Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes

Abstract

Insertion/deletion (InDel) polymorphisms, combined desirable characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), are considerable potential in the fields of forensic practices and population genetics. However, most commercial InDel kits designed based on non-Asians limited extensive forensic applications in East Asian (EAS) populations. Recently, a novel 6-dye direct and multiplex PCR-CE-based typing system was designed on the basis of genome-wide EAS population data, which could amplify 60 molecular genetic markers, consisting of 57 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels), and Amelogenin in a single PCR reaction and detect by capillary electrophoresis, simultaneously. In the present study, the DNA profiles of 279 unrelated individuals from the Hainan Li group were generated by the novel typing system. In addition, we collected two A-InDel sets to evaluate the forensic performances of the novel system in the 1,000 Genomes Project (1KG) populations and Hainan Li group. For the Universal A-InDel set (UAIS, containing 44 A-InDels) the cumulative power of discrimination (CPD) ranged from 1–1.03 × 10–14 to 1–1.27 × 10–18, and the cumulative power of exclusion (CPE) varied from 0.993634 to 0.999908 in the 1KG populations. For the East Asia-based A-InDel set (EAIS, containing 57 A-InDels) the CPD spanned from 1–1.32 × 10–23 to 1–9.42 × 10–24, and the CPE ranged from 0.999965 to 0.999997. In the Hainan Li group, the average heterozygote (He) was 0.4666 (0.2366–0.5448), and the polymorphism information content (PIC) spanned from 0.2116 to 0.3750 (mean PIC: 0.3563 ± 0.0291). In total, the CPD and CPE of 57 A-InDels were 1–1.32 × 10–23 and 0.999965, respectively. Consequently, the novel 6-dye direct and multiplex PCR-CE-based typing system could be considered as the reliable and robust tool for human identification and intercontinental population differentiation, and supplied additional information for kinship analysis in the 1KG populations and Hainan Li group.

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

“…Two commercial InDel kit exist: (1) Investigator DIPlex (QIAGEN, Hilden, Germany) with 30 InDels [ [527] , [528] , [529] , [530] , [531] ] and (2) InnoTyper 21 (InnoGenomics, New Orleans, Louisiana, USA) with 21 autosomal insertion-null (INNUL) markers [ [532] , [533] , [534] , [535] ]. In addition, a number of InDel assays have been published including a 32plex [ 536 ], a 35plex [ 537 ], a 38plex [ 538 ], a 39plex with AIMs [ 539 ], a 43plex [ 540 ], a 57plex [ 541 ], a 60plex with 57 autosomal InDels, 2 Y-chromosome InDels, and amelogenin [ 542 ], a 32plex with X-chromosome InDels [ 543 ], and a 21plex with AIMs [ 544 ].…”

Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures

“…The mean values and standard deviations (SDs) of the DoC, N-1 stutter ratio for Y-STRs, and ACR values for MHs were calculated by SAS ® 9.4 software (SAS Institute Inc., Cary, NC, USA). The other relevant forensic parameters were determined as described in our previous studies [88][89][90][91][92][93][94][95][96][97][98][99]. A e was calculated using the formula proposed by Kidd et al [100], A e = 1 ∑…”

Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel

“…Compared with short tandem repeat (STR) ( Romanini et al, 2015 ), DIP is relatively lower mutation rate, no stutter and shorter amplicon, which is suitable to be genotyped using by capillary electrophoresis (CE) platform and increases the possibility to gain genotype information from compromised sample ( Tie et al, 2022 ). In order to enhance the applicability of the detection system for degraded biological sample from crime scene, forensic researchers always try to design the amplicons of molecular genetic markers with less than 200bp ( Chen et al, 2019 ; Jin R. et al, 2021a ; Fan et al, 2021 ). So far, a series of DIP multiplex amplification systems have been developed to meet different forensic objectives like individual identification and kinship testing over the past decade.…”

“…The Investigator ® DIPplex kit was the first commercial DIPplex panel for forensic individual identification, but the 30 A-DIPs included in this kit were low polymorphic in Chinese different groups in several forensic genetic studies ( He et al, 2019 ; Jian et al, 2019 ; Zou et al, 2020 ; Jin X. et al, 2021b ). Subsequently, several in-house panels including 35 A-DIPs ( Jin et al, 2019 ), and 43 A-DIPs in this study ( Jin R. et al, 2021a ), and commercial kits including 32 X-DIPs ( Gomes et al, 2020 ), 38 X-DIPs ( Chen et al, 2021 ), AGCU DIP 50 kit ( Chen et al, 2019 ), and AGCU DIP 60 kit ( Fan et al, 2021 ) were developed. A new DIP detection system including 39 ancestral informative DIPs exploited by ourselves was also used to infer the biogeographic ancestry ( Jin et al, 2020 ; Zhang et al, 2021 ).…”