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Test Code NOONAN UM Noonan Spectrum Disorders Panel 

Important Note

This panel includes sequencing and CNV detection of 21 genes: A2ML1, BRAF, CBL, HRAS, KAT6B, KRAS, LZTR1, MAP2K1, MAP2K2, MAP3K8, NF1, NRAS, PTPN11, RAF1, RASA2, RIT1, RRAS, SHOC2, SOS1, SOS2, SPRY1

Clinical System Name

Noonan Spectrum Disorders Panel

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: 2-6 C

Storage location:  Do not spin. Affix large Cerner labels to tubes and place in refrigerator send-outs rack.  Store extra labels and copy of requisition in the clear plastic box attached to CPA refrigerator. Alert Send-outs team.

 

Off-site collection:

Stability

Specimen Type Temperature Time
Whole Blood Room temp 48 h
Whole Blood Refrigerated 1 w
Whole Blood Frozen Unacceptable
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

PreventionGenetics

3800 S. Business Park Ave.

Marshfield, WI 54449

 

Phone Number: (715) 387-0484

Department

Department: Sendouts

Phone Number: (206) 987-2563

Reference Range

Interpretive report is provided.

Methodology

Method:

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.

Clinical Utility

The Noonan Spectrum Disorders, also known as RASopathies, are a group of developmental syndromes characterized by extensive clinical and genetic heterogeneity. They include:

1- Noonan syndrome
2- Cardio-facio-cutaneous syndrome
3- Noonan syndrome with multiple lentigines, previously known as LEOPARD syndrome
4- Costello syndrome

 

Although there is a considerable phenotypic overlap among the various syndromes, each syndrome is characterized by distinct clinical features.

Send Out Instructions

Reference Test Name: Noonan Spectrum Disorders/Rasopathies Sequencing Panel with CNV Detection
Reference Test Number: 1309
Instructions: Ship whole blood via FedEx Priority Overnight at ambient temperature. PreventionGenetics accepts Saturday delivery.