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Table 1 Runtime required for GWIS compared to recent CPU and GPU methods.

From: GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS

Method Time for n SNP × n samples Exhaustive Search
  0.45M × 5K 5M × 10K  
CPU Implementation:
(4 cores, 64 bits, 3GHz Intel)
GWIS (1 filter) 2.7 hours* 28 days Yes
GWIS (3 filters) 10.9 hours* 113 days Yes
BOOST [31] 23 hours 8 months Yes
PLINK [53] 89 days 60 years Yes
RAPID [32] 15 mins NA No
SIXPAC [24] 8.0 hours NA No
GPU Implementation:
(448 CUDA cores, 1.215 GHz, NVIDIA GTX 470)
GWIS (1 filter) 13 mins* 2.2 days Yes
GWIS (3 Filters) 22 mins* 3.8 days Yes
GBOOST [7] 1.4 hours 15 days Yes
EpiGPU [8] 17 hours 6 months Yes
SHEsisEPI [9] 28 hours 10 months Yes
EPIBLASTER [6] 8.9 days 6 years Yes
  1. Runtime required for GWIS compared to recent CPU and GPU methods. The first column reports results for WTCCC-sized data (450K SNPs, 5K samples) while the second column shows timings for larger recent GWAS (5M SNPs, 10K samples). The rightmost column denotes whether a method performs exhaustive search of all pairs. Filters run by GWIS are χ 2 alone or in combination with DSS and SS tests. The times indicated by '*' are actual run times, and all other times are estimated by scaling (see Supplement Section 2 for exact calculations). Runtime for non-exhaustive methods has not been estimated as it is difficult to judge how these methods scale with the number of SNPs and samples.