对转换基因组参考联盟的人类构建37的升降工具的评估,以使用ClinVar变体构建38使用ClinVar变体
Kyoung-Jin Park1, Young Ahn Yoon2, Jong-Ho Park3
1Department of Laboratory Medicine & Genetics, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon 51353, Republic of Korea.
Genes
|October 28, 2023
概括
基因组参考联盟的人类构建38 (GRCh38) 从GRCh37转换是使用提升工具非常准确的. UCSC liftOver实现了99.99%的准确性,其中失败的转换主要涉及indels/重复.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 医学遗传学 医学遗传学
背景情况:
- 基因组参考联盟的人类构建38 (GRCh38) 提供了对GRCh37的改进,但面临着缓慢的采用.
- 提升工具通过转换基因组坐标来促进向GRCh38的过渡.
- 准确的基因组坐标转换对于临床遗传变异解释至关重要.
研究的目的:
- 评估常用的升降工具的准确性,用于将基因组坐标从GRCh37转换为GRCh38.
- 为了确定GRCh37到GRCh38基因组构建转换过程中的潜在挑战和局限性.
主要方法:
- 下载的ClinVar变种呼叫格式 (VCF) 文件用于GRCh37和GRCh38.
- 使用了CrossMap,NCBI Remap和UCSC liftOver工具进行基因组坐标转换.
- 分析了转换的准确性,并描述了那些失败的变体.
主要成果:
- 在UCSC liftOver显示的最高准确率为99.99%,其次是CrossMap (99.81%) 和NCBI Remap (99.69%).
- 索引和重复是主要的变体类型,在所有工具中都未能实现转换.
- 八种变异,包括一种致病性/可能致病性,转换失败,并位于ALMS,TTN和CFTR等基因中.
结论:
- 提升工具提供了一个高度准确的方法 (>99%) 转换ClinVar变体之间的GRCh37和GRCh38.
- 这项研究代表了GRCh38.8临床实施的基本步骤.
- 需要进一步的研究来比较提升工具的性能,并在临床环境中验证重新调整策略.
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