Identifying Genetic Variants and Characterizing Their Role In Clubfoot

<p>Clubfoot is a common, complex birth defect affecting 4,000 newborns in the United States and 135,000 world-wide each year. The clubfoot deformity is characterized by inward and rigid downward displacement of one or both feet, along with persistent calf muscle hypoplasia. Despite strong evidence for a genetic liability, there is a limited understanding of the genetic and environmental factors contributing to the etiology of clubfoot. <em>The studies described in this dissertation were performed to identify variants and/or genes associated with clubfoot.</em> Genome-wide linkage scan performed on ten multiplex clubfoot families identified seven new chromosomal regions that provide new areas to search for clubfoot genes. Troponin C (<em>TNNC2</em>) the strongest candidate gene<em>, </em>located in 20q12-q13.11, is involved in muscle contraction. Exon sequencing of <em>TNNC2</em> did not identify any novel coding variants. Interrogation of fifteen muscle contraction genes found strong associations with SNPs located in potential regulatory regions of <em>TPM1 </em>(rs4075583 and<em> </em>rs3805965)<em>, TPM2 </em>(rs2025126 and<em> </em>rs2145925) and<em> TNNC2 </em>(rs383112 and rs437122)<em>.</em> In previous studies, a strong association was found with rs3801776 located in the basal promoter of <em>HOXA9</em>, a gene also involved in muscle development and patterning. Altogether, this data suggests that SNPs located in potential regulatory regions of genes involved in muscle development and function could alter transcription factor binding leading to changes in gene expression. Functional analysis of 3801776/<em>HOXA9, </em>rs2025126/<em>TPM2 </em>and rs2145925/<em>TPM2 </em>showed altered protein binding, which significantly influenced promoter activity. Although the ancestral allele (G) of rs4075583/<em>TPM1 </em>creates a DNA-protein complex, it did not affect <em>TPM1 </em>promoter activity. However and importantly, in the context of a haplotype, rs4075583/G significantly decreased <em>TPM1 </em>promoter activity. These results suggest dysregulation of multiple skeletal muscle genes, <em>TPM1</em>, <em>TPM2</em>, <em>TNNC2</em> and <em>HOXA9, </em>working in concert may contribute to clubfoot. However, specific allelic combinations involving these four regulatory SNPs did not confer a significantly higher risk for clubfoot. Other combinations of these variants are being evaluated. Moreover, these variants may interact with yet to be discovered variants in other genes to confer a higher clubfoot risk. Collectively, we show novel evidence for the role of skeletal muscle genes in clubfoot indicating that there are multiple genetic factors contributing to this complex birth defect.</p>

Name thesis:degree_name

Doctor of Philosophy (PhD)

Level thesis:degree_level

Dissertation (PhD)

Year dc:date.available

2012

Author dc:creator

• Weymouth, Katelyn S

Contributors dc:contributor

• Jacqueline T. Hecht, PhD
• Joseph Alcorn, PhD
• Rebecca Berdeaux, PhD

• Clubfoot
• association
• linkage
• genetic
• EMSA
• luciferase
• SNP
• Genetics
• Medicine and Health Sciences
• Molecular Genetics

Repository record dc:identifier

https://digitalcommons.library.tmc.edu/utgsbs_dissertations/321

OAI identifier oai:identifier

oai:digitalcommons.library.tmc.edu:utgsbs_dissertations-1355