When results of GWAS are published as Manhattan plot, one often sees genomewide line at -log10(5e-08) and suggestive line at -log10(1e-05). Where do these values come from and what do they mean exactly? Many thanks.
Christopher, I am pondering over the same question. My thinking is that GW line is the threshold determined by correcting for multiple testing (e.g. if you have 500,000SNPs, the adjusted P-value would be 0.05/500,000=10E-7=GW threshold ), but i have no clear idea about suggestive line. Any expert here please help.
"The P values of Bonferroni corrected thresholds for suggestive, 5 and 1% genome-wide significant levels were 1, 0.05 and 0.01, respectively, divided by the number of SNPs used in the GWAS. The suggestive level was first proposed by Lander and Kruglyak [17] and represents the threshold where, under the null hypothesis, one false positive is expected per genome scan."
So the suggestive line is calculated as the -log10( 1 / number of variants)
Reference: Guo, Y., Huang, Y., Hou, L., Ma, J., Chen, C., Ai, H., ... & Ren, J. (2017). Genome-wide detection of genetic markers associated with growth and fatness in four pig populations using four approaches. Genetics Selection Evolution, 49(1), 21.
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