• Panel Description
  • Test Descrption
  • CPT Codes
  • Resources
  • Gene Descriptions
  • Appendix

Prostate Cancer Comprehensive Panel

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Panel Description

Hereditary Prostate Cancer
The Prostate Cancer Comprehensive Panel examines 12 genes associated with an increased risk for prostate cancer. This test includes both well-established prostate cancer susceptibility genes, as well as candidate genes with limited evidence of an association with prostate cancer.

Patients with a personal or family history suggestive of a hereditary prostate cancer syndrome. Red flags for hereditary prostate cancer could include onset of cancer prior to the age of 55 years, more than one primary cancer in a single person, and multiple affected people within a family with a history of prostate, breast, ovarian, and/or colon cancer. This test is designed to detect individuals with a germline pathogenic variant, and is not validated to detect mosaicism below the level of 20%. It should not be ordered on tumor tissue.

Patients identified with hereditary prostate cancer can benefit from increased surveillance and preventative steps to better manage their risk for cancer. Also, your patient’s family members can be tested to help define their risk. If a pathogenic variant is identified in your patient, close relatives (children, siblings, parents) could have as high as a 50% risk to also be at increased risk.

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Test Description

  • Sequencing (included)
  • Del/Dup (included)
  • Rush /STAT
2 - 3 weeks
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ATM, BRCA1, BRCA2, CHEK2, EPCAM, HOXB13, MLH1, MSH2, MSH6, NBN, PMS2, TP53 ( 12 genes )
99.99% at 50x
Blood (two 4ml EDTA tubes, lavender top) or Extracted DNA (3ug in TE buffer) or Buccal Swab or Saliva (kits available upon request)
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. trinucletiodess or hexanucleotides), 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.

GeneNotes
MSH2Inversion of MSH2 exons 1-7 is assessed by a MLPA-based assay and is negative unless otherwise noted.
PMS2The 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.
Sequencing 81216x1, 81292x1, 81295x1, 81298x1, 81317x1, 81403x1, 81405x1, 81408x1, 81479x4
Del/Dup 81213x1, 81294x1, 81297x1, 81300x1, 81319x1, 81403x1, 81404x1, 81408x1, 81479x3
Sequencing & Del/Dup 81211x1, 81292x1, 81294x1, 81295x1, 81297x1, 81298x1, 81300x1, 81317x1, 81319x1, 81403x1, 81404x1, 81405x1, 81408x1, 81479x6

NOTE:  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.
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Resources

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Hereditary Prostate Cancer Information for Patients

Gene Descriptions

GeneReasonReference
ATMHeterozygous pathogenic variants in ATM may be associated with an increased risk for prostate cancer, and possibly for a more aggressive form of cancer if it is developed. However, the evidence is contradictory. Additional research is needed. PubMed: 26662178, 27989354, 27595995,1248000, 15928302, 15942625
BRCA1Autosomal dominant pathogenic variants in the BRCA1 gene are associated with an increased risk for prostate cancer. PubMed: 9497246, 12677558, 17416853, 20301425, 22846731
BRCA2Autosomal dominant mutations in the BRCA2 gene are implicated in the hereditary breast and ovarian cancer syndrome (HBOC). Additionally, biallelic mutations in BRCA2 gene are associated with autosomal recessive Fanconi anemia Type D1 .PubMed: 12065746, 12677558, 9497246, 17416853, 18042939, 20301425, 22846731
CHEK2Heterozygous pathogenic variants in CHEK2 are associated with an increased risk for prostate cancer, as well as other CHEK2-related cancers.PubMed: 25431674, 16998506, 18172190, 21876083, 27595995, 15492928, 11719428, 20597917, 21807500, 21876083, 21956126, 23713947, 23296741, 24240112, 24599715, 24879340, 28283864
EPCAMHeterozygous pathogenic variants in the EPCAM gene cause Hereditary Non-Polyposis Colorectal Cancer (HNPCC), also known as Lynch Syndrome, which is associated with an increased risk for prostate cancer.PubMed: 23530095, 24434690, 24425144, 20301390, 23462293
HOXB13Heterozygous pathogenic variants in HOXB13 are associated with an increased risk for prostate cancer.PubMed: 22236224, 24026887, 22841674, 23457453­­­­­­­­­; OMIM: 604607
MLH1Heterozygous pathogenic variants in the MLH1 gene cause Hereditary Non-Polyposis Colorectal Cancer (HNPCC), also known as Lynch Syndrome, which is associated with an increased risk for prostate cancer.PubMed: 23530095, 24434690, 24425144, 20301390, 23462293
MSH2Heterozygous pathogenic variants in the MSH2 gene cause Hereditary Non-Polyposis Colorectal Cancer (HNPCC), also known as Lynch Syndrome, which is associated with an increased risk for prostate cancer.PubMed: 23530095, 24434690, 24425144, 20301390, 23462293
MSH6Heterozygous pathogenic variants in the MSH6 gene cause Hereditary Non-Polyposis Colorectal Cancer (HNPCC), also known as Lynch Syndrome, which is associated with an increased risk for prostate cancer.PubMed: 23530095, 24434690, 24425144, 20301390, 23462293
NBNHeterozygous pathogenic variants in NBN (also known as NBS1) have been associated with a number of malignancies including melanoma, non-Hodkins lymphoma, medulloblastoma, and colorectal, prostate, and breast cancers . Other studies have shown possible associations with aplastic anemia and acute lymphoblastic leukemia. Biallelic pathogenic variants in NBN have been associated with Nijmegen Breakage syndrome (NBS). Individuals with NBS generally have progressive intellectual disability, growth retardation and immunodeficiency, and are at an increased risk for a variety of cancers, including lymphoma, glioma, and medulloblastoma. PubMed: 14973119, 15185344, 16474176, 16770759, 18079974, 19908051, 21514219,15338273,11325820, 20301355; OMIM: 609135, 251260
PMS2Heterozygous pathogenic variants in the PMS2 gene cause Hereditary Non-Polyposis Colorectal Cancer (HNPCC), also known as Lynch Syndrome, which is associated with an increased risk for prostate cancer.PubMed: 23530095, 24434690, 24425144, 20301390, 23462293
TP53Heterozygous pathogenic variants in the TP53 gene are associated with Li-Fraumeni syndrome, a condition that increases risk for many types of cancer.PubMed: 20301488, 26014290, 2614290; OMIM: 151623, 191170

Appendix