Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives

Sun, Shule; Liu, Ying; Li, Jienan; Yang, Zedeng; Wen, Dan; Liang, Weibo; Yan, Yiqing; Hyeong-keun, Yu; Cai, Jinhua; Zha, Lagabaiyila

doi:10.1016/j.fsigen.2020.102255

Cited by 32 publications

(27 citation statements)

References 40 publications

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“…Microhaplotype combines the advantages of STR and SNP, and the rapid development of next-generation sequencing technology makes it possible to accurately determine haplotype. Our previously studies have shown the combined application of the flanking region variants of nonbinary SNP can greatly increase the discrimination power [12,13], and Wendt et al has observed the notedly variations exhibited in the flanking region of 2 piSNP [14]. So, the microhaplotype established on the basis of nonbinary SNP and piSNP may be very useful forensic multifunctional markers.…”

Section: Discussionmentioning

confidence: 93%

“…Our previously studies have shown that the combined application of the flanking region variants of nonbinary SNP can greatly increase the discrimination power [12,13]. Moreover, according to the study published by Wendt et al, the notedly variations were exhibited in the flanking region of two phenotype-informative SNPs (piSNPs), and the diversity of the combined loci increased compared to the target SNPs alone [14].…”

Section: Introductionmentioning

confidence: 98%

“…Therefore, after considering the flanking region variants in nonbinary SNPs and piSNPs, we selected 12 novel and eight previously published highly polymorphic nonbinary SNP-based microhaplotype loci [12] and ten phenotypic microhaplotype loci. Then, we obtained their forensic parameters based on 100 unrelated northern Han Chinese, and analyzed the increased discrimination power after combin-ing the flanking variants.…”

Section: Introductionmentioning

confidence: 99%

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Considering the flanking region variants of nonbinary SNP and phenotype‐informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications

et al. 2021

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The flanking region variants of nonbinary SNPs and phenotype-informative SNPs (piS-NPs) have been observed, which may greatly improve the discriminative ability after constituting microhaplotype. In this study, 30 microhaplotype loci based on the nonbinary SNPs and piSNPs (shown to be related to phenotypes such as hair and eye color) were selected. Genotyping were conducted on 100 unrelated northern Han Chinese, and the 26 populations from the 1000 Genome Project were also included for comparison of populations differentiation. The simulated study was conducted for evaluating the efficiency of kinship testing. These 30 microhaplotype loci we selected had good polymorphism, with a mean effective number of alleles (Ae) of 3.46. The average Ae increase was 1.27 compared with the target SNPs. The populations from the five regions worldwide could also be distinguished using these loci. The results of kinship testing showed that these microhaplotype loci had the similar ability as 15 STR loci of AmpFlSTR R Identifiler R PCR Amplification Kit to identify the biological parent and a stronger ability to exclude the nonbiological parents. So, these 30 microhaplotype loci may be multifunctional for forensic application, including the ability of personal identification and kinship testing equivalent to 15 STR loci, and the power of ancestry inference for distinguishing the main intercontinental population. Moreover, our selected phenotypic microhaplotype loci may theoretically have phenotype prediction capabilities. But the phenotype prediction efficiency of these phenotypic microhaplotype loci may be worse than that of piSNPs and the detailed prediction accuracy of different populations needs to be further studied.

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Section: Discussionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

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Considering the flanking region variants of nonbinary SNP and phenotype‐informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications

et al. 2021

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“…Another useful application of the MH methods is for detection of CNV anomalies in fetal DNA in Non-invasive prenatal testing (NIPT). MH methods are already in use for paternity testing (35)(36)(37)(38). For NIPT, panels can be designed to focus on genomic regions with the most likely copy number variation (e. g. chr 5, 13, 18, or 21) and the frequency of 3 rd MHs in targeted regions compared to the rest of the genome.…”

Section: Discussionmentioning

confidence: 99%

Sensitive detection of DNA contamination in tumor samples via microhaplotypes

Whitty¹,

Thompson²

2020

Preprint

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BackgroundLow levels of sample contamination can have disastrous effects on the accurate identification of somatic variation in tumor samples. Detection of sample contamination in DNA is generally based on observation of low frequency variants that suggest more than a single source of DNA is present. This strategy works with standard DNA samples but is especially problematic in solid tumor FFPE samples because there can be huge variations in allele frequency (AF) due to massive copy number changes arising from large gains and losses across the genome. The tremendously variable allele frequencies make detection of contamination challenging. A method not based on individual AF is needed for accurate determination of whether a sample is contaminated and to what degree.MethodsWe used microhaplotypes to determine whether sample contamination is present. Microhaplotypes are sets of variants on the same sequencing read that can be unambiguously phased. Instead of measuring AF, the number and frequency of microhaplotypes is determined. Contamination detection becomes based on fundamental genomic properties, linkage disequilibrium (LD) and the diploid nature of human DNA, rather than variant frequencies. We optimized microhaplotype content based on 164 single nucleotide variant sets located in genes already sequenced within a cancer panel. Thus, contamination detection uses existing sequence data and does not require sequencing of any extraneous regions. The content is chosen based on LD data from the 1000 Genomes Project to be ancestry agnostic, providing the same sensitivity for contamination detection with samples from individuals of African, East Asian, and European ancestry.ResultsDetection of contamination at 1% and below is possible using this design. The methods described here can also be extended to other DNA mixtures such as forensic and non-invasive prenatal testing samples where DNA mixes of 1% or less can be similarly detected.ConclusionsThe microhaplotype method allows sensitive detection of DNA contamination in FFPE tumor samples. These methods provide a foundation for examining DNA mixtures in a variety of contexts. With the appropriate panels and high sequencing depth, low levels of secondary DNA can be detected and this can be valuable in a variety of applications.

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“…Additionally, the main limitation of microhaplotype markers comprising only two variants is the difficulty with increasing polymorphism. A third method relies on single-stranded haplotypes that are resolved by experimental analyzes such as massively parallel sequencing (MPS), which can directly detect the phases of haplotypes on sequenced strands (Borsting and Morling, 2015;Snyder et al, 2015;Wang et al, 2015;Wendt et al, 2016;Chen et al, 2019;Turchi et al, 2019;Zhu et al, 2019;de la Puente et al, 2020;Pang et al, 2020;Sun et al, 2020). However, forensic scientists face many practical challenges due to the complexity of MPS, extensive data processing requirements, and higher costs.…”

Section: Introductionmentioning

confidence: 99%

Multi-Indel: A Microhaplotype Marker Can Be Typed Using Capillary Electrophoresis Platforms

Xue

et al. 2020

Front. Genet.

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Since the concept of microhaplotypes was proposed by Kidd in 2013, various microhaplotype markers have been investigated for various forensic purposes, such as individual identification, deconvolution of DNA mixtures, or forensic ancestry inference. In our opinion, various compound markers are also regarded as generalized microhaplotypes, encompassing two or more variants in a short segment of DNA (e.g., 200 bp). That is, a set of variants (referred to herein as multi-variants) within a certain length includes single nucleotide polymorphisms (SNP), insertion/deletion polymorphisms (Indels), or short tandem repeat polymorphisms (STRs). At present, multi-variant is mainly aimed at multi-SNPs. However, the haplotype genotyping of multi-variants relies on single-strand analysis, mainly using massively parallel sequencing (MPS). Here, we describe a method based on a capillary electrophoresis (CE) platform that can directly obtain haplotypes of individuals. Several microhaplotypes consisting of three or more Indels with different insertion or deletion lengths in the range of less than 200 bp were screened out, each of which had at least three haplotypes. As a result, the haplotype of an individual was reflected by the length of its polymorphism. Finally, we established a multiplex amplification system containing 18 multi-Indel markers that could identify haplotypes on each chromosome of an individual. The combined power of discrimination (CPD) and the cumulative probability of exclusion (CPE) were 0.999999999997234 and 0.9984, respectively.

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Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives

Cited by 32 publications

References 40 publications

Considering the flanking region variants of nonbinary SNP and phenotype‐informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications

Considering the flanking region variants of nonbinary SNP and phenotype‐informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications

Sensitive detection of DNA contamination in tumor samples via microhaplotypes

Multi-Indel: A Microhaplotype Marker Can Be Typed Using Capillary Electrophoresis Platforms

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