Concurrent genotyping of mitochondrial DNA and nuclear DNA in rootless hair shafts and blood samples for enhanced analysis

IF 3.2 2区医学 Q2 GENETICS & HEREDITY Forensic Science International-Genetics Pub Date : 2024-11-13 DOI:10.1016/j.fsigen.2024.103176

Dan Peng , Nana Wang , Yu Zang , Zhiyong Liu , Zhentang Liu , Jiaojiao Geng , Bin Cong , Hongyu Sun , Riga Wu

{"title":"Concurrent genotyping of mitochondrial DNA and nuclear DNA in rootless hair shafts and blood samples for enhanced analysis","authors":"Dan Peng , Nana Wang , Yu Zang , Zhiyong Liu , Zhentang Liu , Jiaojiao Geng , Bin Cong , Hongyu Sun , Riga Wu","doi":"10.1016/j.fsigen.2024.103176","DOIUrl":null,"url":null,"abstract":"<div><div>Hair is an important type of biological evidence at crime scenes. However, the highly degraded nature of DNA fragments in hair shafts poses challenges for the detection of nuclear DNA (nuDNA) through capillary electrophoresis-based short tandem repeat (STR) genotyping. In this study, an all-in-one multiplex system named MGIEasy Signature Identification Library Prep Kit (MGI Tech, China) was employed to the simultaneous genotyping of both mitochondrial DNA (mtDNA) and nuDNA in hair shafts. This system is based on massively parallel sequencing (MPS) technology and encompasses Amelogenin, STRs, single nucleotide polymorphisms (SNPs) and mtDNA hypervariable regions (HVRs) in a single reaction. A total of 370 hair shafts, together with 180 blood samples as the references, were examined. The mtDNA analysis of 110 unrelated blood samples unveiled a total of 150 homoplasmic variants and 105 distinct haplotypes, revealing population polymorphisms in the Guangdong Han Chinese. The study also delved into the detection of mtDNA heteroplasmy, revealing 8.18 % and 16.36 % of individuals with point heteroplasmies (PHPs) in blood and hair shaft samples, respectively. Additionally, hair shafts with DNA extracted using the Investigator method yielded higher average depth of coverage (DoC), lower drop-out rate for SNP genotyping, higher nuDNA genotyped rates and success rates, than those using the MinElute method. In the longitudinal research, a gradual decrease in the total DoC of mtDNA fragments was observed along the length of the hair shaft, from the proximal root to the distal end. In contrast, the DoC of nuDNA exhibited a relatively stable pattern along the length of the hair shafts. The study contributes valuable insights into the simultaneous detection of nuDNA and mtDNA in hair shafts, emphasizing the need for optimized DNA extraction and detection methods for these highly degraded samples.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"75 ","pages":"Article 103176"},"PeriodicalIF":3.2000,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Forensic Science International-Genetics","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1872497324001728","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}

引用次数: 0

Abstract

Hair is an important type of biological evidence at crime scenes. However, the highly degraded nature of DNA fragments in hair shafts poses challenges for the detection of nuclear DNA (nuDNA) through capillary electrophoresis-based short tandem repeat (STR) genotyping. In this study, an all-in-one multiplex system named MGIEasy Signature Identification Library Prep Kit (MGI Tech, China) was employed to the simultaneous genotyping of both mitochondrial DNA (mtDNA) and nuDNA in hair shafts. This system is based on massively parallel sequencing (MPS) technology and encompasses Amelogenin, STRs, single nucleotide polymorphisms (SNPs) and mtDNA hypervariable regions (HVRs) in a single reaction. A total of 370 hair shafts, together with 180 blood samples as the references, were examined. The mtDNA analysis of 110 unrelated blood samples unveiled a total of 150 homoplasmic variants and 105 distinct haplotypes, revealing population polymorphisms in the Guangdong Han Chinese. The study also delved into the detection of mtDNA heteroplasmy, revealing 8.18 % and 16.36 % of individuals with point heteroplasmies (PHPs) in blood and hair shaft samples, respectively. Additionally, hair shafts with DNA extracted using the Investigator method yielded higher average depth of coverage (DoC), lower drop-out rate for SNP genotyping, higher nuDNA genotyped rates and success rates, than those using the MinElute method. In the longitudinal research, a gradual decrease in the total DoC of mtDNA fragments was observed along the length of the hair shaft, from the proximal root to the distal end. In contrast, the DoC of nuDNA exhibited a relatively stable pattern along the length of the hair shafts. The study contributes valuable insights into the simultaneous detection of nuDNA and mtDNA in hair shafts, emphasizing the need for optimized DNA extraction and detection methods for these highly degraded samples.

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

同时对无根毛轴和血液样本中的线粒体 DNA 和核 DNA 进行基因分型，以加强分析。

头发是犯罪现场的一种重要生物证据。然而，毛发中DNA片段的高度降解性给基于毛细管电泳的短串联重复（STR）基因分型检测核DNA（nuDNA）带来了挑战。本研究采用了一种名为 "MGIEasy Signature Identification Library Prep Kit "的多合一系统（MGIEasy Signature Identification Library Prep Kit，中国）来同时对毛发中的线粒体DNA（mtDNA）和nuDNA进行基因分型。该系统基于大规模并行测序（MPS）技术，在单次反应中包含淀粉样蛋白、STRs、单核苷酸多态性（SNPs）和 mtDNA 超变异区（HVRs）。共检测了 370 根毛干和 180 份血液样本作为参考。对 110 份无血缘关系的血液样本进行的 mtDNA 分析共发现 150 个同质变异和 105 个不同的单倍型，揭示了广东汉族的人群多态性。该研究还深入探讨了 mtDNA 异质体的检测，在血液和毛发样本中分别发现 8.18% 和 16.36% 的个体存在点异质体（PHPs）。此外，与使用 MinElute 方法的样本相比，使用 Investigator 方法提取 DNA 的毛发样本的平均覆盖深度（DoC）更高，SNP 基因分型的丢失率更低，nuDNA 基因分型率和成功率更高。在纵向研究中，观察到 mtDNA 片段的总 DoC 从近端发根到远端沿发干长度逐渐降低。与此相反，nuDNA 的 DoC 沿着毛干的长度呈现出相对稳定的模式。这项研究为同时检测发干中的 nuDNA 和 mtDNA 提供了宝贵的见解，强调了针对这些高度降解样本优化 DNA 提取和检测方法的必要性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

Forensic Science International-Genetics 生物-医学：法

CiteScore

7.50

自引率

32.30%

发文量

132

审稿时长

11.3 weeks

期刊介绍： Forensic Science International: Genetics is the premier journal in the field of Forensic Genetics. This branch of Forensic Science can be defined as the application of genetics to human and non-human material (in the sense of a science with the purpose of studying inherited characteristics for the analysis of inter- and intra-specific variations in populations) for the resolution of legal conflicts. The scope of the journal includes: Forensic applications of human polymorphism. Testing of paternity and other family relationships, immigration cases, typing of biological stains and tissues from criminal casework, identification of human remains by DNA testing methodologies. Description of human polymorphisms of forensic interest, with special interest in DNA polymorphisms. Autosomal DNA polymorphisms, mini- and microsatellites (or short tandem repeats, STRs), single nucleotide polymorphisms (SNPs), X and Y chromosome polymorphisms, mtDNA polymorphisms, and any other type of DNA variation with potential forensic applications. Non-human DNA polymorphisms for crime scene investigation. Population genetics of human polymorphisms of forensic interest. Population data, especially from DNA polymorphisms of interest for the solution of forensic problems. DNA typing methodologies and strategies. Biostatistical methods in forensic genetics. Evaluation of DNA evidence in forensic problems (such as paternity or immigration cases, criminal casework, identification), classical and new statistical approaches. Standards in forensic genetics. Recommendations of regulatory bodies concerning methods, markers, interpretation or strategies or proposals for procedural or technical standards. Quality control. Quality control and quality assurance strategies, proficiency testing for DNA typing methodologies. Criminal DNA databases. Technical, legal and statistical issues. General ethical and legal issues related to forensic genetics.