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Thyroid Cancer Comprehensive Panel

Diseases Targeted:

Hereditary Thyroid Cancer

Overview:

The Thyroid Cancer Comprehensive Panel examines 7 genes associated with an increased risk for thyroid cancer. This test includes both well-established thyroid cancer susceptibility genes.

Who is this test for?

Patients with a personal or family history suggestive of a hereditary thyroid cancer syndrome. Red flags for hereditary thyroid cancer could include onset of cancer prior to the age of 50 years, more than one primary cancer in a single person, and multiple affected people within a family with a history of thyroid, breast and/or colon cancer, as well as others. Also, patients with additional non-cancerous clinical findings, such as abnormal skin pigmentation or macrocephaly, that may indicate a genetic syndrome, may also benefit from this test. After consideration of a patient’s clinical and family history, this testing may be appropriate for some pediatric patients. (If there are specific genes that you do NOT want included, please indicate this on the test requisition form.) 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?

What are the potential benefits for my patient? Patients identified with hereditary thyroid cancer can benefit from increased surveillance and preventative steps to better manage their risk for cancer or other clinical manifestations. 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

APC, CHEK2, DICER1, PRKAR1A, PTEN, RET, TP53 ( 7 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
APC Heterozygous pathogenic variants in APC are associated with both classic and attenuated familial adenomatous polyposis (FAP), Gardner syndrome, Turcot syndrome, and Hereditary Desmoid disease. These conditions are associated with an increased risk for thyroid cancer. PubMed: 20301519; OMIM: 175100
PRKAR1A Heterozygous pathogenic variants in PRKAR1A are associated with Carney Complex. Individuals with this condition have up to a 75% chance of developing thyroid cancer (usually thyroid follicular adenoma), as well as other types of tumors and cancer. PubMed: 20301463; OMIM: 188830
PTEN Individuals with heterozygous pathogenic PTEN variants are at a significantly increased risk for multiple types of cancers, including breast, thyroid, colorectal, endometrial, renal, and others. Autosomal dominant mutations in PTEN have been associated with Cowden syndrome, which is associated with a 35% lifetime risk for thyroid cancer. PubMed: 20301661; OMIM: 601728
RET Autosomal dominant pathogenic variants in the RET gene are associatediwth Multiple endocrine neoplasia type 2 (MEN 2), which is associated with medulary thyroid carcinoma, pheochromocytoma, and other clinical findings. PubMed: 20301434; OMIM: 164761
TP53 Heterozygous pathogenic variants in the TP53 gene are associated with Li-Fraumeni syndrome, a condition that increases risk for many types of cancer, including non-medullary thyroid cancers in some families. PubMed: 20301488, 26014290, 2614290; OMIM: 151623, 191170
CHEK2 Heterozygous pathogenic variants in CHEK2 are associated with an increased risk for thyroid cancer, as well as other CHEK2-related cancers. PubMed: 24599715, 25431674, 16998506, 18172190, 21876083, 27595995, 15492928, 11719428, 20597917, 21807500, 21876083, 21956126, 23713947, 23296741, 24240112, 24879340, 28283864
DICER1 Autosomal dominant mutations in DICER1 have been associated with DICER1 syndrome, a familial tumor susceptibility syndrome which includes susceptibility to many different kinds of tumors. PubMed: 24761742; OMIM: 606241
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