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Molecular investigation in individuals with orofacial clefts and microphthalmia-anophthalmia-coloboma spectrum

Abstract

This study describes genomic findings among individuals with both orofacial clefts (OC) and microphthalmia/anophthalmia/coloboma (MAC) recorded in the Brazilian Database on Craniofacial Anomalies (BDCA). Chromosomal microarray analysis (CMA) and Whole Exome Sequencing (WES) were performed in 17 individuals with OC-MAC. Clinical interpretation of molecular findings was based on data available at the BDCA and on re-examination. No copy number variants (CNVs) classified as likely pathogenic or pathogenic were detected by CMA. WES allowed a conclusive diagnosis in six individuals (35.29%), two of them with variants in the CHD7 gene, and the others with variants in the TFAP2A, POMT1, PTPN11, and TP63 genes with the following syndromes: CHARGE, CHD7-spectrum, Branchiooculofacial, POMT1-spectrum, LEOPARD, and ADULT. Variants of uncertain significance (VUS) possibly associated to the phenotypes were found in six other individuals. Among the individuals with VUSes, three individuals presented variants in genes associated to defects of cilia structure and/or function, including DYNC2H1, KIAA0586, WDR34, INTU, RPGRIP1L, KIF7, and LMNA. These results show that WES was the most effective molecular approach for OC-MAC in this cohort. This study also reinforces the genetic heterogeneity of OC-MAC, and the importance of genes related to ciliopathies in this phenotype.

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Fig. 1: Workflow of Whole Exome Sequencing using Highlander and Varstation.

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All data are available at www.bipmed.org/brave.

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Acknowledgements

This study would not be possible without the dedication of the patients and families and our colleagues from BDCA participant centers.The authors would like to thank the following BDCA participant centers, which provided samples from patients included in this study: Centro de atenção aos defeitos da face (CADEFI), Faculdade de Medicina de São José do Rio Preto (FAMERP), Centrinho Prefeito Luiz Gomes-Joinville, Universidade Federal do Rio Grande do Norte (UFRN), and Hospital de Clínicas de Porto Alegre. We are also indebted to Gabriela Roldão Correia-Costa for her technical support.

Funding

This study was partially supported by the National Council for Scientific and Technological Development (CNPq) (#408504/2018-8 and #309782/2020-1), São Paulo Research Foundation (FAPESP #2018 / 21370-4) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES #001), and by the Fonds de la Recherche Scientifique - FNRS Grant J.0228.20 (to MV). The authors thank the Genomics Platform of University of Louvain for the access to the Next Generation Sequencing data analyses cluster. Eleonore Pairet is a Research Fellow (ASP) grantee of the Fonds de la Recherche Scientifique – FNRS. We also thank the National Lottery, Belgium and the Foundation Against Cancer (2010-101), Belgium for their support to the Genomics Platform of University of Louvain and de Duve Institute, as well as the Fonds de la Recherche Scientifique - FNRS Eguipment Grant U.N035.17 for the «Big data analysis cluster for NGS at UCLouvain».

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Contributions

MAT performed clinical evaluation, clinical interpretation of molecular findings and wrote the manuscript; MMC performed laboratory tests, CMA and WES data analyses through Varstation and revised the manuscript; EP performed the WES data analyses through Highlander and variant evaluation, and wrote the manuscript; ILM collaborated with the design of the study and revised the manuscript; EMR performed clinical evaluation and revised the manuscript; ELM performed clinical evaluation and revised the manuscript; RH developed the data analysis program used for WES analysis; TPV collaborated with the design of the study, CMA analysis and revised the manuscript; MV supervised the WES studies, provided funding and revised the manuscript; VLGSL designed the study, performed clinical evaluation, provided funding, performed clinical interpretation of molecular findings, and revised the manuscript.

Corresponding author

Correspondence to Vera Lúcia Gil-da-Silva-Lopes.

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The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of University of Campinas (protocol numbers: 35316314.9.1001.5404 and 85020018.8.0000.5404). Informed consent was obtained from all subjects involved in the study. Written informed consent has been obtained from the patients to publish this paper.

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Atique Tacla, M., de Mello Copelli, M., Pairet, E. et al. Molecular investigation in individuals with orofacial clefts and microphthalmia-anophthalmia-coloboma spectrum. Eur J Hum Genet (2023). https://doi.org/10.1038/s41431-023-01488-5

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