Dataset Information

Armitage's trend test for genome-wide association analysis: one-sided or two-sided?

ABSTRACT: The importance of considering confounding due to population stratification in genome-wide association analysis using case-control designs has been a source of debate. Armitage's trend test, together with some other methods developed from it, can correct for population stratification to some extent. However, there is a question whether the one-sided or the two-sided alternative hypothesis is appropriate, or to put it another way, whether examining both the one-sided and the two-sided alternative hypotheses can give more information. The dataset for Problem 1 of Genetic Analysis Workshop 16 provides us with a chance to address this question. Because it is a part of a combined sample from the North American Rheumatoid Arthritis Consortium (NARAC) and the Swedish Epidemiological Investigation of Rheumatoid Arthritis (EIRA), the results from the combined sample can be used as references. To test this aim, the last 10,000 single-nucleotide polymorphisms (SNPs) on chromosome 9, which contain the common genetic variant at the TRAF1-C5 locus, were examined by conducting Armitage's trend tests. Examining the two-sided alternative hypothesis shows that SNPs rs12380341 (p = 9.7 x 10-11) and rs872863 (p = 1.7 x 10-15), along with six SNPs across the TRAF1-C5 locus, rs1953126, rs10985073, rs881375, rs3761847, rs10760130, and rs2900180 (p~1 x 10-7), are significantly associated with anti-cyclic citrullinated peptide-positive rheumatoid arthritis. But examining the one-sided alternative hypothesis that the minor allele is positively associated with the disease shows that only those six SNPs across the TRAF1-C5 locus are significantly associated with the disease (p~1 x 10-8), which is consistent with the results from the combined sample of the NARAC and the EIRA.

SUBMITTER: Fang Y

PROVIDER: S-EPMC2795935 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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Armitage's trend test for genome-wide association analysis: one-sided or two-sided?

Fang Yixin Y Wang Yuanjia Y Sha Nanshi N

BMC proceedings 20091215

The importance of considering confounding due to population stratification in genome-wide association analysis using case-control designs has been a source of debate. Armitage's trend test, together with some other methods developed from it, can correct for population stratification to some extent. However, there is a question whether the one-sided or the two-sided alternative hypothesis is appropriate, or to put it another way, whether examining both the one-sided and the two-sided alternative ...[more]

PMID: 20018028

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Project description:ObjectiveAlcohol use disorders are common conditions that have enormous social and economic consequences. Genome-wide association analyses were performed to identify genetic variants associated with a proxy measure of alcohol consumption and alcohol misuse and to explore the shared genetic basis between these measures and other substance use, psychiatric, and behavioral traits.MethodThis study used quantitative measures from the Alcohol Use Disorders Identification Test (AUDIT) from two population-based cohorts of European ancestry (UK Biobank [N=121,604] and 23andMe [N=20,328]) and performed a genome-wide association study (GWAS) meta-analysis. Two additional GWAS analyses were performed, a GWAS for AUDIT scores on items 1-3, which focus on consumption (AUDIT-C), and for scores on items 4-10, which focus on the problematic consequences of drinking (AUDIT-P).ResultsThe GWAS meta-analysis of AUDIT total score identified 10 associated risk loci. Novel associations localized to genes including JCAD and SLC39A13; this study also replicated previously identified signals in the genes ADH1B, ADH1C, KLB, and GCKR. The dimensions of AUDIT showed positive genetic correlations with alcohol consumption (rg=0.76-0.92) and DSM-IV alcohol dependence (rg=0.33-0.63). AUDIT-P and AUDIT-C scores showed significantly different patterns of association across a number of traits, including psychiatric disorders. AUDIT-P score was significantly positively genetically correlated with schizophrenia (rg=0.22), major depressive disorder (rg=0.26), and attention deficit hyperactivity disorder (rg=0.23), whereas AUDIT-C score was significantly negatively genetically correlated with major depressive disorder (rg=-0.24) and ADHD (rg=-0.10). This study also used the AUDIT data in the UK Biobank to identify thresholds for dichotomizing AUDIT total score that optimize genetic correlations with DSM-IV alcohol dependence. Coding individuals with AUDIT total scores ≤4 as control subjects and those with scores ≥12 as case subjects produced a significant high genetic correlation with DSM-IV alcohol dependence (rg=0.82) while retaining most subjects.ConclusionsAUDIT scores ascertained in population-based cohorts can be used to explore the genetic basis of both alcohol consumption and alcohol use disorders.

Project description:BackgroundBovine paratuberculosis (ParaTB) also known as Johne's disease, is a contagious fatal disease resulting from infection by Mycobacterium avium subspecies paratuberculosis (MAP). Previous studies have identified loci associated with ParaTB using different measurements to define cases and controls. The objective of this study was to combine the data from two recent studies to identify genetic loci associated with MAP tissue infection and humoral immune response, defined by MAP ELISA-positive cattle, by comparing cases and control animals for one or both measures of infection.Methodology/principal findingsThe two populations used for the association analyses were a cohort of MAP tissue infected animals and control Holstein cows from the USA and the second cohort composed of ELISA-positive and ELISA-negative Holstein cows from Italy. Altogether 1190 cattle were genotyped with the Illumina BovineSNP50 BeadChip. SNP markers were removed if the minor allele frequency <0.01 or genotyping failure was >5%. Animals were removed with >5% genotyping failure. Whole genome association analyses were conducted with the GRAMMAR-CG method using two different definitions of control populations.Conclusion/significanceThe analyses identified several loci (P<5 e-05) associated with ParaTB, defined by positive ELISA and presence of bacteria in tissue compared to ELISA and tissue negative animals, on chromosomes 1, 12 and 15 and one unassigned SNP. These results confirmed associations on chromosome 12 and the unassigned SNP with ParaTB which had been found in the Italian population alone. Furthermore, several additional genomic regions were found associated with ParaTB when ELISA and tissue positive animals were compared with tissue negative samples. These loci were on chromosomes 1, 6, 7, 13, 16, 21,23 and 25 (P<5 e-05). The results clearly indicate the importance of the phenotype definition when seeking to identify markers associated with different disease responses.

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Armitage's trend test for genome-wide association analysis: one-sided or two-sided?

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Armitage's trend test for genome-wide association analysis: one-sided or two-sided?

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