TY - JOUR T1 - Sensitivity and specificity of loss of heterozygosity analysis for the classification of rare germline variants in <em>BRCA1/2</em>: results of the observational AGO-TR1 study (NCT02222883) JF - Journal of Medical Genetics JO - J Med Genet SP - 248 LP - 252 DO - 10.1136/jmedgenet-2020-107353 VL - 59 IS - 3 AU - Jan Hauke AU - Philipp Harter AU - Corinna Ernst AU - Alexander Burges AU - Sandra Schmidt AU - Alexander Reuss AU - Julika Borde AU - Nikolaus De Gregorio AU - Dimo Dietrich AU - Ahmed El-Balat AU - Mohamad Kayali AU - Heidrun Gevensleben AU - Felix Hilpert AU - Janine Altmüller AU - André Heimbach AU - Werner Meier AU - Birgid Schoemig-Markiefka AU - Holger Thiele AU - Rainer Kimmig AU - Peter Nürnberg AU - Karin Kast AU - Lisa Richters AU - Jalid Sehouli AU - Rita K Schmutzler AU - Eric Hahnen Y1 - 2022/03/01 UR - http://jmg.bmj.com/content/59/3/248.abstract N2 - 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. ER -