A set of 14 DIP-SNP markers to detect unbalanced DNA mixtures

Liu, Zhizhen; Liu, Jinding; Wang, Jiaqi; Chen, Deqing; Liu, Zidong; Shi, Jie; Li, Zeqin; Li, Wenyan; Zhang, Gengqian; Du, Bing

doi:10.1016/j.bbrc.2018.02.109

Cited by 21 publications

(13 citation statements)

References 24 publications

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“…According to the newest report by 1000 Genomes Project, there are 3.6 million short InDels and 84.7 million SNPs in the human genome [26]. Compared with DIP-STRs, SNP-STRs, and DIP-SNPs, abundant SNPs allow an easier discovery of SNP-SNPs [27]. At this stage, the microhaplotype is mainly genotyped by MPS, which has high throughput but is expensive.…”

Section: Discussionmentioning

confidence: 99%

A new approach to detect a set of SNP‐SNP markers: Combining ARMS‐PCR with SNaPshot technology

Zhang

Jian

et al. 2020

Electrophoresis

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Microhaplotypes are a new promising type of forensic genetic marker. Without the interference of stutter and high mutation rates as for STRs, and with short amplification lengths and a higher degree of polymorphism than single SNP, microhaplotypes composed of two SNPs, SNP-SNP, have a strong application potential. Currently, the most common method to detect microhaplotypes is massive parallel sequencing. However, the cost and extensive use of instruments limit its wide application in forensic laboratories. In this study, we screened 23 new SNP-SNP loci and established a new detection method by combining a multiplex amplification refractory mutation system-based PCR (ARMS-PCR) and SNaPshot technology based on CE. First, we introduced an additional deliberate mismatch at the antepenultimate base from the 3 end of primers when designing ARMS-PCR for SNP 1 (the first SNP of the SNP-SNP). Then, single base extension primers for SNaPshot assay were designed next to the position of SNP 2 (the second SNP). Finally, 15 loci were successfully built into four panels and these loci showed a relatively high level of polymorphism in the Southwest Chinese Han population. All the loci had an average probability of informative genotypes (I value) of 0.319 and a combined discrimination power of 0.999999999. Therefore, this new detection system will provide a valuable supplement to current methods.

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Section: Discussionmentioning

confidence: 99%

A new approach to detect a set of SNP‐SNP markers: Combining ARMS‐PCR with SNaPshot technology

Zhang

Jian

et al. 2020

Electrophoresis

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“…Thereafter, two allele-specific sequences are obtained using PCR. The genotype of haplotype markers from an individual can be determined using a capillary electrophoresis (CE) platform and a two-step detection method, but the phase of a haplotype can be unambiguously determined only when the microhaplotypes include two variants (Castella et al, 2013;Cereda et al, 2014;Oldoni et al, 2015;Tan et al, 2017;Liu et al, 2018Liu et al, , 2019Moriot and Hall, 2019;Oldoni and Podini, 2019;Zhang et al, 2020). Additionally, the main limitation of microhaplotype markers comprising only two variants is the difficulty with increasing polymorphism.…”

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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“…Compound marker consists of two different types of genetic markers in the genomic region of 200 bp, which could be classified into STR-DIP, STR-SNP, and SNP-DIP [12,[19][20][21]. In previous studies, some researchers evaluated forensic efficiencies of compound markers and found that these markers were good for detecting the unbalanced two-person mixture [20][21][22].…”

Section: Introductionmentioning

confidence: 99%

Developing and population analysis of a new multiplex panel of 18 microhaplotypes and compound markers using next generation sequencing and its application in the Shaanxi Han population

et al. 2020

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Compound marker consists of two different types of genetic markers, like deletion/insertion polymorphism and single nucleotide polymorphism in the genomic region of 200 bp, and microhaplotype consists of a series of closely linked single nucleotide polymorphisms in a small DNA segment (<300 bp), which show great potential for human identifications and mixture analyses. In this study, we initially selected 23 novel genetic markers comprising 10 microhaplotypes and 13 compound markers according to previously reported single nucleotide polymorphism or deletion/insertion polymorphism loci. Genetic distributions of these 23 loci in different continental populations showed that they could be used as valuable loci for forensic human identification purpose. Besides, high informativeness values (>0.1) were observed in six loci which could be further employed for forensic ancestry analyses. Finally, 18 loci were successfully developed into a multiplex panel and detected by the next generation sequencing (NGS) technology. Further analyses of these 18 loci in the studied Shaanxi Han population showed that 15 loci exhibited relatively high expected heterozygosities (>0.5). Cumulative power of discrimination (0.999 999 999 99 4835) of these 18 loci revealed that the multiplex panel could also be utilized for human identifications in the studied Shaanxi Han population.

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A set of 14 DIP-SNP markers to detect unbalanced DNA mixtures

Cited by 21 publications

References 24 publications

A new approach to detect a set of SNP‐SNP markers: Combining ARMS‐PCR with SNaPshot technology

A new approach to detect a set of SNP‐SNP markers: Combining ARMS‐PCR with SNaPshot technology

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

Developing and population analysis of a new multiplex panel of 18 microhaplotypes and compound markers using next generation sequencing and its application in the Shaanxi Han population

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