SNPassoc: an R package to perform whole genome association studies

González, Juan R.; Armengol, Lluı́s; Solé, Xavier; Guinó, Elisabet; Mercader, Josep M.; Estivill, Xavier; Moreno, Vı́ctor

doi:10.1093/bioinformatics/btm025

Cited by 689 publications

(518 citation statements)

References 3 publications

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“…Analysis was performed using the SNPassoc R package (Catalan Institute of Oncology; http://bioinfo.iconcologia.net/index.php?module=SNPassoc). 33 To avoid false-positive results due to multiple testing, and considering that the SNPs analyzed are not in complete linkage disequilibrium, we applied the Benjamini-Hochberg (BH) method. 34 Power was calculated for the effect detected in previous reports with different diseases at an a level of 0.05, assuming a multiplicative allelic effects model, and a sample number of 2864 cases and 2930 controls.…”

Section: Resultsmentioning

confidence: 99%

The autoimmune disease-associated KIF5A, CD226 and SH2B3 gene variants confer susceptibility for multiple sclerosis

et al. 2010

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Genome-wide association studies (GWAS) have revealed that different diseases share susceptibility variants. Twelve singlenucleotide polymorphisms (SNPs) previously associated with different immune-mediated diseases in GWAS were genotyped in a Caucasian Spanish population of 2864 multiple sclerosis (MS) patients and 2930 controls. Three SNPs were found to be associated with MS: rs1678542 in KIF5A (P ¼ 0.001, odds ratio (OR) ¼ 1.13, 95% confidence interval (CI) ¼ 1.05-1.23); rs3184504 in SH2B3 (P ¼ 0.00001, OR ¼ 1.19, 95% CI ¼ 1.10-1.27) and rs763361 in CD226 (P ¼ 0.00007, OR ¼ 1.16, 95%CI ¼ 1.08-1.25). These variants have previously been associated with rheumatoid arthritis and type 1 diabetes. The SH2B3 polymorphism has additionally been associated with systemic lupus erythematosus. Our results, in addition to validating some of these loci as risk factors for MS, are consistent with shared genetic mechanisms underlying different immune-mediated diseases. These data may help to shape the contribution of each pathway to different disorders.

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Section: Resultsmentioning

confidence: 99%

The autoimmune disease-associated KIF5A, CD226 and SH2B3 gene variants confer susceptibility for multiple sclerosis

et al. 2010

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“…Association analyses were performed assuming a log-additive effect for each polymorphism with SNPassoc software. 23 Multiple tests were corrected by the method proposed by Li et al 24 A level of Po0.0085 was considered statistically significant.…”

Section: Discussionmentioning

confidence: 99%

Association of adiponectin polymorphism with cord blood adiponectin concentrations and intrauterine growth

et al. 2011

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To assess whether adiponectin gene (ADIPOQ) polymorphism is associated with intrauterine fetal growth and cord blood adiponectin, we investigated eight single-nucleotide polymorphisms (SNPs; rs182052, rs710445, rs16861205, rs12495941, rs1501299, rs3774261, rs2082940 and rs266729) in ADIPOQ and birth weight and cord blood adiponectin in 526 healthy neonates. We found that the neonates carrying the G allele of rs266729 had a significantly greater birth weight s.d. score than those homozygous for the C allele (CC: À0.06 ± 0.75 versus CG: 0.20 ± 0.64 versus GG: 0.07 ± 0.78; P¼1.65Â10 À3 , adjusted P¼9.90Â10 À3 ). However, this difference was not significant after adjustment for cord blood adiponectin (P¼0.04, adjusted P¼0.26). The rs266729 SNP was strongly associated with cord blood adiponectin; neonates with rs266729 GG had the highest adiponectin (CC: 34.1 ± 20.2 versus CG: 44.3 ± 26.1 versus GG: 54.1 ± 36.7 lg ml -1 , P¼2.80Â10 À9 , adjusted P¼1.68Â10 À8 ). This association remained after adjustment for birth weight s.d. score (P¼6.63Â10 À8 , adjusted P¼3.98Â10 À7 ). Our results suggest that the influence of the rs266729 SNP in ADIPOQ on birth weight may be dependent on circulating adiponectin.

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“…Statistical evaluations for testing genetic effects of association between the case-control status and each individual SNP, measured by the ORs and its corresponding 95% confidence limits, were estimated using unconditional logistic regression before and after adjusting for age, gender and other covariates. Association analyses were performed assuming codominant, dominant and recessive models using SNPassoc 33 and SPSS (v. 15.0) for Windows. In all analyses, the common homozygote genotype in the control population was defined as the reference category.…”

Section: Discussionmentioning

confidence: 99%

Testing the association of novel meta-analysis-derived diabetes risk genes with type II diabetes and related metabolic traits in Asian Indian Sikhs

et al. 2009

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A recent meta-analysis on three genome-wide association (GWA) scans identified six loci (NOTCH2, THADA, ADAMTS9, JAZF1, CDC123/CAMKID and TSPAN8/LGRS) highly associated with type II diabetes (T2D) in Caucasians. This investigation seeks to confirm this association with diabetes and related metabolic traits in Khatri Sikh diabetics of North India. We genotyped highly significant variants from each locus in a case-control cohort consisting of 680 T2D cases and 637 normoglycemic (NG) controls. Only CDC123/CAMKID (rs12779790) replicated earlier evidence of association with T2D under a dominant model (odds ratio (OR): 1.27; 95% confidence interval (CI): 1.02-1.57; P¼0.031) during initial testing. However, we could not confirm this association using multiple testing corrections. In a multiple linear-regression analysis, the same variant in the CDC123/CAMKID revealed a marked decrease in fasting insulin levels among 'G' (risk) allele carriers independently in NG controls (P¼0.030) and in T2D cases (P¼0.009), as well as in the combined sample (P¼0.003) after adjusting for covariates. Evidence of impaired b-cell function was also observed among 'G' (risk) allele carriers in T2D cases (P¼0.008) and in a combined cohort (P¼0.026). Our data could not confirm the role of the remaining variants with risk either for T2D or quantitative phenotypes measuring insulin secretion or insulin resistance. These findings suggest that CDC123/CAMKID could be a major risk factor for the development of T2D in Sikhs by affecting b-cell function. To our knowledge, this is the first study reporting the role of recently emerging loci in this high-risk population from the South Asian subcontinent.

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SNPassoc: an R package to perform whole genome association studies

Abstract: A tutorial is available on Bioinformatics online and in http://davinci.crg.es/estivill_lab/snpassoc.

Cited by 689 publications

References 3 publications

The autoimmune disease-associated KIF5A, CD226 and SH2B3 gene variants confer susceptibility for multiple sclerosis

The autoimmune disease-associated KIF5A, CD226 and SH2B3 gene variants confer susceptibility for multiple sclerosis

Association of adiponectin polymorphism with cord blood adiponectin concentrations and intrauterine growth

Testing the association of novel meta-analysis-derived diabetes risk genes with type II diabetes and related metabolic traits in Asian Indian Sikhs

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