Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics
Human leukocyte antigen (HLA) are essential components of the immune system that stimulate immune cells to provide protection and defense against cancer. Thousands of HLA alleles have been reported in the literature, but only a specific set of HLA alleles are present in an individual. The capability...
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Frontiers Media S.A.
2020-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00221/full |
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| author | Anjali Dhall Sumeet Patiyal Harpreet Kaur Harpreet Kaur Sherry Bhalla Chakit Arora Gajendra P. S. Raghava |
| author_facet | Anjali Dhall Sumeet Patiyal Harpreet Kaur Harpreet Kaur Sherry Bhalla Chakit Arora Gajendra P. S. Raghava |
| author_sort | Anjali Dhall |
| collection | DOAJ |
| description | Human leukocyte antigen (HLA) are essential components of the immune system that stimulate immune cells to provide protection and defense against cancer. Thousands of HLA alleles have been reported in the literature, but only a specific set of HLA alleles are present in an individual. The capability of the immune system to recognize cancer-associated mutations depends on the presence of a particular set of alleles, which elicit an immune response to fight against cancer. Therefore, the occurrence of specific HLA alleles affects the survival outcome of cancer patients. In the current study, prediction models were developed, using 401 cutaneous melanoma patients, to predict the overall survival (OS) of patients using their clinical data and HLA alleles. We observed that the presence of certain favorable superalleles like HLA-B∗55 (HR = 0.15, 95% CI 0.034–0.67), HLA-A∗01 (HR = 0.5, 95% CI 0.3–0.8), is responsible for the improved OS. In contrast, the presence of certain unfavorable superalleles such as HLA-B∗50 (HR = 2.76, 95% CI 1.284–5.941), HLA-DRB1∗12 (HR = 3.44, 95% CI 1.64–7.2) is responsible for the poor survival. We developed prediction models using key 14 HLA superalleles, demographic, and clinical characteristics for predicting high-risk cutaneous melanoma patients and achieved HR = 4.52 (95% CI 3.088–6.609, p-value = 8.01E-15). Eventually, we also provide a web-based service to the community for predicting the risk status in cutaneous melanoma patients (https://webs.iiitd.edu.in/raghava/skcmhrp/). |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-14T05:36:32Z |
| publishDate | 2020-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-579c125995c24fbd92e55c8371f7d89f2022-12-22T02:09:38ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-03-011110.3389/fgene.2020.00221514918Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical CharacteristicsAnjali Dhall0Sumeet Patiyal1Harpreet Kaur2Harpreet Kaur3Sherry Bhalla4Chakit Arora5Gajendra P. S. Raghava6Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaDepartment of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaDepartment of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaBioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, IndiaDepartment of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaDepartment of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaDepartment of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaHuman leukocyte antigen (HLA) are essential components of the immune system that stimulate immune cells to provide protection and defense against cancer. Thousands of HLA alleles have been reported in the literature, but only a specific set of HLA alleles are present in an individual. The capability of the immune system to recognize cancer-associated mutations depends on the presence of a particular set of alleles, which elicit an immune response to fight against cancer. Therefore, the occurrence of specific HLA alleles affects the survival outcome of cancer patients. In the current study, prediction models were developed, using 401 cutaneous melanoma patients, to predict the overall survival (OS) of patients using their clinical data and HLA alleles. We observed that the presence of certain favorable superalleles like HLA-B∗55 (HR = 0.15, 95% CI 0.034–0.67), HLA-A∗01 (HR = 0.5, 95% CI 0.3–0.8), is responsible for the improved OS. In contrast, the presence of certain unfavorable superalleles such as HLA-B∗50 (HR = 2.76, 95% CI 1.284–5.941), HLA-DRB1∗12 (HR = 3.44, 95% CI 1.64–7.2) is responsible for the poor survival. We developed prediction models using key 14 HLA superalleles, demographic, and clinical characteristics for predicting high-risk cutaneous melanoma patients and achieved HR = 4.52 (95% CI 3.088–6.609, p-value = 8.01E-15). Eventually, we also provide a web-based service to the community for predicting the risk status in cutaneous melanoma patients (https://webs.iiitd.edu.in/raghava/skcmhrp/).https://www.frontiersin.org/article/10.3389/fgene.2020.00221/fullcutaneous melanomasurvival analysisHLAsuperallelesHazard ratioregression |
| spellingShingle | Anjali Dhall Sumeet Patiyal Harpreet Kaur Harpreet Kaur Sherry Bhalla Chakit Arora Gajendra P. S. Raghava Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics Frontiers in Genetics cutaneous melanoma survival analysis HLA superalleles Hazard ratio regression |
| title | Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics |
| title_full | Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics |
| title_fullStr | Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics |
| title_full_unstemmed | Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics |
| title_short | Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics |
| title_sort | computing skin cutaneous melanoma outcome from the hla alleles and clinical characteristics |
| topic | cutaneous melanoma survival analysis HLA superalleles Hazard ratio regression |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00221/full |
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