Nevus Panel | NGS

Genes Sequenced	Focused Panel: BRAF, FGFR1, FGFR2, FGFR3, GNA11, GNAQ, HRAS, KRAS, MAP3K3, NRAS, PIK3CA and TEK Comprehensive Panel*: AKT1, AKT2, AKT3, BRAF, CBL, FGFR1, FGFR2, FGFR3, GNA11, GNAS, GNAQ, HRAS, IDH1, IDH2, KRAS, MAP2K1, MAP2K2, MAP3K3, MTOR, NF1, NRAS, PDGFRB, PIK3CA, PIK3R1, PIK3R2, PTEN, PTPN11, RAF1, RASA1, RIT1, SHOC2, SMO, SOS1, SPRED1, TEK, TSC1 and TSC2
Test Details	Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in Schimmelpenning-Feuerstein-Mims and related syndromes and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology	Next-generation sequencing
Performed	Monday – Friday
Turnaround	3 – 4 weeks
Specimen Requirements	Primary specimen: Affected tissue in fresh or FFPE form or buccal swab (please call the laboratory prior to sending buccal swabs). Secondary specimen: Peripheral blood.
Sample Collection	Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Fresh Tissue: Minimum of 4 mm of affected tissue in tissue culture or transport media. Buccal Swabs: 2-4 buccal swabs (please call lab before sending). Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL.
Minimum Sample Volume	NULL
Storage/Transport Conditions	FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. In seasonal warmer weather, include cold pack with shipment (DO NOT FREEZE). Recommend shipping for overnight delivery. Fresh tissue: please place in tissue culture or transport media and ship refrigerated (cold packs). Overnight shipping required. Blood/Buccal swabs: Ambient/room temperature preferred. However, if delivery/shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery/shipment by overnight delivery. In seasonal warmer weather, include cold pack with shipment (DO NOT FREEZE).
Unacceptable Conditions	Prior acid decalcification (EDTA is acceptable)
CPT Code(s)	81479

*The gene content of each orderable test is not changing, but we have changed the way in which we analyze the sequencing data. Since many of these DoSM share phenotypes related to overgrowth, vascular malformations, and/or skin lesions, we have found that reflexive reanalysis of an expanded set of genes known to be driving DoSM improves the diagnostic yield for compelling cases with initially negative findings. Based on this experience, we believe that client-driven decisions at the time of ordering will result in a faster and more efficient diagnostic outcome. Our revised requisition now contains selectable options for sequence data analysis. A focused order results in analysis and reporting of the genes on the focused panel only. For a comprehensive order, the focused panel is analyzed first – if positive, only the focused panel genes are reported, if negative, then analysis is opened up to the comprehensive panel.

Requisition