Next-Gen Sequencing and Deletion/Duplication Analysis of RASA1 and EPHB4 for CM-AVM / Parkes Weber Syndrome (RASA-NG)
Information for Ordering
{slide=Acceptable Specimen Types}• Fresh blood sample (3-6 ml EDTA; no time limitations associated with receipt)
• Saliva (OGR-575 DNA Genotek; kits are provided upon request)
• DNA (extracted from lymphocyte cells; a minimum volume of 25μL at 3μg; O.D. of 260:280nm ≥1.8; must be extracted in a CLIA or equivalent certified lab)
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Average = 30 working days
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$1000 (USD- institutional/self-pay price)
CPT: 81479 (x2)
Z code: ZB6AB
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{slide=Candidates for Testing}
Patients with features suggestive for Capillary Malformation Arteriovenous Malformation or Parkes Weber syndrome.
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Please find specimen requirement specifications above.
All submitted specimens must be sent at room temperature. DO NOT ship on ice.
Specimens must be packaged to prevent breakage and absorbent material must be included in the package to absorb liquids in the event that breakage occurs. Also, the package must be shipped in double watertight containers (e.g. a specimen pouch + the shipping company’s diagnostic envelope).
To request a sample collection kit, please click here or email medgenomics@uabmc.edu to complete the specimen request form.
Please contact the MGL (via email at medgenomics@uabmc.edu, or via phone at 205-934-5562) prior to sample shipment and provide us with the date of shipment and tracking number of the package so that we can better ensure receipt of the samples.
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Form for Customs
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About
{slide=Disorder Background}Capillary malformation-arteriovenous malformation syndrome (CM-AVM) is a disorder of the vascular system. Parkes Weber syndrome is characterized by congenital vascular abnormalities known as capillary malformations and arteriovenous fistulas (AVFs). Some vascular abnormalities seen in Parkes Weber syndrome are similar to those that occur in capillary malformation-arteriovenous malformation syndrome (CM-AVM). CM-AVM and some cases of Parkes Weber syndrome are caused by variants in the RASA1 gene. (Erola I et al, Am J Hum Genet. 2003;73:1240–9). In addition, loss-of-function variants in the EPHB4 gene have been associated with similar phenotypic presentations (Amyere M et al, Circulation. 2017;136(11):1037-48). EPHB4 interacts with RASA1 and indicates the EPHB4-RAS-ERK signaling pathway as a major cause for AVMs. Therefore, the CM-AVM Syndrome panel includes both RASA1 and EPHB4 sequencing coverage and deletion/duplication analysis of RASA1.
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The RASA1 and EPHB4 by NGS involves sequencing and deletion/duplication analysis for RASA1 and EPHB4. The test uses an extensively customized and optimized set of Agilent HaloPlex capture probes, followed by sequencing of overlapping amplicons within the regions of interest using 300bp paired-end Illumina sequencing chemistry. Each coding exon plus ~50bp of flanking intronic sequence are simultaneously sequenced. 5’ and 3’ untranslated sequences are not included.
The average coverage is ~1500x with 93% of the coding regions ≥350x and 97% ≥200x. This allows for detection of very low-level mosaicism by sequencing (as low as 3-5% of the alleles). Variant and copy number calls are made using a unique bioinformatics pipeline detecting all types of variants including single nucleotide substitutions, indels, and frameshifts caused by deletion/ duplication up to 112bp.
REFERENCES available here.
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For more information, test requisition forms, or sample collection and mailing kits, please call: 205-934-5562.