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Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ Identity Panel on the Ion Torrent PGM™ platform.
Forensic Sci Int Genet. 2016 11; 25:73-84.FS

Abstract

The HID-Ion AmpliSeq™ Identity Panel (the HID Identity Panel) is designed to detect 124-plex single nucleotide polymorphisms (SNPs) with next generation sequencing (NGS) technology on the Ion Torrent PGM™ platform, including 90 individual identification SNPs (IISNPs) on autosomal chromosomes and 34 lineage informative SNPs (LISNPs) on Y chromosome. In this study, we evaluated performance for the HID Identity Panel to provide a reference for NGS-SNP application, focusing on locus strand balance, locus coverage balance, heterozygote balance, and background signals. Besides, several experiments were carried out to find out improvements and limitations of this panel, including studies of species specificity, repeatability and concordance, sensitivity, mixtures, case-type samples and degraded samples, population genetics and pedigrees following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. In addition, Southern and Northern Chinese Han were investigated to assess applicability of this panel. Results showed this panel led to cross-reactivity with primates to some extent but rarely with non-primate animals. Repeatable and concordant genotypes could be obtained in triplicate with one exception at rs7520386. Full profiles could be obtained from 100pg input DNA, but the optimal input DNA would be 1ng-200pg with 21 initial PCR cycles. A sample with ≥20% minor contributor could be considered as a mixture by the number of homozygotes, and full profiles belonging to minor contributors could be detected between 9:1 and 1:9 mixtures with known reference profiles. Also, this assay could be used for case-type samples and degraded samples. For autosomal SNPs (A-SNPs), FST across all 90loci was not significantly different between Southern and Northern Chinese Han or between male and female samples. All A-SNP loci were independent in Chinese Han population. Except for 18loci with He <0.4, most of the A-SNPs in the HID Identity Panel presented high polymorphisms. Forensic parameters were calculated as >99.999% for combined discrimination power (CDP), 0.999999724 for combined power of exclusion (CPE), 1.390×10[11] for combined likelihood ratio (CLR) of trios, and 2.361×10[6] for CLR of motherless duos. For Y-SNPs, a total of 8 haplotypes were observed with the value of 0.684 for haplotype diversity. As a whole, the HID Identity Panel is a well-performed, robust, reliable and high informative NGS-SNP assay and it can fully meet requirements for individual identification and paternity testing in forensic science.

Authors+Show Affiliations

Department of Forensic Medicine, National Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang, Liaoning 110854, PR China; Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China.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.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China; China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China. Electronic address: jiangxianhua_2006@aliyun.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27500651

Citation

Guo, Fei, et al. "Next Generation Sequencing of SNPs Using the HID-Ion AmpliSeq™ Identity Panel On the Ion Torrent PGM™ Platform." Forensic Science International. Genetics, vol. 25, 2016, pp. 73-84.
Guo F, Zhou Y, Song H, et al. Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ Identity Panel on the Ion Torrent PGM™ platform. Forensic Sci Int Genet. 2016;25:73-84.
Guo, F., Zhou, Y., Song, H., Zhao, J., Shen, H., Zhao, B., Liu, F., & Jiang, X. (2016). Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ Identity Panel on the Ion Torrent PGM™ platform. Forensic Science International. Genetics, 25, 73-84. https://doi.org/10.1016/j.fsigen.2016.07.021
Guo F, et al. Next Generation Sequencing of SNPs Using the HID-Ion AmpliSeq™ Identity Panel On the Ion Torrent PGM™ Platform. Forensic Sci Int Genet. 2016;25:73-84. PubMed PMID: 27500651.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ Identity Panel on the Ion Torrent PGM™ platform. AU - Guo,Fei, AU - Zhou,Yishu, AU - Song,He, AU - Zhao,Jinling, AU - Shen,Hongying, AU - Zhao,Bin, AU - Liu,Feng, AU - Jiang,Xianhua, Y1 - 2016/07/29/ PY - 2016/01/20/received PY - 2016/07/10/revised PY - 2016/07/28/accepted PY - 2016/10/23/pubmed PY - 2017/6/15/medline PY - 2016/8/9/entrez KW - Evaluation KW - HID-Ion AmpliSeq™ KW - Identity Panel KW - Ion Torrent PGM™ KW - Next generation sequencing (NGS) KW - Population genetics KW - Single nucleotide polymorphism (SNP) SP - 73 EP - 84 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 25 N2 - The HID-Ion AmpliSeq™ Identity Panel (the HID Identity Panel) is designed to detect 124-plex single nucleotide polymorphisms (SNPs) with next generation sequencing (NGS) technology on the Ion Torrent PGM™ platform, including 90 individual identification SNPs (IISNPs) on autosomal chromosomes and 34 lineage informative SNPs (LISNPs) on Y chromosome. In this study, we evaluated performance for the HID Identity Panel to provide a reference for NGS-SNP application, focusing on locus strand balance, locus coverage balance, heterozygote balance, and background signals. Besides, several experiments were carried out to find out improvements and limitations of this panel, including studies of species specificity, repeatability and concordance, sensitivity, mixtures, case-type samples and degraded samples, population genetics and pedigrees following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. In addition, Southern and Northern Chinese Han were investigated to assess applicability of this panel. Results showed this panel led to cross-reactivity with primates to some extent but rarely with non-primate animals. Repeatable and concordant genotypes could be obtained in triplicate with one exception at rs7520386. Full profiles could be obtained from 100pg input DNA, but the optimal input DNA would be 1ng-200pg with 21 initial PCR cycles. A sample with ≥20% minor contributor could be considered as a mixture by the number of homozygotes, and full profiles belonging to minor contributors could be detected between 9:1 and 1:9 mixtures with known reference profiles. Also, this assay could be used for case-type samples and degraded samples. For autosomal SNPs (A-SNPs), FST across all 90loci was not significantly different between Southern and Northern Chinese Han or between male and female samples. All A-SNP loci were independent in Chinese Han population. Except for 18loci with He <0.4, most of the A-SNPs in the HID Identity Panel presented high polymorphisms. Forensic parameters were calculated as >99.999% for combined discrimination power (CDP), 0.999999724 for combined power of exclusion (CPE), 1.390×10[11] for combined likelihood ratio (CLR) of trios, and 2.361×10[6] for CLR of motherless duos. For Y-SNPs, a total of 8 haplotypes were observed with the value of 0.684 for haplotype diversity. As a whole, the HID Identity Panel is a well-performed, robust, reliable and high informative NGS-SNP assay and it can fully meet requirements for individual identification and paternity testing in forensic science. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/27500651/Next_generation_sequencing_of_SNPs_using_the_HID_Ion_AmpliSeq™_Identity_Panel_on_the_Ion_Torrent_PGM™_platform_ DB - PRIME DP - Unbound Medicine ER -