Further Discussion
A recent review lists NTD genes that have been associated with NTDs in
humans (M. Wang, Marco, Capra, & Kibar, 2019). Except for DVL2 ,
our study may appear not to corroborate findings in their review. We
offer three explanations for this apparent discrepancy. First, the
current study uniquely employs a gene-based mutational burden analysis.
Adopting a similar methodology to those studies summarized in the review
may yield similar results. Second, our subjects differ in ethnicity from
many of the populations discussed in other studies. As the current study
suggests, ancestry may influence which genes associate with
myelomeningocele. Third, any variants that were not equally covered in
both case and control populations were filtered out before analysis. If,
for example, an important variant was discovered in the myelomeningocele
subjects while the variant’s location was not covered in the
corresponding gnomAD control population, that variant would not
contribute to the mutational burden analysis.
The current study introduced 17 genes associated with risk for
myelomeningocele with nominal significance (Fisher exact P values
≤ 0.05). Bonferroni correction for multiple comparisons was applied to
each analysis using the number of compared genes as a denominator (173
in Hispanic comparisons and 189 in European ancestry comparisons) and
0.05 as the numerator alpha to calculate the correction threshold. While
some genes came close, none of the P values fell below the
correction threshold. A large enough group of myelomeningocele subjects
would lend enough statistical power to achieve the strict statistical
significance of a Bonferroni correction, but exome data for 511
myelomeningocele subjects is considerable, given the resource-intensive
nature of gathering samples. The genes discussed above are suggested
candidate genes.
Two of our quality control filters assume that each variant exists in
Hardy-Weinberg equilibrium within the myelomeningocele population
(inbreeding coefficient < -0.3, alternate allele depth ≥
25%). However, if a selective pressure acts on a variant locus, that
Hardy-Weinberg assumption is not met. Therefore, our analysis may
exclude important variant loci that are under intense selective
pressure.
A new approach was taken by limiting our analysis to a subset of human
genes rather than evaluating the entire exome at once. The high
concentration of current NTD candidate genes within the WNT signaling
pathway prompted this focused approach. A more inclusive approach would
also be valuable.
In summary, we report seventeen genes within the known WNT signaling
pathways which may play a role in the development of myelomeningocele.
As discussed above, the genes PORCN , DVL2 , CDH2 ,FUZ are already suspected to play a role in NTD development from
studies in animal models, however the remaining thirteen genes reported
here are new in their possible association with myelomeningocele.