In the original languageTranslation into English
Unveiling the Complex SNP Landscape in Lymphoma Through Comprehensive Analysis for Future Functional Interpretation and Therapeutic Applications
Authors
Ethan Zhang
Rubric:Life Sciences
55
0
Share
55
0
Annotation
The successful management of lymphoma increasingly hinges on a deep understanding of its genomic underpinnings, especially for early detection and targeted treatment strategies. The current study focused on the identification and functional categorization of single nucleotide polymorphisms (SNPs) specifically in lymphoma patients. Utilizing whole-genome sequencing data sourced from the Sequence Read Archive[1] , we employed a rigorous analytical pipeline involving sequence alignment against the Homo sapiens chromosome 4 reference genome, followed by indexing, and variant calling. Our investigation led to the discovery of 1072 SNPs, a significant portion of which remain functionally uncharacterized. Among the categorized SNPs, variants were identified that have potential implications for gene regulation, splicing, and protein function. Statistical analyses revealed a significant association between these SNPs and the lymphoma cohort. Our findings offer nuanced insights into the complex genetic landscape of lymphoma and serve as a foundational platform for future research aimed at functional characterization and potential clinical applications. These identified SNPs could serve as potential biomarkers and contribute to the development of more effective diagnostic and therapeutic strategies for lymphoma.
Keywords
Single Nucleotide Polymorphisms (SNPs)
Lymphoma
TET2
Authors
Ethan Zhang
Rubric:Life Sciences
55
0
Share
55
0
References:
- 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
- Cong, B., Zhang, Q., & Cao, X. (2021). The function and regulation of TET2 in innate immunity and inflammation. Protein & cell, 12(3), 165–173. https://doi.org/10.1007/s13238-020-00796-6
- 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
- Degtyareva, A. O., Antontseva, E. V., & Merkulova, T. I. (2021). Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. International journal of molecular sciences, 22(12), 6454. https://doi.org/10.3390/ijms22126454
- Etebari, M., Navari, M., & Piccaluga, P. P. (2015). SNPs Array Karyotyping in Non-Hodgkin Lymphoma. Microarrays (Basel, Switzerland), 4(4), 551–569. https://doi.org/10.3390/microarrays4040551
- Halim, L., & Maher, J. (2020). CAR T-cell immunotherapy of B-cell malignancy: the story so far. Therapeutic advances in vaccines and immunotherapy, 8, 2515135520927164. https://doi.org/10.1177/2515135520927164
- Hu, L., Zhang, X., Li, H., Lin, S., & Zang, S. (2022, November 20). Targeting TET2 as a therapeutic approach for angioimmunoblastic T cell lymphoma. MDPI. https://www.mdpi.com/2072-6694/14/22/5699
- Jamil A, Mukkamalla SKR. Lymphoma. [Updated 2023 July 17]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK560826/
- Jiang S. (2020). Tet2 at the interface between cancer and immunity. Communications biology, 3(1), 667. https://doi.org/10.1038/s42003-020-01391-5
- Jiraskova K, Hughes DJ, Brezina S, Gumpenberger T, Veskrnova V, Buchler T, Schneiderova M, Levy M, Liska V, Vodenkova S, et al. Functional Polymorphisms in DNA Repair Genes Are Associated with Sporadic Colorectal Cancer Susceptibility and Clinical Outcome. International Journal of Molecular Sciences. 2019; 20(1):97. https://doi.org/10.3390/ijms20010097
- Key statistics for Non-Hodgkin Lymphoma. American Cancer Society. (2023). http://www.cancer.org/cancer/types/non-hodgkin-lymphoma/about/key-statistics.html#:~:text=The%20American%20Cancer%20Society%27s%20estimates,11%2C780%20males%20and%208%2C400%20females).
- 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
- Lymphoma-patient version. National Cancer Institute. (2023). http://www.cancer.gov/types/lymphoma
- National Center for Biotechnology Information (NCBI). (2021). SRA Toolkit v2.10.7. Retrieved from https://github.com/ncbi/sra-tools
- NHL staging. https://www.lls.org/lymphoma/non-hodgkin-lymphoma/diagnosis/nhl-staging. (2023). https://www.lls.org/lymphoma/non-hodgkin-lymphoma/diagnosis/nhl-staging
- Non-hodgkin lymphoma stages: Staging Non-Hodgkin Lymphoma. Staging Non-Hodgkin Lymphoma | American Cancer Society. (n.d.). https://www.cancer.org/cancer/types/non-hodgkin-lymphoma/detection-diagnosis-staging/staging.html
- Philip, M., Schietinger, A. CD8+ T cell differentiation and dysfunction in cancer. Nat Rev Immunol 22, 209–223 (2022). https://doi.org/10.1038/s41577-021-00574-3
- R-CHOP: Combination chemotherapy cancer treatment. City of Hope. (2022, June 14). https://www.cancercenter.com/treatment-options/r-chop#:~:text=Doctors%20use%20R%2DCHOP%20to,other%20cancer%20drugs%20and%20treatments
- Shahrabi, S., Ghanavat, M., Behzad, M. M., Purrahman, D., & Saki, N. (2020). CD markers polymorphisms as prognostic biomarkers in hematological malignancies. Oncology reviews, 14(2), 466. https://doi.org/10.4081/oncol.2020.466
- Shastry B. S. (2009). SNPs: impact on gene function and phenotype. Methods in molecular biology (Clifton, N.J.), 578, 3–22. https://doi.org/10.1007/978-1-60327-411-1_1
- Shi, D.-Q., Ali, I., Tang, J., & Yang, W.-C. (2017, July 5). New insights into 5hmc DNA modification: Generation, distribution and function. Frontiers. https://www.frontiersin.org/articles/10.3389/fgene.2017.00100/full
- Single nucleotide polymorphisms (snps). Genome.gov. (n.d.). https://www.genome.gov/genetics-glossary/Single-Nucleotide-Polymorphisms
- Stages of lymphoma. moffitt. (2023). http://www.moffitt.org/cancers/lymphomas-hodgkin-and-non-hodgkin/diagnosis/stages/.
- Tet2. Tet2 - My Cancer Genome. (2017). https://www.mycancergenome.org/content/gene/tet2/
- Treating Non-Hodgkin Lymphoma: Non-Hodgkin Lymphoma Treatments. Non-Hodgkin Lymphoma Treatments | American Cancer Society. (2023). https://www.cancer.org/cancer/types/non-hodgkin-lymphoma/treating.html
- U.S. National Library of Medicine. (2023). Tet2 gene: Medlineplus Genetics. MedlinePlus. https://medlineplus.gov/genetics/gene/tet2/
- U.S. National Library of Medicine. (2023). Tet2 Tet methylcytosine dioxygenase 2 [homo sapiens (human)] - gene - NCBI. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/gene/54790
Other articles of the issue
