Modeling the minus two base pair stutter ratio of the D1S1656 locus: A sequence-based mixture distribution model
Modeling the minus two base pair stutter ratio of the D1S1656 locus: A sequence-based mixture distribution model
复制标题
对 D1S1656 基因座的负两个碱基对断续率进行建模：基于序列的混合分布模型
DOI：
10.1016/j.fsigen.2020.102450
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Mizuno Natsuko
中科院分区：
文献类型：
--
作者：
Inokuchi Shota;Fujii Koji;Nakanishi Hiroaki;Takada Aya;Saito Kazuyuki;Mizuno Natsuko
在这项研究中，我们提出了一个口吃比为负两个碱基对口吃（-2bpSR）模型的D1 S1656位点的毛细管电泳（CE）为基础的短串联重复序列（STR）分型。通过大规模平行测序分析了来自总共108个日本个体的DNA，以研究涉及侧翼区的重复结构内两个碱基重复基序的最长不间断延伸（2bpLUS值）的长度。此外，使用GlobalFiler试剂盒在3500 xL遗传分析仪上收集~ 2bpSR数据。测序分析结果显示，所有等位基因根据其2bpLUS值分为两类。-2bpSR在不同类型之间差异显著。然后，我们使用基于2bpLUS值的等位基因分类，用混合对数正态分布对-2bpSR进行建模。此外，在混合对数正态分布模型中的每个重复数内的序列类型的概率估计使用逻辑回归的五个主要检测群体的每一个。这项研究预计能够解释STR分型，同时考虑在D1 S1656位点的负两个碱基对口吃。
In this study, we propose a stutter ratio for a minus two base pair stutter (-2bpSR) model of the D1S1656 locus in capillary electrophoresis (CE)-based short tandem repeat (STR) typing. DNA from a total of 108 Japanese individuals was analyzed via massively parallel sequencing to investigate the length of the longest uninterrupted stretch of two base repeat motif (2bpLUS value) within repetitive structures involving the flanking region. Additionally,-2bpSRdata was collected using the GlobalFiler Kit on a 3500xL Genetic Analyzer. As a result of sequencing analysis, all alleles were classified into two types by their 2bpLUS values. The-2bpSRdiffered significantly between the types. Then, we modeled the-2bpSRwith a mixture log-normal distribution using the classification of alleles based on the 2bpLUS values. Furthermore, probabilities of the sequence type within each repeat number in the mixture log-normal distribution model were estimated using logistic regression for each of the five major detected populations. This study is expected to enable interpretation of STR typing while considering minus two base pair stutter at the D1S1656 locus.