Best practices for variant calling in clinical sequencing

被引:207
作者
Koboldt, Daniel C. [1 ,2 ]
机构
[1] Nationwide Childrens Hosp, Steve & Cindy Rasmussen Inst Genom Med, Columbus, OH 43205 USA
[2] Ohio State Univ, Dept Pediat, Columbus, OH 43210 USA
关键词
Next-generation sequencing; Variant calling; Mutation detection; Clinical sequencing; Cancer sequencing; Best practices; COPY-NUMBER VARIATION; SOMATIC POINT MUTATIONS; GENOMIC CHARACTERIZATION; MOSAIC MUTATIONS; READ ALIGNMENT; DNA SAMPLES; CANCER; GENES; VALIDATION; DISCOVERY;
D O I
10.1186/s13073-020-00791-w
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Next-generation sequencing technologies have enabled a dramatic expansion of clinical genetic testing both for inherited conditions and diseases such as cancer. Accurate variant calling in NGS data is a critical step upon which virtually all downstream analysis and interpretation processes rely. Just as NGS technologies have evolved considerably over the past 10 years, so too have the software tools and approaches for detecting sequence variants in clinical samples. In this review, I discuss the current best practices for variant calling in clinical sequencing studies, with a particular emphasis on trio sequencing for inherited disorders and somatic mutation detection in cancer patients. I describe the relative strengths and weaknesses of panel, exome, and whole-genome sequencing for variant detection. Recommended tools and strategies for calling variants of different classes are also provided, along with guidance on variant review, validation, and benchmarking to ensure optimal performance. Although NGS technologies are continually evolving, and new capabilities (such as long-read single-molecule sequencing) are emerging, the "best practice" principles in this review should be relevant to clinical variant calling in the long term.
引用
收藏
页数:13
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