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Related Experiment Video

Updated: Dec 3, 2025

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Best practices for variant calling in clinical sequencing.

Daniel C Koboldt1,2

  • 1Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, USA. Daniel.Koboldt@nationwidechildrens.org.

Genome Medicine
|October 27, 2020
PubMed
Summary
This summary is machine-generated.

Accurate variant calling in next-generation sequencing (NGS) data is crucial for clinical genetic testing. This review outlines best practices for variant detection in inherited disorders and cancer, emphasizing trio sequencing and somatic mutation analysis.

Keywords:
Best practicesCancer sequencingClinical sequencingMutation detectionNext-generation sequencingVariant calling

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Area of Science:

  • Genomics
  • Clinical Genetics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) has revolutionized clinical genetic testing for inherited diseases and cancer.
  • Accurate variant calling is fundamental for downstream analysis and interpretation of NGS data.
  • Software tools for variant detection have significantly evolved alongside NGS technologies.

Purpose of the Study:

  • To review current best practices for variant calling in clinical sequencing studies.
  • To provide guidance on variant detection for inherited disorders (trio sequencing) and cancer (somatic mutation detection).
  • To discuss the strengths and weaknesses of different sequencing approaches (panel, exome, whole-genome).

Main Methods:

  • Review of current literature and software tools for variant calling.
  • Emphasis on strategies for trio sequencing and somatic mutation detection.
  • Discussion of variant classes, review, validation, and benchmarking.

Main Results:

  • Provides recommended tools and strategies for variant calling across different sequencing types.
  • Highlights the relative merits of panel, exome, and whole-genome sequencing for variant detection.
  • Offers guidance on variant review, validation, and benchmarking for optimal performance.

Conclusions:

  • Best practice principles for clinical variant calling remain relevant despite evolving NGS technologies.
  • The review serves as a guide for accurate variant detection in clinical genetic testing.
  • Emerging technologies like long-read sequencing will continue to shape variant calling strategies.