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Functional genomics for curation of variants in telomere biology disorder associated genes: A systematic review

journal contribution
posted on 2023-05-21, 15:56 authored by Niles NelsonNiles Nelson, Feurstein, S, Niaz, N, Truong, J, Holien, JK, Sionne LucasSionne Lucas, Kirsten FairfaxKirsten Fairfax, Joanne DickinsonJoanne Dickinson, Bryan, TM

Purpose: Patients with an underlying telomere biology disorder (TBD) have variable clinical presentations, and they can be challenging to diagnose clinically. A genomic diagnosis for patients presenting with TBD is vital for optimal treatment. Unfortunately, many variants identified during diagnostic testing are variants of uncertain significance. This complicates management decisions, delays treatment, and risks nonuptake of potentially curative therapies. Improved application of functional genomic evidence may reduce variants of uncertain significance classifications.

Methods: We systematically searched the literature for published functional assays interrogating TBD gene variants. When possible, established likely benign/benign and likely pathogenic/pathogenic variants were used to estimate the assay sensitivity, specificity, positive predictive value, negative predictive value, and odds of pathogenicity.

Results: In total, 3131 articles were screened and 151 met inclusion criteria. Sufficient data to enable a PS3/BS3 recommendation were available for TERT variants only. We recommend that PS3 and BS3 can be applied at a moderate and supportive level, respectively. PS3/BS3 application was limited by a lack of assay standardization and limited inclusion of benign variants.

Conclusion: Further assay standardization and assessment of benign variants are required for optimal use of the PS3/BS3 criterion for TBD gene variant classification.

History

Publication title

Genetics in Medicine

Volume

25

Pagination

1-18

ISSN

1098-3600

Department/School

Menzies Institute for Medical Research

Publisher

Lippincott Williams & Wilkins

Place of publication

530 Walnut St, Philadelphia, USA, Pa, 19106-3621

Rights statement

© 2022 American College of Medical Genetics and Genomics.

Repository Status

  • Restricted

Socio-economic Objectives

Diagnosis of human diseases and conditions; Prevention of human diseases and conditions; Treatment of human diseases and conditions

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