Results: 4

1.
Figure 1

Figure 1. SNP-related chromosomal intervals. From: From single-SNP to wide-locus: genome-wide association studies identifying functionally related genes and intragenic regions in small sample studies.

Conceptual structure of chromosomal SNP-related intervals for disease loci in LD with three consecutive SNPs (SNPs X, Y and Z), but not with a more distant SNP (SNP A). SNPs X and Y are part of different LD blocks, separated by a recombination hotspot. Hence, the interval between these two SNPs is excluded. The location indicating LD between SNPs A and X is highlighted in blue. The inter-regional boundaries need not be known.
LD: Linkage disequilibrium.

Knut M Wittkowski, et al. Pharmacogenomics. 2013 March;14(4):391-401.
2.
Figure 3

Figure 3. Published direct relationships between the minimal subset of the NOD/intellectual disability–axonal guidance signaling/ataxin pathway directly related to significant genes by μGWAS (23 of 40, s > 6.5) and lrGWAS (17 of 40, s > 7.0), respectively. From: From single-SNP to wide-locus: genome-wide association studies identifying functionally related genes and intragenic regions in small sample studies.

The members of the pathway are shown and labeled in bold. Methods are indicated in colors (blue: μGWAS; red: lrGWAS; pink: both). The most significant genes (μGWAS: >7.5, lrGWAS: >8.0) are shown in darker shades. (See for details). Supplementary Table 1 Dotted circles relate to functional clusters mentioned in the text. Drugs are indicated in green.
μGWAS: μ-statistics for structured multivariate data; lr: Linear/logistic regression.

Knut M Wittkowski, et al. Pharmacogenomics. 2013 March;14(4):391-401.
3.
Figure 2

Figure 2. Comparison of 185 childhood absence epilepsy cases versus matched controls. From: From single-SNP to wide-locus: genome-wide association studies identifying functionally related genes and intragenic regions in small sample studies.

Unadjusted −log10(p) by chromosomal location; top: μ-statistics for structured multivariate data (μGWAS); bottom: linear/logistic regression (lr; without interaction terms). Univariate results, shown in black, are consistently similar across the approaches, as expected. For μGWAS, dots vary in size by diplotype length and are color coded, with red indicating results with low μ-scores for reliability (high significance, low μIC). Lr results are overlayed with the Cochran–Armitage (squares) and Mantel–Haenszel (×/+) test results. Genes known to be directly related to the NOD/intellectual disability–axonal guidance signaling/ataxin pathway are shown in bold. Genes indicated in the center header row (pink) of each chromosome have support in both μGWAS and lrGWAS; genes ranking higher in μGWAS or linear/logistic regression GWAS appear in the first row (blue) or third row (red), respectively. Darker colors indicate more significant results. Other implicated genes are shown against the dark background of univariate results.
?: No gene in the region implicated; …: Several genes within the same linkage disequilibrium block.

Knut M Wittkowski, et al. Pharmacogenomics. 2013 March;14(4):391-401.
4.
Figure 4

Figure 4. Microarray genotyping results for the linkage disequilibrium block containing ARHGAP32. From: From single-SNP to wide-locus: genome-wide association studies identifying functionally related genes and intragenic regions in small sample studies.

(A) Linkage disequilibrium (LD) map; (B) coding regions; (C) μ-statistics for structured multivariate data (μGWAS) test results by diplotype length followed by the polarities of the SNPs contributing and the SNP pattern (orange: homozygous; yellow: heterozygous; green: wild-type) for controls and cases sorted by μ(E, P) = μ((E1, E2, E4), (P1, P3, P4)) (near right stub). Diplotypes ranked high (red) and low (green) by μ-scores for each region (left stub: μE = μ(E1, E2, E4), μP = μ(P1, P3, P4)) are highlighted as more saturated. Horizontal arrows indicate consistently paired diplotypes. The insert shows the ‘Manhattan plot’ of the −log10(p) values. (D) lrGWAS results followed by the lr coefficients (coeff.) of the SNPs involved. SNP pattern are sorted by lr scores (far right stub). The enlarged profiles with extreme lr scores differ in one the five SNP only (vertical arrow). The insert shows the values based on univariate and stepwise lr. (E) LD between each of the ten SNPs included in the two μGWAS regions (blue) and the lrGWAS region (purple) and the members of the same tag set (gray). Tag set c is represented in both μGWAS diplotypes and the lrGWAS diplotype, which contains two members of tag set e.
Coeff: Coefficient; E: Exon; (E,P): Exon 10 and promoter region; lr: Linear/logistic regression; P: Promoter.

Knut M Wittkowski, et al. Pharmacogenomics. 2013 March;14(4):391-401.

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