Services

Omics Services

Genomics
Epigenomics
Single Cell/Spatial Omics
Metagenomics
Transcriptomics
Proteomics
Bioinformatics
Pre-made Library
CLIA Lab Services
Clinical Genetic Testing
Capabilities
Resources
Promotions
Support
About Us
Let's Connect
Services

Omics Services

Research Services
Genomics
Epigenomics
Single Cell/Spatial Omics
Metagenomics
Transcriptomics
Clinical Services
CLIA Lab Services
Clinical Genetic Testing
Capabilities
Resources
Promotions
Support
About Us
Let's Connect
CLINICAL CAPABILITIES // Genetic testing

Melanoma

Identify genetic risk factors and causes of melanoma.

Clinical at Psomagen

Who Would Benefit from Melanoma Genetic Testing?

1

A person with a strong family history of certain types of cancer

Determine if they carry a gene mutation that increases their risk. If they do have an inherited mutation, they might want to have screening tests to look for cancer early, or even take steps to try to lower their risk.

2

A person already diagnosed with cancer

This is especially true if there are other factors to suggest the cancer might have been caused by an inherited mutation (such as a strong family history or if the cancer was diagnosed at a young age). Genetic testing might show if the person has a higher risk of developing cancer. It can also help other family members decide if they want to be tested for the mutation.  

3

Family members of a person known to have an inherited gene mutation that increases their risk of cancer

Testing can help them know if they need screening tests to look for cancer early, or if they should take steps to try to lower their risk.

How Do I Order a Test?

A printed copy of the requisition form must be submitted with the specimen if you are not placing your order through the online portal. You can find and print a copy of the requisition form here. If you need to modify your order, please contact client services.

Melanoma Panel Best Practices

Preferred Specimen

2mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)

Alternate Specimens

  • Saliva
  • Buccal swab
  • gDNA
Let's get started!

How to Ship Your Samples

Follow IATA Regulations

Please note that Psomagen sample collection kits are built to protect the samples from being damaged during transport and to comply with the International Air Transport Association (IATA) regulation. If you are using packaging other than that provided by Psomagen, please make sure to follow the "three layers of packaging" rule to avoid the risk of having the package destroyed by the courier:

  • A primary sample receptacle sealed (collection tube).
  • A leak-proof specimen bag containing absorbent material.
  • An outer packaging that meets the local postal regulations and is labeled as “Exempt Human Specimen.”

For more information please refer to page 187 of IATA Dangerous Goods Regulation.

Additional Shipment Requirements

For saliva, ship at room temperature (overnight shipping is not necessary).

For blood, we recommend using overnight shipping the same day that the blood is collected.

  • Blood can be kept at room temperature for up to 48 hours.
  • We request that blood is refrigerated no longer than two weeks.
  • Please do not freeze blood as deletion/duplication analysis is not supported for frozen or partially frozen blood.

Please ship the specimen in a crush-proof container via FedEx Priority Overnight (in accordance with the FedEx Packaging Guidelines for Clinical Samples.

Our US Shipping Address

Attn: Clinical Laboratory Testing Personnel
Psomagen Inc.
1330 Piccard Drive, Ste 103
Rockville, MD 20850

Test for 14 related genes

Gene List

BAP1
BRCA2
CDK4
CDKN2A
CHEK2
MC1R
MITF
MUTYH
POT1
PTEN
RB1
SLC45A2
TP53
TYR
 

Test Methodology and Limitations

DNA sequencing involves the extraction of genomic DNA from specimens collected in approved containers and provided the specimen meets required sample minimum quantity (e.g. volume, weight, etc). This is followed by quantification and qualification to ensure the adequacy of amount and purity for sequencing. Subsequently, whole exome sequencing is conducted on an IlluminaTM short read sequencing (SRS) platform (e.g., NovaSeq X PlusTM) at Psomagen, Inc.’s laboratories (CLIA # 21D2062464, CAP # 8742212).

DNA sequence alignment, variant calling, and variant filtering are performed utilizing the Illumina DRAGENTM bioinformatics pipeline (version 4.2.4.) and various tool sets, which align reads to the human reference genome (GRCh38) and identify single nucleotide variants (SNVs) and small insertions/deletions (InDels). Variant annotations are performed using a pipeline available in Fabric Enterprise. Variant review and interpretation are conducted according to the standards and guidelines set forth by the American College of Medical Genetics and Genomics (Richards S, et al., Genet Med., 2015) by Fabric Clinical Labs (CLIA # 45D2281059, CAP # 9619501). Only variants classified as pathogenic or likely pathogenic are reported. The following quality filters are applied to all variants: coverage <40x, allele balance outside 0.3-0.7.

Variants in the following genes are reported: BAP1, BRCA2, CDK4, CDKN2A, CHEK2, MC1R, MITF, MUTYH, POT1, PTEN, RB1, SLC45A2, TP53, TYR. 

This test is designed to detect single nucleotide variants (SNVs) and small insertions/deletions (InDels). Next-Generation Sequencing (NGS) coverage may vary across the genome, potentially resulting in missed variants in regions with low coverage depth. Some genetic abnormalities may be undetectable with the current version of this test. While the DRAGEN bioinformatics pipeline demonstrates high accuracy for variant calling, there remains a possibility of false positive or false negative results due to variant interpretation which relies on current scientific knowledge and available databases. This may lead to the reclassification of reported variants as new information emerges from ongoing research and is updated in the ACMG guidelines. Furthermore, systematic chemical, computational, or human errors may contribute to false positives or false negatives of DNA variants. For any reported variants, confirmation by orthogonal technology and subsequent consultation with a genetic counselor or qualified healthcare provider can help to establish definitive risk. This result should be considered preliminary until such confirmation has been performed.

Clinical management for this individual should be based on personal and family history, along with other relevant information. If considered relevant to this individual’s clinical presentation and/or family history, targeted testing of appropriate family members of this individual for the reported variants may help to interpret these results. For assistance with the interpretation of these results, healthcare professionals may contact Psomagen directly at (301) 251-1007 or support@psomagen.com.

More Resources

  1. Ransohoff KJ, Jaju PD, Tang JY, Carbone M, Leachman S, Sarin KY. Familial skin cancer syndromes increased melanoma risk. Journal of the American Academy of Dermatology. 2016;74(3):423–434. doi: 10.1016/j.jaad.2015.09.070. [PubMed] [CrossRef] [Google Scholar]

  2. Read J, Wadt KAW, Hayward NK. Melanoma genetics. Journal of Medical Genetics. 2015;53:1–14. doi: 10.1136/jmedgenet-2015-103150. [PubMed] [CrossRef] [Google Scholar]

  3. Goldstein AM, Chan M, Harland M, Hayward NK, Demenais F, Bishop DT, et al. Features associated with germline CDKN2A mutations: a GenoMEL study of melanoma-prone families from three continents. Journal of Medical Genetics. 2007;44(2):99–106. doi: 10.1136/jmg.2006.043802. [PMC free article][PubMed] [CrossRef] [Google Scholar]

  4. Taber JM, Aspinwall LG, Stump TK, Kohlmann W, Champine M, Leachman SA. Genetic test reporting enhances understanding of risk information and acceptance of prevention recommendations compared to family history-based counseling alone. Journal of Behavioral Medicine. 2015;38(5):740–753. doi: 10.1007/s10865-015-9648-z. [PMC free article][PubMed] [CrossRef] [Google Scholar]

  5. Aspinwall LG, Taber JM, Kohlmann W, Leaf SL, Leachman SA. Unaffected family members report improvements in daily routine sun-protection 2 years following melanoma genetic testing. Genetics in Medicine. 2014;16:356–372. doi: 10.1038/gim.2014.37. [PMC free article][PubMed] [CrossRef] [Google Scholar]

  6. Goldstein AM, Chan M, Harland M, Gillanders EM, Hayward NK, Avril MF, et al. High-risk melanoma susceptibility genes and pancreatic cancer, neural system tumors, and uveal melanoma across GenoMEL. Cancer Research. 2006;66(20):9818–9828. doi: 10.1158/0008-5472.CAN-06-0494. [PubMed] [CrossRef] [Google Scholar]

  7. Eliason MJ, Larson AA, Florell SR, Zone JJ, Cannon-Albright LA, Samlowski WE, Leachman SA. Population-based prevalence of CDKN2A mutations in Utah melanoma families. The Journal of Investigative Dermatology. 2006;126(3):660–666. doi: 10.1038/sj.jid.5700094. [PubMed] [CrossRef] [Google Scholar]

  8. Hussussian CJ, Struewing JP, Goldstein AM, Higgins PA, Ally DS, Sheahan MD, et al. Germline p16 mutations in familial melanoma. Nature Genetics. 1994;8:15–21. doi: 10.1038/ng0994-15. [PubMed] [CrossRef] [Google Scholar]

  9. Kamb A, Shattuck-Eidens D, Eeles R, Liu Q, Gruis NA, Ding W, et al. Analysis of the p16 gene (CDKN2) as a candidate for the chromosome 9p melanoma susceptibility locus. Nature Genetics. 1994;8(1):22–26. doi: 10.1038/ng0994-22. [PubMed] [CrossRef] [Google Scholar]

  10. Zhang Y, Xiong Y, Yarbrough WG. ARF promotes MDM2 degradation and stabilizes p53: ARF-INK4a locus deletion impairs both the Rb and p53 tumor suppression pathways. Cell. 1998;92(6):725–734. doi: 10.1016/S0092-8674(00)81401-4. [PubMed] [CrossRef] [Google Scholar]

  11. Goldstein AM. Familial melanoma, pancreatic cancer and germline CDKN2A mutations. Human Mutation. 2004;23(September 2003):630. doi: 10.1002/humu.9247. [PubMed] [CrossRef] [Google Scholar]

  12. Vasen HFA, Gruis NA, Frants RR, Van Der Velden PA, Hille ETM, Bergman W. Risk of developing pancreatic cancer in families with familial atypical multiple mole melanoma associated with a specific 19 deletion of p16 (p16-Leiden) International Journal of Cancer. 2000;87(6):809–811. doi: 10.1002/1097-0215(20000915)87:6<809::AID-IJC8>3.0.CO;2-U. [PubMed] [CrossRef] [Google Scholar]

  13. Lynch HT, Shaw TG. Familial atypical multiple mole melanoma (FAMMM) syndrome: history, genetics, and heterogeneity. Familial Cancer. 2016;15(3):487–491. doi: 10.1007/s10689-016-9888-2. [PubMed] [CrossRef] [Google Scholar]

  14. Yang XR, Rotunno M, Xiao Y, Ingvar C, Helgadottir H, Pastorino L, et al. Multiple rare variants in high-risk pancreatic cancer-related genes may increase risk for pancreatic cancer in a subset of patients with and without germline CDKN2A mutations. Human Genetics. 2016;135(11):1241–1249. doi: 10.1007/s00439-016-1715-1. [PMC free article][PubMed] [CrossRef] [Google Scholar]

  15. Soura E, Eliades PJ, Shannon K, Stratigos AJ, Tsao H. Hereditary melanoma: update on syndromes and management genetics of familial atypical multiple mole melanoma syndrome. Journal of the American Academy of Dermatology. 2016;74(3):411–420. doi: 10.1016/j.jaad.2015.08.037. [PMC free article][PubMed] [CrossRef] [Google Scholar]

  16. Borg A, Sandberg T, Nilsson K, Johannsson O, Klinker M, Måsbäck A, et al. High frequency of multiple melanomas and breast and pancreas carcinomas in CDKN2A mutation-positive melanoma families. Journal of the National Cancer Institute. 2000;92(15):1260–1266. doi: 10.1093/jnci/92.15.1260. [PubMed] [CrossRef] [Google Scholar]

  17. Ghiorzo P, Fornarini G, Sciallero S, Battistuzzi L, Belli F, Bernard L, et al. CDKN2A is the main susceptibility gene in Italian pancreatic cancer families. Journal of Medical Genetics. 2012;49(3):164–170. doi: 10.1136/jmedgenet-2011-100281. [PubMed] [CrossRef] [Google Scholar]

  18. Ghiorzo P. Genetic predisposition to pancreatic cancer. World Journal of Gastroenterology. 2014;20(31):10778. doi: 10.3748/wjg.v20.i31.10778. [PMC free article][PubMed] [CrossRef] [Google Scholar]

  19. Leachman SA, Carucci J, Kohlmann W, Banks KC, Asgari MM, Bergman W, et al. Selection criteria for genetic assessment of patients with familial melanoma. Journal of the American Academy of Dermatology. 2009;61(4):677.e1–677.14. doi: 10.1016/j.jaad.2009.03.016. [PMC free article][PubMed] [CrossRef] [Google Scholar]

  20. Bahuau M, Vidaud D, Jenkins RB, Bièche I, Kimmel DW, Assouline B, et al. Germ-line deletion involving the INK4 locus in familial proneness to melanoma and nervous system tumors. Cancer Research. 1998;58(11):2298–2303. [PubMed] [Google Scholar]

Our Certifications

CLIA ID number: 21D2062464
CAP ID number: 8742212