Cargando…

Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage

BACKGROUND: Brain image genetics provides enormous opportunities for examining the effects of genetic variations on the brain. Many studies have shown that the structure, function, and abnormality (e.g., those related to Alzheimer’s disease) of the brain are heritable. However, which genetic variati...

Descripción completa

Detalles Bibliográficos
Autores principales: Li, Jin, Liu, Wenjie, Li, Huang, Chen, Feng, Luo, Haoran, Bao, Peihua, Li, Yanzhao, Jiang, Hailong, Gao, Yue, Liang, Hong, Fang, Shiaofen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8086096/
https://www.ncbi.nlm.nih.gov/pubmed/33931008
http://dx.doi.org/10.1186/s12859-021-04145-0
_version_ 1783686457225904128
author Li, Jin
Liu, Wenjie
Li, Huang
Chen, Feng
Luo, Haoran
Bao, Peihua
Li, Yanzhao
Jiang, Hailong
Gao, Yue
Liang, Hong
Fang, Shiaofen
author_facet Li, Jin
Liu, Wenjie
Li, Huang
Chen, Feng
Luo, Haoran
Bao, Peihua
Li, Yanzhao
Jiang, Hailong
Gao, Yue
Liang, Hong
Fang, Shiaofen
author_sort Li, Jin
collection PubMed
description BACKGROUND: Brain image genetics provides enormous opportunities for examining the effects of genetic variations on the brain. Many studies have shown that the structure, function, and abnormality (e.g., those related to Alzheimer’s disease) of the brain are heritable. However, which genetic variations contribute to these phenotypic changes is not completely clear. Advances in neuroimaging and genetics have led us to obtain detailed brain anatomy and genome-wide information. These data offer us new opportunities to identify genetic variations such as single nucleotide polymorphisms (SNPs) that affect brain structure. In this paper, we perform a genome-wide variant-based study, and aim to identify top SNPs or SNP sets which have genetic effects with the largest neuroanotomic coverage at both voxel and region-of-interest (ROI) levels. Based on the voxelwise genome-wide association study (GWAS) results, we used the exhaustive search to find the top SNPs or SNP sets that have the largest voxel-based or ROI-based neuroanatomic coverage. For SNP sets with >2 SNPs, we proposed an efficient genetic algorithm to identify top SNP sets that can cover all ROIs or a specific ROI. RESULTS: We identified an ensemble of top SNPs, SNP-pairs and SNP-sets, whose effects have the largest neuroanatomic coverage. Experimental results on real imaging genetics data show that the proposed genetic algorithm is superior to the exhaustive search in terms of computational time for identifying top SNP-sets. CONCLUSIONS: We proposed and applied an informatics strategy to identify top SNPs, SNP-pairs and SNP-sets that have genetic effects with the largest neuroanatomic coverage. The proposed genetic algorithm offers an efficient solution to accomplish the task, especially for identifying top SNP-sets. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04145-0.
format Online
Article
Text
id pubmed-8086096
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-80860962021-04-30 Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage Li, Jin Liu, Wenjie Li, Huang Chen, Feng Luo, Haoran Bao, Peihua Li, Yanzhao Jiang, Hailong Gao, Yue Liang, Hong Fang, Shiaofen BMC Bioinformatics Research Article BACKGROUND: Brain image genetics provides enormous opportunities for examining the effects of genetic variations on the brain. Many studies have shown that the structure, function, and abnormality (e.g., those related to Alzheimer’s disease) of the brain are heritable. However, which genetic variations contribute to these phenotypic changes is not completely clear. Advances in neuroimaging and genetics have led us to obtain detailed brain anatomy and genome-wide information. These data offer us new opportunities to identify genetic variations such as single nucleotide polymorphisms (SNPs) that affect brain structure. In this paper, we perform a genome-wide variant-based study, and aim to identify top SNPs or SNP sets which have genetic effects with the largest neuroanotomic coverage at both voxel and region-of-interest (ROI) levels. Based on the voxelwise genome-wide association study (GWAS) results, we used the exhaustive search to find the top SNPs or SNP sets that have the largest voxel-based or ROI-based neuroanatomic coverage. For SNP sets with >2 SNPs, we proposed an efficient genetic algorithm to identify top SNP sets that can cover all ROIs or a specific ROI. RESULTS: We identified an ensemble of top SNPs, SNP-pairs and SNP-sets, whose effects have the largest neuroanatomic coverage. Experimental results on real imaging genetics data show that the proposed genetic algorithm is superior to the exhaustive search in terms of computational time for identifying top SNP-sets. CONCLUSIONS: We proposed and applied an informatics strategy to identify top SNPs, SNP-pairs and SNP-sets that have genetic effects with the largest neuroanatomic coverage. The proposed genetic algorithm offers an efficient solution to accomplish the task, especially for identifying top SNP-sets. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04145-0. BioMed Central 2021-04-30 /pmc/articles/PMC8086096/ /pubmed/33931008 http://dx.doi.org/10.1186/s12859-021-04145-0 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Li, Jin
Liu, Wenjie
Li, Huang
Chen, Feng
Luo, Haoran
Bao, Peihua
Li, Yanzhao
Jiang, Hailong
Gao, Yue
Liang, Hong
Fang, Shiaofen
Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage
title Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage
title_full Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage
title_fullStr Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage
title_full_unstemmed Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage
title_short Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage
title_sort genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8086096/
https://www.ncbi.nlm.nih.gov/pubmed/33931008
http://dx.doi.org/10.1186/s12859-021-04145-0
work_keys_str_mv AT lijin genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT liuwenjie genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT lihuang genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT chenfeng genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT luohaoran genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT baopeihua genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT liyanzhao genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT jianghailong genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT gaoyue genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT lianghong genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage
AT fangshiaofen genomewidevariantbasedstudyofgeneticeffectswiththelargestneuroanatomiccoverage