VEXAS Syndrome

OVERVIEW

VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome is a rare, adult-onset, multisystem inflammatory disorder affecting predominantly male patients. It is caused by somatic loss-of-function mutations in UBA1, an enzyme central to the ubiquitination process (and consequently intracellular protein homeostasis)1,2,3,4. 

INDICATION

UBA1 sequencing offered for patients suspected of being affected with VEXAS syndrome.  Please note that testing is limited to requests made by rheumatologists, hematologists, or hematopathologists.

TEST REQUIREMENTS

  • Completed CGL Myeloid Testing requisition form
  • One of the following specimens (please see our Specimen Guidelines, DNA molecular type)
    • 5mL Peripheral Blood in EDTA tube (purple top)
    • 1 mL Bone Marrow Aspirate in EDTA tube (purple top)

Ordering multiple tests?  Please review our requirements for multiple samples.

METHOD

UBA1 mutation screening is an amplicon-based targeted resequencing assay designed to detect recurrent somatic DNA variations (SNVs and small indels) in UBA1 that are clinically relevant to VEXAS. The test is performed on genomic DNA extracted from either the peripheral blood or bone marrow specimens using the Maxwell RSC instrument. Targeted DNA regions are amplified by multiplex PCR. Paired-end massively parallel sequencing of 300-bp fragments is performed with an illumina MiSeq i100 instrument.  DNA sequences are aligned and compared to reference genome hg38/GRCh38 to identify single nucleotide variants (SNVs) and small insertions and deletions (indels).

Target Space:

Entire coding region (+/- a minimum of 5 bp of adjacent introns):

Reference Sequence: UBA1:NM_003334

Limitations:

This test may not detect all possible variants in UBA1 or its control regulatory elements, as such, a negative result does not rule out the presence of alterations outside the targeted regions. The limit of reliable detection (LOD) for SNVs and indels is a variant allele frequency (VAF) of 5%.  Gross insertions/deletions (CNVs) are not currently detectable.

TURN-AROUND TIME

Results are reported within twenty one (21) days from receipt of specimen, and completed requisition form and all corresponding documentation.

RESULT REPORTING

  • Reports include a list of variants classified into tiers of clinical significance according to AMP/ASCO/CAP guidelines5.
    • TIER I – VARIANTS OF STRONG CLINICAL SIGNIFICANCE 
    • TIER II – VARIANTS OF POTENTIAL CLINICAL SIGNIFICANCE (none anticipated)
    • TIER IIIA –VARIANTS OF UNCERTAIN CLINICAL SIGNIFICANCE (none anticipated) 
    • TIER IIIB – VARIANTS OF UNCERTAIN FUNCTION
  • Note that TIER IV variants (Benign/Likely Benign variants) are not reported.
  • Please see our Variant Classification Guidelines for additional details. 
  • Unless otherwise noted, variant allele frequencies are obtained from The AACR Project GENIE Consortium (PMID: 28572459, mycancergenome.org).

REFERENCES

  1. Beck, DB. et al. Somatic Mutations in UBA1 and Severe Adult-Onset Autoinflammatory Disease. NEJM (2020) 383, 2628-2638. (PMID: 33108101)
  2. Stubbins, RJ. et al. Innovations in Genomics for Undiagnosed Diseases: Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic (VEXAS) Syndrome. CMAJ (2022) 194, E524-E527. (PMID: 35410861)
  3. Beck, DB. et al. Estimated Prevalence and Clinical Manifestations of UBA1 Variants Associated With VEXAS Syndrome in a Clinical Population. JAMA (2023) 329,318-324 (PMID: 36692560)
  4. Koster, MJ. et al. VEXAS syndrome: Clinical, hematologic features and a practical approach to diagnosis and management. Am J Hematol (2023) 99, 284-299. (PMID: 37950858)
  5. Li, MM. et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diag. (2017) 1, 4-23. (PMID: 27993330)