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Combining evidence for and against pathogenicity for variants in cancer susceptibility genes: CanVIG-UK consensus recommendations

by Bowden, Anne Ramsay , Crosby, Charlene , Martin, Rosalind , Ryten, Mina , Tischkowitz, Marc , Torr, Bethany , Barwell, Julian , Brewer, Carole , Wallace, Andrew J , Woodward, Emma , Turnbull, Clare , Eccles, Diana M , Robinson, Rachel , Donaldson, Alan , Mackenzie, Sarah , Tennant, Stephen , Adlard, Julian , Cobbold, Laura , Side, Lucy , Maher, Eamonn , Reay, Kim , Tobal, Khalid , Campbell, Joanna , Burn, John , Thomas, Huw , Taylor-Beadling, Alison , Cubuk, Cankut , Sampson, Julian , Berry, Ian R , Harrison, Rachel , Daniels, Stacey , Mullaney, Brendan , Drummond, James , Ong, Kai-Ren , Callaway, Alison , Hawkes, Lara , Nyanhete, Rodney , Heggarty, Shirley , Tarpey, Patrick , Cranston, Treena , Kumar, Ajith , Eccles, Diana , Cook, Jackie , Izatt, Louise , Chubb, Daniel , Davidson, Rosemarie , Hughes, Lowri , Logan, Peter , Brady, Angela , Tellez, James , Tripathi, Vishakha , Tolmie, Joanna , Jimenez, Ayaovi , Yarram, Laura , Hart, Rachel , Tomlinson, Ian , Hanson, Helen , Lucassen, Anneke , Duff, Marie , Watson, Mark , Garrett, Alice , Ahmed, Munaza , Burghel, George , Dell, Sarah , Field, Joanne , Wright, Ronnie , Clabby, Catherine , Grant, Jonathan , Greenhalgh, Karen-Lynn , Albaba, Sh

in Best practice / Biomarkers / Cancer / Classification / E-cadherin / Evidence-Based Medicine / Genes, Neoplasm / Genetic Predisposition to Disease - genetics / genetic testing / Genetic Variation / Genetics / Genomics / Health risk assessment / Humans / Laboratories / medical / Neoplasms - genetics / p53 Protein / Pathogenicity / Position Statement / PTEN protein

2021

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Combining evidence for and against pathogenicity for variants in cancer susceptibility genes: CanVIG-UK consensus recommendations

2021

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Combining evidence for and against pathogenicity for variants in cancer susceptibility genes: CanVIG-UK consensus recommendations

2021

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Journal Article

Combining evidence for and against pathogenicity for variants in cancer susceptibility genes: CanVIG-UK consensus recommendations

Bowden, Anne Ramsay,

Crosby, Charlene,

Martin, Rosalind,

Ryten, Mina,

Tischkowitz, Marc,

Torr, Bethany,

Barwell, Julian,

Brewer, Carole,

Wallace, Andrew J,

Woodward, Emma,

Turnbull, Clare,

Eccles, Diana M,

Robinson, Rachel,

Donaldson, Alan,

Mackenzie, Sarah,

Tennant, Stephen,

Adlard, Julian,

Cobbold, Laura,

Side, Lucy,

Maher, Eamonn,

Reay, Kim,

Tobal, Khalid,

Campbell, Joanna,

Burn, John,

Thomas, Huw,

Taylor-Beadling, Alison,

Cubuk, Cankut,

Sampson, Julian,

Berry, Ian R,

Harrison, Rachel,

Daniels, Stacey,

Mullaney, Brendan,

Drummond, James,

Ong, Kai-Ren,

Callaway, Alison,

Hawkes, Lara,

Nyanhete, Rodney,

Heggarty, Shirley,

Tarpey, Patrick,

Cranston, Treena,

Kumar, Ajith,

Eccles, Diana,

Cook, Jackie,

Izatt, Louise,

Chubb, Daniel,

Davidson, Rosemarie,

Hughes, Lowri,

Logan, Peter,

Brady, Angela,

Tellez, James,

Tripathi, Vishakha,

Tolmie, Joanna,

Jimenez, Ayaovi,

Yarram, Laura,

Hart, Rachel,

Tomlinson, Ian,

Hanson, Helen,

Lucassen, Anneke,

Duff, Marie,

Watson, Mark,

Garrett, Alice,

Ahmed, Munaza,

Burghel, George,

Dell, Sarah,

Field, Joanne,

Wright, Ronnie,

Clabby, Catherine,

Grant, Jonathan,

Greenhalgh, Karen-Lynn,

Albaba, Sh

2021

Overview

Accurate classification of variants in cancer susceptibility genes (CSGs) is key for correct estimation of cancer risk and management of patients. Consistency in the weighting assigned to individual elements of evidence has been much improved by the American College of Medical Genetics (ACMG) 2015 framework for variant classification, UK Association for Clinical Genomic Science (UK-ACGS) Best Practice Guidelines and subsequent Cancer Variant Interpretation Group UK (CanVIG-UK) consensus specification for CSGs. However, considerable inconsistency persists regarding practice in the combination of evidence elements. CanVIG-UK is a national subspecialist multidisciplinary network for cancer susceptibility genomic variant interpretation, comprising clinical scientist and clinical geneticist representation from each of the 25 diagnostic laboratories/clinical genetic units across the UK and Republic of Ireland. Here, we summarise the aggregated evidence elements and combinations possible within different variant classification schemata currently employed for CSGs (ACMG, UK-ACGS, CanVIG-UK and ClinGen gene-specific guidance for PTEN, TP53 and CDH1). We present consensus recommendations from CanVIG-UK regarding (1) consistent scoring for combinations of evidence elements using a validated numerical ‘exponent score’ (2) new combinations of evidence elements constituting likely pathogenic’ and ‘pathogenic’ classification categories, (3) which evidence elements can and cannot be used in combination for specific variant types and (4) classification of variants for which there are evidence elements for both pathogenicity and benignity.

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Publisher

BMJ Publishing Group Ltd,BMJ Publishing Group LTD,BMJ Publishing Group

Subject

/ Cancer

/ Evidence-Based Medicine

/ Genes, Neoplasm