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Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three East Asian minority ethnicities.
Forensic Sci Int Genet. 2018 Jul; 35:141-148.FS

Abstract

Massively parallel sequencing (MPS) technologies can sequence many targeted regions of multiple samples simultaneously and are gaining great interest in the forensic community. The Precision ID Identity Panel contains 90 autosomal SNPs and 34 upper Y-Clade SNPs, which was designed with small amplicons and optimized for forensic degraded or challenging samples. Here, 184 unrelated individuals from three East Asian minority ethnicities (Tibetan, Uygur and Hui) were analyzed using the Precision ID Identity Panel and the Ion PGM System. The sequencing performance and corresponding forensic statistical parameters of this MPS-SNP panel were investigated. The inter-population relationships and substructures among three investigated populations and 30 worldwide populations were further investigated using PCA, MDS, cladogram and STRUCTURE. No significant deviation from Hardy-Weinberg equilibrium (HWE) and Linkage Disequilibrium (LD) tests was observed across all 90 autosomal SNPs. The combined matching probability (CMP) for Tibetan, Uygur and Hui were 2.5880 × 10-33, 1.7480 × 10-35 and 4.6326 × 10-34 respectively, and the combined power of exclusion (CPE) were 0.999999386152271, 0.999999607712827 and 0.999999696360182 respectively. For 34 Y-SNPs, only 16 haplogroups were obtained, but the haplogroup distributions differ among the three populations. Tibetans from the Sino-Tibetan population and Hui with multiple ethnicities with an admixture population have genetic affinity with East Asian populations, while Uygurs of a Eurasian admixture population have similar genetic components to the South Asian populations and are distributed between East Asian and European populations. The aforementioned results suggest that the Precision ID Identity Panel is informative and polymorphic in three investigated populations and could be used as an effective tool for human forensics.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Liu J
Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
Wang Z
Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
He G
Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
Zhao X
Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.
Wang M
Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
Luo T
Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China.
Li C
Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Science, Ministry of Justice, Shanghai 200063, China.
Hou Y
Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China. Electronic address: forensic@scu.edu.cn.

MeSH

AsiaAsian PeopleChromosomes, Human, YEthnicityGenetics, PopulationHaplotypesHigh-Throughput Nucleotide SequencingHumansPolymorphism, Single NucleotideSequence Analysis, DNA

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

29778045

Citation

Liu, Jing, et al. "Massively Parallel Sequencing of 124 SNPs Included in the Precision ID Identity Panel in Three East Asian Minority Ethnicities." Forensic Science International. Genetics, vol. 35, 2018, pp. 141-148.
Liu J, Wang Z, He G, et al. Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three East Asian minority ethnicities. Forensic Sci Int Genet. 2018;35:141-148.
Liu, J., Wang, Z., He, G., Zhao, X., Wang, M., Luo, T., Li, C., & Hou, Y. (2018). Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three East Asian minority ethnicities. Forensic Science International. Genetics, 35, 141-148. https://doi.org/10.1016/j.fsigen.2018.05.002
Liu J, et al. Massively Parallel Sequencing of 124 SNPs Included in the Precision ID Identity Panel in Three East Asian Minority Ethnicities. Forensic Sci Int Genet. 2018;35:141-148. PubMed PMID: 29778045.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three East Asian minority ethnicities. AU - Liu,Jing, AU - Wang,Zheng, AU - He,Guanglin, AU - Zhao,Xueying, AU - Wang,Mengge, AU - Luo,Tao, AU - Li,Chengtao, AU - Hou,Yiping, Y1 - 2018/05/26/ PY - 2017/12/14/received PY - 2018/5/9/revised PY - 2018/5/10/accepted PY - 2018/5/20/pubmed PY - 2018/12/12/medline PY - 2018/5/20/entrez KW - Forensic genetics KW - Genetic polymorphism KW - Massively parallel sequencing (MPS) KW - Precision ID identity panel SP - 141 EP - 148 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 35 N2 - Massively parallel sequencing (MPS) technologies can sequence many targeted regions of multiple samples simultaneously and are gaining great interest in the forensic community. The Precision ID Identity Panel contains 90 autosomal SNPs and 34 upper Y-Clade SNPs, which was designed with small amplicons and optimized for forensic degraded or challenging samples. Here, 184 unrelated individuals from three East Asian minority ethnicities (Tibetan, Uygur and Hui) were analyzed using the Precision ID Identity Panel and the Ion PGM System. The sequencing performance and corresponding forensic statistical parameters of this MPS-SNP panel were investigated. The inter-population relationships and substructures among three investigated populations and 30 worldwide populations were further investigated using PCA, MDS, cladogram and STRUCTURE. No significant deviation from Hardy-Weinberg equilibrium (HWE) and Linkage Disequilibrium (LD) tests was observed across all 90 autosomal SNPs. The combined matching probability (CMP) for Tibetan, Uygur and Hui were 2.5880 × 10-33, 1.7480 × 10-35 and 4.6326 × 10-34 respectively, and the combined power of exclusion (CPE) were 0.999999386152271, 0.999999607712827 and 0.999999696360182 respectively. For 34 Y-SNPs, only 16 haplogroups were obtained, but the haplogroup distributions differ among the three populations. Tibetans from the Sino-Tibetan population and Hui with multiple ethnicities with an admixture population have genetic affinity with East Asian populations, while Uygurs of a Eurasian admixture population have similar genetic components to the South Asian populations and are distributed between East Asian and European populations. The aforementioned results suggest that the Precision ID Identity Panel is informative and polymorphic in three investigated populations and could be used as an effective tool for human forensics. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/29778045/Massively_parallel_sequencing_of_124_SNPs_included_in_the_precision_ID_identity_panel_in_three_East_Asian_minority_ethnicities_ DB - PRIME DP - Unbound Medicine ER -