Supplementary Figure 1: The use of frequency and size cutoffs in CNV gene set enrichment tests to reduce genomic inflation. | Nature Genetics

Supplementary Figure 1: The use of frequency and size cutoffs in CNV gene set enrichment tests to reduce genomic inflation.

From: The contribution of rare variants to risk of schizophrenia in individuals with and without intellectual disability

Supplementary Figure 1

Quantile–quantile plots were generated based on P values from CNV enrichment tests of random gene sets, using different MAF cutoffs (<0.1%, 1%) and CNV size cutoffs (removing the top 5% and 10% of CNVs overlapping the most genes). Each dot represents a different gene set. The 95% CI assuming uniformly distributed P values is displayed as the gray shaded area. The genomic inflation factor (λ) is provided for each distribution. Inflation followed the reasonable null distribution when more stringent MAF thresholds and size cutoffs were applied (see MAF < 0.1% and removing the 10% of CNVs overlapping the most genes).

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