Variant Curation Expert Panel Recommendations for RYR1 Pathogenicity Assertions in Malignant Hyperthermia Susceptibility

Johnston, J. J.; Dirksen, R. T.; Girard, T.; Gonsalves, S. G.; Hopkins, P. M.; Riazi, S.; Saddic, L. A.; Sambuughin, N.; Saxena, R.; Stowell, K.; Weber, J.; Rosenberg, H.; Biesecker, L. G.

doi:10.1101/2020.11.29.402768

bioRxiv · 10.1101/2020.11.29.402768

Variant Curation Expert Panel Recommendations for RYR1 Pathogenicity Assertions in Malignant Hyperthermia Susceptibility

Johnston, J. J.·Dirksen, R. T.·Girard, T.·Gonsalves, S. G.·Hopkins, P. M.·Riazi, S.·Saddic, L. A.·Sambuughin, N.·Saxena, R.·Stowell, K.·Weber, J.·Rosenberg, H.·Biesecker, L. G.

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Abstract

PurposePrevention of malignant hyperthermia (MH) requires an understanding of RYR1 variant pathogenicity to assess the risk of exposure to triggering agents. Personalized medicine, especially secondary findings and eventually genomic screening, will contribute toward this goal. MethodsWe specified ACMG/AMP criteria for variant interpretation for RYR1 and MH. Proposed rules were piloted on 84 variants. We applied quantitative evidence calibration for several criteria using likelihood ratios based on the Bayesian framework. ResultsSeven ACMG/AMP criteria were adopted without changes, ten were adopted with RYR1-specific modifications, and nine were dropped. The in silico (PP3 and BP4) and hot spot criteria (PM1) were evaluated quantitatively. REVEL gave an OR of 23:1 for PP3 and 16:1 for BP4 using trichotomized cut-offs of >0.85 (pathogenic) and <0.5 (benign). The PM1 hotspot criterion had an OR of 24:1. PP3 and PM1 were implemented at moderate strength. Applying the revised ACMG criteria to 44 recognized MH variants, 30 were assessed as pathogenic, 12 as likely pathogenic, and two as VUS. ConclusionCuration of these variants will facilitate interpretation of RYR1/MH genomic testing results, which is especially important for secondary findings analyses. Our approach to quantitatively calibrating criteria are generalizable to other variant curation expert panels.

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Johnston, J. J., Dirksen, R. T., Girard, T., Gonsalves, S. G., Hopkins, P. M., Riazi, S., Saddic, L. A., Sambuughin, N., Saxena, R., Stowell, K., Weber, J., Rosenberg, H., Biesecker, L. G.. 2020-11-29. Variant Curation Expert Panel Recommendations for RYR1 Pathogenicity Assertions in Malignant Hyperthermia Susceptibility. https://doi.org/10.1101/2020.11.29.402768

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