern Chinese Han (EMP00670) is the first complete mtGenome dataset contributed to the EMPOP from East Asian.
authors.affiliation: China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China.
authors.forename: Yishu
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China; Department of Forensic Medicine, National Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang, Liaoning 110854, PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Guo
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Yu
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Feng
authors.initials: F
authors.lastname: Liu
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Jinling
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Hongying
authors.initials: H
authors.lastname: Shen
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhao
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Jia
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Zhu
authors.initials: Z
authors.lastname: Sun
authors.affiliation: China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China.
authors.forename: He
authors.initials: H
authors.lastname: Song
authors.affiliation: China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China; Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China. Electronic address: jiangxianhua_2006@aliyun.com.
authors.forename: Xianhua
authors.initials: X
authors.lastname: Jiang
mesh_terms: D044466:Asian People / Q000235:genetics; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000032:analysis / Q000235:genetics*; D044707:Forensic Sciences / Q000295:instrumentation / Q000379:methods*; D054629:Genome, Mitochondrial; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008928:Mitochondria / Q000737:chemistry / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004272:DNA, Mitochondrial
keywords: Forensic sciences; Ion Torrent PGM™; Mitochondrial genome (mtGenome); Next generation sequencing (NGS); Northern Chinese Han