Identification of candidate genes and pathways in retinopathy of prematurity by whole exome sequencing of preterm infants enriched in phenotypic extremes

• Published in: Scientific reports Vol. 11; no. 1; pp. 4966 - 11
• Main Authors: Kim, Sang Jin, Sonmez, Kemal, Swan, Ryan, Campbell, J. Peter, Ostmo, Susan, Chan, R. V. Paul, Nagiel, Aaron, Drenser, Kimberly A., Berrocal, Audina M., Horowitz, Jason D., Li, Xiaohui, Chen, Yii-Der Ida, Taylor, Kent D., Simmons, Charles, Rotter, Jerome I., Chiang, Michael F.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 02.03.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208/212/2301; 692/699/3161/3175/3188; Ascorbic acid; Birth weight; Endoplasmic reticulum; Gene set enrichment analysis; Genes; Genetic factors; Genomes; Gestational age; Humanities and Social Sciences; Infants; multidisciplinary; Neonates; Newborn babies; Phenotypes; Premature babies; Premature birth; Retinopathy; Science; Science (multidisciplinary)
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-83552-y

Retinopathy of prematurity (ROP) is a vasoproliferative retinal disease affecting premature infants. In addition to prematurity itself and oxygen treatment, genetic factors have been suggested to predispose to ROP. We aimed to identify potentially pathogenic genes and biological pathways associated with ROP by analyzing variants from whole exome sequencing (WES) data of premature infants. As part of a multicenter ROP cohort study, 100 non-Hispanic Caucasian preterm infants enriched in phenotypic extremes were subjected to WES. Gene-based testing was done on coding nonsynonymous variants. Genes showing enrichment of qualifying variants in severe ROP compared to mild or no ROP from gene-based tests with adjustment for gestational age and birth weight were selected for gene set enrichment analysis (GSEA). Mean BW of included infants with pre-plus, type-1 or type 2 ROP including aggressive posterior ROP (n = 58) and mild or no ROP (n = 42) were 744 g and 995 g, respectively. No single genes reached genome-wide significance that could account for a severe phenotype. GSEA identified two significantly associated pathways (smooth endoplasmic reticulum and vitamin C metabolism) after correction for multiple tests. WES of premature infants revealed potential pathways that may be important in the pathogenesis of ROP and in further genetic studies.