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Cancer Risk Score Prediction Based on a Single-Nucleotide Polymorphism Network

OBJECTIVES: Genome-wide association studies (GWAS) are performed to study the associations between genetic variants with respect to certain phenotypic traits such as cancer. However, the method that is commonly used in GWAS assumes that certain traits are solely affected by a single mutation. We pro...

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Autores principales: Mahesworo, Bharuno, Budiarto, Arif, Hidayat, Alam Ahmad, Pardamean, Bens
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Korean Society of Medical Informatics 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9388919/
https://www.ncbi.nlm.nih.gov/pubmed/35982599
http://dx.doi.org/10.4258/hir.2022.28.3.247
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author Mahesworo, Bharuno
Budiarto, Arif
Hidayat, Alam Ahmad
Pardamean, Bens
author_facet Mahesworo, Bharuno
Budiarto, Arif
Hidayat, Alam Ahmad
Pardamean, Bens
author_sort Mahesworo, Bharuno
collection PubMed
description OBJECTIVES: Genome-wide association studies (GWAS) are performed to study the associations between genetic variants with respect to certain phenotypic traits such as cancer. However, the method that is commonly used in GWAS assumes that certain traits are solely affected by a single mutation. We propose a network analysis method, in which we generate association networks of single-nucleotide polymorphisms (SNPs) that can differentiate case and control groups. We hypothesize that certain phenotypic traits are attributable to mutations in groups of associated SNPs. METHODS: We propose a method based on a network analysis framework to study SNP-SNP interactions related to cancer incidence. We employed logistic regression to measure the significance of all SNP pairs from GWAS for the incidence of colorectal cancer and computed a cancer risk score based on the generated SNP networks. RESULTS: We demonstrated our method in a dataset from a case-control study of colorectal cancer in the South Sulawesi population. From the GWAS results, 20,094 pairs of 200 SNPs were created. We obtained one cluster containing four pairs of five SNPs that passed the filtering threshold based on their p-values. A locus on chromosome 12 (12:54410007) was found to be strongly connected to the four variants on chromosome 1. A polygenic risk score was computed from the five SNPs, and a significant difference in colorectal cancer risk was obtained between the case and control groups. CONCLUSIONS: Our results demonstrate the applicability of our method to understand SNP-SNP interactions and compute risk scores for various types of cancer.
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spelling pubmed-93889192022-08-23 Cancer Risk Score Prediction Based on a Single-Nucleotide Polymorphism Network Mahesworo, Bharuno Budiarto, Arif Hidayat, Alam Ahmad Pardamean, Bens Healthc Inform Res Original Article OBJECTIVES: Genome-wide association studies (GWAS) are performed to study the associations between genetic variants with respect to certain phenotypic traits such as cancer. However, the method that is commonly used in GWAS assumes that certain traits are solely affected by a single mutation. We propose a network analysis method, in which we generate association networks of single-nucleotide polymorphisms (SNPs) that can differentiate case and control groups. We hypothesize that certain phenotypic traits are attributable to mutations in groups of associated SNPs. METHODS: We propose a method based on a network analysis framework to study SNP-SNP interactions related to cancer incidence. We employed logistic regression to measure the significance of all SNP pairs from GWAS for the incidence of colorectal cancer and computed a cancer risk score based on the generated SNP networks. RESULTS: We demonstrated our method in a dataset from a case-control study of colorectal cancer in the South Sulawesi population. From the GWAS results, 20,094 pairs of 200 SNPs were created. We obtained one cluster containing four pairs of five SNPs that passed the filtering threshold based on their p-values. A locus on chromosome 12 (12:54410007) was found to be strongly connected to the four variants on chromosome 1. A polygenic risk score was computed from the five SNPs, and a significant difference in colorectal cancer risk was obtained between the case and control groups. CONCLUSIONS: Our results demonstrate the applicability of our method to understand SNP-SNP interactions and compute risk scores for various types of cancer. Korean Society of Medical Informatics 2022-07 2022-07-31 /pmc/articles/PMC9388919/ /pubmed/35982599 http://dx.doi.org/10.4258/hir.2022.28.3.247 Text en © 2022 The Korean Society of Medical Informatics https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Mahesworo, Bharuno
Budiarto, Arif
Hidayat, Alam Ahmad
Pardamean, Bens
Cancer Risk Score Prediction Based on a Single-Nucleotide Polymorphism Network
title Cancer Risk Score Prediction Based on a Single-Nucleotide Polymorphism Network
title_full Cancer Risk Score Prediction Based on a Single-Nucleotide Polymorphism Network
title_fullStr Cancer Risk Score Prediction Based on a Single-Nucleotide Polymorphism Network
title_full_unstemmed Cancer Risk Score Prediction Based on a Single-Nucleotide Polymorphism Network
title_short Cancer Risk Score Prediction Based on a Single-Nucleotide Polymorphism Network
title_sort cancer risk score prediction based on a single-nucleotide polymorphism network
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9388919/
https://www.ncbi.nlm.nih.gov/pubmed/35982599
http://dx.doi.org/10.4258/hir.2022.28.3.247
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