A functional assay-based procedure to classify mismatch repair gene variants in Lynch syndrome

被引：34

作者：

Drost, Mark ^{[1
]}

Tiersma, Yvonne ^{[1
]}

Thompson, Bryony A. ^{[2
,3
]}

Frederiksen, Jane H. ^{[4
]}

Keijzers, Guido ^{[4
]}

Glubb, Dylan ^{[5
]}

Kathe, Scott ^{[6
]}

Osinga, Jan ^{[7
]}

Westers, Helga ^{[7
]}

Pappas, Lisa ^{[8
]}

Boucher, Kenneth M. ^{[8
]}

Molenkamp, Siska ^{[9
]}

Zonneveld, Jose B. ^{[9
]}

van Asperen, Christi J. ^{[9
]}

Goldgar, David E. ^{[10
]}

Wallace, Susan S. ^{[6
]}

Sijmons, Rolf H. ^{[7
]}

Spurdle, Amanda B. ^{[5
]}

Rasmussen, Lene J. ^{[4
]}

Greenblatt, Marc S. ^{[11
,12
]}

de Wind, Niels ^{[1
]}

Tavtigian, Sean V. ^{[2
]}

机构：

[1] Leiden Univ, Med Ctr, Dept Human Genet, Leiden, Netherlands

[2] Univ Utah, Sch Med, Huntsman Canc Inst, Dept Oncol Sci, Salt Lake City, UT 84112 USA

[3] Univ Melbourne, Sch Populat & Global Hlth, Ctr Epidemiol & Biostat, Melbourne, Vic, Australia

[4] Univ Copenhagen, Dept Cellular & Mol Med, Ctr Hlth Aging, Copenhagen, Denmark

[5] QIMR Berghofer Med Res Inst, Dept Genet & Computat Biol, Brisbane, Qld, Australia

[6] Univ Vermont, Robert Larner MD Coll Med, Dept Microbiol & Mol Genet, Burlington, VT USA

[7] Univ Groningen, Univ Med Ctr Groningen, Dept Genet, Groningen, Netherlands

[8] Univ Utah, Sch Med, Dept Med, Div Epidemiol,Huntsman Canc Inst, Salt Lake City, UT USA

[9] Leiden Univ, Med Ctr, Dept Clin Genet, Leiden, Netherlands

[10] Univ Utah, Sch Med, Huntsman Canc Inst, Dept Dermatol, Salt Lake City, UT USA

[11] Univ Vermont, Robert Larner MD Coll Med, Dept Med, Burlington, VT 05405 USA

[12] Univ Vermont, Robert Larner MD Coll Med, Ctr Canc, Burlington, VT 05405 USA

来源：

GENETICS IN MEDICINE | 2019年 / 21卷 / 07期

基金：

美国国家卫生研究院; 英国医学研究理事会; 澳大利亚国家健康与医学研究理事会;

关键词：

Lynch syndrome; variants of uncertain significance; functional assay; variant classification; assay calibration; UNKNOWN CLINICAL-SIGNIFICANCE; CELL-FREE ASSAY; SEQUENCE VARIANTS; MISSENSE SUBSTITUTIONS; CLASSIFICATION; PATHOGENICITY; SUSCEPTIBILITY; MUTATIONS; BRCA1; MSH2;

D O I：

10.1038/s41436-018-0372-2

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Purpose: To enhance classification of variants of uncertain significance (VUS) in the DNA mismatch repair (MMR) genes in the cancer predisposition Lynch syndrome, we developed the cellfree in vitro MMR activity (CIMRA) assay. Here, we calibrate and validate the assay, enabling its integration with in silico and clinical data. Methods: Two sets of previously classified MLH1 and MSH2 variants were selected from a curated MMR gene database, and their biochemical activity determined by the CIMRA assay. The assay was calibrated by regression analysis followed by symmetric cross-validation and Bayesian integration with in silico predictions of pathogenicity. CIMRA assay reproducibility was assessed in four laboratories. Results: Concordance between the training runs met our prespecified validation criterion. The CIMRA assay alone correctly classified 65% of variants, with only 3% discordant classification. Bayesian integration with in silico predictions of pathogenicity increased the proportion of correctly classified variants to 87%, without changing the discordance rate. Interlaboratory results were highly reproducible. Conclusion: The CIMRA assay accurately predicts pathogenic and benign MMR gene variants. Quantitative combination of assay results with in silico analysis correctly classified the majority of variants. Using this calibration, CIMRA assay results can be integrated into the diagnostic algorithm for MMR gene variants.

引用

页码：1486 / 1496

页数：11

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