CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting

Genome Medicine
Márton MünzNazneen Rahman

Abstract

Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical data. Provision of consistent, clinically applicable variant annotation of NGS data has proved difficult, particularly of indels, an important variant class in clinical genomics. Annotation in relation to a reference genome sequence, the DNA strand of coding transcripts and potential alternative variant representations has not been well addressed. Here we present tools that address these challenges to provide rapid, standardized, clinically appropriate annotation of NGS data in line with existing clinical standards. We developed a clinical sequencing nomenclature (CSN), a fixed variant annotation consistent with the principles of the Human Genome Variation Society (HGVS) guidelines, optimized for automated variant annotation of NGS data. To deliver high-throughput CSN annotation we created CAVA (Clinical Annotation of VAriants), a fast, lightweight tool designed for easy incorporation into NGS pipelines. CAVA allows transcript specification, appropriately accommodates the strand of a gene transcript and flags variants with ...Continue Reading

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Citations

Jan 11, 2016·American Journal of Human Genetics·Tychele N TurnerEvan E Eichler
Aug 4, 2016·Scientific Reports·Elise RuarkNazneen Rahman
May 30, 2017·Nature Genetics·Shawn YostNazneen Rahman
Mar 1, 2017·BMC Bioinformatics·Sarah SandmannMartin Dugas
Oct 13, 2018·Human Mutation·Piotr PawliczekClinical Genome (ClinGen) Resource
May 20, 2020·Journal of the National Cancer Institute·Julie R PalmerFergus J Couch
Apr 11, 2017·PeerJ·Miika J AhdesmäkiJustin H Johnson
Jun 9, 2018·Wellcome Open Research·Márton MünzNazneen Rahman
Aug 25, 2020·JCO Precision Oncology·Marco MatejcicChristopher A Haiman
Nov 7, 2017·Frontiers in Microbiology·Camilla SekseJianxin Shi
Jun 21, 2018·JAMA : the Journal of the American Medical Association·Chunling HuFergus J Couch
Oct 9, 2020·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Siddhartha YadavRobert R McWilliams

Related Concepts

BRCA1-IRIS protein, human
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