Background: Evidence suggests that common complex diseases may be partially due to SNP-SNP interactions, but such detection is yet to be fully established in a high-dimensional small-sample (small-n-large-p) study. A number of penalized regression techniques are gaining popularity within the statistical community, and are now being applied to detect interactions. These techniques tend to be over-fitting, and are prone to false positives. The recently developed stability least absolute shrinkage and selection operator (SLASSO) has been used to control family-wise error rate, but often at the expense of power (and thus false negative results).
Results: Here, we propose an alternative stability selection procedure known as stability smoothly clipped absolute deviation (SSCAD). Briefly, this method applies a smoothly clipped absolute deviation (SCAD) algorithm to multiple sub-samples, and then identifies cluster ensemble of interactions across the sub-samples. The proposed method was compared with SLASSO and two kinds of traditional penalized methods by intensive simulation. The simulation revealed higher power and lower false discovery rate (FDR) with SSCAD. An analysis using the new method on the previously published GWAS of lung cancer confirmed all significant interactions identified with SLASSO, and identified two additional interactions not reported with SLASSO analysis.
Conclusions: Based on the results obtained in this study, SSCAD presents to be a powerful procedure for the detection of SNP-SNP interactions in large-scale genomic data.