Practical considerations in the clinical application of whole-exome sequencing.

Despite the exciting advent of whole-exome sequencing (WES) in medical genetics practices, the optimal interpretation of results requires further actions such as reconsidering clinical information and obtaining further laboratory testing. There are no published data to guide clinicians in this process. In a retrospective study on 93 patients who underwent clinical WES, we set out to assess and resolve these practical challenges. With the laboratories reporting a molecular diagnostic rate of 25.8%, the medical geneticists and the laboratories were 90% concordant in their interpretation of the WES results. Divergence occurred when the medical geneticist reconsidered clinical information and/or additional information regarding pathogenicity of a variant. Variants of uncertain significance were reported in 86% of patients, with 53.7% needing follow-up, such as additional laboratory tests and genotyping of family members. By layering clinical data (e.g. mode of inheritance and phenotypic fit) on to the laboratory results, we developed clinical categories for the WES results. These categories of definite diagnosis (14/93), likely diagnosis (8/93), possible diagnosis (13/93) and no diagnosis (58/93) could be used to convey results to patients uniformly. Our framework for a clinically informed interpretation of the results enhances the utility of WES within medical genetics practices.

Prenatal diagnosis of Pompe disease: enzyme assay or molecular testing?

We report two cases which illustrate that enzyme assay results alone, may at times be equivocal and inconclusive in the prenatal diagnosis of storage disorders like Pompe disease and therefore, if the probands mutation is known, targeted mutation analysis of fetal DNA is the most reliable method for fetal evaluation.

Comparison of methods for obtaining serum opacity factor from group A streptococci.

Streptococcal serum opacity factor (OF) is an important type-specific strain marker produced by certain serotypes of group A streptococci (GAS). The accurate determination of OF production and subsequent serotyping of a strain require a reliable method for extracting OF. Traditional OF extraction methods have utilized either culture supernatants or Lancefield HCl extracts. However, these methods do not consistently yield adequate amounts of OF for accurate characterization of all strains. To improve the accuracy of OF utilized and found to be reproducibly sensitive and suitable for routine laboratory use. A total of 3,014 GAS were examined for OF production by each of the three methods. The SDS extraction method accurately detected OF in all 1,302 OF-producing strains, whereas the HCl extraction method correctly identified 1,202 (92%) and the supernatant method identified only 1,141 (88%) of the isolates. When the 1,302 OF-producing strains were further evaluated to determine if sufficient OF had been extracted for reliable OF serotyping, 1,147 (88%) of the SDS extracts were found to be satisfying compared with 1,081 (83%) of the HCl extracts and only 936 (72%) of the culture supernatants. The improved ability to characterize OF-producing strains by using SDS was statistically significant compared with the results obtained by the other two techniques. This technique offers distinct advantages, including enhanced detection of OF production and improved reliability of serotyping OF-producing GAS.