Sensitivity and specificity of loss of heterozygosity analysis for the classification of rare germline variants in BRCA1/2: results of the observational AGO-TR1 study (NCT02222883). Issue 3 (3rd December 2020)

• Record Type: Journal Article
• Authors: Hauke, Jan; Harter, Philipp; Ernst, Corinna; Burges, Alexander; Schmidt, Sandra; Reuss, Alexander; Borde, Julika; De Gregorio, Nikolaus; Dietrich, Dimo; El-Balat, Ahmed; Kayali, Mohamad; Gevensleben, Heidrun; Hilpert, Felix; Altmüller, Janine; Heimbach, André; Meier, Werner; Schoemig-Markiefka, Birgid; Thiele, Holger; Kimmig, Rainer; Nürnberg, Peter; Kast, Karin; Richters, Lisa; Sehouli, Jalid; Schmutzler, Rita K; Hahnen, Eric
• Is Part Of: Journal of medical genetics. Volume 59:Issue 3(2022)
• Page Start: 248
• Page End: 252
• Publication Date: 2020-12-03
• Subjects: genetic predisposition to disease -- genetic testing -- genetic research -- germ-line mutation; Medical genetics -- Periodicals; 616.042
• DOI: 10.1136/jmedgenet-2020-107353
• Languages: English
• ISSNs: 1468-6244

Abstract

Abstract : Variant-specific loss of heterozygosity (LOH) analyses may be useful to classify BRCA1/2 germline variants of unknown significance (VUS). The sensitivity and specificity of this approach, however, remains unknown. We performed comparative next-generation sequencing analyses of the BRCA1/2 genes using blood-derived and tumour-derived DNA of 488 patients with ovarian cancer enrolled in the observational AGO-TR1 trial (NCT02222883 ). Overall, 94 pathogenic, 90 benign and 24 VUS were identified in the germline. A significantly increased variant fraction (VF) of a germline variant in the tumour indicates loss of the wild-type allele; a decreased VF indicates loss of the variant allele. We demonstrate that significantly increased VFs predict pathogenicity with high sensitivity (0.84, 95% CI 0.77 to 0.91), poor specificity (0.63, 95% CI 0.53 to 0.73) and poor positive predictive value (PPV; 0.71, 95% CI 0.62 to 0.79). Significantly decreased VFs predict benignity with low sensitivity (0.26, 95% CI 0.17 to 0.35), high specificity (1.0, 95% CI 0.96 to 1.00) and PPV (1.0, 95% CI 0.85 to 1.00). Variant classification based on significantly increased VFs results in an unacceptable proportion of false-positive results. A significantly decreased VF in the tumour may be exploited as a reliable predictor for benignity, with no false-negative result observed. When applying the latter approach, VUS identified in four patients can now be considered benign. Trial registration number NCT02222883 .