title: Exome sequencing and pathway analysis for identification of genetic variability relevant for bronchopulmonary dysplasia (BPD) in preterm newborns: A pilot study.
abstract: BACKGROUND
  Bronchopulmonary dysplasia (BPD) is the most common chronic lung disease in infancy, affecting preterm children with low birth weight. The disease has a multifactorial aetiology with a significant genetic component; until now published association studies have identified several candidate genes but only few of these data has been replicated. In this pilot study, we approached exome sequencing aimed at identifying non-common variants, which are expected to have a stronger phenotypic effect.
  
  
  METHODS
  We performed this study on 26 Italian severely affected BPD preterm unrelated newborns, homogeneously selected from a large prospective cohort. We used an Illumina HiSeq 2000 for sequencing. Data analysis was focussed on genes previously associated to BPD susceptibility and to new candidates in related pathways, highlighted by a prioritization analysis performed using ToppGene Suite.
  
  
  RESULTS
  By exome sequencing, we identified 3369 novel variants, with a median of 400 variations per sample. The top candidate genes highlighted were NOS2, MMP1, CRP, LBP and the toll-like receptor (TLR) family. All of them have been confirmed with Sanger sequencing.
  
  
  CONCLUSIONS
  Potential candidate genes have been discovered in this preliminary study; the pathogenic role of identified variants will need to be confirmed with functional and segregation studies and possibly with further methods, able to evaluate the collective influence of rare variants. Moreover, additional candidates will be tested and genetic analysis will be extended to all affected children.
authors.affiliation: Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milano, Italy. Electronic address: carrera.paola@hsr.it.
authors.forename: Paola
authors.initials: P
authors.lastname: Carrera
authors.affiliation: Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Di Resta
authors.affiliation: Vita-Salute San Raffaele University, Milano, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Volonteri
authors.affiliation: Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy.
authors.forename: Emanuela
authors.initials: E
authors.lastname: Castiglioni
authors.affiliation: Centre for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Bonfiglio
authors.affiliation: Centre for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy.
authors.forename: Dejan
authors.initials: D
authors.lastname: Lazarevic
authors.affiliation: Centre for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Cittaro
authors.affiliation: Centre for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy.
authors.forename: Elia
authors.initials: E
authors.lastname: Stupka
authors.affiliation: Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milano, Italy; Vita-Salute San Raffaele University, Milano, Italy.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Ferrari
authors.affiliation: Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Somaschini
mesh_terms: D001483:Base Sequence; D001997:Bronchopulmonary Dysplasia / Q000175:diagnosis / Q000235:genetics*; D004247:DNA / Q000235:genetics; D059472:Exome / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007234:Infant, Premature / Q000097:blood / Q000378:metabolism*; D007363:Intensive Care Units, Neonatal; D010865:Pilot Projects
chemical_list: D004247:DNA
keywords: Bronchopulmonary dysplasia; Exome sequencing; Genetics