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FeedbackMassively Parallel Sequencing
- Use to confirm a clinical diagnosis of a hereditary vascular malformation disorder if no single specific diagnosis is strongly suspected.
- If an individual meets clinical criteria for a specific disorder or if a specific diagnosis is suspected, consider more targeted gene testing first.
If a familial sequence variant has been previously identified, targeted sequencing for that variant may be appropriate; refer to the Laboratory Test Directory for additional information.
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.
Test Interpretation
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
| Variant Class | Analytic Sensitivity (PPA) Estimatea (%) and 95% Credibility Region | Analytic Specificity (NPA) Estimate (%) |
|---|---|---|
|
SNVs |
>99 (96.9-99.4) |
>99.9 |
|
Deletions 1-10 bpb |
93.8 (84.3-98.2) |
>99.9 |
|
Insertions 1-10 bpb |
94.8 (86.8-98.5) |
>99.9 |
|
Exon-levelc deletions |
97.8 (90.3-99.8) [2 exons or larger] 62.5 (38.3-82.6) [Single exon] |
>99.9 |
|
Exon-levelc duplications |
83.3 (56.4-96.4) [3 exons or larger] |
>99.9 |
|
aPPA values are derived from larger methods-based MPS and/or Sanger validations. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA) unless otherwise indicated. bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced. cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp. bp, base pairs; PPA, positive percent agreement; NPA, negative percent agreement; SNVs, single nucleotide variants |
||
Limitations
- 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
| Gene | MIM Number | Disorder | Inheritance |
|---|---|---|---|
|
ACVRL1 |
601284 |
Hereditary hemorrhagic telangiectasia, type 2 |
AD |
|
AKT1 |
164730 |
Proteus syndrome |
AD with somatic mosaicism |
|
BMPR2 |
600799 |
Primary pulmonary hypertension 1 Pulmonary venoocclusive disease 1, autosomal dominant |
AD |
|
CCBE1 |
612753 |
Hennekam lymphangiectasia-lymphedema syndrome 1 |
AR |
|
CCM2 |
607929 |
Cerebral cavernous malformations 2 |
AD |
|
EIF2AK4 |
609280 |
Pulmonary venoocclusive disease 2, autosomal recessive |
AR |
|
ELMO2 |
606421 |
Primary intraosseous vascular malformation |
AR |
|
ENG |
131195 |
Hereditary hemorrhagic telangiectasia type 1 |
AD |
|
EPHB4 |
600011 |
Capillary malformation-arteriovenous malformation syndrome |
AD |
|
FAT4 |
612411 |
Van Maldergem syndrome 2 Hennekam lymphangiectasia-lymphedema syndrome 2 |
AR |
|
FLT4 |
136352 |
Hereditary lymphedema IA Capillary infantile hemangioma |
AD |
|
FOXC2 |
602402 |
Lymphedema-distichiasis syndrome |
AD |
|
GATA2 |
137295 |
Primary lymphedema with myelodysplasia Emberger syndrome |
AD |
|
GDF2 (BMP9) |
605120 |
Hereditary hemorrhagic telangiectasia type 5 |
AD |
|
GJC2 |
608803 |
Hereditary lymphedema IC |
AD |
|
GLMN |
601749 |
Glomuvenous malformations |
AD |
|
KCNK3 |
603220 |
Primary pulmonary hypertension 4 |
AD |
|
KRIT1 |
604214 |
Cerebral cavernous malformations |
AD |
|
PDCD10 |
609118 |
Cerebral cavernous malformations 3 |
AD |
|
PIEZO1 |
611184 |
Hereditary lymphedema III |
AR |
|
PTEN |
601728 |
PTEN hamartoma tumor syndrome PTEN-related Proteus syndrome |
AD |
|
RASA1 |
139150 |
Capillary malformation-arteriovenous malformation syndrome Parkes Weber syndrome |
AD |
|
SMAD4 |
600993 |
Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome |
AD |
|
SMAD9 |
603295 |
Primary pulmonary hypertension 2 |
AD |
|
SOX18 |
601618 |
Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome |
AD |
| Hypotrichosis-lymphedema-telangiectasia syndrome | AR | ||
|
STAMBP |
606247 |
Microcephaly-capillary malformation syndrome |
AR |
|
TEK |
600221 |
Multiple cutaneous and mucosal venous malformations |
AD |
|
VEGFC |
601528 |
Hereditary lymphedema ID |
AD |
| AD, autosomal dominant; AR, autosomal recessive | |||
References
-
GeneReviews - Hereditary Hemorrhagic Telangiectasia
McDonald J, Pyeritz RE. Hereditary hemorrhagic telangiectasia. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews. University of Washington, Seattle. Updated Feb 2017; accessed Oct 2020.
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32894695
Faughnan ME, Mager JJ, Hetts SW, et al. Second international guidelines for the diagnosis and management of hereditary hemorrhagic telangiectasia. Ann Intern Med. 2020;173(12):989-1001.
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30909834
Zafar A, Quadri SA, Farooqui M, et al. Familial cerebral cavernous malformations. Stroke. 2019;50(5):1294-1301.
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28687708
Amyere M, Revencu N, Helaers R, et al. Germline loss-of-function mutations in EPHB4 cause a second form of capillary malformation-arteriovenous malformation (CM-AVM2) deregulating RAS-MAPK signaling. Circulation. 2017;136(11):1037-1048.
-
10234502
Nelen MR, Kremer H, Konings IB, et al. Novel PTEN mutations in patients with Cowden disease: absence of clear genotype-phenotype correlations. Eur J Hum Genet. 1999;7(3):267-73.
-
GeneReviews - Proteus Syndrome
Biesecker LG, Sapp JC. Proteus syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews. University of Washington, Seattle. Last update Jan 2019; accessed Mar 2022.