title: Genetic variant characterization in intron 4 of the surfactant protein B gene.
abstract: Genetic variants in intron 4 of the surfactant protein B gene SFTPB have been associated with pulmonary morbidity in newborn infants and adults. Genetic variant discovery in intron 4 requires high fidelity polymerase amplification due to a variable number of intermotif dinucleotide repeats and reliable characterization of alleles genetically distinct due to insertion, deletion, or both of 11 conserved sequence motifs. To optimize genetic variant discovery, we selected a high fidelity polymerase enzyme by replicate amplification and compared automated sequencing with agarose gel electrophoresis for all variant alleles (N=68) in a cohort of Missouri infants with (N=187) and without (N=53) respiratory distress. We identified and characterized six new alleles based on sequence motifs and two pairs of variant alleles with similar mobilities by agarose gel electrophoresis but distinct motif sequences. We confirmed uniformity of invariant alleles by sequencing (N=77). Logistic regression using race and intron 4 genotype for infants > or = 35 weeks gestation suggested that the invariant allele was independently associated with increased risk of respiratory distress (OR for the invariant allele 2.7, 95% CI 1.0-7.2). Reliable characterization of genetic variants in intron 4 requires both a high fidelity polymerase and sequencing of variant alleles.
authors.affiliation: Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, Missouri, USA.
authors.forename: Aaron
authors.initials: A
authors.lastname: Hamvas
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Wegner
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Trusgnich
authors.forename: Katherine
authors.initials: K
authors.lastname: Madden
authors.forename: Hillary
authors.initials: H
authors.lastname: Heins
authors.forename: Ying
authors.initials: Y
authors.lastname: Liu
authors.forename: Treva
authors.initials: T
authors.lastname: Rice
authors.forename: Ping
authors.initials: P
authors.lastname: An
authors.forename: Julie
authors.initials: J
authors.lastname: Watkins-Torry
authors.forename: F Sessions
authors.initials: FS
authors.lastname: Cole
mesh_terms: D001483:Base Sequence; D015331:Cohort Studies; D017124:Conserved Sequence; D004252:DNA Mutational Analysis; D004259:DNA-Directed DNA Polymerase; D018900:Dinucleotide Repeats; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007231:Infant, Newborn; D007438:Introns; D008923:Missouri; D008969:Molecular Sequence Data; D009154:Mutation; D037701:Pulmonary Surfactant-Associated Protein B / Q000235:genetics*; D012131:Respiratory Insufficiency / Q000235:genetics*; D012307:Risk Factors
chemical_list: D037701:Pulmonary Surfactant-Associated Protein B; D004259:DNA-Directed DNA Polymerase