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Background  Persistent pulmonary hypertension of the newborn (PPHN) is a severe clinical problem among neonatal intensive care unit (NICU) patients. The genetic pathogenesis of PPHN is unclear. Only a few genetic polymorphisms have been identified in infants with PPHN. Our study aimed to investigate the potential genetic etiology of PPHN.    Methods  This study recruited PPHN patients admitted to the NICU of the Children’s Hospital of Fudan University from Jan 2016 to Dec 2017. Exome sequencing was performed for all patients. Variants in reported PPHN/pulmonary arterial hypertension (PAH)-related genes were assessed. Single nucleotide polymorphism (SNP) association and gene-level analyses were carried out in 74 PPHN cases and 115 non-PPHN controls with matched baseline characteristics.    Results  Among the patient cohort, 74 (64.3%) patients were late preterm and term infants (≥ 34 weeks gestation) and 41 (35.7%) were preterm infants (< 34 weeks gestation). Preterm infants with PPHN exhibited low birth weight and a high frequency of bronchopulmonary dysplasia, respiratory distress syndrome (RDS) and mortality. Nine patients (only one preterm infant) were identified as harboring genetic variants, including three with pathogenic/likely pathogenic variants in  TBX4  and  BMPR2  and six with variants of unknown significance in  BMPR2 ,  SMAD9 ,  TGFB1 ,  KCNA5  and  TRPC6 . Three SNPs (rs192759073, rs1047883 and rs2229589) in  CPS1  and one SNP (rs1044008) in  NOTCH3  were significantly associated with PPHN ( p  < 0.05).  CPS1  and  SMAD9  were identified as risk genes for PPHN ( p  < 0.05).    Conclusions  In this study, we identified genetic variants in PPHN patients, and we reported  CPS1 ,  NOTCH3  and  SMAD9  as risk genes for late preterm and term PPHN in a single-center Chinese cohort. Our findings provide additional genetic evidence of the pathogenesis of PPHN and new insight into potential strategies for disease treatment.    Electronic supplementary material  The online version of this article (10.1186/s12931-019-1148-1) contains supplementary material, which is available to authorized users.

Identification of genetic factors underlying persistent pulmonary hypertension of newborns in a cohort of Chinese neonates