SNP typing using the HID-Ion AmpliSeq™ Identity Panel in a southern Chinese population
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.
KeywordsSingle nucleotide polymorphism (SNP) Next generation sequencing (NGS) Ion torrent PGM™ Population genetics Miscalled reads
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.
Informed consent was obtained from all individual participants included in the study.
- 4.Sanchez JJ, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27:1713–1724CrossRefPubMedGoogle Scholar
- 11.Eduardoff M, Santos C, de la Puente M, Gross TE, Fondevila M, Strobl C, Sobrino B, Ballard D, Schneider PM, Carracedo Á, Lareu MV, Parson W, Phillips C (2015) Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™. Forensic Sci Int Genet 17:110–121CrossRefPubMedGoogle Scholar
- 12.Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352CrossRefPubMedGoogle Scholar
- 16.Athey TW (2006) Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach. J Genet Geneal 2:34–39Google Scholar
- 17.Athey TW (2005) Haplogroup prediction from Y-STR values using an allele-frequency approach. J Genet Geneal 1:1–7Google Scholar
- 21.International Society of Genetic Genealogy (ISOGG): Y-DNA Haplogroup Tree 2017, Version: 12.128. In, 2017. Available at: http://www.isogg.org/tree/
- 22.Wright S (1978) Evolution and the genetics of populations. Vol. 4. Variability within and among natural populations. University of Chicago Press, ChicagoGoogle Scholar
- 23.Phillips C, García-Magariños M, Salas A, Carracedo Á, Lareu MV (2012) SNPs as supplements in simple kinship analysis or as core markers in distant pairwise relationship tests: when do SNPs add value or replace well-established and powerful STR tests? Transfus Med Hemoth 39:202–210CrossRefGoogle Scholar
- 29.Athey W (2011) Comments on the article, “Software for Y haplogroup predictions, a word of caution”. Int J Legal Med 125(901–903):905–906Google Scholar