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Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: the case of hypertrophic cardiomyopathy

dc.contributor.authorWalsh, Roddy
dc.contributor.authorMazzarotto, Francesco
dc.contributor.authorWhiffin, Nicola
dc.contributor.authorBuchan, Rachel
dc.contributor.authorMidwinter, William
dc.contributor.authorWilk, Alicja
dc.contributor.authorLi, Nicholas
dc.contributor.authorFelkin, Leanne
dc.contributor.authorIngold, Nathan
dc.contributor.authorGovind, Risha
dc.contributor.authorAhmad, Mian
dc.contributor.authorMazaika, Erica
dc.contributor.authorAllouba, Mona
dc.contributor.authorZhang, Xiaolei
dc.contributor.authorde Marvao, Antonio
dc.contributor.authorDay, Sharlene M
dc.contributor.authorAshley, Euan
dc.contributor.authorColan, Steven D
dc.contributor.authorMichels, Michelle
dc.contributor.authorPereira, Alexandre C
dc.contributor.authorJacoby, Daniel
dc.contributor.authorHo, Carolyn Y
dc.contributor.authorThomson, Kate L
dc.contributor.authorWatkins, Hugh
dc.contributor.authorBarton, Paul J R
dc.contributor.authorOlivotto, Iacopo
dc.contributor.authorCook, Stuart A
dc.contributor.authorWare, James S
dc.date.accessioned2019-02-03T04:16:56Z
dc.date.available2019-02-03T04:16:56Z
dc.date.issued2019-01-29
dc.identifier.citationGenome Medicine. 2019 Jan 29;11(1):5
dc.identifier.urihttps://doi.org/10.1186/s13073-019-0616-z
dc.identifier.urihttps://hdl.handle.net/2027.42/147462
dc.description.abstractAbstract 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.
dc.titleQuantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: the case of hypertrophic cardiomyopathy
dc.typeArticleen_US
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/147462/1/13073_2019_Article_616.pdf
dc.language.rfc3066en
dc.rights.holderThe Author(s).
dc.date.updated2019-02-03T04:17:01Z
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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