1. Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants
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Lucy Loong, Cankut Cubuk, Subin Choi, Sophie Allen, Beth Torr, Alice Garrett, Chey Loveday, Miranda Durkie, Alison Callaway, George J. Burghel, James Drummond, Rachel Robinson, Ian R. Berry, Andrew Wallace, Diana M. Eccles, Marc Tischkowitz, Sian Ellard, James S. Ware, Helen Hanson, Clare Turnbull, S. Samant, A. Lucassen, A. Znaczko, A. Shaw, A. Ansari, A. Kumar, A. Donaldson, A. Murray, A. Ross, A. Taylor-Beadling, A. Taylor, A. Innes, A. Brady, A. Kulkarni, A.-C. Hogg, A. Ramsay Bowden, A. Hadonou, B. Coad, B. McIldowie, B. Speight, B. DeSouza, B. Mullaney, C. McKenna, C. Brewer, C. Olimpio, C. Clabby, C. Crosby, C. Jenkins, C. Armstrong, C. Bowles, C. Brooks, C. Byrne, C. Maurer, D. Baralle, D. Chubb, D. Stobo, D. Moore, D. O'Sullivan, D. Donnelly, D. Randhawa, D. Halliday, E. Atkinson, E. Baple, E. Rauter, E. Johnston, E. Woodward, E. Maher, E. Sofianopoulou, E. Petrides, F. Lalloo, F. McRonald, F. Pelz, I. Frayling, G. Evans, G. Corbett, G. Rea, H. Clouston, H. Powell, H. Williamson, H. Carley, H.J.W. Thomas, I. Tomlinson, J. Cook, J. Hoyle, J. Tellez, J. Whitworth, J. Williams, J. Murray, J. Campbell, J. Tolmie, J. Field, J. Mason, J. Burn, J. Bruty, J. Callaway, J. Grant, J. Del Rey Jimenez, J. Pagan, J. VanCampen, J. Barwell, K. Monahan, K. Tatton-Brown, K.-R. Ong, K. Murphy, K. Andrews, K. Mokretar, K. Cadoo, K. Smith, K. Baker, K. Brown, K. Reay, K. McKay Bounford, K. Bradshaw, K. Russell, K. Stone, K. Snape, L. Crookes, L. Reed, L. Taggart, L. Yarram, L. Cobbold, L. Walker, L. Hawkes, L. Busby, L. Izatt, L. Kiely, L. Hughes, L. Side, L. Sarkies, K.-L. Greenhalgh, M. Shanmugasundaram, M. Duff, M. Bartlett, M. Watson, M. Owens, M. Bradford, M. Huxley, M. Slean, M. Ryten, M. Smith, M. Ahmed, N. Roberts, C. O'Brien, O. Middleton, P. Tarpey, P. Logan, P. Dean, P. May, P. Brace, R. Tredwell, R. Harrison, R. Hart, R. Kirk, R. Martin, R. Nyanhete, R. Wright, R. Davidson, R. Cleaver, S. Talukdar, S. Butler, J. Sampson, S. Ribeiro, S. Dell, S. Mackenzie, S. Hegarty, S. Albaba, S. McKee, S. Palmer-Smith, S. Heggarty, S. MacParland, S. Greville-Heygate, S. Daniels, S. Prapa, S. Abbs, S. Tennant, S. Hardy, S. MacMahon, T. McVeigh, T. Foo, T. Bedenham, T. Cranston, T. McDevitt, V. Clowes, V. Tripathi, V. McConnell, N. Woodwaer, Y. Wallis, Z. Kemp, G. Mullan, L. Pierson, L. Rainey, C. Joyce, A. Timbs, A.-M. Reuther, B. Frugtniet, C. Husher, C. Lawn, C. Corbett, D. Nocera-Jijon, D. Reay, E. Cross, F. Ryan, H. Lindsay, J. Oliver, J. Dring, J. Spiers, J. Harper, K. Ciucias, L. Connolly, M. Tsang, R. Brown, S. Shepherd, S. Begum, T. Tadiso, T. Linton-Willoughby, H. Heppell, K. Sahan, L. Worrillow, Z. Allen, M. Barlett, C. Watt, M. Hegarty, British Heart Foundation, and Wellcome Trust
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Concordance ,Mutation, Missense ,Biology ,PM5 ,CanVIG-UK ,Humans ,Missense mutation ,Genetic Predisposition to Disease ,Variant ,Codon ,Genetics (clinical) ,Genetics ,Genetics & Heredity ,0604 Genetics ,BRCA1 Protein ,Genetic Variation ,1103 Clinical Sciences ,Pathogenicity ,Classification ,MutS Homolog 2 Protein ,Genetic Variation/genetics ,Mutation, Missense/genetics ,MSH2 ,ACMG ,BRCA1 Protein/genetics ,MutS Homolog 2 Protein/genetics - Abstract
Purpose: Conditions and thresholds applied for evidence weighting of within-codon concordance (PM5) for pathogenicity vary widely between laboratories and expert groups. Because of the sparseness of available clinical classifications, there is little evidence for variation in practice. Methods: We used as a truthset 7541 dichotomous functional classifications of BRCA1 and MSH2, spanning 311 codons of BRCA1 and 918 codons of MSH2, generated from large-scale functional assays that have been shown to correlate excellently with clinical classifications. We assessed PM5 at 5 stringencies with incorporation of 8 in silico tools. For each analysis, we quantified a positive likelihood ratio (pLR, true positive rate/false positive rate), the predictive value of PM5-lookup in ClinVar compared with the functional truthset. Results: pLR was 16.3 (10.6-24.9) for variants for which there was exactly 1 additional colocated deleterious variant on ClinVar, and the variant under examination was equally or more damaging when analyzed using BLOSUM62. pLR was 71.5 (37.8-135.3) for variants for which there were 2 or more colocated deleterious ClinVar variants, and the variant under examination was equally or more damaging than at least 1 colocated variant when analyzed using BLOSUM62. Conclusion: These analyses support the graded use of PM5, with potential to use it at higher evidence weighting where more stringent criteria are met.
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- 2021