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Test Code RAI1 S+D/D RAI1 Seq and Del/Dup

Important Note

This test includes sequencing and CNV analysis of the RAI1 gene.

Clinical System Name

RAI1 Seq and Del/Dup

Sample Requirements

Specimen: Whole Blood

Container(s): Lavender/EDTA or Yellow/ACD

Preferred Vol: 3.0 - 5.0 mL

Minimum Vol: 1.0 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 - 4 C

Storage location: Do not spin. Affix large Cerner label to tube and store in CPA refrigerator, Send Outs rack.

 

Off-site collection: Send whole blood refrigerated.

Stability

Specimen Type Temperature Time
Whole Blood Room temp

48 h

  Refrigerated 7 d
  Frozen

Unacceptable

 

Availability

STAT Performed TAT
N   20 d

 

Performing Laboratory

PreventionGenetics

3800 S. Business Park Ave.

Marshfield, WI 54449

 

Phone Number: (715) 387-0484

Department

Department: Send Outs

Phone Number: (206) 987-2563

Reference Range

Interpretive report is 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 RAI1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Special Instructions

PreventionGenetics

Clinical Utility

Smith-Magenis GeneReviews

Send Out Instructions

Reference Test Name:

Smith-Magenis and Potocki-Lupski syndromes via RAI1 Gene Sequencing with CNV Detection

Reference Test Number: 8107
Instructions: Ship whole blood via FedEx Priority Overnight at ambient temperature. PreventionGenetics accepts Saturday delivery.

 

Update Date

This page was last updated 12/5/2018.