PIK3CA-Related Overgrowth Spectrum Disorders | NGS

Genes SequencedFocused Option
1 gene: PIK3CA
Comprehensive Option
75 genes: ACTB, ACVRL1, AKT1, AKT2, AKT3, ARAF, BRAF, CCBE1, CCM2, CCND2, CDKN1C, CELSR1, CLDN14, CTNNB1, DCHS1, ELMO2, ENG, EPHB4, FAT4, FGFR1, FGFR2, FLT4, FOXC2, GATA2, GDF2, GJA4, GJC2, GLMN, GNA11, GNA14, GNAQ, GNAS, HGF, HRAS, IDH1, IDH2, KDR, KEL, KIF11, KRAS, KRIT1, LZTR1, MAP2K1, MAP2K2, MAP3K3, MET, MTOR, NF1, NF2, NRAS, PDCD10, PDGFRB, PIEZO1, PIK3CA,  PIK3CD, PIK3R1, PIK3R2, PRKACA, PTEN, PTPN11, PTPN14, RASA1, RHOA, SHOC2, SMAD3, SMAD4, SMO, SOS1, SOX18, SPRED1, STAMBP, TEK, TSC1, TSC2 and VEGFC). 
Test DetailsFocused vs. Comprehensive Analysis – Clinicians ordering the PIK3CA-Related Overgrowth Spectrum panel may choose between a focused or comprehensive panel option. Selection of a focused analysis will result in the evaluation of ONLY the gene(s) included in the ordered subset. A negative result will trigger reporting of a negative finding (no pathogenic or likely pathogenic variants) or inconclusive finding (variants of unknown significance). Selection of comprehensive analysis includes an initial evaluation of the focused gene(s) only, and if a pathogenic or likely pathogenic (P/LP) variant is identified, the analysis ends and a report is generated. However, if no P/LP variants are initially identified from the ordered subset, then a comprehensive analysis automatically occurs, and any P/LP variants identified from our comprehensive list of 75 DoSM-associated genes is reported. If no P/LP variants are identified after comprehensive analysis, we generate a report with negative or inconclusive findings.

This targeted hybrid capture-based test is designed to detect somatic single nucleotide variants, insertions and deletions (indels). At a mean depth of coverage of at least 4000x across the captured region, this test has 89.84% sensitivity for variants at a variant allelic fraction (VAF) of 1.25% and 99.48% for variants at a VAF of at least 2.5%. Identified variants classified using ACMG/AMP, ClinGen and internally developed guidelines.
MethodologyNext Generation Sequencing
PerformedMonday – Friday
Turnaround3 weeks
Specimen RequirementsFresh or Formalin fixed paraffin embedded tissue from the affected area.
Sample CollectionFresh tissue placed in media (4 mm skin punch or tissue 4 mm in size).
Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block or 15 unstained slides with matched H&E slide.
Minimum Sample Volume 3 millimeters
Storage/Transport ConditionsFresh tissue: Refrigerated temperature (cold packs). Please ship in media for overnight delivery.
FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope for overnight delivery. In seasonal warmer weather, include cold pack.
Unacceptable ConditionsFFPE specimens processed using acid decalcification are not acceptable (EDTA is acceptable)
CPT Code(s) 81479