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. 2022 Aug 11;8(5):e200012. doi: 10.1212/NXG.0000000000200012

Figure 4. Metrics of Variants Removed by the Proposed Center-Based/Platform-Based Variant Filters.

Figure 4

(A.a, A.b, and B) ADSP WES. (C.a, C.b, and D) ADSP WGS. (A.a and C.a) Variants that passed filters showed largely consistent p values across model 1 and model 2 case-control association analyses, with only few variants remaining that reach suggestive significance in model 1 but lose suggestive significance on center/platform adjustment in model 2 (lower right quadrant). (A.b and C.b) Variants that were removed by filters showed many inconsistent p values across models 1 and 2, consistent with center-related/platform-related variant artifacts that could not fully be accounted for by model 2. (B and D) Frequency density plots, comparing variants that were filtered/removed with those that were not filtered. Note that variants were consistently filtered across the full frequency range, with increased density at frequencies <1% or >10% in ADSP WES. ADSP, Alzheimer Disease Sequencing Project; WES, whole-exome sequencing; WGS, whole-genome sequencing.