Results: 3

1.
Figure 1

Figure 1. From: Genome-wide association study identifies three loci associated with melanoma risk.

Results of Cochran-Armitage (CA) trend test for all SNPs passing quality control reported as −log10 p-values. The analysis stratified by geographic region is on the top with the unstratified analysis on the bottom (see Methods for details). The solid horizontal line indicates p-value of 10−5 and the dashed line indicates p-value of 5×10−7.

D Timothy Bishop, et al. Nat Genet. ;41(8):920-925.
2.
Figure 2

Figure 2. From: Genome-wide association study identifies three loci associated with melanoma risk.

Stratified CA trend tests. The −log10 p-values are from the CA trend test stratified (by geographical region) for genotyped and imputed SNPs in candidate regions for follow-up. Genotyped SNPs are shown in black and imputed SNPs in red; those SNPs that were followed up in the replication stage are indicated by a cross. The solid horizontal line indicates a p-value of 10−5 and the dashed line indicates a p-value of 5×10−7. The grey scale plots indicate extent of pairwise linkage disequilibrium (measured by r2) between SNPs, estimated from our data using Haploview23. Imputed data were not used for this. The darkest shading (black) indicates r2≥0.9, the next darkest 0.8≥ r2 > 0.9, etc. The position of the SNPs relative to the graph is indicated by the lines between the two.

D Timothy Bishop, et al. Nat Genet. ;41(8):920-925.
3.
Figure 3

Figure 3. From: Genome-wide association study identifies three loci associated with melanoma risk.

Forest plot of associations by geography and case category. The forest plot of the estimated per-allele OR from the CA trend test across geographical regions and overall for (i) chromosome 9 (rs7023329, top left), (ii) chromosome 11 (rsl393350, top right), (iii) chromosome 16 (rs258322, middle left), (iv) by case-category for these three SNPs (middle right), (v) chromosome 20 (rsl885120, only genotyped in replication set, bottom left) and (vi) chromosome 22 (rs2284063, bottom right). Overall the associations are consistent across populations. The case categories show some limited variation for both chromosome 9 and chromosome 16 with family history and multiple primaries being associated with more extreme risk than early onset.

D Timothy Bishop, et al. Nat Genet. ;41(8):920-925.

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