Table 2.

Description of the prognostic germline variants identified in this study

Aa
VariantChromPosRefAltPopulation frequencySample sizeNumber of heterozygotesNumber of homozygotesGene nameMedian expression (FPKM)PHR
rs617579551775318086AG5.01%291210GRB242.27.08E-1020.4
rs28672782111446622CT16.27%50155BRSK27.29<1E-161.15E-10
Bb
VariantChromPosRefAltPopulation frequencyCADD ScorePhyloP ScoreGene nameDatasetSample sizeNumber of heterozygotesNumber of homozygotesPHR
rs349881931564943580AG30.90%328.42ANKDD1aTCGA450199520.001131.73
CGGA761820.07431.79
  • aA description of the two prognostic germline variants (FDR < 0.10) in the TCGA dataset identified when testing all 196,022 germline variants.

  • bA description of the prognostic germline variant (FDR < 0.10) rs34988193 in ANKDD1a identified when the analysis was restricted to only germline variants with a combined annotation dependent depletion (CADD) score greater than 30 in the TCGA and CGGA datasets.