CDKN2A and CDK4 Testing

CDKN2A and CDK4 are tumor suppressor genes which are associated with increased risk of developing melanoma skin cancer and multiple dysplastic or atypical nevi.

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CDKN2A and CDK4 are tumor suppressor genes which are associated with increased risk of developing melanoma skin cancer and multiple dysplastic or atypical nevi.

Two genes are well documented to be associated with hereditary melanoma, cyclin-dependent kinase inhibitor 2A gene (CDKN2A) and cyclin-dependent kinase 4 gene (CDK4).  Individuals with a mutation in one of these genes may have up to a 67% or 74% lifetime risk for melanoma, respectively, and may also have multiple dysplastic or atypical nevi.  Individuals with CDKN2A mutations also have an increased risk for pancreatic cancer.

Disease Name 
Melanoma
Cutaneous malignant melanoma syndrome
Familial atypical mole-malignant melanoma syndrome (FAMMM)
Melanoma-Pancreatic cancer syndrome (M-PCS)
Pancreatic cancer
Disease Information 

Melanoma skin cancer (also called malignant melanoma or cutaneous melanoma) refers to cancer that begins in the melanocytes (pigment-producing cells of the skin). It is less common than other forms of skin cancer, such as basal and squamous cell carcinomas. Because melanoma is more likely to spread (metastasize) than these other forms of skin cancer, it carries greater health risks. When detected at an early stage, melanoma is treatable and greater than 90% of individuals survive more than 5 years after diagnosis.1 Typically, melanoma develops in sun-exposed areas such as on the back, arms, legs, chest, neck, or face. In rare cases, however, melanoma can develop in the eye, mouth, and genitalia.2, 3

The lifetime risk of getting melanoma is about 2% (1 in 50) for Caucasians, 0.5% (1 in 200) for Hispanics, and 0.1% (1 in 1,000) for African Americans, but the risk for each individual can vary greatly.2-4 While the majority of melanoma cases are sporadic or related to excessive sun exposure, there are families in which multiple individuals are affected. It is estimated that approximately 10% of melanoma cases are due to a hereditary cause.2, 4-8 An essential part of managing patients with melanoma is early diagnosis.

CDKN2A
CDKN2A mutations contribute to 10-39% of hereditary melanoma; the more members of the same family have melanoma, the more likely it is due to a CDKN2A mutation.2, 5, 8-11 The majority of the information regarding mutations in CDKN2A refers to those affecting the p16 transcript. Mutations affecting the p14 transcript are rare and, hence, not much information is known about the clinical features.8, 12-14 It is estimated that individuals with a CDKN2A mutation have an approximate 28-67% lifetime risk of developing melanoma, with penetrance estimates varying widely based on study design and geographic region.4, 6-8 Those with a CDKN2A mutation also have an approximate 17-25% lifetime risk of developing pancreatic cancer; however, recent reports suggest this risk may be as high as 58%, and are potentially higher in smokers. 8, 14-16

CDK4
CDK4 is estimated to account for ~1% of hereditary melanoma.17 Individuals with a CDK4 mutation demonstrate a higher frequency of atypical nevi, an earlier age at melanoma diagnosis (mean age 32-39 years), and an increased likelihood for multiple primary melanomas as compared to individuals without a CDK4 mutation.8, 18 It is estimated that those with a CDK4 mutation have up to a 74% risk for malignant melanoma by age 50.18

Since CDKN2A and CDK4 do not account for all hereditary cases of melanoma, there are other genes (some still unidentified) that account for the remaining cases.

Testing Benefits & Indication 

Genetic testing for CDKN2A and CDK4 mutations can identify those with hereditary risk of developing melanoma and possibly pancreatic cancer, which helps target increased medical surveillance. Increased surveillance for individuals with a CDKN2A or CDK4 mutation may help reduce morbidity and mortality associated with melanoma. Early detection of melanoma is a critical part of patient management. It is important to detect melanomas early by recognizing and performing a biopsy on clinically suspicious lesions.3, 19

It is generally best for an individual who has had melanoma or pancreatic cancer to have genetic testing first in a family. Individuals who may be suitable for testing include those who have:

  • Multiple primary melanomas
  • Multiple family members with melanoma with/without pancreatic cancer
  • A family history of a CDKN2A and CDK4 mutation.  In a family with a mutation, those who do not have the familial mutation may still have elevated cancer risks due to other contributing risk factors.2
Test Description 

CDKN2A coding exons1α-3 and CDK4 coding exons 1-7 and well into the 5’ and 3’ ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis determines gene copy number for CDKN2A coding exons 1α-3 and CDK4 coding exons 1-7. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology, using long biotinylated oligonucleotide probes followed by polymerase chain reaction (PCR) and next generation sequencing (NGS). Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing.20 Gross deletion/duplication analysis of CDKN2A and CDK4 using read-depth from NGS data is also performed. Any copy number changes detected by NGS are confirmed by targeted chromosomal microarray and/or multiplex ligation-dependent probe amplification (MLPA).

Mutation Detection Rate 

Mutations in the CDKN2A gene can be detected in 10-40% of familial melanoma families. Mutations in the CDK4 gene have been identified in appromimately 1% of familial melanoma families (clinical sensitivity). Ambry's CDKN2A and CDK4 analyses can detect >99.9% of described mutations in both genes, when present (analytic sensitivity).

Specimen Requirements 

Complete specimen requirements are available here or by downloading the PDF found above on this page.

Turnaround Time 
TEST CODE Technique CALENDAR DAYS
4708 CDKN2A p16INK4a/p14ARF and CDK4 gene sequence and deletion/duplication analysis 14-21 
9036 CDK4 gene sequence & deletion/duplication analysis 14-21 

 

Specialty 
Genes 
CDKN2A
CDK4
Techniques 
References 
  1. Surveillance E., and End Results Program. SEER Stat Fact Sheets: Melanoma of the Skin. Available from: http://seer.cancer.gov/statfacts/html/kidrp.html#risks.
  2. Gabree M, Patel D, and Rodgers L. Clinical applications of melanoma genetics. Curr Treat Options Oncol. 2014. 15(2): p. 336-50.
  3. Society AC. Melanoma Skin Cancer. Available from: http://www.cancer.org/cancer/skincancer-melanoma/.
  4. Bishop DT, et al., Geographical variation in the penetrance of CDKN2A mutations for melanoma. J Natl Cancer Inst. 2002. 94(12): p. 894-903.
  5. Goldstein AM, et al., Features associated with germline CDKN2A mutations: a GenoMEL study of melanoma-prone families from three continents. J Med Genet. 2007. 44(2): p. 99-106.
  6. Begg CB, et al., Lifetime risk of melanoma in CDKN2A mutation carriers in a population-based sample. J Natl Cancer Inst. 2005. 97(20): p. 1507-15.
  7. Cust AE, et al., Melanoma risk for CDKN2A mutation carriers who are relatives of population-based case carriers in Australia and the UK. J Med Genet. 2011. 48(4): p. 266-72.
  8. Goldstein AM, et al., High-risk melanoma susceptibility genes and pancreatic cancer, neural system tumors, and uveal melanoma across GenoMEL. Cancer Res. 2006. 66(20): p. 9818-28.
  9. Goldstein AM and Tucker MA. Screening for CDKN2A mutations in hereditary melanoma. J Natl Cancer Inst. 1997. 89(10): p. 676-8.
  10. Hayward NK. Genetics of melanoma predisposition. Oncogene. 2003. 22(20): p. 3053-62.
  11. Maubec E, et al., Familial melanoma: clinical factors associated with germline CDKN2A mutations according to the number of patients affected by melanoma in a family. J Am Acad Dermatol. 2012. 67(6): p. 1257-64.
  12. Binni F, et al., Novel and recurrent p14 mutations in Italian familial melanoma. Clin Genet. 2010. 77(6): p. 581-6.
  13. Laud K, et al., Comprehensive analysis of CDKN2A (p16INK4A/p14ARF) and CDKN2B genes in 53 melanoma index cases considered to be at heightened risk of melanoma. J Med Genet. 2006. 43(1): p. 39-47.
  14. McWilliams RR, et al., Prevalence of CDKN2A mutations in pancreatic cancer patients: implications for genetic counseling. Eur J Hum Genet. 2011. 19(4): p. 472-8.
  15. Vasen HF, et al., Risk of developing pancreatic cancer in families with familial atypical multiple mole melanoma associated with a specific 19 deletion of p16 (p16-Leiden). Int J Cancer. 2000. 87(6): p. 809-11.
  16. de Snoo FA, et al., Increased risk of cancer other than melanoma in CDKN2A founder mutation (p16-Leiden)-positive melanoma families. Clin Cancer Res. 2008. 14(21): p. 7151-7.
  17. Soufir N. Prevalence of p16 and CDK4 germline mutations in 48 melanoma-prone families in France. The French Familial Melanoma Study Group [published erratum appears in Hum Mol Genet 1998 May;7(5):941]. Hum Mol Genet. 1998. 7(2): p. 209-216.
  18. Ward KA, Lazovich D, and Hordinsky MK. Germline melanoma susceptibility and prognostic genes: a review of the literature. J Am Acad Dermatol. 2012. 67(5): p. 1055-67.
  19. Moloney FJ, et al., Detection of primary melanoma in individuals at extreme high risk: a prospective 5-year follow-up study. JAMA Dermatol. 2014. 150(8): p. 819-27.
  20. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932.