PUBLICATION
Exome sequencing provides additional evidence for the involvement of ARHGAP29 in Mendelian orofacial clefting and extends the phenotypic spectrum to isolated cleft palate
- Authors
- Liu, H., Busch, T., Eliason, S., Anand, D., Bullard, S., Gowans, L.J., Nidey, N., Petrin, A., Augustine-Akpan, E.A., Saadi, I., Dunnwald, M., Lachke, S.A., Zhu, Y., Adeyemo, A., Amendt, B., Roscioli, T., Cornell, R., Murray, J., Butali, A.
- ID
- ZDB-PUB-161229-1
- Date
- 2017
- Source
- Birth defects research. Part A, Clinical and molecular teratology 109(1): 27-37 (Journal)
- Registered Authors
- Cornell, Robert
- Keywords
- cleft palate, exome, missense mutation
- MeSH Terms
-
- Alleles
- Animals
- Cleft Lip/genetics
- Cleft Palate/genetics*
- Computational Biology
- Disease Models, Animal
- Exome
- Exome Sequencing
- Female
- GTPase-Activating Proteins/genetics*
- GTPase-Activating Proteins/metabolism
- Gene Frequency/genetics
- Genome-Wide Association Study
- High-Throughput Nucleotide Sequencing
- Humans
- Male
- Pedigree
- Polymorphism, Single Nucleotide/genetics
- Risk Factors
- Sequence Analysis, DNA/methods
- Zebrafish/embryology
- Zebrafish/genetics
- PubMed
- 28029220 Full text @ Birth Defects Res. Part A Clin. Mol. Teratol.
Citation
Liu, H., Busch, T., Eliason, S., Anand, D., Bullard, S., Gowans, L.J., Nidey, N., Petrin, A., Augustine-Akpan, E.A., Saadi, I., Dunnwald, M., Lachke, S.A., Zhu, Y., Adeyemo, A., Amendt, B., Roscioli, T., Cornell, R., Murray, J., Butali, A. (2017) Exome sequencing provides additional evidence for the involvement of ARHGAP29 in Mendelian orofacial clefting and extends the phenotypic spectrum to isolated cleft palate. Birth defects research. Part A, Clinical and molecular teratology. 109(1):27-37.
Abstract
Background Recent advances in genomics methodologies, in particular the availability of next-generation sequencing approaches have made it possible to identify risk loci throughout the genome, in particular the exome. In the current study, we present findings from an exome study conducted in five affected individuals of a multiplex family with cleft palate only.
Methods The GEnome MINIng (GEMINI) pipeline was used to functionally annotate the single nucleotide polymorphisms, insertions and deletions. Filtering methods were applied to identify variants that are clinically relevant and present in affected individuals at minor allele frequencies (≤1%) in the 1000 Genomes Project single nucleotide polymorphism database, Exome Aggregation Consortium, and Exome Variant Server databases. The bioinformatics tool Systems Tool for Craniofacial Expression-Based Gene Discovery was used to prioritize cleft candidates in our list of variants, and Sanger sequencing was used to validate the presence of identified variants in affected and unaffected relatives.
Results Our analyses approach narrowed the candidates down to the novel missense variant in ARHGAP29 (GenBank: NM_004815.3, NP_004806.3;c.1654T>C [p.Ser552Pro]. A functional assay in zebrafish embryos showed that the encoded protein lacks the activity possessed by its wild-type counterpart, and migration assays revealed that keratinocytes transfected with wild-type ARHGAP29 migrated faster than counterparts transfected with the p.Ser552Pro ARHGAP29 variant or empty vector (control).
Conclusion These findings reveal ARHGAP29 to be a regulatory protein essential for proper development of the face, identifies an amino acid that is key for this, and provides a potential new diagnostic tool.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping