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Table 2 Retaining confirmed AMD associations in a candidate SNP analysis when batch is completely confounded with AMD status

From: Identifying and mitigating batch effects in whole genome sequencing data

CHR Positiona p-value Percent missing GQ20M05 GQ20M30 Diff GQ LD corrected p-value
1 196,710,325 0.002199 4.928 NF NF NF 0.002122
3 64,719,689 NS 5.027 F NF NF NS
3 99,762,695 NS 5.027 F NF NF NS
6 43,858,890 NS 6.57 F NF F NS
6 116,122,572 NS 6.471 F NF NF NS
8 23,225,458 NS 6.72 F NF NF NS
9 99,146,083 NS 5.475 F NF NF NS
10 122,454,932 1.60E-05 0.6969 NF NF NF 1.79E-05
13 31,245,188 NS 5.625 F NF NF NS
14 68,318,360 NS 5.226 F NF NF NS
15 58,396,268 NS 5.625 F NF NF NS
16 56,963,321 NS 3.833 NF NF F NS
19 6,718,376 NS 3.534 NF NF NF NS
19 44,919,689 2.30E-21b 6.67 F NF NF 3.16E-21
22 32,663,679 NS 6.521 F NF NF NS
22 38,080,269 NS 6.272 F NF NF NS
  1. NF is not filtered, F is filtered, GQ20M05 filter, filter sites with more than 5% missingness after setting genotypes with GQ < 20 to missing; GQ20M30 filter, filter sites with more than 30% missingness after setting genotypes with GQ < 20 to missing
  2. Diff GQ, differential genotype quality filter, LD linkage disequilibrium, NS not significant in candidate SNP analysis at Bonferroni adjusted significance level: 0.05/16 = 0.00312
  3. aSites are reported in GRCh38 coordinates
  4. bWe detect APOE because our controls are enriched for Alzheimer’s cases