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Test Code SGSH S+D/D SGSH Seq and Del/Dup

Important Note

This test includes sequencing and CNV analysis for the SGSH gene.

Clinical System Name

SGSH Seq and Del/Dup

Synonyms

Sanfilippo Syndrome

Mucopolysaccharidosis Type IIIA

Sample Requirements

Specimen: Whole Blood

Container(s): Lavender Top/EDTA, Yellow/ACD

Preferred Vol: 5 mL

Minimum Vol: 3 mL (1 mL for small infants)

 

Specimen: DNA

Container(s): Sterile plastic tube

Preferred Vol: 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml

Saliva: Isohelix™ or GeneFiX™ Saliva Collection kit used according to manufacturer instructions.

Specimens & Shipping

Processing Instructions

Reject due to:

Spin: N

Aliquot: N

Temp: 2-8 C

Storage location: Deliver blood to Sendouts refrigerator rack. Store labels in the clear plastic box on front of the CPA fridge.

 

Off-site collection: Send whole blood refrigerated.

Stability

Specimen Type Temperature Time
Whole Blood Room temp Y
Whold Blood Refrigerated Y
Whole Blood Frozen N
Extracted DNA Room temp 3-4 d
Extracted DNA Refrigerated  1 y
Extracted DNA Frozen Indefinitely

 

Availability

STAT Performed TAT
N   20 d

 

Performing Laboratory

Department:     PreventionGenetics, 3800 S. Business Park Ave., Marshfield, Wisconsin 54449

Phone Number:    (715) 387-0484

Department

Department: Send Outs

Phone: (206) 987-2563

Reference Range

Interpretive report provided.
 

Methodology

For this Next Generation Sequencing (NGS) test, sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for regions not captured or with insufficient number of sequence reads.

For Sanger sequencing, polymerase chain reaction (PCR) is used to amplify targeted regions. After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

This test provides full coverage of all coding exons of the SGSH gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Special Instructions

PreventionGenetics

Clinical Utility

Sanfilippo syndrome is caused by a defect in one of four enzymes required for the modification and removal of glucosamine residues from heparan sulfate. A defect in one of these four enzymes (types A-D) results in the accumulation of heparan sulfate in the patient’s cells and organs which overtime leads to the clinical phenotype. Patients with Sanfilippo syndrome experience delayed development with a progressively deteriorating mental status. Behavior and sleep problems are common as well as coarse facial features and stiff joints. The four types of Sanfilippo syndrome (A-D) are clinically indistinguishable, thus enzyme testing is recommended as an initial diagnostic test

Send Out Instructions

 

Reference Test Name:

Mucopolysaccharidosis Type IIIA / Sanfilippo Syndrome A via SGSH Gene Sequencing with CNV Detection

Reference Test Number: 7821
Instructions: Ship whole blood overnight, ambient temperature. PreventionGenetics accepts Saturday delivery

 

Update Date

This page was last updated 12/4/2018.