SNPs rs11240569, rs708727, and rs823156 in SLC41A1 Do Not Discriminate Between Slovak Patients with Idiopathic Parkinson’s Disease and Healthy Controls: Statistics and Machine-Learning Evidence
Open Access
- 21 September 2019
- journal article
- research article
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 20 (19), 4688
- https://doi.org/10.3390/ijms20194688
Abstract
Gene SLC41A1 (A1) is localized within Parkinson’s disease-(PD)-susceptibility locus PARK16 and encodes for the Na+/Mg2+-exchanger. The association of several A1 SNPs with PD has been studied. Two, rs11240569 and rs823156, have been associated with reduced PD-susceptibility primarily in Asian populations. Here, we examined the association of rs11240569, rs708727, and rs823156 with PD in the Slovak population and their power to discriminate between PD patients and healthy controls. The study included 150 PD patients and 120 controls. Genotyping was performed with the TaqMan® approach. Data were analyzed by conventional statistics and Random Forest machine-learning (ML) algorithm. Individually, none of the three SNPs is associated with an altered risk for PD-onset in Slovaks. However, a combination of genotypes of SNP-triplet GG(rs11240569)/AG(rs708727)/AA(rs823156) is significantly (p < 0.05) more frequent in the PD (13.3%) than in the control (5%) cohort. ML identified the power of the tested SNPs in isolation or of their singlets (joined), duplets and triplets to discriminate between PD-patients and healthy controls as zero. Our data further substantiate differences between diverse populations regarding the association of A1 polymorphisms with PD-susceptibility. Lack of power of the tested SNPs to discriminate between PD and healthy cases render their clinical/diagnostic relevance in the Slovak population negligible.This publication has 58 references indexed in Scilit:
- Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription RegulationCell, 2012
- Cellular magnesium homeostasisArchives of Biochemistry and Biophysics, 2011
- Replication of MAPT and SNCA, but not PARK16‐18, as susceptibility genes for Parkinson's diseaseMovement Disorders, 2011
- Analysis of GWAS-linked loci in Parkinson disease reaffirms PARK16 as a susceptibility locusNeurology, 2010
- Genetic variability at the PARK16 locusEuropean Journal of Human Genetics, 2010
- Genome-wide association study reveals genetic risk underlying Parkinson's diseaseNature Genetics, 2009
- Genomic views of distant-acting enhancersNature, 2009
- Hardy-Weinberg Equilibrium Testing of Biological Ascertainment for Mendelian Randomization StudiesAmerican Journal of Epidemiology, 2009
- SLC41A1 Is a Novel Mammalian Mg2+ CarrierOnline Journal of Public Health Informatics, 2008
- ParkinsonismNeurology, 1967