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Results: 5

1.
Figure 3

Figure 3. From: Novel Genes Identified in a High Density Genome Wide Association Study for Nicotine Dependence.

Scatter plot of the allele frequencies from pooling and individual genotyping from the Stage I sample.

Laura Jean Bierut, et al. Hum Mol Genet. ;16(1):24-35.
2.
Figure 4

Figure 4. From: Novel Genes Identified in a High Density Genome Wide Association Study for Nicotine Dependence.

Plot of distributions of standard errors of SNPs selected using different criteria. The plot illustrates that delta cutoff selects preferentially SNPs with high standard errors of delta , regular t-test preferentially selects SNPs with low standard errors and the corrected t-test is centered on the standard error distribution from all SNPs.

Laura Jean Bierut, et al. Hum Mol Genet. ;16(1):24-35.
3.

Figure 2. From: Novel Genes Identified in a High Density Genome Wide Association Study for Nicotine Dependence.

a) Distribution of p-values from the Stage I sample of the 31,960 individually genotyped SNPs that were selected from pooled genotyping stage. The distribution shows that the pooled genotyping produced an enrichment of SNPs with small p-values. A uniform distribution from 0-1 would be expected if there were no correlation between pooled genotyping and individual genotyping.
b) Distribution of p-values from the additional samples added in Stage II. The distribution is fairly uniform with only a slight enrichment of small p-values.

Laura Jean Bierut, et al. Hum Mol Genet. ;16(1):24-35.
4.
Figure 1

Figure 1. From: Novel Genes Identified in a High Density Genome Wide Association Study for Nicotine Dependence.

P values of genome-wide association scan for genes that affect the risk of developing nicotine dependence. -log10 (p) is plotted for each SNP in chromosomal order. The spacing between SNPs on the plot is based on physical map length. The horizontal lines show P values for logistic analysis. The vertical lines show chromosomal boundaries. Black diamonds represent SNPs that result in non-synonymous amino acid changes.

Laura Jean Bierut, et al. Hum Mol Genet. ;16(1):24-35.
5.
Figure 5

Figure 5. From: Novel Genes Identified in a High Density Genome Wide Association Study for Nicotine Dependence.

Q-Q plot of logistic regression ANOVA deviance produced from samples added to Stage I samples at Stage II. Because these samples are independent of Stage I samples used for the SNP selection from pooled genotyping the test statistic is expected to largely follow the null distribution (Chi-square distribution with 2 degrees of freedom). Due to the lower power of this sample set compared to the combined set of samples and the small effect sizes found in this study, any possible associations are not expected to cluster together at low p-values, thereby changing the linear shape of this Q-Q plot. The dotted line represents 95% point-wise confidence envelope of expected null distribution.

Laura Jean Bierut, et al. Hum Mol Genet. ;16(1):24-35.

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