<abstract xmlns="http://www.w3.org/1999/xhtml">

<p>Diffuse large B-cell lymphoma (DLBCL) is a common B-lymphocyte tumor in dogs, making up 60-70% of cases. We assessed the utility of DNA methylation data for the diagnostic classification of DLBCL in dogs. We also assessed the utility of the classification features identified in cDLBCL for diagnostic classification of DLBCL in humans. The GSE94913 cDLBCL DNA methylation dataset from the Gene Expression Omnibus (GEO) was used for analysis. Differential methylation analysis was performed between the 37 cDLBCL and seven control lymph node samples in the dataset. 1701 differentially methylated probes were identified between the cDLBCL and control lymph nodes groups. Applying recursive feature elimination on the 1701 significant probes, 20 probes were selected for machine learning classification tasks. The methylation values of these 20 probes were used to build an SVM model and create the training and testing set. 100% of the test samples were accurately classified by the SVM model. The diagnostic classification utility of the identified differentially methylated CpGs/CDS was also assessed in humans using the GSE28094 human DLBCL dataset. 95% of 98 DLBCL and leukocyte samples obtained from this dataset was correctly classified using clustering techniques on 11 CpG sites of 5 genes (<italic>ERBB4</italic>, <italic>IGF2</italic>, <italic>PGF</italic>, <italic>PITX2</italic>, <italic>TJP1</italic>). The utility of DNA methylation data for the diagnostic classification of DLBCL in dogs is demonstrated. Further exploration of this data type for potential biomarker discovery in cDLBCL is necessary.</p>
</abstract>

Diffuse large B-cell lymphoma (DLBCL) is a common B-lymphocyte tumor in dogs, making up 60-70% of cases. We assessed the utility of DNA methylation data for the diagnostic classification of DLBCL in dogs. We also assessed the utility of the classification features identified in cDLBCL for diagnostic classification of DLBCL in humans. The GSE94913 cDLBCL DNA methylation dataset from the Gene Expression Omnibus (GEO) was used for analysis. Differential methylation analysis was performed between the 37 cDLBCL and seven control lymph node samples in the dataset. 1701 differentially methylated probes were identified between the cDLBCL and control lymph nodes groups. Applying recursive feature elimination on the 1701 significant probes, 20 probes were selected for machine learning classification tasks. The methylation values of these 20 probes were used to build an SVM model and create the training and testing set. 100% of the test samples were accurately classified by the SVM model. The diagnostic classification utility of the identified differentially methylated CpGs/CDS was also assessed in humans using the GSE28094 human DLBCL dataset. 95% of 98 DLBCL and leukocyte samples obtained from this dataset was correctly classified using clustering techniques on 11 CpG sites of 5 genes (ERBB4, IGF2, PGF, PITX2, TJP1). The utility of DNA methylation data for the diagnostic classification of DLBCL in dogs is demonstrated. Further exploration of this data type for potential biomarker discovery in cDLBCL is necessary.

Exploring DNA methylation data for diagnostic classification of Diffuse large B-cell lymphoma in Dogs

Department of Zoology and Environmental Biology

Annals of Science and Technology

This work is licensed under the Creative Commons Attribution 4.0 International License.

Diffuse large B-cell lymphoma (DLBCL) is a common B-lymphocyte tumor in dogs, making up 60-70% of cases. We assessed the utility of DNA methylation data for...

Exploring DNA methylation data for diagnostic classification of Diffuse large B-cell lymphoma in Dogs

Published Online: May 27, 2023

Page range: 8 - 15

Received: May 13, 2022

Accepted: Dec 24, 2022

DOI: https://doi.org/10.2478/ast-2023-0002

Keywords
Biomarkers, Classification, DNA methylation, Dogs, Machine learning

© 2023 Abdulazeez Giwa et al., published by Sciendo

This work is licensed under the Creative Commons Attribution 4.0 International License.

Exploring DNA methylation data for diagnostic classification of Diffuse large B-cell lymphoma in Dogs

Published Online: May 27, 2023

Page range: 8 - 15

Received: May 13, 2022

Accepted: Dec 24, 2022

DOI: https://doi.org/10.2478/ast-2023-0002

KeywordsBiomarkers, Classification, DNA methylation, Dogs, Machine learning

© 2023 Abdulazeez Giwa et al., published by Sciendo

This work is licensed under the Creative Commons Attribution 4.0 International License.

Keywords
Biomarkers, Classification, DNA methylation, Dogs, Machine learning