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Genetic investigation of 124 SNPs in a Myanmar population using the Precision ID Identity Panel and the Illumina MiSeq

Authors
 Su Min Joo  ;  Ye-Lim Kwon  ;  Mi Hyeon Moon  ;  Kyoung-Jin Shin 
Citation
 LEGAL MEDICINE, Vol.63 : 102256, 2023-07 
Journal Title
LEGAL MEDICINE
ISSN
 1344-6223 
Issue Date
2023-07
MeSH
Asian People / genetics ; DNA Fingerprinting* ; Genetics, Population ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Microsatellite Repeats ; Myanmar ; Polymorphism, Single Nucleotide* / genetics ; Sequence Analysis, DNA ; Southeast Asian People* / genetics
Keywords
Human identification ; Illumina platform ; Myanmar population ; Next-generation sequencing ; Precision ID Identity Panel ; Single nucleotide polymorphisms
Abstract
Single nucleotide polymorphisms (SNPs) have become popular in forensic genetics as an alternative to short tandem repeats (STRs). The Precision ID Identity Panel (Thermo Fisher Scientific), consisting of 90 autosomal SNPs and 34 Y-chromosomal SNPs, enabled human identification studies on global populations through next-generation sequencing (NGS). However, most previous studies on the panel have used the Ion Torrent platform, and there are few reports on the Southeast Asian population. Here, a total of 96 unrelated males from Myanmar (Yangon) were analyzed with the Precision ID Identity Panel on a MiSeq (Illumina) using an in-house TruSeq compatible universal adapter and a custom variant caller, Visual SNP. The sequencing performance evaluated by locus balance and heterozygote balance was comparable to that of the Ion Torrent platform. For 90 autosomal SNPs, the combined match probability (CMP) was 6.994 × 10-34, lower than that of 22 PowerPlex Fusion autosomal STRs (3.130 × 10-26). For 34 Y-SNPs, 14 Y-haplogroups (mostly O2 and O1b) were observed. We found 51 cryptic variations (42 haplotypes) around target SNPs, of which haplotypes corresponding to 33 autosomal SNPs decreased CMP. Interpopulation analysis revealed that the Myanmar population is genetically closer to the East and Southeast Asian populations. In conclusion, the Precision ID Identity Panel can be successfully analyzed on the Illumina MiSeq and provides high discrimination power for human identification in the Myanmar population. This study broadened the accessibility of the NGS-based SNP panel by expanding the available NGS platforms and adopting a robust NGS data analysis tool.
Full Text
https://www.sciencedirect.com/science/article/pii/S1344622323000664
DOI
10.1016/j.legalmed.2023.102256
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Forensic Medicine (법의학과) > 1. Journal Papers
Yonsei Authors
Shin, Kyoung Jin(신경진) ORCID logo https://orcid.org/0000-0002-1059-9665
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/196554
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