Cargando…
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...
Autores principales: | , , , |
---|---|
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 |
_version_ | 1784770320096296960 |
---|---|
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. |
format | Online Article Text |
id | pubmed-9388919 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Korean Society of Medical Informatics |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT mahesworobharuno cancerriskscorepredictionbasedonasinglenucleotidepolymorphismnetwork AT budiartoarif cancerriskscorepredictionbasedonasinglenucleotidepolymorphismnetwork AT hidayatalamahmad cancerriskscorepredictionbasedonasinglenucleotidepolymorphismnetwork AT pardameanbens cancerriskscorepredictionbasedonasinglenucleotidepolymorphismnetwork |