Optimization of weights and features in use of AHP for SNP prioritization

Date

2018

Author

Yılmaz, Arif

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Single Nucleotide Polymorphisms (SNP) holds a promise in identification of genomic footprints of complex diseases such as cancer and diabetes. However identification of SNPs associated to complex diseases is a challenging problem due to the high number and variety of SNPs present in individual genomes. Analysis of genome wide studies of SNP datasets mainly focus on statistical evidence. As there are close to hundred million SNPs in human genome, incorporating biological and functional knowledge about statistically significant SNPs provides valuable features for further selection of SNPs. Analytical Hierarchy Process (AHP) based SNP prioritization approach is a method developed for this purpose. However, AHP requires expert knowledge, which results in subjective decisions. In this work, we propose a novel approach for AHP design and optimization by utilizing Random Forest based AHP (RF-AHP) assessment on categories. We utilized the results of previously developed genomic model on Prostate Cancer. Proposed RF-AHP approach was compared with Delphi-AHP based method on Schizophrenia, Prostate Cancer, Type 2 Diabetes and Alzheimer’s disease genomic datasets and same performance was achieved. Additionally, RegulomeDB database was integrated to RF-AHP. While similar performance was obtained in most of the datasets better prioritization scoring is achieved for Schizophrenia disease.

Subject Keywords

Single nucleotide polymorphisms., Prostate, Diabetes., Bioinformatics.

URI

http://etd.lib.metu.edu.tr/upload/12621874/index.pdf
https://hdl.handle.net/11511/27086

Collections

Graduate School of Informatics, Thesis

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Citation Formats

A. Yılmaz, “Optimization of weights and features in use of AHP for SNP prioritization,” Ph.D. - Doctoral Program, Middle East Technical University, 2018.