TY - JOUR
T1 - Development of a SNP set for human identification
T2 - A set with high powers of discrimination which yields high genetic information from naturally degraded DNA samples in the Thai population
AU - Boonyarit, Hathaichanoke
AU - Mahasirimongkol, Surakameth
AU - Chavalvechakul, Nuttama
AU - Aoki, Masayuki
AU - Amitani, Hanae
AU - Hosono, Naoya
AU - Kamatani, Naoyuki
AU - Kubo, Michiaki
AU - Lertrit, Patcharee
N1 - Funding Information:
This study was supported by the Laboratory for Genotyping Development, RIKEN Center for Genomic Medicine, Yokohama, Japan , through the Department of Medical Science (DMSc)-RIKEN collaboration and by the Thailand Research Fund (TRF) through the Royal Golden Jubilee (RGJ) Ph.D. Program (Grant number PHD/0328/2550 ) to H. Boonyarit and P. Lertrit. We would like to thank Dr Jim Stankovich for the proof reading of this manuscript and Dr Bhoom Suktitipat for the calculation of median matched probability of STR and SNPs genotyping used in the plot of Fig. 4 , and the two anonymous reviewers for their critical and constructive comments of the manuscript. We would also like to thank the Institute of Forensic Medicine, Police General Hospital, Royal Thai Police, Thailand for supporting the sample collection from deceased individuals. Finally, we thank all participants who gave samples for this research and we thank everyone for their help and support during the sample collection. P. Lertrit is supported by " Chalermphrakiat" Grant, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand.
PY - 2014/7
Y1 - 2014/7
N2 - 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.
AB - 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.
KW - Degraded DNA
KW - Human identification
KW - Invader assay
KW - Short tandem repeat (STR)
KW - Single nucleotide polymorphism (SNP)
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U2 - 10.1016/j.fsigen.2014.03.010
DO - 10.1016/j.fsigen.2014.03.010
M3 - Article
C2 - 24747184
AN - SCOPUS:84898943653
SN - 1872-4973
VL - 11
SP - 166
EP - 173
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
IS - 1
ER -