A highly polymorphic panel of 40-plex microhaplotypes for the Chinese Han population and its application in estimating the number of contributors in DNA mixtures

Yang, Jiawen; Chen, Ji; Ji, Qiang; Yu, Youjia; Li, Kai; Kong, Xiaochao; Xie, Sumei; Zhan, Wenxuan; Mao, Zhengsheng; Yu, Yizhen; Ding, Li; Chen, Peng; Chen, Feng

doi:10.1016/j.fsigen.2021.102600

Cited by 12 publications

(11 citation statements)

References 35 publications

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“…Early studies using MHs showed the same patterns of population relationships that were shown by large SNP panels with broad geographic coverage [ 17 ]. However, the most recent panels of MHs allow more detailed groupings of populations.…”

Section: Ancestry Inferencementioning

confidence: 90%

“…This is reflected in most studies of SNPs and of microhaplotypes (e.g., [ 15 , 16 ]). Whatever the cause, there is some potential counter effort, since many studies are ascertaining larger numbers of MHs using East Asian populations (e.g., [ 10 , 12 , 17 ]). Thus, more MHs with higher A e values in East Asian populations are becoming available.…”

Section: Individualizationmentioning

confidence: 99%

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State of the Art for Microhaplotypes

Kídd

Pakstis

2022

Genes

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In recent years, the number of publications on microhaplotypes has averaged more than a dozen papers annually. Many have contributed to a significant increase in the number of highly polymorphic microhaplotype loci. This increase allows microhaplotypes to be very informative in four main areas of forensic uses of DNA: individualization, ancestry inference, kinship analysis, and mixture deconvolution. The random match Probability (RMP) can be as small as 10−100 for a large panel of microhaplotypes. It is possible to measure the heterozygosity of an MH as the effective number of alleles (Ae). Ae > 7.5 exists for African populations and >4.5 exists for Native American populations for a smaller panel of two dozen selected microhaplotypes. Using STRUCTURE, at least 10 different ancestral clusters can be defined by microhaplotypes. The Ae for a locus is also identical to the Paternity Index (PI), the measure of how informative a locus will be in parentage testing. High Ae loci can also be useful in missing persons cases. Finally, high Ae microhaplotypes allow the near certainty of seeing multiple additional alleles in a mixture of two or more individuals in a DNA sample. In summary, a panel of higher Ae microhaplotypes can outperform the standard CODIS markers.

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Section: Ancestry Inferencementioning

confidence: 90%

Section: Individualizationmentioning

confidence: 99%

State of the Art for Microhaplotypes

Kídd

Pakstis

2022

Genes

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“…Microhaps assays are highly sensitive, requiring as little as 50pg (8 cells) of DNA sample, and it could also differentiate mixtures with 2 donors up to a 49:1 ratio and mixtures with up to 6 DNA donors. The number of contributors was accurately defined for 2- to 4-person mixtures in more than 95% of the evaluated samples, and more than 83% accuracy was obtained for 2- to 6-person mixtures ( Yang et al, 2022 ). Usually, when using electrophoretic methods, very little or no information can be gathered from mixtures where less than 5-10% of total DNA belongs to the minor donor.…”

Section: Polymorphic Markers For Forensic Identification Purposesmentioning

confidence: 99%

“…They consist of three or more genetic markers found nearby, in DNA segments of around 150 to 300 bp, in which the haplotype is made of the allelic combinations observed in the same amplicon. This characteristic makes possible the existence of multiple genotypes even when only bi-allelic SNPs are present ( Oldoni et al, 2020 ; Pang et al, 2020 ; Yang et al, 2022 ).…”

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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“…Various MH panels have been evaluated for effectiveness with kinship analysis [ [521] , [522] , [523] ]. Likewise the ability to detect minor contributors in DNA mixtures has been assessed [ [524] , [525] , [526] ].…”

Section: Emerging Technologies Research Studies and Other Topicsmentioning

confidence: 99%

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

Butler

2023

Forensic Science International: Synergy

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A highly polymorphic panel of 40-plex microhaplotypes for the Chinese Han population and its application in estimating the number of contributors in DNA mixtures

Cited by 12 publications

References 35 publications

State of the Art for Microhaplotypes

State of the Art for Microhaplotypes

Applications of massively parallel sequencing in forensic genetics

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

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