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Prostate Cancer Comprehensive Panel

Genes:

ATM, BRCA1, BRCA2, CHEK2, EPCAM, HOXB13, MLH1, MSH2, MSH6, NBN, PMS2, TP53 - 12 genes

Coverage:

99.99% at 50x



CPT Codes:

CPT Codes**
Seq81216x1, 81292x1*, 81295x1*, 81298x1*, 81317x1*, 81403x1, 81405x1, 81479x4
Del/Dup81213x1*, 81294x1*, 81297x1*, 81300x1*, 81319x1*, 81403x1, 81404x1, 81479x3
Seq & Del/Dup81211x1*, 81292x1*, 81294x1*, 81295x1*, 81297x1*, 81298x1*, 81300x1*, 81317x1*, 81319x1*, 81403x1, 81404x1, 81405x1, 81479x6
* CPTs listed under CLAB2016 can be found on CMS.gov Fee Schedule released in January 2016. (Reference: https://www.cms.gov/Medicare/Medicare-Fee-for-Service-Payment/ClinicalLabFeeSched/Clinical-Laboratory-Fee-Schedule-Files.html, Alternative: http://fulgentgenetics.com/public/cptdocs/CLAB2016v1.xls)
** CPTs are based on the genes listed. Adding or removing genes will change the CPTs. In some cases, a CPT may require a specific list of genes while performing both sequencing and deldup to qualify. Fulgent bases the CPT for each Gene on multiple sources: CLAB2016v1, AMA Molecular Pathology Tier 2 Gene Designation Chart, and AMA CPT 2016. Call for more details.

Specimen Requirements:

Blood (two 4ml EDTA tubes, lavender top) or Extracted DNA (3ug in TE buffer) or Buccal Swab or Saliva (kits available upon request). See How to Order for more details.


Test Limitations:

All sequencing technologies have limitations. This analysis is performed by Next Generation Sequencing (NGS) and is designed to examine coding regions and splicing junctions. Although next generation sequencing technologies and our bioinformatics analysis significantly reduce the contribution of pseudogene sequences or other highly-homologous sequences, these may still occasionally interfere with the technical ability of the assay to identify pathogenic variant alleles in both sequencing and deletion/duplication analyses. Sanger sequencing is used to confirm variants with low quality scores and to meet coverage standards. If ordered, Del/Dup analysis is designed to identify deletion or duplication which is one exon in size. Identified putative deletions or duplications are confirmed by an orthogonal method (qPCR or MLPA). This assay will not detect certain types of genomic alterations which may cause disease such as, but not limited to, translocations or inversions, most repeat expansions (eg. trinucleodes or hexanucleodes), alternations in most regulatory regions (promoter regions) or deep intronic regions (greater than 20bp from an exon). If performed, repeat expansion analysis may not elicit the precise number of repeats present in large expansions. This assay is not designed or validated for the detection of somatic mosaicism or somatic mutations.


Gene Limitations:

  • PMS2: The sequence in the region of exons 12 – 15 of the PMS2 gene is highly homologous to the PMS2 pseudogene, namely PMS2CL. NGS technology is currently unable to distinguish sequencing variants within exons 12 - 15 in the PMS2 gene from the PMS2CL pseudogene. A long range PCR assay is used to confirm variants identified in this region. Variants are reported when they are confirmed to be located in the PMS2 gene.

Addtional Notes:

  • MSH2: Inversion of MSH2 exons 1-7 is assessed by a MLPA-based assay and is negative unless otherwise noted.