ERAP1 polymorphisms interactions and their association with Behçet's disease susceptibly: Application of Model-Based Multifactor Dimension Reduction Algorithm (MB-MDR).
Adult
Algorithms
Aminopeptidases
/ genetics
Behcet Syndrome
/ genetics
Entropy
Female
Gene Frequency
/ genetics
Gene Regulatory Networks
Genetic Association Studies
Genetic Predisposition to Disease
Humans
Iran
Male
Minor Histocompatibility Antigens
/ genetics
Models, Genetic
Multifactor Dimensionality Reduction
Polymorphism, Single Nucleotide
/ genetics
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2020
2020
Historique:
received:
14
10
2019
accepted:
03
01
2020
entrez:
6
2
2020
pubmed:
6
2
2020
medline:
23
4
2020
Statut:
epublish
Résumé
Behçet's disease (BD) is a chronic multi-systemic vasculitis with a considerable prevalence in Asian countries. There are many genes associated with a higher risk of developing BD, one of which is endoplasmic reticulum aminopeptidase-1 (ERAP1). In this study, we aimed to investigate the interactions of ERAP1 single nucleotide polymorphisms (SNPs) using a novel data mining method called Model-based multifactor dimensionality reduction (MB-MDR). We have included 748 BD patients and 776 healthy controls. A peripheral blood sample was collected, and eleven SNPs were assessed. Furthermore, we have applied the MB-MDR method to evaluate the interactions of ERAP1 gene polymorphisms. The TT genotype of rs1065407 had a synergistic effect on BD susceptibility, considering the significant main effect. In the second order of interactions, CC genotype of rs2287987 and GG genotype of rs1065407 had the most prominent synergistic effect (β = 12.74). The mentioned genotypes also had significant interactions with CC genotype of rs26653 and TT genotype of rs30187 in the third-order (β = 12.74 and β = 12.73, respectively). To the best of our knowledge, this is the first study investigating the interaction of a particular gene's SNPs in BD patients by applying a novel data mining method. However, future studies investigating the interactions of various genes could clarify this issue.
Sections du résumé
BACKGROUND
Behçet's disease (BD) is a chronic multi-systemic vasculitis with a considerable prevalence in Asian countries. There are many genes associated with a higher risk of developing BD, one of which is endoplasmic reticulum aminopeptidase-1 (ERAP1). In this study, we aimed to investigate the interactions of ERAP1 single nucleotide polymorphisms (SNPs) using a novel data mining method called Model-based multifactor dimensionality reduction (MB-MDR).
METHODS
We have included 748 BD patients and 776 healthy controls. A peripheral blood sample was collected, and eleven SNPs were assessed. Furthermore, we have applied the MB-MDR method to evaluate the interactions of ERAP1 gene polymorphisms.
RESULTS
The TT genotype of rs1065407 had a synergistic effect on BD susceptibility, considering the significant main effect. In the second order of interactions, CC genotype of rs2287987 and GG genotype of rs1065407 had the most prominent synergistic effect (β = 12.74). The mentioned genotypes also had significant interactions with CC genotype of rs26653 and TT genotype of rs30187 in the third-order (β = 12.74 and β = 12.73, respectively).
CONCLUSION
To the best of our knowledge, this is the first study investigating the interaction of a particular gene's SNPs in BD patients by applying a novel data mining method. However, future studies investigating the interactions of various genes could clarify this issue.
Identifiants
pubmed: 32023277
doi: 10.1371/journal.pone.0227997
pii: PONE-D-19-28263
pmc: PMC7001967
doi:
Substances chimiques
Minor Histocompatibility Antigens
0
Aminopeptidases
EC 3.4.11.-
ERAP1 protein, human
EC 3.4.11.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0227997Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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