Abstract 4629: QClampTM Plex VEXAS syndrome UBA1 mutation detection assay: A noval XNA based assay to simultaneously detect eight UBA1 somatic mutations associated with VEXAS syndrome

Abstract

Abstract VEXAS syndrome (acronym for Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) is a monogenic disease discovered in December 2020. It is an adult-onset systemic inflammatory disorder genetically characterized by somatic mutation of the UBA1 gene which encodes the ubiquitin like modifier activating enzyme 1. VEXAS patients have overlapping rheumatologic and hematologic manifestations, including increased risk for myelodysplastic syndrome (MDS). It is critically important to diagnose VEXAS syndrome, but UBA1 mutation test is still not commercially available. The three most frequent mutations of UBA1 gene are p.M41T(122T>C), p.M41V (c.121A>G), and p.M41L (c.121A>C) in codon 41 of exon 3. Other mutations including splice site mutations at exon 3 (c.118-2A>C, c.118-1G>C and c.118- 9_118-2del), p.S56F (c.167C>T) in codon 56 of exon 3, and p.S621C (c.1861A>T) in codon 621 of exon 16 have been reported. Based on XNA technology, we developed a QClampTM Plex platform to detect all the eight mutations in a single reaction with Luminex system. XNA technology enriches mutant target sequence in a PCR reaction by using synthetic DNA analog XNA (xenonucleic acid) to block wild type DNA. With spiking synthetic mutant DNA in GM24385 cell line DNA, we determined that this assay can detect mutations with a detection limit of variant allele frequency (VAF) for M41T at 0.1%, M41V at 0.1%, M41L at 0.25%, c.118-2A>C at 1%, c.118-1G>C at 1%, c.118- 9_118-2del at 1%, S56F at 0.25% and S621C at 1%, respectively, and specificity of 100% for all mutations. We tested saved DNA samples extracted from whole blood previously collected from suspected VEXAS patients and tested at the National Cancer Institute by Sanger sequencing, including 13 positive and 20 negative samples. Our assay detected all corresponding UBA1 mutations in the 13 positive patient samples, and did not detect UBA1 mutation in 18 of the 20 negative patient samples. Two of the 20 negative samples were also tested positive for UBA1 M41T and M41L on our assay, respectively, due to its significantly higher sensitivity than the Sanger sequencing platform, which has a detection limit of 15-20% VAF. Citation Format: Yunqing Ma. QClampTM Plex VEXAS syndrome UBA1 mutation detection assay: A noval XNA based assay to simultaneously detect eight UBA1 somatic mutations associated with VEXAS syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4629.