Cargando…
Automated construction and testing of multi-locus gene–gene associations
Summary: It has been argued that the missing heritability in common diseases may be in part due to rare variants and gene–gene effects. Haplotype analyses provide more power for rare variants and joint analyses across genes can address multi-gene effects. Currently, methods are lacking to perform jo...
Autores principales: | , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008644/ https://www.ncbi.nlm.nih.gov/pubmed/21076150 http://dx.doi.org/10.1093/bioinformatics/btq616 |
_version_ | 1782194529547321344 |
---|---|
author | Abo, Ryan Knight, Stacey Thomas, Alun Camp, Nicola J. |
author_facet | Abo, Ryan Knight, Stacey Thomas, Alun Camp, Nicola J. |
author_sort | Abo, Ryan |
collection | PubMed |
description | Summary: It has been argued that the missing heritability in common diseases may be in part due to rare variants and gene–gene effects. Haplotype analyses provide more power for rare variants and joint analyses across genes can address multi-gene effects. Currently, methods are lacking to perform joint multi-locus association analyses across more than one gene/region. Here, we present a haplotype-mining gene–gene analysis method, which considers multi-locus data for two genes/regions simultaneously. This approach extends our single region haplotype-mining algorithm, hapConstructor, to two genes/regions. It allows construction of multi-locus SNP sets at both genes and tests joint gene–gene effects and interactions between single variants or haplotype combinations. A Monte Carlo framework is used to provide statistical significance assessment of the joint and interaction statistics, thus the method can also be used with related individuals. This tool provides a flexible data-mining approach to identifying gene–gene effects that otherwise is currently unavailable. Availability: http://bioinformatics.med.utah.edu/Genie/hapConstructor.html Contact: ryan.abo@hsc.utah.edu |
format | Text |
id | pubmed-3008644 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30086442010-12-29 Automated construction and testing of multi-locus gene–gene associations Abo, Ryan Knight, Stacey Thomas, Alun Camp, Nicola J. Bioinformatics Applications Note Summary: It has been argued that the missing heritability in common diseases may be in part due to rare variants and gene–gene effects. Haplotype analyses provide more power for rare variants and joint analyses across genes can address multi-gene effects. Currently, methods are lacking to perform joint multi-locus association analyses across more than one gene/region. Here, we present a haplotype-mining gene–gene analysis method, which considers multi-locus data for two genes/regions simultaneously. This approach extends our single region haplotype-mining algorithm, hapConstructor, to two genes/regions. It allows construction of multi-locus SNP sets at both genes and tests joint gene–gene effects and interactions between single variants or haplotype combinations. A Monte Carlo framework is used to provide statistical significance assessment of the joint and interaction statistics, thus the method can also be used with related individuals. This tool provides a flexible data-mining approach to identifying gene–gene effects that otherwise is currently unavailable. Availability: http://bioinformatics.med.utah.edu/Genie/hapConstructor.html Contact: ryan.abo@hsc.utah.edu Oxford University Press 2011-01-01 2010-11-13 /pmc/articles/PMC3008644/ /pubmed/21076150 http://dx.doi.org/10.1093/bioinformatics/btq616 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Abo, Ryan Knight, Stacey Thomas, Alun Camp, Nicola J. Automated construction and testing of multi-locus gene–gene associations |
title | Automated construction and testing of multi-locus gene–gene associations |
title_full | Automated construction and testing of multi-locus gene–gene associations |
title_fullStr | Automated construction and testing of multi-locus gene–gene associations |
title_full_unstemmed | Automated construction and testing of multi-locus gene–gene associations |
title_short | Automated construction and testing of multi-locus gene–gene associations |
title_sort | automated construction and testing of multi-locus gene–gene associations |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008644/ https://www.ncbi.nlm.nih.gov/pubmed/21076150 http://dx.doi.org/10.1093/bioinformatics/btq616 |
work_keys_str_mv | AT aboryan automatedconstructionandtestingofmultilocusgenegeneassociations AT knightstacey automatedconstructionandtestingofmultilocusgenegeneassociations AT thomasalun automatedconstructionandtestingofmultilocusgenegeneassociations AT campnicolaj automatedconstructionandtestingofmultilocusgenegeneassociations |