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

Li, Ran; Shen, Xuefeng; Chen, Hui; Peng, Dan; Wu, Riga; Sun, Hongyu

doi:10.1007/s00414-021-02507-0

Cited by 24 publications

(8 citation statements)

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“…To our knowledge, the CPM of the 133 iiSNPs was lower than that of the 94 iiSNPs in the ForenSeq ™ DNA signature Prep Kit (Delest et al, 2020). With 54 A-STR and 133 iiSNP loci simultaneously detected, cumulative discrimination power of the novel assay was significantly elevated, which was comparable to efficiencies of 74-90 A-STRs as previously described (Li et al, 2021) and further proved in this study. We also put forward that another advantage of the MGI identification system was the relatively small amplicons in the panel, to show a better performance in challenging DNA profiling, such as degraded DNA samples.…”

Section: Discussionsupporting

confidence: 86%

“…The allele frequencies of the 54 A-STRs and 133 iiSNPs in the Yugu and NMH populations were used to simulate genotype data of each 1,000 full sibling and half sibling cases to generate LR distributions. During the simulation, we determined the recombination ratio of pairwise loci by referring to data reported by Li et al (2021). LR distributions of the Yugu and NMH populations were plotted with the density plot function in the R program.…”

Section: Statistical Analysesmentioning

confidence: 99%

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Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set

et al. 2022

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The MPS technology has expanded the potential applications of DNA markers and increased the discrimination power of the targeted loci by taking variations in their flanking regions into consideration. Here, a collection of nuclear and extranuclear DNA markers (totally six kinds of nuclear genetic markers and mtDNA hypervariable region variations) were comprehensively and systematically assessed for polymorphism detections, further employed to dissect the population backgrounds in the Yugu ethnic group from Gansu province (Yugu) and Han population from the Inner Mongolia Autonomous Region (NMH) of China. The elevated efficiencies of the marker set in separating full sibling and challenging half sibling determination cases in parentage tests (iiSNPs), as well as predicting ancestry origins of unknown individuals from at least four continental populations (aiSNPs) and providing informative characteristic-related clues for Chinese populations (piSNPs) are highlighted in the present study. To sum up, different sets of DNA markers revealed sufficient effciencies to serve as promising tools in forensic applications. Genetic insights from the perspectives of autosomal DNA, Y chromosomal DNA, and mtDNA variations yielded that the Yugu ethnic group was genetically close related to the Han populations of the northern region. But we admit that more reference populations (like Mongolian, Tibetan, Hui, and Tu) should be incorporated to gain a refined genetic background landscape of the Yugu group in future studies.

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Section: Discussionsupporting

confidence: 86%

Section: Statistical Analysesmentioning

confidence: 99%

Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set

et al. 2022

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“…Notably, the latest application of SNPs is investigative genetic genealogy where dense SNP data are jointly analysed to infer distant relationships (which in forensics indicate relatedness exceeding that of first cousins) [69]. For these reasons, an increasing number of commercial NGS-based kits have included X chromosomal SNPs and/or STRs to address complex kinship scenarios [14,18,[70][71][72][73][74][75][76]. Nevertheless, complex kinship cases relying on many and mixed types of X chromosomal genetic markers cannot be addressed using the previous implementations for the inference of recombination rates, which are used, albeit with limitations, for STR markers.…”

Section: Discussionmentioning

confidence: 99%

Recombulator-X: a fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Aneli

Fariselli

Chierto

et al. 2023

Preprint

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Background and Objective: Genetic markers (especially short tandem repeats or STRs) located on the X chromosome are a valuable resource to solve complex kinship cases in forensic genetics in addition or alternatively to autosomal STRs. Groups of tightly linked markers are combined into haplotypes, thus increasing the discriminating power of tests. However, this approach requires precise knowledge of the recombination rates between adjacent markers. Recombination rates vary across the human genome and cannot be automatically derived from linkage physical maps. The International Society of Forensic Genetics recommends that recombination rate estimation on the X chromosome is performed from pedigree genetic data while taking into account the confounding effect of mutations. However, the only existing implementations that satisfy these requirements have several drawbacks: they were never publicly released, they are very slow and/or need cluster-level hardware and strong computational expertise to use. In order to address these key concerns, we developed Recombulator-X, a new open-source Python tool. Methods: The most challenging issue, namely the running time, was addressed with dynamic programming techniques to greatly reduce the computational complexity of the algorithm, coupled with JIT compilation to further increase performance. We also extended the statistical framework from STR to any polymorphic marker. Results: Compared to the previous methods, Recombulator-X reduces the estimation times from weeks or months to less than one hour for typical datasets. Moreover, the estimation process, including preprocessing, has been streamlined and packaged into a simple command-line tool that can be run on a normal PC. Where previous approaches were limited to small panels of STR markers (up to 15), our tool can handle greater numbers (up to 100) of mixed STR and non-STR markers. Conclusions: In the genetic forensic community, state-of-the-art estimation methods for X chromosome recombination rates have seen limited usage due to the technical hurdles posed by previous implementations. Recombulator-X makes the process much simpler, faster and accessible to researchers without a computational background, hopefully spurring increased adoption of best practices. Moreover, it extends the estimation framework to larger panels of genetic markers (not only STRs), allowing analyses of sequencing-based data.

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“…The standard WGS library construction method for MGISEQ-2000RS includes the following major steps: (1) DNA fragmentation; (2) end repair and A-tailing; (3) indexed adapter ligation; (4) post-ligation cleanup; (5) library amplification; (6) post-amplification cleanup; and (7) DNB preparation. The libraries were then pooled, and a number of DNBs were generated; the products were measured using Qubit with the use of an ssDNA kit and were finally sequenced using an MGISEQ-2000RS (MGI Tech, Shenzhen, China), with an average depth of 30× [ 15 ]. Bioinformatic analyses were performed using both public software and software developed in-house.…”

Section: Methodsmentioning

confidence: 99%

Novel Exon 7 Deletions in TSPAN12 in a Three-Generation FEVR Family: A Case Report and Literature Review

Jiang

Wang

2023

Genes

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Familial exudative vitreoretinopathy (FEVR) is a severe clinically and genetically heterogeneous disease that is characterized by vascular disorder. FEVR exhibits strikingly variable clinical phenotypes, ranging from asymptomatic to total blindness. In this case, we present a patient who was first treated as having high myopia and retinopathy but was finally diagnosed with FEVR caused by the heterozygous deletion of exon 7 in TSPAN12 with the aid of whole genome sequencing (WGS). Typical vascular changes, including vascular leakage and an avascular zone in the peripheral retina, were observed in the proband using fundus fluorescein angiography (FFA), and the macular dragging was shown to be progressing in the follow-up visit. Furthermore, the proband showed unreported TSPAN12-related phenotypes of FEVR: ERG (full-field electroretinogram) abnormalities and retinoschisis. Only mild vascular changes were exhibited in the FFA for the other three family members who carried the same deletion of exon 7 in TSPAN12. This case expands our understanding of the phenotype resulting from TSPAN12 mutations and signifies the importance of combining both clinical and molecular analysis approaches to establish a complete diagnosis.

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

Cited by 24 publications

References 50 publications

Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set

Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set

Recombulator-X: a fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Novel Exon 7 Deletions in TSPAN12 in a Three-Generation FEVR Family: A Case Report and Literature Review

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