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Nutrients 2017, 9(4), 390; doi:10.3390/nu9040390

Novel Genetic Variants Associated with Child Refractory Esophageal Stricture with Food Allergy by Exome Sequencing

1
Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou 510623, China
2
Division of Experimental and Translational Genetics, Children’s Mercy Hospital, University of Missouri Kansas City School of Medicine, 2401 Gillham Road, Kansas City, MO 64108, USA
3
Division of Gastroenterology, Children’s Mercy Hospital, University of Missouri Kansas City School of Medicine, 2401 Gillham Road, Kansas City, MO 64108, USA
*
Authors to whom correspondence should be addressed.
Received: 26 January 2017 / Revised: 5 April 2017 / Accepted: 13 April 2017 / Published: 15 April 2017
(This article belongs to the Special Issue Nutrigenetics)
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Abstract

Background: Refractory esophageal stricture (RES) may be attributed to food allergy. Its etiology and pathogenesis are not fully understood. Identification of novel genetic variants associated with this disease by exome sequencing (exome-seq) may provide new mechanistic insights and new therapeutic targets. Methods: To identify new and novel disease-associating variants, whole-exome sequencing was performed on an Illumina NGS platform in three children with RES as well as food allergy. Results: A total of 91,024 variants were identified. By filtering out ‘normal variants’ against those of the 1000 Genomes Project, we identified 12,741 remaining variants which are potentially associated with RES plus food allergy. Among these variants, there are 11,539 single nucleotide polymorphisms (SNPs), 627 deletions, 551 insertions and 24 mixture variants. These variants are located in 1370 genes. They are enriched in biological processes or pathways such as cell adhesion, digestion, receptor metabolic process, bile acid transport and the neurological system. By the PubMatrix analysis, 50 out of the top 100 genes, which contain most variants, have not been previously associated with any of the 17 allergy-associated diseases. These 50 genes represent newly identified allergy-associated genes. Those variants of 627 deletions and 551 insertions have also not been reported before in RES with food allergy. Conclusions: Exome-seq is potentially a powerful tool to identify potential new biomarkers for RES with food allergy. This study has identified a number of novel genetic variants, opening new avenues of research in RES plus food allergy. Additional validation in larger and different patient populations and further exploration of the underlying molecular mechanisms are warranted. View Full-Text
Keywords: children; exome-seq; food allergy; genetic variants; refractory esophageal stricture children; exome-seq; food allergy; genetic variants; refractory esophageal stricture
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Yang, M.; Xiong, M.; Chen, H.; Geng, L.; Chen, P.; Xie, J.; Ye, S.Q.; Li, D.-Y.; Gong, S. Novel Genetic Variants Associated with Child Refractory Esophageal Stricture with Food Allergy by Exome Sequencing. Nutrients 2017, 9, 390.

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