Table 1.

Case–control GWA-based PEGASUS gene hits

Gene IDChromosomeStart position (hg19)End position (hg19)Discovery stage PEGASUS P values: GWA P values (15)Replication stage PEGASUS P values: GWA P values (14)
ARID5Ba1063661012638567072.22E−162.22E−16
IKZF1750343678504727982.22E−162.22E−16
FIGNL1750511826505180882.22E−162.22E−16
CDKN2A921967750219944901.97E−070.000928457
DDC750526133506331541.14E−054.82E−12
PIP4K2A1022823765230035032.36E−054.45E−07
CDKN2B922002901220093120.0001408481.66E−05
HLA-DQB1632627240326344660.0008701770.005309704
  • NOTE: Table 1 shows case–control GWA-based PEGASUS gene hits. In the discovery-stage analysis, we apply PEGASUS to case–control GWA P values (15) using the 1000 Genomes Project EUR population (30) as a reference for LD. We then replicated eight of the 42 resulting gene hits (P < 10−3; Bonferroni-corrected for the number of haplotype blocks in the genome; ref. 38), shown in bold above, by applying PEGASUS to a second dataset of case–control GWA P values (replication P < 0.05; ref. 14). The full list of 42 gene hits is shown in Supplementary Table S3.

  • aARID5B was also replicated using the trio analysis-based PEGASUS replication test (replication P = 1.61 × 10−6; Supplementary Table S4). ARID5B, IKZF1, CDKN2A/2B, and PIP4K2A all contain SNPs previously associated with ALL in GWA studies (8–13).