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SNP typing using the HID-Ion AmpliSeq™ Identity Panel in a southern Chinese population.
Int J Legal Med. 2018 Jul; 132(4):997-1006.IJ

Abstract

In the present study, 90 autosomal single nucleotide polymorphisms (SNPs) and 34 Y chromosomal SNPs were sequenced simultaneously using HID-Ion AmpliSeq™ Identity Panel on the Ion PGM™ platform for 125 samples in a southern Chinese population. Raw data were analyzed and forensic parameters were calculated. Haplogrouping concordance was also assessed using alternative methods based on Y-SNP haplotypes and Y-STR haplotypes. The results showed that allelic imbalance occurred more frequently with low coverage while several SNPs with high coverage were also observed with poor allelic balance, including rs214955, rs430046, rs7520386, rs876724, rs9171188, rs16981290, and rs2032631. Totally, 21,261 miscalled reads (0.28%) were observed. The rate of allele-specific miscalled reads (ASMRs) was higher than that of allele nonspecific miscalled reads (ANMRs) and associated with genetic diversity of the SNP. The ASMRs of major allele were lower than that of minor allele while there was no difference for ANMRs. The combined discrimination power (CDP) was 1-4.81 × 10-34 and the combined power of exclusion (CPE) was 0.99989 and 0.99999992 for duo and trio paternity testing, respectively. No significant genetic difference was detected between southern and northern Chinese populations. For haplogroup study, O2 was the predominant haplogroup and 97.01% of samples were assigned consistent haplogoups with Y-SNP and Y-STR haplotypes. In conclusion, the AmpliSeq™ Identity Panel was powerful for individual identification and trio paternity testing. ASMRs were associated with the genetic diversity and allele frequency while neither was related for ANMRs. High concordance of haplogrouping assignment can be obtained with Y-STR and Y-SNP haplotypes.

Authors+Show Affiliations

Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.The Center of Criminal Technology of Guangdong Province, Guangzhou, 510050, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.The Center of Criminal Technology of Guangdong Province, Guangzhou, 510050, People's Republic of China.The Second Clinical Medical School (Zhujiang Hospital), Southern Medical University, Guangzhou, 510280, People's Republic of China.Thermo Fisher Scientific Inc, South San Francisco, CA, 94080, USA.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.The Center of Criminal Technology of Guangdong Province, Guangzhou, 510050, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China. sunhy@mail.sysu.edu.cn. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510089, Guangdong, People's Republic of China. sunhy@mail.sysu.edu.cn.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29046953

Citation

Li, Ran, et al. "SNP Typing Using the HID-Ion AmpliSeq™ Identity Panel in a Southern Chinese Population." International Journal of Legal Medicine, vol. 132, no. 4, 2018, pp. 997-1006.
Li R, Zhang C, Li H, et al. SNP typing using the HID-Ion AmpliSeq™ Identity Panel in a southern Chinese population. Int J Legal Med. 2018;132(4):997-1006.
Li, R., Zhang, C., Li, H., Wu, R., Li, H., Tang, Z., Zhen, C., Ge, J., Peng, D., Wang, Y., Chen, H., & Sun, H. (2018). SNP typing using the HID-Ion AmpliSeq™ Identity Panel in a southern Chinese population. International Journal of Legal Medicine, 132(4), 997-1006. https://doi.org/10.1007/s00414-017-1706-3
Li R, et al. SNP Typing Using the HID-Ion AmpliSeq™ Identity Panel in a Southern Chinese Population. Int J Legal Med. 2018;132(4):997-1006. PubMed PMID: 29046953.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - SNP typing using the HID-Ion AmpliSeq™ Identity Panel in a southern Chinese population. AU - Li,Ran, AU - Zhang,Chuchu, AU - Li,Haiyan, AU - Wu,Riga, AU - Li,Haixia, AU - Tang,Zhenya, AU - Zhen,Chenhao, AU - Ge,Jianye, AU - Peng,Dan, AU - Wang,Ying, AU - Chen,Hongying, AU - Sun,Hongyu, Y1 - 2017/10/18/ PY - 2017/03/19/received PY - 2017/10/11/accepted PY - 2017/10/20/pubmed PY - 2018/10/17/medline PY - 2017/10/20/entrez KW - Ion torrent PGM™ KW - Miscalled reads KW - Next generation sequencing (NGS) KW - Population genetics KW - Single nucleotide polymorphism (SNP) SP - 997 EP - 1006 JF - International journal of legal medicine JO - Int J Legal Med VL - 132 IS - 4 N2 - In the present study, 90 autosomal single nucleotide polymorphisms (SNPs) and 34 Y chromosomal SNPs were sequenced simultaneously using HID-Ion AmpliSeq™ Identity Panel on the Ion PGM™ platform for 125 samples in a southern Chinese population. Raw data were analyzed and forensic parameters were calculated. Haplogrouping concordance was also assessed using alternative methods based on Y-SNP haplotypes and Y-STR haplotypes. The results showed that allelic imbalance occurred more frequently with low coverage while several SNPs with high coverage were also observed with poor allelic balance, including rs214955, rs430046, rs7520386, rs876724, rs9171188, rs16981290, and rs2032631. Totally, 21,261 miscalled reads (0.28%) were observed. The rate of allele-specific miscalled reads (ASMRs) was higher than that of allele nonspecific miscalled reads (ANMRs) and associated with genetic diversity of the SNP. The ASMRs of major allele were lower than that of minor allele while there was no difference for ANMRs. The combined discrimination power (CDP) was 1-4.81 × 10-34 and the combined power of exclusion (CPE) was 0.99989 and 0.99999992 for duo and trio paternity testing, respectively. No significant genetic difference was detected between southern and northern Chinese populations. For haplogroup study, O2 was the predominant haplogroup and 97.01% of samples were assigned consistent haplogoups with Y-SNP and Y-STR haplotypes. In conclusion, the AmpliSeq™ Identity Panel was powerful for individual identification and trio paternity testing. ASMRs were associated with the genetic diversity and allele frequency while neither was related for ANMRs. High concordance of haplogrouping assignment can be obtained with Y-STR and Y-SNP haplotypes. SN - 1437-1596 UR - https://www.unboundmedicine.com/medline/citation/29046953/SNP_typing_using_the_HID_Ion_AmpliSeq™_Identity_Panel_in_a_southern_Chinese_population_ L2 - https://dx.doi.org/10.1007/s00414-017-1706-3 DB - PRIME DP - Unbound Medicine ER -