title: The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia.
abstract: BACKGROUND
  Mutational analysis is commonly used to support the diagnosis and management of haemophilia. This has allowed for the generation of large mutation databases which provide unparalleled insight into genotype-phenotype relationships. Haemophilia is associated with inversions, deletions, insertions, nonsense and missense mutations. Both synonymous and non-synonymous mutations influence the base pairing of messenger RNA (mRNA), which can alter mRNA structure, cellular half-life and ribosome processivity/elongation. However, the role of mRNA structure in determining the pathogenicity of point mutations in haemophilia has not been evaluated.
  
  
  OBJECTIVE
  To evaluate mRNA thermodynamic stability and associated RNA prediction software as a means to distinguish between neutral and disease-associated mutations in haemophilia.
  
  
  METHODS
  Five mRNA structure prediction software programs were used to assess the thermodynamic stability of mRNA fragments carrying neutral vs. disease-associated and synonymous vs. non-synonymous point mutations in F8, F9 and a third X-linked gene, DMD (dystrophin).
  
  
  RESULTS
  In F8 and DMD, disease-associated mutations tend to occur in more structurally stable mRNA regions, represented by lower MFE (minimum free energy) levels. In comparing multiple software packages for mRNA structure prediction, a 101-151 nucleotide fragment length appears to be a feasible range for structuring future studies.
  
  
  CONCLUSIONS
  mRNA thermodynamic stability is one predictive characteristic, which when combined with other RNA and protein features, may offer significant insight when screening sequencing data for novel disease-associated mutations. Our results also suggest potential utility in evaluating the mRNA thermodynamic stability profile of a gene when determining the viability of interchanging codons for biological and therapeutic applications.
authors.affiliation: Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation & Research, United States Food and Drug Administration, Silver Spring, MD, USA.
authors.forename: N
authors.initials: N
authors.lastname: Hamasaki-Katagiri
authors.affiliation: Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation & Research, United States Food and Drug Administration, Silver Spring, MD, USA.
authors.forename: B C
authors.initials: BC
authors.lastname: Lin
authors.affiliation: Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation & Research, United States Food and Drug Administration, Silver Spring, MD, USA.
authors.forename: J
authors.initials: J
authors.lastname: Simon
authors.affiliation: Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation & Research, United States Food and Drug Administration, Silver Spring, MD, USA.
authors.forename: R C
authors.initials: RC
authors.lastname: Hunt
authors.affiliation: Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation & Research, United States Food and Drug Administration, Silver Spring, MD, USA.
authors.forename: T
authors.initials: T
authors.lastname: Schiller
authors.affiliation: Division of Biostatistics, Center for Biologics Evaluation & Research, United States Food and Drug Administration, Silver Spring, MD, USA.
authors.forename: E
authors.initials: E
authors.lastname: Russek-Cohen
authors.affiliation: Center for Gene Regulation in Health and Disease, Department of Biological, Geological & Environmental Sciences, Cleveland State University, Cleveland, OH, USA.
authors.forename: A A
authors.initials: AA
authors.lastname: Komar
authors.affiliation: Department of Statistics, College of Liberal Arts and Sciences, University of Connecticut, Storrs, CT, USA.
authors.forename: H
authors.initials: H
authors.lastname: Bar
authors.affiliation: Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation & Research, United States Food and Drug Administration, Silver Spring, MD, USA.
authors.forename: C
authors.initials: C
authors.lastname: Kimchi-Sarfaty
mesh_terms: D004252:DNA Mutational Analysis / Q000379:methods*; D006467:Hemophilia A / Q000235:genetics*; D006801:Humans; D009154:Mutation; D012333:RNA, Messenger / Q000235:genetics*
chemical_list: D012333:RNA, Messenger
keywords: 
  F8
  ; 
  MFE
  ; RNA prediction software; haemophilia; mRNA thermodynamic stability; synonymous mutations