title: A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer.
abstract: BACKGROUND
  Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significantly increases the number of VUS detected. While prior studies have emphasized protein coding variants, non-coding sequence variants have also been proven to significantly contribute to high penetrance disorders, such as hereditary breast and ovarian cancer (HBOC). We present a strategy for analyzing different functional classes of non-coding variants based on information theory (IT) and prioritizing patients with large intragenic deletions.
  
  
  METHODS
  We captured and enriched for coding and non-coding variants in genes known to harbor mutations that increase HBOC risk. Custom oligonucleotide baits spanning the complete coding, non-coding, and intergenic regions 10 kb up- and downstream of ATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2, and TP53 were synthesized for solution hybridization enrichment. Unique and divergent repetitive sequences were sequenced in 102 high-risk, anonymized patients without identified mutations in BRCA1/2. Aside from protein coding and copy number changes, IT-based sequence analysis was used to identify and prioritize pathogenic non-coding variants that occurred within sequence elements predicted to be recognized by proteins or protein complexes involved in mRNA splicing, transcription, and untranslated region (UTR) binding and structure. This approach was supplemented by in silico and laboratory analysis of UTR structure.
  
  
  RESULTS
  15,311 unique variants were identified, of which 245 occurred in coding regions. With the unified IT-framework, 132 variants were identified and 87 functionally significant VUS were further prioritized. An intragenic 32.1 kb interval in BRCA2 that was likely hemizygous was detected in one patient. We also identified 4 stop-gain variants and 3 reading-frame altering exonic insertions/deletions (indels).
  
  
  CONCLUSIONS
  We have presented a strategy for complete gene sequence analysis followed by a unified framework for interpreting non-coding variants that may affect gene expression. This approach distills large numbers of variants detected by NGS to a limited set of variants prioritized as potential deleterious changes.
authors.affiliation: Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada.
authors.forename: Eliseos J
authors.initials: EJ
authors.lastname: Mucaki
authors.affiliation: Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada.
authors.forename: Natasha G
authors.initials: NG
authors.lastname: Caminsky
authors.affiliation: Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada.
authors.forename: Ami M
authors.initials: AM
authors.lastname: Perri
authors.affiliation: Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada.
authors.forename: Ruipeng
authors.initials: R
authors.lastname: Lu
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3290, USA.
authors.forename: Alain
authors.initials: A
authors.lastname: Laederach
authors.affiliation: Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, 10032, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Halvorsen
authors.affiliation: Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada.|Cytognomix Inc., London, Canada.
authors.forename: Joan H M
authors.initials: JH
authors.lastname: Knoll
authors.affiliation: Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada. progan@uwo.ca.|Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada. progan@uwo.ca.|Cytognomix Inc., London, Canada. progan@uwo.ca.|Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada. progan@uwo.ca.
authors.forename: Peter K
authors.initials: PK
authors.lastname: Rogan
mesh_terms: D001483:Base Sequence; D001943:Breast Neoplasms / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics*; D005091:Exons / Q000235:genetics; D005260:Female; D020022:Genetic Predisposition to Disease; D006801:Humans; D007257:Information Theory; D040582:Inheritance Patterns / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D009690:Nucleic Acid Conformation; D010051:Ovarian Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011485:Protein Binding / Q000235:genetics; D020033:Protein Isoforms / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion / Q000235:genetics; D020506:Untranslated Regions / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D020033:Protein Isoforms; D022821:RNA Splice Sites; D020506:Untranslated Regions
keywords: Hereditary breast and ovarian cancer; Information theory; Next-generation sequencing; Non-coding; Prioritization; RNA-binding protein; Splicing; Transcription factor binding; Variants of uncertain significance