Melanoma Panel

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesCPT Code Copy CPT Codes
5473 BAP1 81479,81479 Add to Order
BRCA2 81216,81167
CDK4 81479,81479
CDKN2A 81404,81479
CHEK2 81479,81479
MITF 81479,81479
POT1 81479,81479
PTEN 81321,81323
RB1 81479,81479
TP53 81405,81479
Full Panel Price* $540
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
5473 Genes x (10) $540 81167, 81216, 81321, 81323, 81404, 81405, 81479(x14) Add to Order

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available.

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

Turnaround Time

The great majority of tests are completed within 20 days.

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Malignant melanoma, also known as cutaneous malignant melanoma, results from new and abnormal growth of melanocytes most frequently occurring in the skin, but can also occur in the eyes, ears, and gastrointestinal tract. Malignant melanoma is characterized by atypical or numerous nevi (moles) often present in non-sun exposed areas. These moles are often larger than other moles and display an abnormal shape or color. Melanomas can develop anywhere on the skin, but often start on the chest and back in men and on the legs in women. A major risk factor for melanoma is UV exposure, which damages the DNA of skin cells. Unlike common skin cancers which are associated with total cumulative UV exposure, melanomas are associated with intense intermittent exposure. Other risk factors include having a weakened immune system, being male, and being older. In the United States, there is an overall higher rate of melanoma in males after age 50, and the risk of melanoma is higher in women before age 50.

Germline variants in the CDKN2A gene have been known to be most associated with high risk susceptibility to malignant melanoma; however, germline variant frequencies in this gene among melanoma families is variable with 46% in French familial melanoma (Soufir et al. 1998. PubMed ID: 9425228), 18% in American familial melanoma (Soufir et al. 1998. PubMed ID: 9425228; Fitzgerald et al. 1996. PubMed ID: 8710906) and 8% in Swedish familial melanoma (Platz et al. 1997. PubMed ID: 9168184; Platz et al. 1998. PubMed ID: 9724087). Changes in the CDK4 gene are also responsible for a small fraction of familial melanoma (Debniak. 2004. PubMed ID: 20233466).

In addition to germline variants in high penetrance genes, multiple studies have documented familial predisposition to malignant melanoma, noting that an individual has a higher risk of developing melanoma if an immediate family member has had the disease (Tucker et al. 2002. PubMed ID: 12115352; Debniak. 2004. PubMed ID: 20233466; Nelson et al. 2009. PubMed ID: 19095153). This increased risk might be due to shared lifestyle of sun exposure, fair skin, certain genetic variants, or a combination of these factors.

Genetics

Melanoma is inherited in an autosomal dominant manner (Greene et al. 1983. PubMed ID: 6577466; Debniak. 2004. PubMed ID: 20233466). The locus for susceptibility for cutaneous malignant melanoma-1 (CMM1) was mapped to chromosome 1p36 (Cannon-Albright et al. 1990. PubMed ID: 2339690). To our knowledge, no gene of interest has been mapped to the CMM1 locus that is implicated in susceptibility to malignant melanoma-1. Subsequently, several other susceptibility loci were identified including CMM2 caused by variants in the CDKN2A gene; CMM3 caused by variants in CDK4; CMM4 mapped to chromosome 1p22; CMM5 caused by variants in MC1R gene; CMM6 caused by variants in XRCC3 gene; CMM7 mapped to chromosome 20q11; CMM8 caused by variants in MITF; CCM9 caused by variants in TERT; and CCM10 caused by variants in POT1. Though most familial cases of melanoma are a result of variants in CDKN2A, variants in CDK4 and RB1 have also been identified in familial melanoma families (Nelson et al. 2009. PubMed ID: 19095153).

The cyclin-dependent kinase inhibitor 2A (CDKN2A) gene encodes proteins that regulate two critical cell cycle regulatory pathways, namely TP53 and RB1. Two major separate but related proteins are produced from the CDKN2A gene as a result of shared coding regions and alternate reading frames: p16(INK4) which functions to inhibit CDK4/6-mediated phosphorylation of the Rb protein (active in dephosphorylated state), and p14(ARF) that binds MDM2, the p53-stabilizing protein, thereby inhibiting its function of marking proteins for degradation through ubiquitination (Nelson et al. 2009. PubMed ID: 19095153). TP53 functions to sense DNA damage and allow for repair, as well as to activate cellular apoptosis. Decreased levels of TP53 result in genetic instability and lead to a higher risk of melanoma in individuals with disruptions to the CDKN2A gene (Nelson et al. 2009. PubMed ID: 19095153). p16(INK4a) is formed by the fusion of exon 1α with exons 2 and 3, while p14(ARF) originated through alternate splicing of exon 1B with exons 2 and 3 (Nelson et al. 2009. PubMed ID: 19095153).

Tumor Protein p53 (TP53) encodes p53, the well-studied, ubiquitously expressed DNA-binding protein that plays significant roles in regulation of the cell cycle, DNA repair and programmed cells death. TP53 has 2 transcriptional start sites in exon 1, and alternative splicing occurs in intron 2 and between exon 9 and 10 (Bourdon et al. 2005. PubMed ID: 16131611). Germline TP53 pathogenic variants are found in patients with hereditary Li-Fraumeni syndrome, leading to early onset of several cancers, including melanoma (Platz et al. 1998. PubMed ID: 9724087).

Phosphatase and Tensin homolog deleted from chromosome 10 (PTEN) encodes a dual lipid and protein phosphatase. Loss of cancer suppressor genes located on chromosome 10 is highly implicated in melanoma tumorigenesis and is reported to contribute to 30-60% of non-inherited melanomas (Stahl et al. 2003. PubMed ID: 12782594). The 3’ end of exon 8 is subject to alternative splicing (Sharrard et al. 2000. PubMed ID: 11121587). PTEN also has a processed pseudogene PTENP1 that also exerts a tumor suppressive function (Poliseno et al. 2010. PubMed ID: 20577206).

BRCA2 is a tumor suppressor gene that is associated with a high risk for breast and ovarian cancer. Melanoma risk is elevated in some families with pathogenic variants in BRCA2 (Van Aperen et al. 2005. PubMed ID: 16141007). The most commonly reported cancers after breast and ovarian with BRCA2 variants are pancreas, prostate and melanoma (Mersch et al. 2015. PubMed ID: 25224030).

Microphthalmia-Associated Transcription Factor (MITF) is a basic helix-loop-helix-leucine zipper protein, and a melanocyte-specific transcription factor (Hartman and Czyz. 2015. PubMed ID: 25433395). It has been shown to play important developmental roles in various cell types including neural crest-derived melanocytes and optic cup-derived retinal epithelial cells (Fuse et al. 1999. PubMed ID: 10578055). It also helps to control the development and function of melanocytes which allow for the production of melanin that contributes to hair, eye and skin color. MITF acts as a melanoma oncogene, and controls the expression of CDKN2A/p16(INK4a) which has key roles in melanoma development. The germline missense variant c.952G>A (p.Glu318Lys) occurs at high frequency in patients affected with melanoma and renal cell carcinoma, and a >4 fold relative risk for melanoma observed in groups carrying the p.Glu318Lys variant compared to controls (Bertolotto et al. 2011. PubMed ID: 22012259; Yokoyama et al. 1999. PubMed ID: 22080950).

CDK4 is a protein-serine kinase that allows for orderly progression through the cell cycle. CDK4 encodes the cyclin dependent kinase 4 protein which is inhibited by p16(INK4a). Variants in CDK4 allow cells to skip the G1/S cell cycle checkpoint, thereby leading to uncontrolled cell proliferation (Ibrahim et al. 2009. PubMed ID: 19400696). Alterations in CDK4 are responsible for a very small proportion of familial melanoma (Debniak. 2004. PubMed ID: 20233466). The most common variants in CDK4 that are known to be involved in melanoma occur in codon 24 (p.Arg24Cys and p.Arg24His) (Soufir et al. 1998. PubMed ID: 9425228). When the amino acid substitutions occur, CDK4 is resistant to the inhibition of p16(INK4a) resulting in the phosphorylation of the Rb protein, allowing for the release of transcription factor E2F, and further resulting in uncontrolled cell proliferation (Ibrahim et al. 2009. PubMed ID: 19400696).

BRCA1-Associated Protein 1 (BAP1) gene encodes the deubiquitinating enzyme, nuclear ubiquitin carboxy-terminal hydrolase. It contains BRCA1 and BARD1 binding domains that together form a tumor suppressor heterodimeric complex. BAP1 has roles in chromatin dynamics, DNA damage response and cell cycle regulation (Goldstein et al. 2011. PubMed ID: 21956388). Germline variants in BAP1 have been reported to cause several types of cancer including uveal melanoma, cutaneous melanoma, non-melanoma skin, ovarian, breast, pancreatic, lung carcinoma and meningiomas.

Retinoblastoma 1 (RB1) is a tumor suppressor gene and a negative regulator of the cell cycle through repression of transcription of genes needed in S-phase. Retinoblastoma is an autosomal dominant disorder, and about 40% of cases are inherited or caused by germline variants in the RB1 gene. Families have also been reported with variants in the RB1 gene with an increased risk of melanoma. Germline variants in RB1 disrupt the ability of the RB1 protein to bind E2F and prevent unregulated cell division. It has been shown that though retinoblastoma is the most severe phenotype for carriers of RB1 variants, individuals who survive retinoblastoma tumors are at a 4-80 relative risk of developing melanoma later in life (Chin et al. 2006. PubMed ID: 16912270).

CHEK2 is involved in recognizing double-strand breaks in DNA, and allows for activation of downstream targets, such as p53 and BRCA2 (Weischer et al. 2012. PubMed ID: 2195612). Variants in CHEK2 have been frequently found in patients who have hereditary breast cancer, but do not have detectable variants in BRCA1 and BRCA2 (Desrichard et al. 2011. PubMed ID: 22114986), but has also been shown to associate with melanoma (Weischer et al. 2012. PubMed ID: 21956126). CHEK2 is upregulated in response to UV exposure, suggesting a role for the protein in control of UV damage (Yajima et al. 2009. PubMed ID: 19071136; Weischer et al. 2012. PubMed ID: 21956126). The CHEK2 c.1100delC variant has been shown to increase the risk of malignant melanoma ~2 fold in patients who are heterozygous for this variant, as these individuals have an impaired ability to repair DNA double-strand breaks induced by UV radiation (Weischer et al. 2012. PubMed ID: 21956126).

POT1 encodes a protein that is widely conserved across eukaryotic species and is associated with the telomere shelterin complex that regulates the protection of telomeres by preventing incorrect processing of chromosome ends. Studies have identified POT1 variants in individuals affected with malignant melanoma (Shi et al. 2014. PubMed ID: 24686846; Robles-Espinoza et al. 2014. PubMed ID: 24686849; Wilson et al. 2017. PubMed ID: 28389767). To date, approximately 15 missense variants have been reported to be associated with melanoma (Human Gene Mutation Database).

See individual gene test descriptions for further information on molecular biology of gene products and mutation spectra.

Testing Strategy

For this Next Generation Sequencing (NGS) test, sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments.

For Sanger sequencing, polymerase chain reaction (PCR) is used to amplify targeted regions. After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

This panel typically provides ≥98% coverage of all coding exons of the genes listed, plus ~10 bases of flanking noncoding DNA. We define coverage as ≥20X NGS reads or Sanger sequencing.

Clinical Sensitivity - Sequencing and CNV

Genes tested in this panel have been associated with cutaneous malignant melanoma. Up to 50% of familial melanoma cases have causative germline variants in CDKN2A, and there is a 1-3% chance that an individual with primary melanoma has a causative germline variant in CDKN2A (Nelson et al. 2009. PubMed ID: 19095153; Ibrahim et al. 2009. PubMed ID: 19400696). CDKN2A variants were detected in 46%, 18%, and 8% of French, US and Swedish familial melanoma cases, respectively (Platz et al. 1997. PubMed ID: 9168184; Platz et al. 1998. PubMed ID: 9724087; Debiak. 2004. PubMed ID: 20233466). One study determined that 18% of men over age 50 with invasive melanoma are due to abnormal expression of p53 (Whiteman et al. 1998. PubMed ID: 9714052). Melanoma cell lines have been shown to contain approximately 10% of inactivating variants in PTEN (Stahl et al. 2003. PubMed ID: 12782594). The prevalence of causative variants in BRCA2 is 3% in patients with familial ocular melanoma (Scott et al. 2002. PubMed ID: 12385017; Debniak. 2004. PubMed ID: 20233466). MITF variant p.Glu318Lys was detected in 2.2% of melanoma prone families (n=270) (Yokoyama et al. 1999. PubMed ID: 22080950). The Geno-Mel study revealed that only 2% of families were carriers of CDK4 variants (Goldstein et al. 2006. PubMed ID: 17047042). Clinical sensitivity of BAP1 in malignant melanoma is unknown. Clinical sensitivity for detecting RB1 in retinoblastoma is ~95% (Rushlow et al. 2009. PubMed ID: 19280657), and is unknown at this time for malignant melanoma. Germline POT1 variants were identified in ~ 4% of melanoma patients who were negative for variants in CDKN2A or CDK4 (Robles-Espinoza. 2014. PubMed ID: 24686849). Therefore, a pathogenic variant in one of the ten genes in this panel would be expected in ~2-50% of individuals with a personal or family history of malignant melanoma.

Indications for Test

Candidates for this test are Individuals who have multiple family members with melanoma. Some members of the melanoma families may have other forms of cancer, particularly pancreatic cancer (Goldstein et al. 2006. PubMed ID:17047042). In such families, it is best to test an affected individual first. Other candidates are patients with multiple primary melanomas. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.

Genes

Official Gene Symbol OMIM ID
BAP1 603089
BRCA2 600185
CDK4 123829
CDKN2A 600160
CHEK2 604373
MITF 156845
POT1 606478
PTEN 601728
RB1 614041
TP53 191170
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
PGxome®

Citations

  • Bertolotto et al. 2011. PubMed ID: 22012259
  • Bourdon et al. 2005. PubMed ID: 16131611
  • Cannon-Albright et al. 1990. PubMed ID: 2339690
  • Chin et al. 2006. PubMed ID: 16912270
  • Debniak. 2004. PubMed ID: 20233466
  • Desrichard et al. 2011. PubMed ID: 22114986
  • Fitzgerald et al. 1996. PubMed ID: 8710906
  • Fuse et al. 1999. PubMed ID: 10578055
  • Goldstein et al. 2006. PubMed ID: 17047042
  • Goldstein et al. 2011. PubMed ID: 21956388
  • Greene et al. 1983. PubMed ID: 6577466
  • Hartman and Czyz. 2015. PubMed ID: 25433395
  • Human Gene Mutation Database (Bio-base).
  • Ibrahim et al. 2009. PubMed ID: 19400696
  • Mersch et al. 2015. PubMed ID: 25224030
  • Nelson et al. 2009. PubMed ID: 19095153
  • Platz et al. 1997. PubMed ID: 9168184
  • Platz et al. 1998. PubMed ID: 9724087
  • Poliseno et al. 2010. PubMed ID: 20577206
  • Robles-Espinoza et al. 2014. PubMed ID: 24686849
  • Rushlow et al. 2009. PubMed ID: 19280657
  • Scott et al. 2002. PubMed ID: 12385017
  • Sharrard et al. 2000. PubMed ID: 11121587
  • Shi et al. 2014. PubMed ID: 24686846
  • Soufir et al. 1998. PubMed ID: 9425228
  • Stahl et al. 2003. PubMed ID: 12782594
  • Tucker et al. 2002. PubMed ID: 12115352
  • Van Aperen et al. 2005. PubMed ID: 16141007
  • Weischer et al. 2012. PubMed ID: 21956126
  • Whiteman et al. 1998. PubMed ID: 9714052
  • Wilson et al. 2017. PubMed ID: 28389767
  • Yajima et al. 2009. PubMed ID: 19071136
  • Yokoyama et al. 1999. PubMed ID: 22080950

Ordering/Specimens

Ordering Options

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

Specimen Types

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