For rare variants rs139667828 and rs61737326 located in DISC1, differences in MAF between OD cases and controls were very similar when observed at the sequencing stage and again at the genotyping stage. Because the direction of the association was the same for the two rare variants, we used a regular collapsing method to test their association with OD. Based on the Fisher’s exact test, the association p-value was 0.035 in the sequencing stage and 0.0028 in the genotyping stage. When subjects from the two stages were combined, the association p-value was 0.0001. Although combining the subjects yielded a smaller p-value, we posit that it was not, most likely, because of bias from including subjects from the first stage, but due to increased sample size. This is supported by the allele frequency similarities noted above.
