Genetics Research
rs7517357
Population Frequencies12
African
C 0.9162T 0.0838CC 0.838791CT/TC 0.154732TT 0.006477pop=5,558
African American
C 0.9153T 0.0847CC 0.837383CT/TC 0.155888TT 0.006729pop=5,350
African Others
C 0.938T 0.062CC 0.875CT/TC 0.125TT 0pop=208
Asian
C 0.921T 0.079CC 0.842105CT/TC 0.157895TT 0pop=114
East Asian
C 0.92T 0.08CC 0.840909CT/TC 0.159091TT 0pop=88
European
C 0.8288T 0.1712CC 0.691714CT/TC 0.274162TT 0.034124pop=17,114
Latin American 1
C 0.886T 0.114CC 0.798246CT/TC 0.175439TT 0.026316pop=228
Latin American 2
C 0.892T 0.108CC 0.800499CT/TC 0.182045TT 0.017456pop=802
Other
C 0.876T 0.124CC 0.769401CT/TC 0.21286TT 0.017738pop=902
Other Asian
C 0.92T 0.08CC 0.846154CT/TC 0.153846TT 0pop=26
South Asian
C 0.922T 0.078CC 0.843137CT/TC 0.156863TT 0pop=102
Studies11
Unread Studies11 ▼
1
Celiac disease (CD) is highly prevalent in the wheat eating population of India. While HLA-DQ genotype is the strongest genetic determinant of CD, other genetic factors are likely contribute to genesis of CD. In this case-control study, we determined the frequencies of single nucleotide polymorphisms (SNP) in non-HLA candidate genes that influence the development of CD. DNA obtained from peripheral blood of 376 patients with CD and 736 controls was used for the studies. Fifty-one candidate gene polymorphisms were identified for evaluation. Competitive allele-specific polymerase chain reactions were designed to genotype biallelic SNPs at the selected loci. The genotype and allelotype was determined using KASP genotyping technology in a real-time PCR instrument. Eighteen of the 51 SNPs tested associated strongly with CD. The strongest association was found with the HLA DQ2.5 haplotype. HLA DQ2.2 haplotype and HLA-DQ8 haplotype were also strongly associated with CD. Non-HLA genes that were significantly associated with CD included those associated with T cell receptor signaling and T cell activation - CD247, CD80, CD28, PRKCQ, TNFAIP3, UBASH3 and ARHGAP31; genes involved in inflammatory cell migration - CCR3 and CCR4; those involved in epithelial protection - GATD3, PARK7 and INAVA (C1orf106); and those influencing RNA - DDX6 and PUS10. We concluded that the non-HLA genes associated with CD in this Indian population were mostly those associated with molecules involved in the T cell receptor signaling pathway downstream to HLA-DQ2/8, which lead to immune and subsequent inflammatory activation.
2
DNA methylation (DNAm) provides a crucial epigenetic mark linking genetic variations to environmental influence. We analyzed array-based DNAm profiles of 160 human retinas with co-measured RNA-seq and > 8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 mQTLs and 12,505 eQTLs) and 13,747 eQTMs (DNAm loci affecting gene expression), with over one-third specific to the retina. mQTLs and eQTMs show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration (AMD). Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of AMD pathology by genotype–environment interaction in retina.
3
Summary statistics for discovery GWAS of 22,473 varicose veins cases and 379,183 non-varicose veins controls in UK Biobank. Related publication: Ahmed W. et al., Nature Communications, 2022. SNP= SNP name CHR= Chromosome number BP= Genomic position (GRCh37) ALLELE1= effect allele ALLELE0= non-effect allele A1FREQ= frequency of allele A INFO= INFO score for imputed SNPs BETA= beta coefficient SE= standard error PVAL= p-value
4
We analyzed the DJ1 gene in a large consecutive series (N = 163) of Italian unrelated Early Onset Parkinson Disease (EOPD: onset ≤40 years of age) patients and 100 healthy controls (mean age 64 ± 7 years). No homozygous or compound heterozygous mutations with an obvious pathogenic effect were found. Several variants were identified, some of which were novels. All variants had similar frequency in patients and in controls. Our data suggest that DJ1 mutations are very rare in Italian EOPD. Other genes and risk factors for PD are still to be identified.
5
Parkinson's disease (PD) is a common neurodegenerative movement disorder. Among the candidate genes, DJ-1 accounts for about 1% of the cases in different populations. We aim to …
6
Parkinson's disease (PD) is a common neurodegenerative movement disorder. Among the candidate genes, DJ-1 accounts for about 1% of the cases in different populations. We aim to …
7
Parkinson’s disease (PD) is a common neurodegenerative movement disorder. Among the candidate genes, DJ-1 accounts for about 1% of the cases in different populations. We aim to …
8
Parkinson’s disease (PD) is a common neurodegenerative movement disorder. Among the candidate genes, DJ-1 accounts for about 1% of the cases in different populations. We aim to find the contribution of the gene towards PD among Indians. By screening DJ-1 in 308 PD patients of eastern India and 248 ethnically matched controls, a total of 21 nucleotide variants – including two nonsynonymous changes – were detected. p.Arg98Gln was identified in 6 unrelated patients and 2 controls while p.Val35Ile, a novel change, was found only in 2 unrelated patients. A SNP (rs7517357) was observed to be moderately associated with increased risk of PD (p < 0.05). The deletion allele (g.168–185del) of a known 18 bp del/ins/dup polymorphism was found to be over represented (p < 0.05) among older patients (> 40 years) compared to the controls (> 45 years). Two of the patients, also heterozygotes for PINK1 mutation, had more severe disease phenotypes, consistent with the reported interaction between PINK1 and DJ-1 gene products [19]. Our results demonstrate that up to 3.9% (12/308) of PD patients of eastern India harbor DJ-1 variants that should be explored further for any causal relationship with PD.
9
Parkinson’s disease (PD) is a common neurodegenerative movement disorder. Among the candidate genes, DJ-1 accounts for about 1% of the cases in different populations. We aim to find the contribution of the gene towards PD among Indians. By screening DJ-1 in 308 PD patients of eastern India and 248 ethnically matched controls, a total of 21 nucleotide variants – including two nonsynonymous changes – were detected. p.Arg98Gln was identified in 6 unrelated patients and 2 controls while p.Val35Ile, a novel change, was found only in 2 unrelated patients. A SNP (rs7517357) was observed to be moderately associated with increased risk of PD (p < 0.05). The deletion allele (g.168–185del) of a known 18 bp del/ins/dup polymorphism was found to be over represented (p < 0.05) among older patients (> 40 years) compared to the controls (> 45 years). Two of the patients, also heterozygotes for PINK1 mutation, had more severe disease phenotypes, consistent with the reported interaction between PINK1 and DJ-1 gene products [19]. Our results demonstrate that up to 3.9% (12/308) of PD patients of eastern India harbor DJ-1 variants that should be explored further for any causal relationship with PD.
10
… SNPs rs3766606 and rs7517357 were genotyped using TaqMan 5′ fluorogenic nuclease assays on an ABI7900 real-time PCR instrument (Applied Biosystems Inc, Foster City, CA). …
11
De Marco EV, Annesi G, Tarantino P, Nicoletti G, Civitelli D, Messina D, Annesi F, Arabia G, Salsone M, Condino F, Novellino F, Provenzano G, Rocca FE, Colica C, Morelli M, Scornaienchi V, Greco V, Giofrè L, Quattrone A. DJ‐1 is a Parkinson's disease susceptibility gene in southern Italy.
Curated Studies0 ▼
These studies were determined to be useful for this variant — check "Unused Studies" further down if curious what didn't make the cut.
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Unused Studies0 ▼
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