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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)

Authors

  • J. Hauke
  • P. Harter
  • C. Ernst
  • A. Burges
  • S. Schmidt
  • A. Reuss
  • J. Borde
  • N. De Gregorio
  • D. Dietrich
  • A. El-Balat
  • M. Kayali
  • H. Gevensleben
  • F. Hilpert
  • J. Altmüller
  • A. Heimbach
  • W. Meier
  • B. Schoemig-Markiefka
  • H. Thiele
  • R. Kimmig
  • P. Nürnberg
  • K. Kast
  • L. Richters
  • J. Sehouli
  • R.K. Schmutzler
  • E. Hahnen

Journal

  • Journal of Medical Genetics

Citation

  • J Med Genet 59 (3): 248-252

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.


DOI

doi:10.1136/jmedgenet-2020-107353