MelanomaNext

MelanomaNext is a next generation sequencing panel that simultaneously analyzes 8 genes associated with increased risk for melanoma and other cancers.

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MelanomaNext is a next generation sequencing panel that simultaneously analyzes 8 genes associated with increased risk for melanoma and other cancers.

MelanomaNext is a next generation sequencing (NGS) panel of 8 genes associated with melanoma: BAP1, BRCA2, CDK4, CDKN2A, MITF, PTEN, RB1, TP53. Full gene sequencing and gross deletion/duplication analysis are performed for all genes with the exception of MITF. Specific Site Analysis is available for individual gene mutations identified in a family.

Disease Name 
Hereditary cancer
Melanoma
Disease Information 

Melanoma (also called malignant melanoma or cutaneous melanoma) refers to skin 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 cell and squamous cell carcinomas. Because melanoma is more likely to spread (metastasize) than these other forms of skin cancer, it carries greater health risks and is responsible for the majority of skin cancer related deaths. When detected at an early stage, melanoma is treatable and >90% of individuals survives more than 5 years after diagnosis.1 Typically, melanoma develops in sun-exposed areas of the skin 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 average lifetime risk for getting melanoma is 2% for Caucasians, 0.5% for Hispanics, and 0.1% for African Americans, but the risk for each individual can vary greatly.2-4 While the majority of melanoma cases is sporadic or related to excessive sun exposure, there are families in which multiple individuals are affected. It is estimated that ~10% of melanoma cases are due to a hereditary cause.2, 4-8 An essential part of managing patients with melanoma is early diagnosis to implement appropriate medical screening.

MelanomaNext Genes 

BAP1 mutations have been shown to cause a tumor predisposition syndrome characterized by uveal melanoma, cutaneous melanoma, renal cell carcinoma, asbestos exposure-induced mesothelioma, and non-malignant melanocytic BAP1-mutated atypical intradermal tumors (MBAITs).9-12 Lifetime cancer risks are increased, but are not well defined. 

BRCA2 is a tumor suppressor gene inherited in an autosomal dominant pattern. Mutations in this highly penetrant gene increase the chance for cancer of the breast (female and male), ovaries (including primary peritoneal and Fallopian tube), pancreas, prostate, and melanoma. Studies suggest female BRCA2 mutation carriers have a 45-84% risk to develop breast cancer and an 11-18% risk to develop ovarian cancer by age 70.13-17 Male BRCA2 mutation carriers have up a 15% prostate cancer risk and a cumulative breast cancer risk of 6.8% by ages 65 and 70 respectively.17-19,20 BRCA2 mutation carriers may also be at an increased risk for melanoma, pancreatic cancer, and potentially other cancers.21 BRCA2 is also known as FANCD1.  Individuals who inherit a BRCA2/FANCD1 mutation from each parent may have a rare autosomal recessive condition called Fanconi anemia type D1 (FA-D1), which affects multiple body systems.

CDK4 is one of the genes associated with cutaneous malignant melanoma (CMM) syndrome. Individuals with CDK4 mutations demonstrate a higher frequency of atypical nevi, an earlier age of melanoma diagnosis (mean age 32-39 years), and an increased likelihood for multiple primary melanomas, as compared to individuals without CDK4 mutations.8,22 It is estimated that CDK4 mutation carriers have up to a 74% lifetime risk for malignant melanoma by age 50.22

CDKN2A encodes two distinct proteins, p16 and p14ARF, which are both involved in cell cycle regulation. Germline p16/CDKN2A mutations are associated with familial atypical multiple mole melanoma (FAMMM) syndrome. FAMMM is an autosomal dominant disorder characterized by an increased risk for atypical mole malignant melanoma, often associated with dysplastic or atypical nevi. CDKN2A mutation carriers have an approximate 28-67% lifetime risk of developing melanoma, with penetrance estimates varying widely based on study design and geographic region.4,6,7 Individuals carrying CDKN2A mutations also have an approximate17-25% lifetime risk for pancreatic cancer; however, recent reports suggest this risk may be as high as 58% and elevated further in smokers.23-25 Rare mutations that affect the p14ARF mutations have also been reported to predispose to melanoma and possibly pancreatic cancer.24,26,27

MITF is a gene implicated in both melanoma and renal cell carcinoma (RCC) development pathways.28,29 As such, MITF mutation carriers have an increased predisposition to developing melanoma and/or RCC. A specific mutation with unique functional consequences, p.E318K, has been detected at increased frequency in both melanoma and RCC cohorts.28,29  MITF mutation carriers are estimated to have a 2-8 fold increased risk for melanoma and a 5-fold increased risk for RCC compared to the general population. 40

PTEN is a gene associated with Cowden syndrome (CS), PTEN hamartoma tumor syndrome (PHTS), Bannayan-Riley-Ruvalcaba syndrome, Proteus syndrome, and autism spectrum disorder. CS is a multiple hamartoma syndrome with a high risk of developing tumors of the thyroid, breast, and endometrium. Mucocutaneous lesions, thyroid abnormalities, fibrocystic disease, multiple uterine leiomyomata, and macrocephaly can also be seen. Historically, individuals with PTEN mutations were thought to have a lifetime risk of up to 50% for breast cancer, 10% for thyroid cancer, and 5-10% for endometrial cancer.30 However, data from a large study of PTEN mutation carriers by Tan et al. suggests much higher lifetime risks (up to 85% for breast cancer, 35% for thyroid cancer, 28% for endometrial cancer) in individuals with PHTS and significantly increased lifetime risks of renal cancer (34%), colorectal cancer (9%), and melanoma (6%) as compared to the general population.31

RB1 encodes a 928 amino acid nuclear phosphoprotein pRB, which functions as a negative regulator of the cell cycle and cell proliferation. Heterozygous pathogenic mutations in RB1 cause retinoblastoma, a malignant tumor of the developing retina. Individuals with germline mutations in RB1 typically present with bilateral tumors, though some individuals develop unilateral or trilateral (involving the pineal gland) disease. The majority of mutations is highly penetrant and confer a 90% risk for retinoblastoma.32 However, a subset of mutations is moderately penetrant and result in lower and variable risk of disease.33 Individuals with hereditary retinoblastoma are at increased risk to develop second primary malignancies including osteosarcomas, soft tissue sarcomas, and melanoma, as well as other common epithelial malignancies. Risks for such malignancies vary based on laterality of tumor, family history, age at initial diagnosis, and treatment course. 34,35

TP53 is a tumor suppressor gene, and germline mutations within it are associated with Li-Fraumeni syndrome (LFS). An individual carrying a TP53 mutation has a 21-49% lifetime risk of developing cancer by age 30 and a lifetime cancer risk of 68-93%.36 The most common tumor types observed in LFS families include soft tissue and osteosarcomas, breast cancer, brain tumors (including astrocytomas, glioblastomas, medulloblastomas and choroid plexus carcinomas), and adrenocortical carcinoma (ACC); other cancers, including colorectal, gastric, ovarian, pancreatic, and renal, have also been reported.37,38

Testing Benefits & Indication 

Indications for Testing:

Individuals and families with a combination of the cancers below and/or some common red flags for hereditary cancer may be appropriate to consider for MelanomaNext.

  • Multiple primary melanomas
  • Multiple family members* with melanoma, with or without pancreatic cancer
  • Melanoma and kidney cancer in the same person, or close relatives*
  • Melanoma and mesothelioma in the same person, or close relatives*
  • A family history of a mutation in a gene that predisposes to melanoma
    *On the same side of the family

Common Red Flags for Hereditary Cancer:

  • Cancer diagnosed at a younger age than expected for the general population (≤ 50 years, for most cancers)
  • Cancer diagnosed across generations, and in multiple generations within a family, especially if diagnosed younger than average
  • Individual with multiple primary cancers (either in paired organs or in different organs)
  • A pattern of cancer in the family that is typical of a known cancer predisposition syndrome (for example, breast and diffuse gastric cancer with CDH1 mutations, or breast and thyroid cancer with PTEN mutations)

If increased risk of a hereditary cancer syndrome is suspected, the American Congress (formerly College) of Obstetricians and Gynecologists (ACOG) recommends referral to a specialist in cancer genetics or a healthcare provider with expertise in genetics for complete hereditary cancer risk assessment, which may lead to genetic testing.39 Establishing a molecular diagnosis can help guide preventive measures, direct surgical options and estimate personal and familial cancer risk.

Benefits of Testing:

Identifying patients with an inherited susceptibility for certain cancers can help with medical management. For example, this information can:

  • Modify skin cancer surveillance options and age of initial screening
  • Suggest specific risk-reduction measures, when applicable 
  • Offer treatment guidance (e.g. avoidance of radiation-based treatment methods for individuals with a TP53 mutation)
  • Identify other at-risk family members
  • Provide guidance with new gene-specific treatment options and risk reduction measures as they emerge
Test Description 

MelanomaNext analyzes 8 genes (listed above). All genes are evaluated by next generation sequencing (NGS) or Sanger sequencing of all coding domains, and well into the flanking 5’ and 3’ ends of all the introns and untranslated regions. In addition, sequencing of the promoter region is performed for PTEN (c.-1300 to c.-745). The BRCA2 Portuguese founder mutation, c.156_157insAlu (also known as 384insAlu) is detected by NGS and confirmed by PCR and agarose gel electrophoresis. For MITF, only the status of the c.952G>A (p.E318K) alteration is analyzed and reported. 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. Additional 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.41  Gross deletion/duplication analysis is performed for the covered exons and untranslated regions of all 7 genes (excluding MITF) using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray.

Mutation Detection Rate 

MelanomaNext can detect >99.9% of described mutations in the included genes listed above, when present (analytic sensitivity).

Specimen Requirements 

Complete specimen requirements are available here or by downloading the PDF found above in the Quick Links section at the top of this page.

Turnaround Time 
TEST CODE TECHNIQUE TURNAROUND TIME (days)
8849 MelanomaNext 14-21 

 

Specialty 
Genes 
BAP1
BRCA2
CDK4
CDKN2A
MITF
PTEN
RB1
TP53
References 
  1. National Cancer Institute. Surveillance, Epidemiology, and End Results Program. SEER Stat Fact Sheets: Melanoma of the Skin. [Internet}. Available from: http://seer.cancer.gov/statfacts/html/melan.html .
  2. Gabree M, et al. Clinical applications of melanoma genetics. Curr Treat Options Oncol. 2014 Jun. 15(2):336-50.
  3. American Cancer Society. Melanoma Skin Cancer. [Internet]. 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 Jun 19;94(12):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 Feb;44(2):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 Oct 19;97(20):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 Apr;48(4):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 Oct 15;66(20):9818-28.
  9. Pilarski R, et al. Expanding the clinical phenotype of hereditary BAP1 cancer predisposition syndrome, reporting three new cases. Genes Chromosomes Cancer. 2014;53:177-82.
  10. Popova T, et al. Germline BAP1 mutations predispose to renal cell carcinomas. Am J Hum Genet. 2013;92:974-80.
  11. Testa JR, et al. Germline BAP1 mutations predispose to malignant mesothelioma. Nat Genet. 2011;43(10):1022-5.
  12. Wiesner T, et al. Germline mutations in BAP1 predispose to melanocytic tumors. Nat Genet. 2011;43(10):1018-21.
  13. Antoniou A, et al. Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: a combined analysis of 22 studies. Am J Hum Genet. 2003;72(5):1117-30. 
  14. Chen S, Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol.2007;25(11):1329-33. 
  15. Ford D, et al. Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet. 1998;62(3):676-89.
  16. Folkins AK, Longacre TA. Hereditary gynaecological malignancies: advances in screening and treatment. Histopathology. 2013;62(1):2-30. 
  17. Shannon KM, Chittenden A. Genetic testing by cancer site: breast. Cancer Journal. 2012;18(4):310-9.
  18. Tai YC, et al. Breast cancer risk among male BRCA1 and BRCA2 mutation carriers. J Nat Cancer Inst. 2007;99(23):1811-4.
  19. Thompson D, Easton DF, Breast Cancer Linkage Consortium. Cancer Incidence in BRCA1 mutation carriers. J Natl Cancer Inst. 2002;94(18):1358-65. 
  20. Kote-Jarai Z, et al. BRCA2 is a moderate penetrance gene contributing to young-onset prostate cancer: implications for genetic testing in prostate cancer patients. Br J Cancer. 2011;105(8):1230-4.
  21. van Asperen CJ, et al. Cancer risks in BRCA2 families: estimates for sites other than breast and ovary. J Med Genet. 2005;42(9):711-9.
  22. Puntervoll HE, et al. Melanoma prone families with CDK4 germline mutation: phenotypic profile and associations with MC1R variants. J Med Genet. 2013;50(4):264-70. 
  23. 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):809-11. 
  24. McWilliams RR, et al. Prevalence of CDKN2A mutations in pancreatic cancer patients: implications for genetic counseling. Eur J Hum Genet. 2011;19(4):472-8. 
  25. 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):7151-7.
  26. 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):39-47. 
  27. Binni F, et al. Novel and recurrent p14 mutations in Italian familial melanoma. Clin Genet. 2010;77(6):581-6. 
  28. Bertolotto C, et al. A SUMOylation-defective MITF germline mutation predisposes to melanoma and renal carcinoma. Nature. 2011;480(7375):94-8. 
  29. Yokoyama S, et al. A novel recurrent mutation in MITF predisposes to familial and sporadic melanoma. Nature. 2011; 480(7375):99-103.
  30. Hobert JA and End C. PTEN hamartoma tumor syndrome: an overview. Genet Med. 2009;11(10):687-94. 
  31. Tan MH, et al., Lifetime cancer risks in individuals with germline PTEN mutations. Clin Cancer Res. 2012;18(2)400-7.
  32. Lohmann DR, et al. The spectrum of RB1 germline mutations in hereditary retinoblastoma. Am J Hum Genet. 1996;58(5):940-9. 
  33. Harbour JW. Molecular basis of low-penetrance retinoblastoma. Arch Ophthalmol. 2001;119(11):1699-704.
  34. Kleinerman RA, et al. Variation of second cancer risk by family history of retinoblastoma among long-term survivors. J Clin Oncol. 2012;30(9):950-7.
  35. Wong JR, et al. Risk of subsequent malignant neoplasms in long-term hereditary retinoblastoma survivors after chemotherapy and radiotherapy. J Clin Oncol. 2014;32(29):3284-90.
  36. Hwang SJ, et al. Germline p53 mutations in a cohort with childhood sarcoma: sex differences in cancer risk. Am J Hum Genet. 2003. 72(4):975-83.
  37. Olivier M, et al. Li-Fraumeni and related syndromes: correlation between tumor type, family structure, and TP53 genotype. Cancer Res. 2003. 63(20):6643-50.
  38. Birch JM, et al. Prevalence and diversity of constitutional mutations in the p53 gene among 21 Li-Fraumeni families. Cancer Res. 1994. 54(5):1298-304.
  39. American Congress of Obstetricians and Gynecologists Committee on Genetics. Committee Opinion No. 634: Hereditary cancer syndromes and risk assessment. Obstet Gynecol. June 2015. 125(6):1538-1543.
  40. Potrony M, et al. Prevalence of MITF p.E318K in patients with melanoma independent of the presence of CDKN2A causative mutations. JAMA Dermatol. 2016. 152(4):405-12.
  41. 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.