A 21‐Locus Autosomal SNP Multiplex and its Application in Forensic Science

Abstract

To develop a cost-effective technique for single-nucleotide polymorphism (SNP) genotyping and improve the efficiency to analyze degraded DNA, we have established a novel multiplex system including 21-locus autosomal SNPs and amelogenin locus, which was based on allele-specific amplification (ASA) and universal reporter primers (URP). The target amplicons for each of the 21 SNPs arranged from 63 base pair (bp) to 192 bp. The system was tested in 539 samples from three ethnic groups (Han, Mongolian, and Zhuang population) in China, and the total power of discrimination (TPD) and cumulative probability of exclusion (CPE) were more than 0.99999999 and 0.98, respectively. The system was further validated with forensic samples and full profiles could be achieved from degraded DNA and 63 case-type samples. In summary, the multiplex system offers an effective technique for individual identification of forensic samples and is much more efficient in the analysis of degraded DNA compared with standard STR typing.

Massively parallel sequencing of 231 autosomal SNPs with a custom panel: a SNP typing assay developed for human identification with Ion Torrent PGM

“…In this study, 129 polymorphic universal SNPs from database of SNPforID [ 11 ] and IISNP [ 12 ] with MAF > 0.1 in Chinese Han [ 9 ] were included first. With published references of [ 13–20 ], 25 new SNPs with MAF > 0.3 in CHB or Asian population were found. Three SNPs (rs1029047, rs3808378 and rs1108414) of them were located within long homopolymers with sequence-checking and should be excluded from the panel.…”

“…The newly developed panel we present here allows simultaneous sequencing of 231 SNPs chosen from SNPforID [ 11 ], IISNP [ 12 ], HapMap, dbSNP and published literatures [ 13–20 ] for forensic application. The library length ranges from 125 to 175 bp, which is suitable for sequencing of degraded DNA.…”

“…The following steps of SNP screening were applied: Universal SNPs included in SNPforID [ 11 ] and IISNP [ 12 ] with minor allele frequency (MAF) above 0.1 in Chinese Han population [ 9 ] were included. SNPs reported with MAF > 0.3 in Han population of China or Asian populations by extensive studies [ 13–20 ] were included. SNPs should follow Hardy–Weinberg equilibrium (HWE).…”

“…SNPs reported with MAF > 0.3 in Han population of China or Asian populations by extensive studies [ 13–20 ] were included. SNPs should follow Hardy–Weinberg equilibrium (HWE).…”

Genotyping of 75 SNPs using arrays for individual identification in five population groups

“…Lou et al reported the performance of a 44 SNPs individual identification assay for Chinese based on an IISNP panel established by Pakstis et al [8,14]. There are other combinations of IISNPs for different Asian populations reported [18][19][20]. An IISNP panel for global forensic casework was established recently [21].…”