title: Exome Sequencing of Neonatal Blood Spots and the Identification of Genes Implicated in Bronchopulmonary Dysplasia.
abstract: BACKGROUND
  Bronchopulmonary dysplasia (BPD), a prevalent severe lung disease of premature infants, has a strong genetic component. Large-scale genome-wide association studies for common variants have not revealed its genetic basis.
  
  
  OBJECTIVE
  Given the historical high mortality rate of extremely preterm infants who now survive and develop BPD, we hypothesized that risk loci underlying this disease are under severe purifying selection during evolution; thus, rare variants likely explain greater risk of the disease.
  
  
  METHODS
  We performed exome sequencing on 50 BPD-affected and unaffected twin pairs using DNA isolated from neonatal blood spots and identified genes affected by extremely rare nonsynonymous mutations. Functional genomic approaches were then used to systematically compare these affected genes.
  
  
  RESULTS
  We identified 258 genes with rare nonsynonymous mutations in patients with BPD. These genes were highly enriched for processes involved in pulmonary structure and function including collagen fibril organization, morphogenesis of embryonic epithelium, and regulation of Wnt signaling pathway; displayed significantly elevated expression in fetal and adult lungs; and were substantially up-regulated in a murine model of BPD. Analyses of mouse mutants revealed their phenotypic enrichment for embryonic development and the cyanosis phenotype, a clinical manifestation of BPD.
  
  
  CONCLUSIONS
  Our study supports the role of rare variants in BPD, in contrast with the role of common variants targeted by genome-wide association studies. Overall, our study is the first to sequence BPD exomes from newborn blood spot samples and identify with high confidence genes implicated in BPD, thereby providing important insights into its biology and molecular etiology.
authors.affiliation: 1 Department of Genetics, Center for Genomics and Personalized Medicine.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Li
authors.affiliation: 1 Department of Genetics, Center for Genomics and Personalized Medicine.|2 Biomedical Informatics Program, and.
authors.forename: Kun-Hsing
authors.identifier: http://orcid.org/0000-0001-9892-8218
authors.initials: KH
authors.lastname: Yu
authors.affiliation: 3 Department of Pediatrics, Stanford University School of Medicine, Stanford, California.
authors.forename: John
authors.initials: J
authors.lastname: Oehlert
authors.affiliation: 4 California Department of Public Health, Richmond, California; and.|5 Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.
authors.forename: Laura L
authors.initials: LL
authors.lastname: Jeliffe-Pawlowski
authors.affiliation: 3 Department of Pediatrics, Stanford University School of Medicine, Stanford, California.
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Gould
authors.affiliation: 3 Department of Pediatrics, Stanford University School of Medicine, Stanford, California.
authors.forename: David K
authors.initials: DK
authors.lastname: Stevenson
authors.affiliation: 1 Department of Genetics, Center for Genomics and Personalized Medicine.
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.affiliation: 3 Department of Pediatrics, Stanford University School of Medicine, Stanford, California.
authors.forename: Gary M
authors.initials: GM
authors.lastname: Shaw
authors.affiliation: 3 Department of Pediatrics, Stanford University School of Medicine, Stanford, California.
authors.forename: Hugh M
authors.initials: HM
authors.lastname: O'Brodovich
mesh_terms: D000818:Animals; D001800:Blood Specimen Collection; D001997:Bronchopulmonary Dysplasia / Q000235:genetics*; D016022:Case-Control Studies; D059472:Exome / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D057895:Haploinsufficiency; D006801:Humans; D007223:Infant; D062071:Infant, Extremely Premature; D007231:Infant, Newborn; D007234:Infant, Premature; D008168:Lung / Q000196:embryology*; D008297:Male; D051379:Mice; D009024:Morphogenesis / Q000235:genetics*; D015997:Neonatal Screening; D017422:Sequence Analysis, DNA; D014429:Twins, Dizygotic / Q000235:genetics*; D014430:Twins, Monozygotic / Q000235:genetics*; D060449:Wnt Signaling Pathway / Q000235:genetics*
keywords: bronchopulmonary dysplasia; chronic lung disease; exome sequencing; genetic predisposition to disease; premature