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Table 1 Significant true-positive genes by pedigree found using PSGS analysis

From: Pairwise shared genomic segment analysis in high-risk pedigrees: application to Genetic Analysis Workshop 17 exome-sequencing SNP data

Replicate Chromosome p-value Causal gene Causal SNP Frequency in cases (%) Frequency in population (%) Run length range in causal gene
25 1 1 × 10–4 PIK3C2B C1S9189 4.35 0.65 1,152.577–1,192.443
  9 1 × 10–5 VLDLR C9S444 17.39 0.14 793.933–802.051
27 9 1 × 10–4 VLDLR C9S444 14.29 0.14 798.038–816.491
29 1 0.001 PIK3C2B C1S9189 4.76 0.65 1,065.976–1,106.357
  4 0.001 VEGFC C4S4935 90.48 0.07 639.6238
  9 1 × 10–6 VLDLR C9S444 9.52 0.14 801.038–809.448
  10 0.001 SIRT1 C10S3109 61.90 0.07 870.229–870.229
49 10 0.001 SIRT1 C10S3109 56.52 0.07 919.134–919.134
75 1 2 × 10–4 PIK3C2B C1S9189 4.76 0.65 1,127.395–1,159.105
85 1 2 × 10–4 PIK3C2B C1S9189 4.35 0.65 1,159.779–1,188.854
  9 1 × 10–4 VLDLR C9S444 13.04 0.14 764.763–770.269
94 1 1 × 10–4 PIK3C2B C1S9189 4.76 0.55 1,232.038–1,256.771
116 9 4 × 10–4 VLDLR C9S444 13.64 0.14 772.983–776.619
129 9 5 × 10–4 VLDLR C9S444 20.83 0.14 712.761–728.337
142 9 9 × 10–4 VLDLR C9S444 19.05 0.14 708.8238–711.8381
  10 3 × 10–4 SIRT1 C10S3109 57.14 0.07 863.629–863.629
184 9 7 × 10–4 VLDLR C9S444 23.81 0.14 734.410–750.419
190 9 4 × 10–5 VLDLR C9S444 18.18 0.14 779.281–782.654
199 10 6 × 10–4 SIRT1 C10S3109 71.43 0.07 984.443–984.443
  1. Replicates 15, 101, 144, 182, and 200 did not identify any true-positive genes. Significance threshold = 0.001. Frequencies of causal SNPs in case subjects were calculated from 18 pedigree replicates.