Investigation of the role of SNVs (single nucleotide variants) in the etiology of nonsyndromic cleft lip with or without cleft palate

Author(s)

Carolina Malcher Amorim de Carvalho Silva

• Document type: Master's Dissertation
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Instituto de Biociências (IBIOC/SB)
• Defense date: 2013-04-04

Examining board members

Maria Rita dos Santos e Passos Bueno

• Advisor: Maria Rita dos Santos e Passos Bueno

Abstract

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a frequent craniofacial malformation, with a multifactorial model of inheritance, in which genetic and environmental risk factors act in disease manifestation. Variation of gene expression has been pointed as an important susceptibility mechanism to complex diseases, and DNA variants that regulate expression levels (eQTLs) have been combined with association studies to help elucidate the etiology of some diseases. In the present work, we integrate eQTL and association studies to 1) verify if variants associated with NSCL/P have a regulatory role in orbicularis oris muscle mesenchymal stem cells (OOMMSC, a tissue affected by NSCL/P); and 2) verify if eQTLs mapped in OOMMSC are associated with the disease. For the first goal, we verified the correlation of the rs642961 and rs590223 genotype variants with IRF6 expression levels, and also between the rs987525 genotype and MYC expression levels. We did not find correlation for any of the three variants tested. Possibly, these variants have a functional role in specific moments of embryogenesis, or sample size (N=46) was insufficient to detect correlation. For the second goal, we did a case-control association study for eQTLs rs5011163, rs1505443, rs4793213, rs4793229 and rs1242500. We did not find association between these variants and NSCL/P. The negative association could be explained by the marginal significance of these variants as eQTLs in OOMMSC. Besides, low-power studies, as the OOMMSC eQTL mapping performed in another project by our group, usually detect eQTLs of larger effect, which are frequently shared among tissues; therefore, they may not be relevant for the disease itself. Other eQTLs, selected under different criteria, are currently being tested for association with NSCL/P, which will enable us to evaluate the relevance of this approach to detect susceptibility variants for NSCL/P (AU)

• FAPESP's process: 11/04260-1 - Impact of SNPs (single nucleotide polymorphisms) on the levels of expression of IRF6 in patient cells with cleft lip with or without cleft palate
• Grantee: Carolina Malcher Amorim de Carvalho Silva
• Support Opportunities: Scholarships in Brazil - Master