Abstract P4-12-07: Technical evaluation of multigene testing for hereditary breast and ovarian cancer
Authors: Lincoln Stephen , Kurian Allison , Desmond Andrea , Nilsen Geoffrey , Jacobs Kevin , Yang Shan , Hart Reece , Monzon Federico , Ellisen Leif , Ford James 
Published: May 2015

Abstract
Introduction: Next Generation Sequencing, or NGS technology is gaining acceptance in diagnostic laboratories for multigene panel testing. However questions remain about the sensitivity, specificity and clinical implications of this new technology and the expanded testing it enables. Moreover, questions are raised as to whether new laboratories using these methods, typically without the benefit of large historical proprietary databases, can provide similar assessments of pathogenicity as do the previously established providers. Expanding on our recently published work (Kurian et al., JCO 2014) we considered whether NGS testing in an independent laboratory can replace traditional BRCA1/2 tests in patients indicated for hereditary breast/ovarian cancer testing.
Methods: We recruited over 800 patients who were indicated for BRCA1/BRCA2 testing under clinical management guidelines, and collected over 200 additional samples to increase the power of this ongoing study. All were tested using an NGS-based multigene panel which reported both DNA sequence and copy-number alterations for BRCA1/2 and 27 other known cancer risk genes. Traditional genetic testing results using established technologies were also available for comparison. In this report we focus on the results for BRCA1/2 and 27 other known cancer risk genes.
Results: Sensitivity was high: 261 alterations (196 pathogenic and 65 others) were reported in the traditional genetic data, and all were detected by NGS when the corresponding test was available. In this set are 141 alterations considered technically challenging for NGS: insertions, deletions, and complex sequence changes, as well as very large (chromosome) and small (single exon) copy number changes. Specificity was also high: all NGS variants for which we sought confirmation using independent methods (n&gt;2000) were confirmed, including 51 alterations not previously reported. Determination of pathogenicity was also highly concordant: in all but 2 cases positive reports agreed, and in these 2 cases data were available in the literature to support pathogenicity, although not at a level which meets recent guidelines from the American College of Medical Genetics (ACMG). It is not clear from the diagnostic reports exactly what evidence supported pathogenicity in the traditional data for these 2 cases. Rates of Variants of Unknown Significance (VUS) in BRCA1/2 were somewhat different: about 7% of cases in the NGS data vs. about 4% of fully tested cases in the traditional data had an uncertain report. The root of this difference is also unclear as details are not provided in the traditional reports.
Conclusions: NGS can be a viable replacement for traditional genetic testing for hereditary breast and ovarian cancer. Interpretation concordance is high but fully evaluating the details of this is hampered by the limited reporting of proprietary data by some established laboratories. Recent efforts to establish large public databases of genetic information (particularly ClinVar) will promote greater transparency and accountability and thus can help improve access to high quality care for hereditary conditions.
Note: All of the variants in this study and their interpretations will be released to public databases by the time of the meeting.
Citation Format: Stephen Lincoln, Allison Kurian, Andrea Desmond, Geoffrey Nilsen, Kevin Jacobs, Shan Yang, Reece Hart, Federico Monzon, Leif Ellisen, James Ford. Technical evaluation of multigene testing for hereditary breast and ovarian cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-12-07.