Analyzing Single Nucleotide Polymorphisms and Their Chromosomal Distribution to Unravel the Genetic Landscape of Melanoma

Authors

  • Angelina Huang Ridge High School
  • Roberto Aguilar

DOI:

https://doi.org/10.47611/jsrhs.v13i1.6297

Keywords:

Melanoma, Single Nucleotide Polymorphisms (SNPs), Genomic Variants, Personalized Medicine, Therapeutic Targets, Early Detection.

Abstract

Melanoma, a malignant skin cancer, continues to pose significant challenges in early detection, optimal treatment strategies, and understanding its etiology. This study aimed to elucidate the complex genetic landscape of melanoma by analyzing 2,641 Single Nucleotide Polymorphisms (SNPs) across 18 genomic variant categories within a melanoma cohort. The analysis revealed diverse genetic variations, including Missense and Frameshift Variants, with a significant number of unknown variants that require further exploration. A significant association (p < 0.05) was found between the identified variants and the melanoma cohort. The study's findings underscore the heterogeneous nature of melanoma and emphasize the potential need for personalized therapeutic approaches. This comprehensive study contributes valuable insights into melanoma's genetic landscape and holds promise for future interventions and personalized prevention and treatment strategies.

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References or Bibliography

Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Retrieved from http://www.bioinformatics.babraham.ac.uk/projects/fastqc

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. https://doi.org/10.1093/bioinformatics/btu170

Cannon-Albright, L. A., Teerlink, C. C., Farnham, J. M., Thomas, A. W., Zone, J. J., & Leachman, S. A. (2013). Linkage analysis of extended high-risk pedigrees replicates a cutaneous malignant melanoma predisposition locus on chromosome 9q21. The Journal of investigative dermatology, 133(1), 128–134. https://doi.org/10.1038/jid.2012.271

Centers for Disease Control and Prevention. (2023, April 18). What are the symptoms of skin cancer?. Centers for Disease Control and Prevention. https://www.cdc.gov/cancer/skin/basic_info/symptoms.htm#:~:text=Border%3A%20Is%20the%20border%20irregular,past%20few%20weeks%20or%20months%3F

Cunningham, F., Achuthan, P., Akanni, W., Allen, J., Amode, M. R., Armean, I. M., ... & Flicek, P. (2021). Ensembl 2021. Nucleic Acids Research, 49(D1), D884-D891. https://doi.org/10.1093/nar/gkaa942

Cust, A. E., Goumas, C., Vuong, K., Davies, J. R., Barrett, J. H., Holland, E. A., Schmid, H., Agha-Hamilton, C., Armstrong, B. K., Kefford, R. F., Mann, G. J., & Investigators, G. (2011). MC1R genotype as a predictor of early-onset melanoma, compared with self-reported and physician-measured traditional risk factors: An Australian case-control-family study. BMC cancer, 11, 283.

Deng, L., Xu, X., Li, Y., Yang, F., & Wei, Z. (2017). Exploration and practice of using exome sequencing in routine genetic diagnosis. Yi chuan= Hereditas, 39(11), 1033–1041.

Deng, N., Zhou, H., Fan, H., & Yuan, Y. (2017, November 7). Single nucleotide polymorphisms and cancer susceptibility. Oncotarget. https://www.oncotarget.com/article/22372/text/#:~:text=SNPs%20are%20located%20in%20gene,the%20individual%20SNPs%20are%20located

Gandini, S., Sera, F., Cattaruzza, M. S., Pasquini, P., Abeni, D., Boyle, P., & Melchi, C. F. (2005). Meta-analysis of risk factors for cutaneous melanoma: II. Sun exposure. European journal of cancer (Oxford, England: 1990), 41(1), 45–60.

Han, J., Kraft, P., Nan, H., Guo, Q., Chen, C., Qureshi, A., Hankinson, S. E., Hu, F. B., Duffy, D. L., Zhao, Z. Z., Martin, N. G., Montgomery, G. W., Hayward, N. K., Thomas, G., Hoover, R. N., & Chanock, S. J. (2008). A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. PLoS genetics, 4(5), e1000074.

Immune checkpoint inhibitors. National Cancer Institute. (n.d.). https://www.cancer.gov/about-cancer/treatment/types/immunotherapy/checkpoint-inhibitors

Immunotherapy for Melanoma. Pennmedicine.org. (n.d.). https://www.pennmedicine.org/cancer/types-of-cancer/melanoma/melanoma-treatments/melanoma-immunotherapy#:~:text=These%20medications%20help%20T%20cells,support%20the%20overall%20immune%20system.

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357-359. https://doi.org/10.1038/nmeth.1923

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. https://doi.org/10.1093/bioinformatics/btp352

Liu, X.-Y., Petska, S., & Shi, Y.-F. (2012). Recent Advances in Cancer Research and Therapy.

Mayo Foundation for Medical Education and Research. (2023, July 22). Melanoma. Mayo Clinic. https://www.mayoclinic.org/diseases-conditions/melanoma/symptoms-causes/syc-20374884#:~:text=Melanomas%20can%20develop%20anywhere%20on,your%20hands%20and%20fingernail%20beds.

Melanoma skin cancer statistics. Melanoma Skin Cancer Statistics | American Cancer Society. (n.d.). https://www.cancer.org/cancer/types/melanoma-skin-cancer/about/key-statistics.html

Menchaca, C. (2021, October 11). The cost of skin cancer: Diagnosis, treatment, and care. HealthMatch. https://healthmatch.io/skin-cancer/cost-of-skin-cancer-treatment

Morton, D. L., Essner, R., Kirkwood J. M., Wollman R. C. (2003). Home - books - NCBI.

National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/books

National Center for Biotechnology Information (NCBI). (2021). SRA Toolkit v2.10.7. Retrieved from https://github.com/ncbi/sra-tools

Radiation therapy for melanoma. Memorial Sloan Kettering Cancer Center. (1970, January 1). https://www.mskcc.org/cancer-care/types/melanoma/treatment/radiation-therapy-melanoma

Rossi, M., Pellegrini, C., Cardelli, L., Ciciarelli, V., Di Nardo, L., & Fargnoli, M. C. (2019, January 31). Familial melanoma: Diagnostic and management implications. Dermatology practical & conceptual. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368081/#:~:text=CDKN2A%20is%20the%20major%20high,early%20age%20at%20melanoma%20onset.

Shastry, B. S. (n.d.). SNPs: Impact on gene function and phenotype. Methods in molecular biology (Clifton, N.J.). https://pubmed.ncbi.nlm.nih.gov/19768584/#:~:text=They%20may%20influence%20promoter%20activity,and%20hence%20may%20produce%20disease

Skin cancer facts & statistics. The Skin Cancer Foundation. (2023, March 6). https://www.skincancer.org/skin-cancer-information/skin-cancer-facts/#:~:text=The%20annual%20cost%20of%20treating,and%20%243.3%20billion%20for%20melanoma.

Stages of melanoma. AIM at Melanoma Foundation. (2023, May 9). https://www.aimatmelanoma.org/stages-of-melanoma/

Strachan, T., & Read, A. P. (2015). Human Molecular Genetics (4th ed.). Garland Science.

Published

02-29-2024

How to Cite

Huang, A., & Aguilar, R. (2024). Analyzing Single Nucleotide Polymorphisms and Their Chromosomal Distribution to Unravel the Genetic Landscape of Melanoma. Journal of Student Research, 13(1). https://doi.org/10.47611/jsrhs.v13i1.6297

Issue

Section

HS Research Articles