A review of the potential of the MinION™ single‐molecule sequencing system for forensic applications

Analyzing genetic markers in nuclear and mitochondrial genomes is helpful in various forensic applications, such as individual identifications and kinship analyses However, most commercial kits detect these markers separately, which is time-consuming, laborious, and more error-prone (mislabelling, contamination, ) The MGIEasy Signature Identification Library Prep Kit (hereinafter “MGIEasy identification system”; MGI Tech, Shenzhen, China) has been designed to provide a simple, fast, and robust way to detect appropriate markers in one multiplex PCR reaction: 52 autosomal STRs, 27 X-chromosomal STRs, 48 Y-chromosomal STRs, 145 identity-informative SNPs, 53 ancestry-informative SNPs, 29 phenotype-informative SNPs, and the hypervariable regions of mitochondrial DNA (mtDNA) Here, we validated the performance of MGIEasy identification system following the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), assessing species specificity, sensitivity, mixture identification, stability under non-optimal conditions (degraded samples, inhibitor contamination, and various substrates), repeatability, and concordance Libraries prepared using MGIEasy identification system were sequenced on a MGISEQ-2000 instrument (MGI Tech) MGIEasy-derived STR, SNP, and mtDNA genotypes were highly concordant with CE-based STR genotypes (9979%), MiSeq FGx-based SNP genotypes (9978%), and Sanger-based mtDNA genotypes (100%), respectively This system was strongly human-specific, resistant to four common PCR inhibitors, and reliably amplified both low quantities of DNA (as low as 0125 ng) and degraded DNA (~ 150 nt) Most of the unique alleles from the minor contributor were detected in 1:10 male-female and male-male mixtures; some minor Y-STR alleles were even detected in 1:1000 male-female mixtures MGIEasy also successfully directly amplified markers from blood stains on FTA cards, filter papers, and swabs Thus, our results demonstrated that MGIEasy identification system was suitable for use in forensic analyses due to its robust and reliable performance on samples of varying quality and quantity

Developmental validation of the MGIEasy Signature Identification Library Prep Kit, an all-in-one multiplex system for forensic applications

A biogeographic estimate of a certain population can not only discern population substructure in the whole genome association study, but also provide informative clues for forensic investigations when obtained DNA genotypes do not find a match in the available forensic DNA database. In this study, 100 ancestry informative single nucleotide polymorphisms (AISNPs) were first presented to differentiate three continental ancestries (African, East Asian and European). Ultimately, forty-two AISNPs were chosen from the 100 AISNPs. Distinguishing power of the 100 and 42 AISNPs for differentiating continental populations was further evaluated with population cluster analyses. Results indicated both of AISNP sets could efficiently differentiate 11 training populations from the three continents. Further validation of 42 AISNPs in testing population set indicated these 42 AISNPs performed well for ancestry inferences of these testing individuals. Ancestry components of Uyghur group were assessed by comparing with different continental populations based on these 42 AISNPs. Results revealed that East Asian populations contributed more ancestry components to the studied Uyghur group than European populations. In conclusion, our study is expected to provide more AISNP markers and enrich extant reference database.

Biogeographic origin prediction of three continental populations through 42 ancestry informative SNPs.

Could routine forensic STR genotyping data leak personal phenotypic information?

The Forensic Databases Advisory Board (FDAB), an independent board that assists the International Society for Forensic Genetics (ISFG), has presented a First Report on ethical aspects of the following Forensic Genetic Frequency Databases (FGFD): EMPOP, STRidER and YHRD. The FDAB designed an ethical framework to evaluate the content of these FGFD, and the factors to be considered for retention and acceptance of submissions. The FDAB framework proposes to categorize submissions according to the risk of having contravened the universal ethical principles outlined by international organizations, and the guidelines adopted by the ISFG. The report has been open to discussion by the scientific community since 2023. Herein we present the conception and development of the First Report along with a summary of its content, with consideration of the feedback received. 

Ethical considerations for Forensic Genetic Frequency databases

Inferring an unknown DNA's ancestry using a set of ancestry-informative single nucleotide polymorphisms (SNPs) in forensic science is useful to provide investigative leads. This is especially true when there is no DNA database match or specified suspect. Thus, a set of SNPs with highly robust and balanced differential power is strongly demanded in forensic science. In addition, it is also necessary to build a genotyping database for estimating the ancestry of an individual or an unknown DNA. For the differentiation of Africans, Europeans, East Asians, Native Americans, and Oceanians, the Global Nano set that includes just 31 SNPs was developed by de la Puente et al. Its ability for differentiation and balance was evaluated using the genotype data of the 1000 Genomes Phase III project and the Stanford University HGDP-CEPH. Just 402 samples were genotyped and analyzed as a reference set based on statistical methods. To validate the differentiating capacity using more samples, we developed a single-tube 28-plex SNP assay in which the SNPs were chosen from the 31 allelic loci of the Global AIMs Nano set. Three tri-allelic SNPs used to differentiate mixed-source DNA contribute little to population differentiation and were excluded here. Then, 998 individuals from 21 populations were typed, and these genotypes were combined with the genotype data obtained from 1000 Genomes Phase III and the Stanford University HGDP-CEPH (3090 total samples,43 populations) to estimate the power of this multiplex assay and build a database for the further inference of an individual or an unknown DNA sample in forensic practice.

Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs.

Inferring an unknown DNA’s ancestry using a set of ancestry-informative single nucleotide polymorphisms (SNPs) in forensic science is useful to provide investigative leads. This is especially true when there is no DNA database match or specified suspect. Thus, a set of SNPs with highly robust and balanced differential power is strongly demanded in forensic science. In addition, it is also necessary to build a genotyping database for estimating the ancestry of an individual or an unknown DNA. For the differentiation of Africans, Europeans, East Asians, Native Americans, and Oceanians, the Global Nano set that includes just 31 SNPs was developed by de la Puente et al. Its ability for differentiation and balance was evaluated using the genotype data of the 1000 Genomes Phase III project and the Stanford University HGDP-CEPH. Just 402 samples were genotyped and analyzed as a reference set based on statistical methods. To validate the differentiating capacity using more samples, we developed a single-tube 28-plex SNP assay in which the SNPs were chosen from the 31 allelic loci of the Global AIMs Nano set. Three tri-allelic SNPs used to differentiate mixed-source DNA contribute little to population differentiation and were excluded here. Then, 998 individuals from 21 populations were typed, and these genotypes were combined with the genotype data obtained from 1000 Genomes Phase III and the Stanford University HGDP-CEPH (3090 total samples,43 populations) to estimate the power of this multiplex assay and build a database for the further inference of an individual or an unknown DNA sample in forensic practice.

/pdf/retraction-note-exploring-the-ancestry-differentiation-and-2b5j39ffe1.pdf

Retraction Note: Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs

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Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs.

Retraction Note: Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs