Although we are encouraged by our findings, we recognize that there were several limitations to our study. We had a relatively small population size and therefore did not have sufficient power to detect disease variants occurring at a low frequency or that have a small effect size. We also did not have access to an independent dataset for replication of our finding. In addition, we may not have sufficiently covered all the variation in DOCK3 and SLC9A9 as a result of selecting only SNPs that were present on the Illumina chip. Finally, we were unable to adequately address all aspects of the phenotype that cosegregated with the 3p21 : 3q24 inversion as we excluded individuals in our study with extreme developmental delay (IQ<70). Thus, one area for future study would be to focus on individuals with a lower IQ to determine whether the association with SLC9A9 extends to other IQ levels.
