Power and Sample Size Calculations for Genetic Case/Control Studies Using Gene-Centric SNP Maps: Application to Human Chromosomes 6, 21, and 22 in Three Populations

Applied Biosystems, Foster City, CA 94404, USA.
Human Heredity (Impact Factor: 1.64). 02/2005; 60(1):43-60. DOI: 10.1159/000087918
Source: PubMed

ABSTRACT Power and sample size calculations are critical parts of any research design for genetic association. We present a method that utilizes haplotype frequency information and average marker-marker linkage disequilibrium on SNPs typed in and around all genes on a chromosome. The test statistic used is the classic likelihood ratio test applied to haplotypes in case/control populations. Haplotype frequencies are computed through specification of genetic model parameters. Power is determined by computation of the test's non-centrality parameter. Power per gene is computed as a weighted average of the power assuming each haplotype is associated with the trait. We apply our method to genotype data from dense SNP maps across three entire chromosomes (6, 21, and 22) for three different human populations (African-American, Caucasian, Chinese), three different models of disease (additive, dominant, and multiplicative) and two trait allele frequencies (rare, common). We perform a regression analysis using these factors, average marker-marker disequilibrium, and the haplotype diversity across the gene region to determine which factors most significantly affect average power for a gene in our data. Also, as a 'proof of principle' calculation, we perform power and sample size calculations for all genes within 100 kb of the PSORS1 locus (chromosome 6) for a previously published association study of psoriasis. Results of our regression analysis indicate that four highly significant factors that determine average power to detect association are: disease model, average marker-marker disequilibrium, haplotype diversity, and the trait allele frequency. These findings may have important implications for the design of well-powered candidate gene association studies. Our power and sample size calculations for the PSORS1 gene appear consistent with published findings, namely that there is substantial power (>0.99) for most genes within 100 kb of the PSORS1 locus at the 0.01 significance level.

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    • "For the SNPs rs2694861, rs1465073, rs1534284, rs4759054, rs4325348, rs2279025, rs1545650, and 4759281 the Applied Biosystems (Foster City, California) SNPlex assay pool was used. The ZipCode probes were detected with an Applied Biosystems 3730 DNA Analyzer, and data interpretation was performed with the Applied Biosystems Genemapper v4.0 software [13]. SNPbrowser version 3.5 was used for SNP selection and SNPlex assay pool design. "
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    ABSTRACT: MYG1 (Melanocyte proliferating gene 1, also C12orf10 in human) is a ubiquitous nucleo-mitochondrial protein, involved in early developmental processes and in adult stress/illness conditions. We recently showed that MYG1 mRNA expression is elevated in the skin of vitiligo patients. Our aim was to examine nine known polymorphisms in the MYG1 gene, to investigate their functionality, and to study their association with vitiligo susceptibility. Nine single nucleotide polymorphisms (SNPs) in the MYG1 locus were investigated by SNPlex assay and/or sequencing in vitiligo patients (n = 124) and controls (n = 325). MYG1 expression in skin biopsies was detected by quantitative-real time PCR (Q-RT-PCR) and polymorphisms were further analysed using luciferase and YFP reporters in the cell culture. Control subjects with -119G promoter allele (rs1465073) exhibited significantly higher MYG1 mRNA levels than controls with -119C allele (P = 0.01). Higher activity of -119G promoter was confirmed by luciferase assay. Single marker association analysis showed that the -119G allele was more frequent in vitiligo patients (47.1%) compared to controls (39.3%, P < 0.05, OR 1.37, 95%CI 1.02-1.85). Analysis based on the stage of progression of the vitiligo revealed that the increased frequency of -119G allele occurred prevalently in the group of patients with active vitiligo (n = 86) compared to the control group (48.2% versus 39.3%, P < 0.05; OR 1.44, 95%CI 1.02-2.03). Additionally, we showed that glutamine in the fourth position (in Arg4Gln polymorphism) completely eliminated mitochondrial entrance of YFP-tagged Myg1 protein in cell culture. The analysis of available EST, cDNA and genomic DNA sequences revealed that Myg1 4Gln allele is remarkably present in human populations but is never detected in homozygous state according to the HapMap database. Our study demonstrated that both MYG1 promoter polymorphism -119C/G and Arg4Gln polymorphism in the mitochondrial signal of Myg1 have a functional impact on the regulation of the MYG1 gene and promoter polymorphism (-119C/G) is related with suspectibility for actively progressing vitiligo.
    BMC Medical Genetics 04/2010; 11(1):56. DOI:10.1186/1471-2350-11-56 · 2.45 Impact Factor
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    • "Research suggesting that association studies may have success in finding complex trait genes (De La Vega et al., 2005 ; Risch and Merikangas, 1996) and the discovery and validation of large numbers of SNPs in the human genome (HapMap, 2003), have elicited a growing interest in the performance of large-scale genetic association studies using SNPs at the candidate-gene , whole-chromosome, and eventually wholegenome level (De La Vega et al., 2005). Genetic association studies require a large sample size and strict investigation methodologies (Risch and Merikangas, 1996) given that the reliably observed gene variants odd ratios range around 1.2–1.5 (Kendler, 2005; Lasky-Su et al., 2005). "
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    ABSTRACT: 5-HT1A receptors are key components of the serotonin system, acting both pre- and post- synaptically in different brain areas. There is a growing amount of evidence showing the importance of 5-HT1A in different psychiatric disorders, from mood to anxiety disorders, moving through suicidal behaviour and psychotic disorders. Findings in the literature are not consistent with any definite 5-HT1A influence in psychiatric disorders. 5-HT1A gene variants have been reported to play some role in mood disorders, anxiety disorders and psychotic disorders. Again, the literature findings are not unequivocal. Concerning response to treatment, the C(-1019)G variant seems to be of primary interest in antidepressant response: C allele carriers generally show a better response to treatment, especially in Caucasian samples. Together with the C(-1019)G (rs6295) variant, the Ile28Val (rs1799921), Arg219Leu (rs1800044) and Gly22Ser (rs1799920) variants have been investigated in possible associations with psychiatric disorders, also with no definitive results. This lack of consistency can be also due to an incomplete gene investigation. To make progress on this point, a list of validated single nucleotide polymorphisms (SNPs) covering the whole gene is proposed for further investigations.
    The International Journal of Neuropsychopharmacology 09/2008; 11(5):701-21. DOI:10.1017/S1461145707008218 · 5.26 Impact Factor
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    • "This study is limited by the use of instruments such as the SF-36, MFI, and SI which are based on patient responses and a small sample size which may not detect associations of small or moderate effect. It should be noted, however, that SNPbrowser software, which was used for SNP selection, showed 480% power to detect an association with HTR2A polymorphisms in Caucasian subjects with 250 cases and 250 controls, assuming a disease allele frequency of 0.20 (De La Vega et al., 2005a, b). Further, MFI and SF-36 instruments have been rigorously tested for psychometric properties in both healthy and ill individuals (Smets et al., 1995; Keller et al., 1998), and the subjects were classified according to the most conservative CFS case definition following thorough hospital-based clinical evaluation of both cases and controls. "
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    ABSTRACT: Chronic fatigue syndrome (CFS) is a debilitating disorder of unknown etiology with no known lesions, diagnostic markers or therapeutic intervention. The pathophysiology of CFS remains elusive, although abnormalities in the central nervous system (CNS) have been implicated, particularly hyperactivity of the serotonergic (5-hydroxytryptamine; 5-HT) system and hypoactivity of the hypothalamic-pituitary-adrenal (HPA) axis. Since alterations in 5-HT signaling can lead to physiologic and behavioral changes, a genetic evaluation of the 5-HT system was undertaken to identify serotonergic markers associated with CFS and potential mechanisms for CNS abnormality. A total of 77 polymorphisms in genes related to serotonin synthesis (TPH2), signaling (HTR1A, HTR1E, HTR2A, HTR2B, HTR2C, HTR3A, HTR3B, HTR4, HTR5A, HTR6, and HTR7), transport (SLC6A4), and catabolism (MAOA) were examined in 137 clinically evaluated subjects (40 CFS, 55 with insufficient fatigue, and 42 non-fatigued, NF, controls) derived from a population-based CFS surveillance study in Wichita, Kansas. Of the polymorphisms examined, three markers (-1438G/A, C102T, and rs1923884) all located in the 5-HT receptor subtype HTR2A were associated with CFS when compared to NF controls. Additionally, consistent associations were observed between HTR2A variants and quantitative measures of disability and fatigue in all subjects. The most compelling of these associations was with the A allele of -1438G/A (rs6311) which is suggested to have increased promoter activity in functional studies. Further, in silico analysis revealed that the -1438 A allele creates a consensus binding site for Th1/E47, a transcription factor implicated in the development of the nervous system. Electrophoretic mobility shift assay supports allele-specific binding of E47 to the A allele but not the G allele at this locus. These data indicate that sequence variation in HTR2A, potentially resulting in its enhanced activity, may be involved in the pathophysiology of CFS.
    Psychoneuroendocrinology 03/2008; 33(2):188-97. DOI:10.1016/j.psyneuen.2007.11.001 · 5.59 Impact Factor
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