LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants.
LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants.
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DOI：
10.1186/s12864-023-09935-9
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发表时间：
2024-01-26
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
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短串联重复序列（STR）广泛分布于人类基因组中，与许多神经系统疾病相关。然而，STR对疾病的贡献程度可能被低估，因为在短读下一代测序数据中调用这些变体存在挑战。已经开发了几种计算工具用于STR变体调用，但没有一种完全解决与这种变体类别相关的所有复杂性。在这里，我们介绍了LUSTR，它旨在通过在定义STR基因座方面实现更大的灵活性，允许可定制的模块来定制分析，并扩展调用体细胞和多等位基因STR变体的能力，来解决与STR变体调用相关的一些挑战。LUSTR是一种用户友好且易于定制的工具，用于靶向或无偏见的全基因组STR变体筛选，可以使用预定义的或新的基因组构建。使用模拟和真实的数据集，我们证明了LUSTR准确地推断出有和没有疾病的个体的种系和体细胞STR扩增。LUSTR提供了一种强大且用户友好的方法，可以识别STR变异，并可以促进更全面的研究，评估致病性STR变异在人类疾病中的作用。在线版本包含补充材料，可通过10.1186/s12864-023-09935-9获得。
Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class. Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases. LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases. The online version contains supplementary material available at 10.1186/s12864-023-09935-9.
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DOI：
10.1073/pnas.79.21.6465
发表时间：
1982-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
HAMADA, H;PETRINO, MG;KAKUNAGA, T
通讯作者：
KAKUNAGA, T
影响因子：
64.5
作者：
FU, YH;KUHL, DPA;CASKEY, CT
通讯作者：
CASKEY, CT
影响因子：
12.3
作者：
Dolzhenko, Egor;Bennett, Mark F.;Eberle, Michael A.
通讯作者：
Eberle, Michael A.
影响因子：
3.7
作者：
Wang, Xuewen;Huang, Meng;Budowle, Bruce;Ge, Jianye
通讯作者：
Ge, Jianye
影响因子：
14.9
作者：
Benson, G
通讯作者：
Benson, G