Development of a SNP set for human identification: A set with high powers of discrimination which yields high genetic information from naturally degraded DNA samples in the Thai population

Hathaichanoke Boonyarit, Surakameth Mahasirimongkol, Nuttama Chavalvechakul, Masayuki Aoki, Hanae Amitani, Naoya Hosono, Naoyuki Kamatani, Michiaki Kubo, Patcharee Lertrit

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

This study describes the development of a SNP typing system for human identification in the Thai population, in particular for extremely degraded DNA samples. A highly informative SNP marker set for forensic identification was identified, and a multiplex PCR-based Invader assay was developed. Fifty-one highly informative autosomal SNP markers and three sex determination SNP markers were amplified in two multiplex PCR reactions and then detected using Invader assay reactions. The average PCR product size was 71 base pairs. The match probability of the 54-SNP marker set in 124 Thai individuals was 1.48 × 10 -21 , higher than that of STR typing, suggesting that this 54-SNP marker set is beneficial for forensic identification in the Thai population. The selected SNP marker set was also evaluated in 90 artificially degraded samples, and in 128 naturally degraded DNA samples from real forensic casework which had shown no profiles or incomplete profiles when examined using a commercial STR typing system. A total of 56 degraded samples (44%) achieved the matching probability (PM) equivalent to STR gold standard analysis (successful genotyping of 44 SNP markers) for human identification. These data indicated that our novel 54-SNP marker set provides a very useful and valuable approach for forensic identification in the Thai population, especially in the case of highly to extremely degraded DNA. In summary, we have developed a set of 54 Thai-specific SNPs for human identification which have higher discrimination power than STR genotyping. The PCRs for these 54 SNP markers were successfully combined into two multiplex reactions and detected with an Invader assay. This novel SNP genotyping system also yields high levels of genetic information from naturally degraded samples, even though there are much more difficult to recover than artificially degraded samples.

Original languageEnglish
Pages (from-to)166-173
Number of pages8
JournalForensic Science International: Genetics
Volume11
Issue number1
DOIs
Publication statusPublished - 01-01-2014

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Forensic Anthropology
Single Nucleotide Polymorphism
DNA
Population
Multiplex Polymerase Chain Reaction
Polymerase Chain Reaction
Base Pairing

All Science Journal Classification (ASJC) codes

  • Pathology and Forensic Medicine
  • Genetics

Cite this

Boonyarit, Hathaichanoke ; Mahasirimongkol, Surakameth ; Chavalvechakul, Nuttama ; Aoki, Masayuki ; Amitani, Hanae ; Hosono, Naoya ; Kamatani, Naoyuki ; Kubo, Michiaki ; Lertrit, Patcharee. / Development of a SNP set for human identification : A set with high powers of discrimination which yields high genetic information from naturally degraded DNA samples in the Thai population. In: Forensic Science International: Genetics. 2014 ; Vol. 11, No. 1. pp. 166-173.
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abstract = "This study describes the development of a SNP typing system for human identification in the Thai population, in particular for extremely degraded DNA samples. A highly informative SNP marker set for forensic identification was identified, and a multiplex PCR-based Invader assay was developed. Fifty-one highly informative autosomal SNP markers and three sex determination SNP markers were amplified in two multiplex PCR reactions and then detected using Invader assay reactions. The average PCR product size was 71 base pairs. The match probability of the 54-SNP marker set in 124 Thai individuals was 1.48 × 10 -21 , higher than that of STR typing, suggesting that this 54-SNP marker set is beneficial for forensic identification in the Thai population. The selected SNP marker set was also evaluated in 90 artificially degraded samples, and in 128 naturally degraded DNA samples from real forensic casework which had shown no profiles or incomplete profiles when examined using a commercial STR typing system. A total of 56 degraded samples (44{\%}) achieved the matching probability (PM) equivalent to STR gold standard analysis (successful genotyping of 44 SNP markers) for human identification. These data indicated that our novel 54-SNP marker set provides a very useful and valuable approach for forensic identification in the Thai population, especially in the case of highly to extremely degraded DNA. In summary, we have developed a set of 54 Thai-specific SNPs for human identification which have higher discrimination power than STR genotyping. The PCRs for these 54 SNP markers were successfully combined into two multiplex reactions and detected with an Invader assay. This novel SNP genotyping system also yields high levels of genetic information from naturally degraded samples, even though there are much more difficult to recover than artificially degraded samples.",
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Development of a SNP set for human identification : A set with high powers of discrimination which yields high genetic information from naturally degraded DNA samples in the Thai population. / Boonyarit, Hathaichanoke; Mahasirimongkol, Surakameth; Chavalvechakul, Nuttama; Aoki, Masayuki; Amitani, Hanae; Hosono, Naoya; Kamatani, Naoyuki; Kubo, Michiaki; Lertrit, Patcharee.

In: Forensic Science International: Genetics, Vol. 11, No. 1, 01.01.2014, p. 166-173.

Research output: Contribution to journalArticle

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AU - Amitani, Hanae

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