New Validation Framework to Optimize Specificity and Sensitivity in WES-Based Diagnostics

CENTOGENE, a rare disease company committed to improving the lives of rare disease patients by providing solutions that accelerate the development of drugs, has published the development of a rationale framework to optimize sensitivity and specificity in whole exome sequencing (WES)-based diagnostics of a clinically heterogeneous patient population using orthogonal Sanger sequencing validation.

While next generation sequencing (NGS) is clearly replacing the Sanger DNA sequencing method not only for research but also for routine genetic diagnostic tests, studies have shown it is not as reliable as a standalone genetic test. Since NGS introduces a relevant number of false positives and false negatives, CENTOGENE has determined how to optimize the use of orthogonal Sanger sequencing of variants in parallel when looking at borderline cases. In the January 2019 issue of Genetics in Medicine, CENTOGENE outlined in the manuscript entitled ‘Development of an evidence-based algorithm that optimizes sensitivity and specificity in ES-based diagnostics of a clinically heterogeneous patient population’ a framework where NGS variant calls can be consistently assessed and monitored, bringing down significantly the burden of this additional validation.

CENTOGENE has developed a decision tree that takes into consideration three variant specific features: quality score, read number and frequency. By using this predictor, itis possible to classify 91.7% of variants with 100% specificity and 99.8% sensitivity, leaving only 8.3% of variants to be confirmed with additional Sanger sequencing. This result avoids over and under filtering results, enabling the generation of  a more accurate diagnosis for patients suffering from rare diseases that otherwise would have been missed. The implications of this increase in specificity and sensitivity also translates into more consistent monitoring capabilities.

“The new framework that we have developed to optimize sensitivity and specificity in WES-based diagnostics underscores the strategic focus of CENTOGENE— transforming clinical and genetic data in order to drive rapid medical diagnosis of inherited diseases,” said Professor Peter Bauer, M.D., Chief Scientific Officer of CENTOGENE and lead author of the study. “This framework can be optimized across the industry, academia, and in the clinic without compromising the accuracy of genetic diagnosis.”

The study was performed on a widespread real-world patient population, and incorporates data from approximately 1,000 candidate genomic variants. Patient samples were provided as EDTA blood or as dried blood spots on filter cards using CENTOGENE’s CentoCard® —  a global logistic solution developed by CENTOGENE to simplify the worldwide collection of samples.