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

ABSTRACT: 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.

SUBMITTER: Qu S

PROVIDER: S-EPMC7649793 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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

Qu Shengqiu S Lv Meili M Xue Jiaming J Zhu Jing J Wang Li L Jian Hui H Liu Yuqing Y Zhang Ranran R Zha Lagabaiyila L Liang Weibo W Zhang Lin L

Frontiers in genetics 20201023

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 ...[more]

PMID: 33193656

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Project description:Surface oxidation improves the dispersion of carbon nanotubes in aqueous solutions and plays a key role in the development of biosensors, electrochemical detectors and polymer composites. Accurate characterization of the carbon nanotube surface is important because the development of these nano-based applications depends on the degree of functionalization, in particular the amount of carboxylation. Affinity capillary electrophoresis is used to characterize the oxidation of multi-walled carbon nanotubes. A polytryptophan peptide that contains a single arginine residue (WRWWWW) serves as a receptor in affinity capillary electrophoresis to assess the degree of carboxylation. The formation of peptide-nanotube receptor-ligand complex was detected with a UV absorbance detector. Apparent dissociation constants (KD) are obtained by observing the migration shift of the WRWWWW peptide through background electrolyte at increasing concentrations of multi-walled carbon nanotubes. A 20% relative standard deviation in method reproducibility and repeatability is determined with triplicate analysis within a single sample preparation and across multiple sample preparations for a commercially available carbon nanotube. Affinity capillary electrophoresis is applied to assess differences in degree of carboxylation across two manufacturers and to analyze acid treated carbon nanotubes. The results of these studies are compared to X-ray photoelectron spectroscopy and zeta potential. Affinity capillary electrophoresis comparisons of carbon nanotube samples prepared by varying acid treatment time from 30 min to 3 h yielded significant differences in degree of carboxylation. X-ray photoelectron spectroscopy analysis was inconclusive due to potential acid contamination, while zeta potential showed no change based on surface charge. This work is significant to research involving carbon nanotube-based applications because it provides a new metric to rapidly characterize carbon nanotubes obtained from different vendors, or synthesized in laboratories using different procedures.

Dataset Information

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

Publications

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

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