Vascular Malformations Panel, Sequencing and Deletion/Duplication

Vascular malformation syndromes are caused by defects of blood vessels, which can affect multiple vessel types (venous, arterial, capillary, or combined). Examples include capillary malformation, arteriovenous malformation, cerebral cavernous malformation (CCM), glomuvenous malformation, hereditary hemorrhagic telangiectasia (HHT), multiple cutaneous and mucosal venous malformations, pulmonary arterial hypertension, and hereditary lymphedema syndromes. Potential findings of vascular malformation syndromes include hemorrhage and/or epistaxis, localized pain and/or lymphedema, destruction or deformation of surrounding tissue, localized intravascular coagulopathy (LIC), stroke, and congestive heart failure. If no single specific diagnosis is strongly suspected, a multigene panel test can confirm a clinical diagnosis of a hereditary vascular malformation disorder.

Genetics

Genes

Analysis includes the coding regions and intron-exon boundaries of the genes tested (see Genes Tested table), the 5' untranslated region of ENG, a region of ACVRL1 intron 9 encompassing the CT-rich variant hotspot region, and select PTEN promoter variants.

Etiology

Pathogenic variants in vascular malformation genes lead to defects of blood vessels that can cause fast-flow or slow-flow lesions, shunting, swelling, or skin findings. For some disorders, this may lead to potentially life-threatening hemorrhage, stroke, or heart failure.

Prevalence

Genotype-Phenotype Correlation

• Vascular malformation syndromes are typically categorized according to vessel type affected and fast- versus slow-flow lesions.
• Most vascular malformations are sporadic.
• Inherited forms are characterized by multiple lesions, which are often smaller and less often congenital than their sporadic counterparts.
• Penetrance is often age-related and variable.

Methodology

This test is performed using the following sequence of steps:

• Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
• Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
• Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
• Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.
• Bidirectional Sanger sequencing is performed on the following gene(s):
  • PTEN (NM_000314) 9

Clinical Sensitivity

Variable and dependent upon specific disorder

Analytic Sensitivity

• A negative result does not exclude a heritable form of a vascular malformation disorder.
• Diagnostic errors can occur due to rare sequence variations.
• Interpretation of this test result may be impacted if this individual has had an allogeneic stem cell transplantation.
• The following will not be evaluated:
  • Variants outside the coding regions and intron-exon boundaries of the targeted genes
  • Regulatory region variants and deep intronic variants
  • Breakpoints of large deletions/duplications
  • The following exons are not sequenced due to technical limitations of the assay:
    • CCM2 (NM_001363458) exon(s) 7
    • CCM2 (NM_001363459) exon(s) 6
    • FLT4 (NM_001354989) exon(s) 30
    • GJC2 (NM_020435) partial exon(s) 2(Chr1:228346380-228346419)
    • PTEN (NM_000314) exon(s) 9
    • PTEN (NM_001304717) exon(s) 10
    • PTEN (NM_001304718) exon(s) 9
    • SOX18 (NM_018419) partial exon(s) 1(Chr20:62680707-62680791)
    • STAMBP (NM_001353969) exon(s) 10
    • STAMBP (NM_001353970) exon(s) 11
    • STAMBP (NM_001353976) exon(s) 10
• The following may not be detected:
  • Deletions/duplications/insertions of any size by MPS
  • Large duplications less than 3 exons in size
  • Noncoding transcripts
  • Deletions/duplications less than 1kb in the targeted genes by array
  • Some variants due to technical limitations in the presence of pseudogenes and/or repetitive/homologous regions
  • Low-level somatic variants
  • Single exon deletions/duplications in the following exons:
    • CCM2 (NM_001363458) 7; CCM2 (NM_001363459) 6; ENG (NM_001114753) 1; ENG (NM_000118) 1; FLT4 (NM_001354989) 30; GLMN (NM_053274) 16; GLMN (NM_001319683) 15; PIEZO1 (NM_001142864) 1,25,47; PTEN (NM_000314) 9; PTEN (NM_001304717) 1,10; PTEN (NM_001304718) 9; STAMBP (NM_001353969) 10; STAMBP (NM_001353970) 11; STAMBP (NM_001353976) 10

Genes Tested