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Prostate Cancer Comprehensive Panel

Diseases Targeted:

Hereditary Prostate Cancer

Overview:

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.

Who is this test for?

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.

What are the potential benefits for my patient?

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.

Order Options

Sequencing (included)
Del/Dup (included)

 

Genes

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

Coverage:

99% at 50x

Specimen Requirements:

Blood (two 4ml EDTA tubes, lavender top) or Extracted DNA (3ug in EB buffer) or Buccal Swab or Saliva (kits available upon request)

Test Limitations:

Test results and variant interpretation are based on the proper identification of the submitted specimen and use of correct human reference sequences at the queried loci. In very rare instances, errors may result due to mix-up or co-mingling of specimens. Positive results do not imply that there are no other contributions, genetic or otherwise, to the patient's phenotype, and negative results do not rule out a genetic cause for the indication for testing. Result interpretation is based on the collected information and Alamut annotation available at the time of reporting. This assay is not designed or validated for the detection of mosaicism. DNA alterations in regulatory regions or deep intronic regions (greater than 20bp from an exon) will not be detected by this test. There are technical limitations on the ability of DNA sequencing to detect small insertions and deletions. Our laboratory uses a sensitive detection algorithm, however these types of alterations are not detected as reliably as single nucleotide variants. Rarely, due to systematic chemical, computational, or human error, DNA variants may be missed. Although next generation sequencing technologies and our bioinformatics analysis significantly reduce the confounding contribution of pseudogene sequences or other highly-homologous sequences, sometimes these may still interfere with the technical ability of the assay to identify pathogenic variant alleles in both sequencing and deletion/duplication analyses. Deletion/duplication analysis can identify alterations of genomic regions which are a single exon in size. When novel DNA duplications are identified, it is not possible to discern the genomic location or orientation of the duplicated segment, hence the effect of the duplication cannot be predicted. Where deletions are detected, it is not always possible to determine whether the predicted product will remain in-frame or not. Unless otherwise indicated, in regions that have been sequenced by Sanger, deletion/duplication analysis has not been performed.

Patients with Bone Marrow Transplants:
DNA extracted from cultured fibroblasts should be submitted instead of blood/saliva/buccal samples from individuals who have undergone allogeneic bone marrow transplant and from patients with hematologic malignancy.

Gene Specifics:

Gene Notes
MSH2 Inversion of MSH2 exons 1-7 ("Boland" inversion) is assessed for Lynch Syndrome, Colorectal, Endometrial, and Prostate Cancer Panel testing (for both Focus and Comprehensive Panels) as well as Comprehensive Gastric Cancer Panel testing. Unless otherwise specified, this testing is not performed for other cancer panels, but is available upon request.

CPT Codes:

CPT Code 81445, 81479

NOTE: The CPT codes listed on the website are in accordance with Current Procedural Terminology, a publication of the American Medical Association. CPT codes are provided here for the convenience of our clients. Clients who bill for services should make the final decision on which codes to use.

Gene Descriptions:

Gene Reason Reference
ATM Heterozygous 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
BRCA1 Autosomal dominant pathogenic variants in the BRCA1 gene are associated with an increased risk for prostate cancer. PubMed: 9497246, 12677558, 17416853, 20301425, 22846731
BRCA2 Autosomal 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
MSH6 Heterozygous 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
EPCAM Heterozygous 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
MLH1 Heterozygous 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
MSH2 Heterozygous 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
NBN Heterozygous 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
PMS2 Heterozygous 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
TP53 Heterozygous 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
HOXB13 Heterozygous pathogenic variants in HOXB13 are associated with an increased risk for prostate cancer. PubMed: 22236224, 24026887, 22841674, 23457453­­­­­­­­­; OMIM: 604607
CHEK2 Heterozygous 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
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