What variables are plotted on a Manhattan plot?
What variables are plotted on a Manhattan plot?
Manhattan Plots The plot shows on the y-axis the negative log-base-10 of the P value for each of the polymorphisms in the genome (along the x-axis), when tested for differences in frequency between 17,008 cases and 37,154 controls. The line shows the threshold for genome-wide significance (P < 5 × 10–8).
What are the horizontal lines on a Manhattan plot?
The horizontal dotted line represents the genome-wide significance threshold which is labeled in the figure. Single variant analysis in genome-wide association studies (GWAS) has been proven to be successful in identifying thousands of genetic variants associated with hundreds of complex diseases.
How do you interpret Manhattan plot GWAS?
Manhattan plots represent the P values of the entire GWAS on a genomic scale (Fig. 2a). The P values are represented in genomic order by chromosome and position on the chromosome (x-axis). The value on the y-axis represents the −log10 of the P value (equivalent to the number of zeros after the decimal point plus one).
What does a high LOD score mean?
A statistical estimate of whether two genetic loci are physically near enough to each other (or “linked”) on a particular chromosome that they are likely to be inherited together. A LOD score of 3 or higher is generally understood to mean that two genes are located close to each other on the chromosome.
What causes linkage disequilibrium?
Linkage disequilibrium arises when a mutation event gives rise to a new allele on a particular chromosome in an individual. The new allele will be associated with the alleles already present on that individual’s chromosome for all other loci.
How many SNPs are in a haplotype?
The estimated number of SNPs required for a genome-wide haplotype survey ranges from 180K (based on a European sample of 16 chromosomes) to 600K (based on an ethnically diverse sample of 164 chromosomes).
What does a LOD score 3.0 mean?
A LOD score of 3 or higher is generally understood to mean that two genes are located close to each other on the chromosome. In terms of significance, a LOD score of 3 means the odds are 1,000:1 that the two genes are linked and therefore inherited together.
How do you analyze a LOD score?
For interpretation of LOD score, a LOD score greater than 3.0 is considered evidence for linkage. A LOD score of +3 indicates 1000 to 1 odds that the linkage being observed did not occur by chance.
