PIK3CA-Related Overgrowth Spectrum Disorders | NGS
| Genes Sequenced | Focused 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 Details | Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region on the Illumina platform. Identified variants previously described and other potentially pathogenic non-synonymous variants are reported with interpretations. 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%. |
| Methodology | Next Generation Sequencing |
| Performed | Monday – Friday |
| Turnaround | 3 weeks from receipt of specimen |
| Specimen Requirements | Tissue from the affected area. Formalin fixed paraffin embedded affected tissue or fresh affected tissue in transport or tissue culture media. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Fresh tissue placed in media (4 mm skin punch or tissue 4 mm in size). |
| Minimum Sample Volume | 3 millimeters |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE). Fresh tissue: Refrigerated temperature (cold packs). Please ship in media for overnight delivery. |
| Unacceptable Conditions | FFPE specimens processed using acid decalcification are not acceptable (EDTA is acceptable) |
| CPT Code(s) | 81479 |