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Test Code NF1 UM NF1 Sequencing and Deletion Duplication

Clinical System Name

NF1 Sequencing and Deletion Duplication

Synonyms

Neurofibromatosis, type 1

Description

NF1

 

 

Sample Requirements

Preferred sample type is whole blood

 

Specimen: Whole Blood

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

Preferred Vol: 3 mL

Minimum Vol: 2 mL

 

Notes: No micro collection.

 

Specimen: DNA extracted from lymphocyte cells

Container(s): Sterile plastic tube

Preferred Vol: 3μg, O.D. value at 260:280nm ≥1.8

Minimum Vol:  3μg, O.D. value at 260:280nm ≥1.8

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 3 d
Whole blood Refrigerated 7 d
Whole blood Frozen N
Extracted DNA Room temp 3-4 d
Extracted DNA Refrigerated 1 y
Extracted DNA Frozen Indefinitely

 

Availability

STAT TAT
N 25 d

 

Performing Laboratory

University of Alabama (UAB) Medical Genomics Laboratory

Department

Department:  University of Alabama (UAB) Medical Genomics Laboratory, 720 South Twentieth Street, Suite 330, Birmingham, Alabama 35294-0005

Phone Number: (205) 934-5562

Fax Number: (205) 996-2929

 

Reference Range

Interpretive report is provided.

Methodology

Method: The NF1-only by NGS involves sequencing as well as deletion/duplication analysis of the entire coding NF1 region plus the alternatively spliced exons 9br, 23a and 48a (60 exons total). 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 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 >2000x with >99.8% of the NF1 coding region ≥350x and 100% ≥200x, allowing detection of very low level mosaicism, down to 3-5% MAF respectively (regions covered by ≥350x respectively ≥200x). Variant and copy number calls are made using a unique bioinformatics pipeline detecting all types of mutations including single nucleotide substitutions, indels, and frameshifts caused by deletion/ duplication up to 112bp.

Special Instructions

Link to ref lab website

 

Required Form:

Requistion with Clinical History

 

 

Clinical Utility

NF1 GeneReviews

Send Out Instructions

Reference Test Name: Next-Gen Sequencing and Deletion/Duplication Analysis of NF1 Only
Reference Test Number: NF1-NG
Instructions: Send samples to arrive Monday through Friday. If you wish to ship a sample on Friday for Saturday delivery, you must call the lab by 2:00 CST on Friday to get special Saturday delivery instructions. Whole blood specimens may be stored refrigerated for up to 5 days prior to shipping. Ship whole blood overnight via FedEx, ambient temperature. Keep a copy of the completed forms and the airbill for our files.