A Novel Panel of 43 Insertion/Deletion Loci for Human Identifications of Forensic Degraded DNA Samples: Development and Validation

Jin, Rui; Cui, Wei; Fang, Yingying; Jin, Xiaoye; Wang, Hongdan; Lan, Qiong; Guo, Yuxin; Chen, Chong; Zhang, Xingru; Zhu, Bofeng

doi:10.3389/fgene.2021.610540

Cited by 32 publications

(32 citation statements)

References 31 publications

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“…For Asian populations, there are two additional InDel panels, comprising 12 and 21 markers, respectively ( Sun et al, 2016 ; Zhu et al, 2021 ). Other InDel panels have been recently developed and validated for mixture interpretation and human identification on degraded samples, proving to be informative, robust, reliable, and sensitive ( Jin et al, 2021 ; Chen L et al, 2021 ).…”

Section: Polymorphic Markers For Forensic Identification Purposesmentioning

confidence: 99%

Applications of massively parallel sequencing in forensic genetics

et al. 2022

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Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.

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Section: Polymorphic Markers For Forensic Identification Purposesmentioning

confidence: 99%

Applications of massively parallel sequencing in forensic genetics

et al. 2022

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“…If primer sets across InDels (>20 bp) can be designed, an InDel polymorphism can be determined with conventional agarose gel electrophoresis, as reported in some plant species [ 24 ]. Detection of InDel markers is especially useful for sun- or rain-damaged samples for wildlife since the method is widely used for individual identification in forensic samples of humans [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

Conventional Gel Electrophoresis-Resolvable Insertion/Deletion Markers for Individual Identification and Analysis of Population Genetics in Red-Crowned Cranes in Eastern Hokkaido, Japan

Kawasaki

Dong

Sawada

et al. 2022

Animals

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Red-crowned crane Grus japonensis is an endangered species in two separate populations: the mainland population in the Eurasian continent and the island population in eastern Hokkaido, Japan. We found 11 insertion/deletion (InDel) markers in the genome of the red-crowned crane and designed primer sets across these InDels that can be analyzed with conventional agarose gel electrophoresis. Sixty-six samples of whole blood and skeletal muscle obtained from red-crowned cranes, including 12 families in eastern Hokkaido from 1994 to 2021, showed different patterns in gel images of 11 InDel PCR reactions except for two pairs. The combined non-exclusion probability of the 11 markers indicates that individuals can be determined with a probability of 99.9%. In 39 non-relative chicks, the expected heterozygosity (He) was 0.316, suggesting low genetic diversity. This might not be caused by high levels of inbreeding since the average FIS was not significantly different from zero (0.095, p = 0.075). The results suggest that the 11 InDel primer sets can be used for fairly accurate individual identification as well as genetic population analyses in red-crowned cranes in the island population.

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“…Insertion/Deletion (InDel) polymorphism is a special type of diallelic genetic marker caused by the insertion or deletion of one or more nucleotides, ranking the second-most abundant DNA marker after single nucleotide polymorphism (SNP), approximately one InDel per 7.2 kb of the human genome [4][5][6]. InDels are characterized by their combination of both lower mutation rates and shorter length compared with STR, which means they may serve as markers for typing of degraded forensic samples when STR failed [7,8]. Discrimination power (PD) value is defined as the probability that two individuals have different phenotypes of genetic markers.…”

Section: Introductionmentioning

confidence: 99%

A new set of 20 Multi‐InDel markers for forensic application

Liu

Zhang

et al. 2022

Electrophoresis

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Insertion/deletion markers (InDels) become an important marker for forensic medicine because of their compatible typing techniques with STRs and lower mutation rates. Recent years, a new kind of DNA marker named Multi-InDel was reported as characterized by two or more tightly linked InDel loci within a short length of physical position, usually 200-300 nucleotides. Many pieces of research showed that Multi-InDels had excellent application values in ancestry inference and forensic medicine. Since the identical number of insertion/deletion nucleotides of the InDel markers that composing the Multi-InDel marker, the genotypes of most reported Multi-InDels could not be directly typed by capillary electrophoresis (CE) due to the lack of length discrepancy among the composing InDel sequence. In this study, we applied a typing system of 20 Multi-InDels including 41 InDels, whose genotypes could be deduced by CE and assessed their potential applications in forensic medicine. A total of 200 unrelated Chinese Han individuals and five mother-child-father trios with proven paternity with one STR locus transmission incompatibilities from Shanxi province were genotyped by the multiplex system. The results showed that a total of 70 specific alleles were observed, more than three alleles were observed in 19 loci and seven alleles were observed in one locus. The combined probability of exclusion and the combined power of discrimination were 0.992 and 0.99999999993, respectively. This study demonstrates their potential usefulness for individual identification and paternity tests. The development of Multi-InDels provided another genetic tool inherent in higher polymorphic and lower mutation rates.

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A Novel Panel of 43 Insertion/Deletion Loci for Human Identifications of Forensic Degraded DNA Samples: Development and Validation

Cited by 32 publications

References 31 publications

Applications of massively parallel sequencing in forensic genetics

Applications of massively parallel sequencing in forensic genetics

Conventional Gel Electrophoresis-Resolvable Insertion/Deletion Markers for Individual Identification and Analysis of Population Genetics in Red-Crowned Cranes in Eastern Hokkaido, Japan

A new set of 20 Multi‐InDel markers for forensic application

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