Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 \(\times\) 10–7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p = 0.0009), and created binding sites for 23 TFs, including Pax6 (p = 6.12 \(\times\) 10–5) and Pax9 (p = 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study indicates that rare genetic variation may contribute to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Data availability
The data analyzed and reported in this manuscript is publicly available and can be accessed from the database of Genotypes and Phenotypes (dbGaP; phs001168.v2.p2) and from the Kids First Data Resource Center.
References
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Acknowledgements
The authors thank the dedicated field staff, collaborators, and participating families for their important contributions to this study.
Funding
This work was supported by grants from the National Institutes of Health (NIH) including: F32-DE032260 [SWC], R00-DE025060 [EJL], R21- DE029698 [MPE], X01-HG007485 [MLM, EF], R01-DE016148 [MLM, SMW], U01-DE024425 [MLM], R37- DE008559 [JCM, MLM], R01-DE009886 [MLM], R21-DE016930 [MLM], R01- DE012472 [MLM], R01-DE014581 [THB], U01-DE018993 [THB]. National Institute of Dental and Craniofacial Research (U01-DE020078; R01-DE027023 [SMW]). Funding for genotyping by the National Human Genome Research Institute (X01-HG007821) and funding for initial genomic data cleaning by the University of Washington provided by contract HHSN268201200008I from the National Institute for Dental and Craniofacial Research awarded to the Center for Inherited Disease Research.
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Curtis, S.W., Carlson, J.C., Beaty, T.H. et al. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes. Hum. Genet. 142, 1531–1541 (2023). https://doi.org/10.1007/s00439-023-02596-4
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DOI: https://doi.org/10.1007/s00439-023-02596-4