Best Practices for Variant Calling in Clinical Next-Generation Sequencing
This review provides comprehensive guidance on variant calling in clinical NGS studies, covering trio sequencing for inherited disorders and somatic mutation detection in cancer. The author evaluates the relative strengths of panel, exome, and whole-genome sequencing for variant detection and recommends specific tools and strategies for different variant classes, including guidance on validation and benchmarking. The principles presented remain broadly applicable despite the evolving technology landscape, including emerging long-read sequencing platforms.
The original study
Best practices for variant calling in clinical sequencing.
- Authors
- Koboldt DC
- Journal
- Genome medicine
- Type
- Journal Article, Research Support, Non-U.S. Gov't, Review
- PMID
- 33106175
Original abstract
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.