Sequence-based assessment of expediency of tri-, tetra-, and penta-nucleotides repeat autosomal STR markers in the central Indian population using Next Generation Sequencing (NGS)

IF 0.8 Q4 GENETICS & HEREDITY Meta Gene Pub Date : 2022-02-01 DOI:10.1016/j.mgene.2021.100983
Hirak Ranjan Dash , Kamayani Vajpayee , Ritesh Shukla , Ankit Srivastava , Pankaj Shrivastava , Surajit Das
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Abstract

Present-day forensic DNA analysis is witnessing a paradigm shift from size-based allele determination by capillary electrophoresis (CE) to sequence-based allele determination by Next Generation Sequencing (NGS). An attempt has been made to evaluate the sequence-based allelic data at two tri (D12ATA63, D22S1045), two tetra (D18S51, D1S1656), and two penta- (Penta D, Penta E) nucleotides repeat STR markers in the central Indian population. 183.33 times allele gain has been observed in D1S1656 after evaluating individual allelic sequences in comparison to the size-based alleles. Despite not witnessing any sequence-based allele gain, highest power of discrimination (0.978), Polymorphic Information Content (0.9), Power of Exclusion (0.807), typical paternity index (5.31), Expected heterozygosity (0.906), and lowest matching probability (0.022) was observed at Penta E marker suggesting its more usefulness among the considered markers for forensic and paternity applications. A giant leap in sequence-based allelic information showed a significant increase in forensic and paternity parameters (p = 0.646) in D1S1656. Substitution of TAGA with either TAGG or TAGC was found to be responsible for the generation of sequence variant alleles in D1S1656. Besides, the observation of rs4847015 SNP in 11.5% of sequences further increases the evidentiary value of D1S1656 in comparison to other STR markers analyzed in this study.

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利用下一代测序(NGS)对印度中部人群中三、四、五核苷酸重复常染色体STR标记的便利性进行基于序列的评估
目前法医DNA分析正见证着从毛细管电泳(CE)的基于大小的等位基因测定到下一代测序(NGS)的基于序列的等位基因测定的范式转变。在印度中部人群中,对两个三核苷酸(D12ATA63, D22S1045),两个四核苷酸(D18S51, D1S1656)和两个五核苷酸(penta D, penta E)重复STR标记进行了基于序列的等位基因数据评估。与基于大小的等位基因相比,对单个等位基因序列进行评估后,在D1S1656中观察到183.33倍的等位基因增益。尽管没有观察到任何基于序列的等位基因获得,但在Penta E标记上观察到最高的辨别力(0.978),多态信息含量(0.9),排除力(0.807),典型父系指数(5.31),预期杂合度(0.906)和最低的匹配概率(0.022),这表明它在法医和父系鉴定应用中更有用。基于序列的等位基因信息的巨大飞跃显示,D1S1656的法医和父权参数显著增加(p = 0.646)。在D1S1656中,TAGG或TAGC替代TAGA可导致序列变异等位基因的产生。此外,在11.5%的序列中发现rs4847015 SNP,与本研究分析的其他STR标记相比,进一步增加了D1S1656的证据价值。
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来源期刊
Meta Gene
Meta Gene Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
1.10
自引率
0.00%
发文量
20
期刊介绍: Meta Gene publishes meta-analysis, polymorphism and population study papers that are relevant to both human and non-human species. Examples include but are not limited to: (Relevant to human specimens): 1Meta-Analysis Papers - statistical reviews of the published literature of human genetic variation (typically linked to medical conditionals and/or congenital diseases) 2Genome Wide Association Studies (GWAS) - examination of large patient cohorts to identify common genetic factors that influence health and disease 3Human Genetics Papers - original studies describing new data on genetic variation in smaller patient populations 4Genetic Case Reports - short communications describing novel and in formative genetic mutations or chromosomal aberrations (e.g., probands) in very small demographic groups (e.g., family or unique ethnic group). (Relevant to non-human specimens): 1Small Genome Papers - Analysis of genetic variation in organelle genomes (e.g., mitochondrial DNA) 2Microbiota Papers - Analysis of microbiological variation through analysis of DNA sequencing in different biological environments 3Ecological Diversity Papers - Geographical distribution of genetic diversity of zoological or botanical species.
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