GWAS Analysis
Last updated
Last updated
GWAS analysis interface
Choose BED file: Click to select a BED file containing genotype data for Genome-wide association study (GWAS).
Choose phenotype: Click to select a file with phenotype data that will be used in the GWAS analysis.
Algorithm dropdown menu: Select the algorithm for GWAS.
Run GWAS button: Initiate the GWAS process with the selected BED file, phenotype data, and algorithm.
The Manhattan plot shows the association between genetic markers (SNPs) and the trait of interest. The x-axis represents the genomic position, while the y-axis displays the negative logarithm of the p-value for each SNP. Peaks identify genomic regions that are significantly associated with the trait, highlighting potential loci for further research.
This quantile-quantile plot compares the distribution of observed p-values from the GWAS against the expected distribution under the null hypothesis. If no significant genetic associations are present, the points should align closely with a diagonal line. Deviations from the line suggest population stratification or true associations.
In the context of a Q-Q plot, particularly in genome-wide association studies (GWAS), the lambda (often referred to as the genomic inflation factor, or GIF) is a measure of the inflation of test statistics due to population stratification, technical artifacts, or other confounding factors:
Lambda < 1.05: Generally considered very good, indicating minimal inflation. Such values suggest that there is little to no unaccounted confounding or bias affecting the results.
Lambda between 1.05 and 1.10: Often acceptable, especially in large-scale studies involving complex traits where some degree of polygenicity and residual population structure can cause slight inflation.
Lambda > 1.10 but < 1.15: Mild inflation is indicated, prompting a review of data and methods. While this range is still often acceptable, it suggests that there might be factors such as subtle population stratification or model misspecification affecting the results.
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