| Autor: |
Roddy Walsh, Francesco Mazzarotto, Nicola Whiffin, Rachel Buchan, William Midwinter, Alicja Wilk, Nicholas Li, Leanne Felkin, Nathan Ingold, Risha Govind, Mian Ahmad, Erica Mazaika, Mona Allouba, Xiaolei Zhang, Antonio de Marvao, Sharlene M. Day, Euan Ashley, Steven D. Colan, Michelle Michels, Alexandre C. Pereira, Daniel Jacoby, Carolyn Y. Ho, Kate L. Thomson, Hugh Watkins, Paul J. R. Barton, Iacopo Olivotto, Stuart A. Cook, James S. Ware |
| Jazyk: |
angličtina |
| Rok vydání: |
2019 |
| Předmět: |
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| Zdroj: |
Genome Medicine, Vol 11, Iss 1, Pp 1-18 (2019) |
| Druh dokumentu: |
article |
| ISSN: |
1756-994X |
| DOI: |
10.1186/s13073-019-0616-z |
| Popis: |
Abstract Background International guidelines for variant interpretation in Mendelian disease set stringent criteria to report a variant as (likely) pathogenic, prioritising control of false-positive rate over test sensitivity and diagnostic yield. Genetic testing is also more likely informative in individuals with well-characterised variants from extensively studied European-ancestry populations. Inherited cardiomyopathies are relatively common Mendelian diseases that allow empirical calibration and assessment of this framework. Methods We compared rare variants in large hypertrophic cardiomyopathy (HCM) cohorts (up to 6179 cases) to reference populations to identify variant classes with high prior likelihoods of pathogenicity, as defined by etiological fraction (EF). We analysed the distribution of variants using a bespoke unsupervised clustering algorithm to identify gene regions in which variants are significantly clustered in cases. Results Analysis of variant distribution identified regions in which variants are significantly enriched in cases and variant location was a better discriminator of pathogenicity than generic computational functional prediction algorithms. Non-truncating variant classes with an EF ≥ 0.95 were identified in five established HCM genes. Applying this approach leads to an estimated 14–20% increase in cases with actionable HCM variants, i.e. variants classified as pathogenic/likely pathogenic that might be used for predictive testing in probands’ relatives. Conclusions When found in a patient confirmed to have disease, novel variants in some genes and regions are empirically shown to have a sufficiently high probability of pathogenicity to support a “likely pathogenic” classification, even without additional segregation or functional data. This could increase the yield of high confidence actionable variants, consistent with the framework and recommendations of current guidelines. The techniques outlined offer a consistent and unbiased approach to variant interpretation for Mendelian disease genetic testing. We propose adaptations to ACMG/AMP guidelines to incorporate such evidence in a quantitative and transparent manner. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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