Genetic Testing for the VEXAS Syndrome

Feb 6, 2024 | Blog

Diagnosis of the VEXAS syndrome improves medical management of the disease and provides more effective treatment of the disease, although there is no cure currently. The diagnosis relies on the VEXAS syndrome genetic testing, a test for a mutation present in the UBA1 gene, mostly at codon41. The most common testing methods are Sanger sequencing and Next Generation Sequencing (NGS). Quantitative PCR (qPCR) and digital PCR (dPCR) can also be used.

We have developed a different detection method, QClamps™ Plex, that combines our proprietary XNA technology with Luminex’s xMAP technology for the benefit of (1) Early detection when the variant allele frequency (VAF) is still low (as low as 0.1%); (2) Short turn-around time: one-day detection without the need for bioinformatics.

Sanger sequencing is a traditional DNA sequencing method that allows for the direct and accurate determination of the sequence of the UBA1 gene fragment. It is particularly well-suited for identifying point mutations or small insertions/deletions in genetic analysis of hereditary diseases (germline mutations). However, the technique has limitations for low-frequency somatic mutations as the test sensitivity is only 15 to 20% VAF.

Next-generation sequencing (NGS) has become more prevalent and has gradually been adopted in clinical settings. NGS is a high-throughput sequencing technology that can analyze multiple DNA sequences from multiple samples simultaneously. It is much faster and more cost-effective than Sanger sequencing for large-scale genomic profiling. Therefore, NGS can detect multiple mutations in the UBA1 gene in many patients at the same time. Despite the technical evolution in the last few years, NGS still suffers from long turn-around time and complex bioinformatics analysis from experts.

qPCR and dPCR can also be used in UBA1 mutation tests, but they are limited by the low throughput of target detection. One of the applications that use dPCR is to detect UBA1 mutation at an early stage of the VEXAS syndrome for monitoring disease progression and the right time of therapy, which can’t be achieved by Sanger sequencing. Both qPCR and NGS have been used for early detection of the UBA1 gene in a few publications.

DiaCarta’s QClamps Plex platform for UBA1 mutation testing leverages our XNA technology for mutation enrichment. Combined with sequence-specific ligation, the assay has great sensitivity and specificity. Using Luminex’s xMAP technology as a detection module, we have been able to detect all the 20 known mutations in UBA1 from the clinical samples of the VEXAS syndrome. The limit of detection for specific targets can reach as low as 0.1% VAF, lower than regular NGS and much lower than Sanger sequencing. The assay sensitivity can benefit the early detection of the disease and provide guidance for physicians for disease progress monitoring and proper therapy decisions. In addition, rather than waiting a week or more for confident results, our test delivers the results on the same day, reducing the waiting time and patient anxiety. This platform can be customized for different panels of mutation detection with up to 100 targets on the MIGPIX and other Luminex devices.

Contact us to learn more about our VEXAS syndrome genetic test on the QClamps Plex platform. If you want to use this platform for your specific gene panels. assay development, you are welcome to work with us.

 

 

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