VARista: a free web platform for streamlined whole-genome variant analysis across T2T, hg38, and hg19

IF 3.8 2区生物学 Q2 GENETICS & HEREDITY

Human Genetics Pub Date : 2024-04-12 DOI:10.1007/s00439-024-02671-4

Noam Hadar, Vadim Dolgin, Katya Oustinov, Yuval Yogev, Tomer Poleg, Amit Safran, Ofek Freund, Nadav Agam, Matan M. Jean, Regina Proskorovski-Ohayon, Ohad Wormser, Max Drabkin, Daniel Halperin, Marina Eskin-Schwartz, Ginat Narkis, Sufa Sued-Hendrickson, Ilana Aminov, Maya Gombosh, Sarit Aharoni, Ohad S. Birk

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引用次数: 0

Abstract

With the increasing importance of genomic data in understanding genetic diseases, there is an essential need for efficient and user-friendly tools that simplify variant analysis. Although multiple tools exist, many present barriers such as steep learning curves, limited reference genome compatibility, or costs. We developed VARista, a free web-based tool, to address these challenges and provide a streamlined solution for researchers, particularly those focusing on rare monogenic diseases. VARista offers a user-centric interface that eliminates much of the technical complexity typically associated with variant analysis. The tool directly supports VCF files generated using reference genomes hg19, hg38, and the emerging T2T, with seamless remapping capabilities between them. Features such as gene summaries and links, tissue and cell-specific gene expression data for both adults and fetuses, as well as automated PCR design and integration with tools such as SpliceAI and AlphaMissense, enable users to focus on the biology and the case itself. As we demonstrate, VARista proved effective in narrowing down potential disease-causing variants, prioritizing them effectively, and providing meaningful biological context, facilitating rapid decision-making. VARista stands out as a freely available and comprehensive tool that consolidates various aspects of variant analysis into a single platform that embraces the forefront of genomic advancements. Its design inherently supports a shift in focus from technicalities to critical thinking, thereby promoting better-informed decisions in genetic disease research. Given its unique capabilities and user-centric design, VARista has the potential to become an essential asset for the genomic research community. https://VARista.link

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VARista：跨 T2T、hg38 和 hg19 的简化全基因组变异分析免费网络平台

随着基因组数据在了解遗传疾病方面的重要性与日俱增，我们亟需高效且用户友好的工具来简化变异分析。虽然目前已有多种工具，但许多工具都存在学习曲线陡峭、参考基因组兼容性有限或成本高昂等障碍。我们开发了基于网络的免费工具 VARista，以应对这些挑战，并为研究人员，尤其是关注罕见单基因疾病的研究人员提供简化的解决方案。VARista 提供了一个以用户为中心的界面，消除了通常与变异分析相关的大量复杂技术。该工具直接支持使用参考基因组 hg19、hg38 和新出现的 T2T 生成的 VCF 文件，并支持它们之间的无缝重映射功能。基因摘要和链接、成人和胎儿的组织和细胞特异性基因表达数据、自动 PCR 设计以及与 SpliceAI 和 AlphaMissense 等工具的集成等功能，使用户能够专注于生物学和病例本身。正如我们所展示的，VARista 在缩小潜在致病变异范围、有效确定优先级以及提供有意义的生物学背景方面证明是有效的，有助于快速决策。VARista 是一款可免费使用的综合工具，它将变异分析的各个方面整合到一个平台中，引领了基因组学的前沿发展。它的设计本质上支持将重点从技术性问题转移到批判性思维，从而促进遗传疾病研究做出更明智的决策。鉴于其独特的功能和以用户为中心的设计，VARista 有潜力成为基因组研究界的重要资产。https://VARista.link

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来源期刊

Human Genetics 生物-遗传学

CiteScore

10.80

自引率

3.80%

发文量

审稿时长

1 months

期刊介绍： Human Genetics is a monthly journal publishing original and timely articles on all aspects of human genetics. The Journal particularly welcomes articles in the areas of Behavioral genetics, Bioinformatics, Cancer genetics and genomics, Cytogenetics, Developmental genetics, Disease association studies, Dysmorphology, ELSI (ethical, legal and social issues), Evolutionary genetics, Gene expression, Gene structure and organization, Genetics of complex diseases and epistatic interactions, Genetic epidemiology, Genome biology, Genome structure and organization, Genotype-phenotype relationships, Human Genomics, Immunogenetics and genomics, Linkage analysis and genetic mapping, Methods in Statistical Genetics, Molecular diagnostics, Mutation detection and analysis, Neurogenetics, Physical mapping and Population Genetics. Articles reporting animal models relevant to human biology or disease are also welcome. Preference will be given to those articles which address clinically relevant questions or which provide new insights into human biology. Unless reporting entirely novel and unusual aspects of a topic, clinical case reports, cytogenetic case reports, papers on descriptive population genetics, articles dealing with the frequency of polymorphisms or additional mutations within genes in which numerous lesions have already been described, and papers that report meta-analyses of previously published datasets will normally not be accepted. The Journal typically will not consider for publication manuscripts that report merely the isolation, map position, structure, and tissue expression profile of a gene of unknown function unless the gene is of particular interest or is a candidate gene involved in a human trait or disorder.