Test Code LAB3281 Megalencephaly Panel

Additional Codes

MEGPX

Clinical System Name

Megalencephaly Panel

Synonyms

Megaplex

Description

This panel is useful for the evaluation of patients with suspected overgrowth syndromes including:

body overgrowth syndromes such as Proteus, fibroadipose hyperplasia, and CLOVES (Congenital Lipomatous Overgrowth, Vascular malformations, Epidermal nevi and Scoliosis/Skeletal/Spinal anomalies)
brain overgrowth/megalencephaly syndromes such as PTEN-hamartoma spectrum of disorders (Cowden, Bannayan-Riley-Ruvalcaba, and megalencephaly with autism)
vascular malformation syndromes such as Klippel-Trenaunay syndrome

The panel uses next-generation sequencing to detect most mutations in the genes listed below. The assay completely sequences all exons of these genes, detects large deletions and duplications, and has the potential to detect mosaicism.

Genes in panel: ABCC9, AKT1, AKT2, AKT3, BRWD3, CCND2, CDKN1C, CUL4B, DEPDC5, DNMT3A, EED, EZH2, GLI3, GNAQ, GNAS, GPC3, HEPACAM, KCNJ8, KIF7, MED12, MLC1, MTOR, NFIA, NFIX, NSD1, PIK3CA, PIK3R2, PTCH1, PTEN, RAB39B, RIN2, RNF135, SETD2, STRADA, TBC1D7, TSC1, and TSC2

Sample Requirements

Specimen: Fresh Frozen Tissue

Container(s): Sterile cup or tube

Preferred Vol: 200-300mg

Minimum Vol: 50mg

Specimen: Formalin-fixed paraffin embedded tissue

Container(s): EITHER (a) formalin-fixed slides, OR (b) formalin-fixed tissue block

Preferred Vol:

(a) Instructions for slide specimens: 1 slide at 4-micron thickness stained with hematoxylin-and-eosin AND 10 unstained, non-baked slides at 10-micron thickness. Unstained slides can be on charged or uncharged slides. Note: In order to ensure that enough DNA is obtained, the minimum acceptable tissue area is 10 square millimeters when ten 10-micron slides are supplied (1 cubic millimeter of tissue). Tissue sections should contain as much lesional tissue as possible; to ensure detection of all types of mutations, there should be at least 10% lesional cells in the tissue area processed for DNA.

(b) Instructions for tissue block specimen: Provide complete formalin-fixed tissue block containing lesional tissue. If there is more than one tissue block, please provide the block that has the greatest amount of lesional tissue. Tissue block will be returned at completion of testing.

Specimen: DNA (from lesional tissue or skin preferred)

Container(s): Sterile plastic tube

Preferred Vol: 6 micrograms, concentration: at least 25 nanograms/microliter

Minimum Vol: 3 micrograms

Specimen: Whole Blood

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

Preferred Vol: 10.0 mL

Minimum Vol: 5.0 mL

Specimen: Cultured Cells

Acceptable: Fibroblasts

Container(s): T-25 flasks

Preferred Vol: 2 flasks

Alternative Specimen (e.g. saliva or buccal): Alternate Specimen Collection Kits for Genetic Testing

Processing Instructions

Reject due to: Decalcified samples; tissue samples treated with fixatives other than formalin.

Spin: N

Aliquot: N

Temp: 2 - 4 C

Storage location: Place whole blood sample in CPA refrigerator, Send Outs rack.

Off-site collection: Send at room temperature for overnight delivery. Ok to hold blood up to 7 days before shipping if refrigerated.

Stability

Specimen Type	Temperature	Time
Whole Blood	Room Temp	5 d
	Refrigerated	7 d
	Frozen	Unacceptable
Extracted DNA from Blood or Cultured Fibroblasts	Room Temp	3-4 d
	Refrigerated	1 y
	Frozen	Indefinitely
Fresh Frozen Tissue	Frozen	Indefinitely
Cultured cells	Room Temp	3 d

Availability

STAT	TAT
N	6 w

Performing Laboratory

University of Washington Medical Center

Department of Laboratory Medicine

Genetics Lab
1959 NE Pacific St, NW220
Seattle, WA 98195

Phone Number: (206) 520-4600

Department

Department: Send Outs

Phone Number: (206) 987-2563

Methodology

Method: Next-Generation Sequencing

The assay completely sequences all exons of these genes and detects large deletions, duplications and mosaicism. A total of 1.1Mb of DNA is sequenced and the average coverage ranges from 320 to >1,000 sequencing reads per bp. Genomic regions are captured using biotinylated RNA oliognucleotides (SureSelect), prepared in paired-end libraries with ~200 bp insert size, and sequenced on an Illumina HiSeq2500 instrument with 100 bp read lengths, in a modification of a procedure described by Pritchard et al. 2012. Large deletions and duplications are detected using methods described by Nord et al. 2011.

Reference Range

Interpretive report provided.

Special Instructions

UWMC

Clinical Utility