Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.

IF 3.8 3区 医学 Q2 GENETICS & HEREDITY Human Genomics Pub Date : 2024-11-05 DOI:10.1186/s40246-024-00684-8
Ferdinando Bonfiglio, Andrea Legati, Vito Alessandro Lasorsa, Flavia Palombo, Giulia De Riso, Federica Isidori, Silvia Russo, Simone Furini, Giuseppe Merla, Fabio Coppedè, Marco Tartaglia, Alessandro Bruselles, Tommaso Pippucci, Andrea Ciolfi, Michele Pinelli, Mario Capasso
{"title":"Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.","authors":"Ferdinando Bonfiglio, Andrea Legati, Vito Alessandro Lasorsa, Flavia Palombo, Giulia De Riso, Federica Isidori, Silvia Russo, Simone Furini, Giuseppe Merla, Fabio Coppedè, Marco Tartaglia, Alessandro Bruselles, Tommaso Pippucci, Andrea Ciolfi, Michele Pinelli, Mario Capasso","doi":"10.1186/s40246-024-00684-8","DOIUrl":null,"url":null,"abstract":"<p><p>This comprehensive review provides insights and suggested strategies for the analysis of germline variants using second- and third-generation sequencing technologies (SGS and TGS). It addresses the critical stages of data processing, starting from alignment and preprocessing to quality control, variant calling, and the removal of artifacts. The document emphasized the importance of meticulous data handling, highlighting advanced methodologies for annotating variants and identifying structural variations and methylated DNA sites. Special attention is given to the inspection of problematic variants, a step that is crucial for ensuring the accuracy of the analysis, particularly in clinical settings where genetic diagnostics can inform patient care. Additionally, the document covers the use of various bioinformatics tools and software that enhance the precision and reliability of these analyses. It outlines best practices for the annotation of variants, including considerations for problematic genetic alterations such as those in the human leukocyte antigen region, runs of homozygosity, and mitochondrial DNA alterations. The document also explores the complexities associated with identifying structural variants and copy number variations, underscoring the challenges posed by these large-scale genomic alterations. The objective is to offer a comprehensive framework for researchers and clinicians, ensuring that genetic analyses conducted with SGS and TGS are both accurate and reproducible. By following these best practices, the document aims to increase the diagnostic accuracy for hereditary diseases, facilitating early diagnosis, prevention, and personalized treatment strategies. This review serves as a valuable resource for both novices and experts in the field, providing insights into the latest advancements and methodologies in genetic analysis. It also aims to encourage the adoption of these practices in diverse research and clinical contexts, promoting consistency and reliability across studies.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"18 1","pages":"120"},"PeriodicalIF":3.8000,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536923/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Human Genomics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1186/s40246-024-00684-8","RegionNum":3,"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

This comprehensive review provides insights and suggested strategies for the analysis of germline variants using second- and third-generation sequencing technologies (SGS and TGS). It addresses the critical stages of data processing, starting from alignment and preprocessing to quality control, variant calling, and the removal of artifacts. The document emphasized the importance of meticulous data handling, highlighting advanced methodologies for annotating variants and identifying structural variations and methylated DNA sites. Special attention is given to the inspection of problematic variants, a step that is crucial for ensuring the accuracy of the analysis, particularly in clinical settings where genetic diagnostics can inform patient care. Additionally, the document covers the use of various bioinformatics tools and software that enhance the precision and reliability of these analyses. It outlines best practices for the annotation of variants, including considerations for problematic genetic alterations such as those in the human leukocyte antigen region, runs of homozygosity, and mitochondrial DNA alterations. The document also explores the complexities associated with identifying structural variants and copy number variations, underscoring the challenges posed by these large-scale genomic alterations. The objective is to offer a comprehensive framework for researchers and clinicians, ensuring that genetic analyses conducted with SGS and TGS are both accurate and reproducible. By following these best practices, the document aims to increase the diagnostic accuracy for hereditary diseases, facilitating early diagnosis, prevention, and personalized treatment strategies. This review serves as a valuable resource for both novices and experts in the field, providing insights into the latest advancements and methodologies in genetic analysis. It also aims to encourage the adoption of these practices in diverse research and clinical contexts, promoting consistency and reliability across studies.

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
对第二代和第三代测序数据进行种系变异和 DNA 甲基化分析的最佳实践。
这篇综合性综述为使用第二代和第三代测序技术(SGS 和 TGS)分析种系变异提供了见解和建议策略。它探讨了数据处理的关键阶段,从比对和预处理到质量控制、变异调用和去除伪影。文件强调了细致数据处理的重要性,重点介绍了注释变异、识别结构变异和甲基化 DNA 位点的先进方法。文件特别关注对有问题变异的检查,这一步骤对于确保分析的准确性至关重要,尤其是在临床环境中,因为基因诊断可为患者护理提供依据。此外,文件还介绍了各种生物信息学工具和软件的使用方法,以提高这些分析的准确性和可靠性。文件概述了变异注释的最佳实践,包括对有问题的基因改变的考虑,如人类白细胞抗原区域的基因改变、同基因遗传变异和线粒体 DNA 改变。文件还探讨了与识别结构变异和拷贝数变异相关的复杂性,强调了这些大规模基因组改变所带来的挑战。其目的是为研究人员和临床医生提供一个全面的框架,确保使用 SGS 和 TGS 进行的基因分析既准确又具有可重复性。通过遵循这些最佳实践,本文件旨在提高遗传性疾病诊断的准确性,促进早期诊断、预防和个性化治疗策略。本综述为该领域的新手和专家提供了宝贵的资源,让他们深入了解遗传分析的最新进展和方法。它还旨在鼓励在不同的研究和临床环境中采用这些方法,促进各项研究的一致性和可靠性。
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
Human Genomics
Human Genomics GENETICS & HEREDITY-
CiteScore
6.00
自引率
2.20%
发文量
55
审稿时长
11 weeks
期刊介绍: Human Genomics is a peer-reviewed, open access, online journal that focuses on the application of genomic analysis in all aspects of human health and disease, as well as genomic analysis of drug efficacy and safety, and comparative genomics. Topics covered by the journal include, but are not limited to: pharmacogenomics, genome-wide association studies, genome-wide sequencing, exome sequencing, next-generation deep-sequencing, functional genomics, epigenomics, translational genomics, expression profiling, proteomics, bioinformatics, animal models, statistical genetics, genetic epidemiology, human population genetics and comparative genomics.
期刊最新文献
Advancing understanding of human variability through toxicokinetic modeling, in vitro-in vivo extrapolation, and new approach methodologies. Genetic heterogeneity in familial forms of genetic generalized epilepsy: from mono- to oligogenism. Analysis of public perceptions on the use of artificial intelligence in genomic medicine. Global transcriptome modulation by xenobiotics: the role of alternative splicing in adaptive responses to chemical exposures. Ralationship between polymorphisms and diplotypes of HLA-G 3'UTR and fetuses with abnormal chromosomes or unexplained pregnancy loss (UPL).
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1