Research paperA newly devised multiplex assay of novel polymorphic non-CODIS STRs as a valuable tool for forensic application
Introduction
The study of genetic markers allows a better understanding of the history and diversity of humans and provides a technique for forensic application [[1], [2], [3], [4]]. Short tandem repeats (STRs) are common genetic markers used in forensic DNA typing and were first used in 1991 in a forensic case [5]. Capillary electrophoresis (CE) technology allows more than two dozen STRs to be profiled at once, providing DNA evidence for personal identification, paternity and relationship-testing applications [6,7]. A variety of commercially available autosomal STR kits were developed in the forensic community, which mainly detect STR loci from the databases of the Combined DNA Index System (CODIS), Interpol Standard of Loci (ISSL) and European Standard Set (ESS) [[8], [9], [10]]. Supplementary Table S1 lists the main commercialized STR kits. Twenty-four autosomal STR loci from the above databases are mainly included in these kits, which are widely used for forensic applications.
Decades ago, many Chinese families were forced to send their children away, and their families became fragmented due to difficult periods such as “the great famine” or “the great cultural revolution”. Currently, these parents want to find their “lost” children, and brothers and sisters want to find their “lost” siblings. Therefore, the demand for resolving complex parentage testing in China’s forensic community is rising. However, available commercial STR kits cannot provide enough STR markers for such cases and often result in low likelihood ratio (LR) calculations [[11], [12], [13]]. In these cases, it is becoming necessary to increase the number of loci analysed to reach an adequate number of LRs [[11], [12], [13]].
In the present study, non-CODIS STR kits such as AGCU 21 + 1 (AGCU ScienTech Incorporation, China) [14], Goldeneye DNA ID 22NC (Goldeneye Technology Ltd., China) [15,16] and Microreader 23sp ID (Suzhou Microread Genetics, China) [17] are available. Some of the non-CODIS STRs included in the kits above are less polymorphic in the Chinese population and are physically close to the above twenty-four autosomal STRs that are commonly used [9,10,[14], [15], [16], [17]]. Kits including non-CODIS STRs that are based on massively parallel sequencing (MPS) technology, such as Precision ID GlobalFiler NGS STR (20 CODIS STRs and nine non-CODIS STRs) (Thermo Fisher Scientific, Waltham, USA) [18] and ForenSeq DNA Signature Prep kit (20 CODIS STRs, seven non-CODIS STRs, 24 Y-STRs, seven X-STRs and 94 identity informative SNPs) (Verogen, San Diego, USA) [19], can also be utilized to increase the power of kinship testing. It is expensive to establish these systems, which partially explains their uncommon application in laboratories. In light of the above, we try to discover more polymorphic, independent, suitable non-CODIS STRs and, on the basis of these STRs, develop a novel multiplex typing system to provide a new tool for DNA analysis in the forensic community. The developmental validation references the following: “Validation Guidelines for DNA Analysis Methods” [20] and “Basic Quality Requirements of Forensic Science Human Fluorescent STR Multiplex PCR Testing Reagent (GA/T815-2009)” [21].
Section snippets
STR candidate selection
The screening of candidates consists of two steps: (1) web scanning and (2) experimental screening.
- (1)
Web scanning: First, we scanned the Ensembl Genomes Database [22] (http://ensemblgenomes.org/) and UCSC (University of California Santa Cruz) Genome Browser [23] (http://genome.ucsc.edu/) and found 169,871 STS (Sequence-Tagged Sites) at 22 human autochromosomes. Second, we used Bedtools software (https://bedtools.readthedocs.io/) and obtained 15,645 STS markers within the intron region. Third, we
Construction and optimization of the novel non-CODIS multiplex system
Web scanning and experimental screening produced 18 promising polymorphic non-CODIS autosomal STRs (D1S1616, D1S1608, D2S437, D3S2457, D4S2406, D4S3249, D5S2843, D5S2501, D6S1010, D8S1039, D12S1301, D14S586, D15S815, SHGC-145653, CHLC.GATA14D12, D1S1603, HUMUT7148, and CHLC.GATA84D07). Since there are no studies or documents that describe the repeat motifs of these markers, we followed the rules in [37,38] to name the alleles of the 18 STRs. The detailed genetic information and motif repeats
Conclusion
This article outlines the development and validation of a novel multiplex system named the SiFaSTR 21plex_NCII Typing System. First, through web scanning and experimental screening, we discovered 18 new autosomal non-CODIS STR loci (D1S1616, D1S1608, D2S437, D3S2457, D4S2406, D4S3249, D5S2843, D5S2501, D6S1010, D8S1039, D12S1301, D14S586, D15S815, SHGC-145653, CHLC.GATA14D12, D1S1603, HUMUT7148, and CHLC.GATA84D07). The 18 newly discovered autosomal STRs are informative in the Chinese Han
Declaration of Competing Interest
The authors declare that they have no conflicts of interest.
Acknowledgments
This study was supported by grants from the National Natural Science Fund of China (Nos. 81625013 and 81930056), and the Shanghai Science and Technology Innovation Fund (18DZ1200300 and 19DZ2201400).
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2023, Forensic Science International: GeneticsCitation Excerpt :Match scores of true pairs all reached the top 3 places in all possible pairs and 80 % of true pairs had the highest match score. STR is the most widely used genetic marker for personal identification or kinship analysis in the world [19]. With the popularization of massively parallel sequencing technology, other genetic markers have also been used, such as SNP [20–23] and MH [12, 24–27].