title: Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families.
abstract: BACKGROUND
  Ataxia telangiectasia-mutated and Rad3-related (ATR) is a member of the PIK-related family which plays, along with ATM, a central role in cell-cycle regulation. ATR has been shown to phosphorylate several tumor suppressors like BRCA1, CHEK1 and TP53. ATR appears as a good candidate breast cancer susceptibility gene and the current study was designed to screen for ATR germline mutations potentially involved in breast cancer predisposition.
  
  
  METHODS
  ATR direct sequencing was performed using a fluorescent method while widely available programs were used for linkage disequilibrium (LD), haplotype analyses, and tagging SNP (tSNP) identification. Expression analyses were carried out using real-time PCR.
  
  
  RESULTS
  The complete sequence of all exons and flanking intronic sequences were analyzed in DNA samples from 54 individuals affected with breast cancer from non-BRCA1/2 high-risk French Canadian breast/ovarian families. Although no germline mutation has been identified in the coding region, we identified 41 sequence variants, including 16 coding variants, 3 of which are not reported in public databases. SNP haplotypes were established and tSNPs were identified in 73 healthy unrelated French Canadians, providing a valuable tool for further association studies involving the ATR gene, using large cohorts. Our analyses led to the identification of two novel alternative splice transcripts. In contrast to the transcript generated by an alternative splicing site in the intron 41, the one resulting from a deletion of 121 nucleotides in exon 33 is widely expressed, at significant but relatively low levels, in both normal and tumoral cells including normal breast and ovarian tissue.
  
  
  CONCLUSIONS
  Although no deleterious mutations were identified in the ATR gene, the current study provides an haplotype analysis of the ATR gene polymorphisms, which allowed the identification of a set of SNPs that could be used as tSNPs for large-scale association studies. In addition, our study led to the characterization of a novel Delta33 splice form, which could generate a putative truncated protein lacking several functional domains. Additional studies in large cohorts and other populations will be needed to further evaluate if common and/or rare ATR sequence variants can be associated with a modest or intermediate breast cancer risk.
authors.affiliation: Cancer Genomics Laboratory, Oncology and Molecular Endocrinology Research Centre, Centre Hospitalier Universitaire de Québec and Laval University, Québec, G1V 4G2, Canada. Francine.durocher@crchul.ulaval.ca
authors.forename: Francine
authors.initials: F
authors.lastname: Durocher
authors.forename: Yvan
authors.initials: Y
authors.lastname: Labrie
authors.forename: Penny
authors.initials: P
authors.lastname: Soucy
authors.forename: Olga
authors.initials: O
authors.lastname: Sinilnikova
authors.forename: Damian
authors.initials: D
authors.lastname: Labuda
authors.forename: Paul
authors.initials: P
authors.lastname: Bessette
authors.forename: Jocelyne
authors.initials: J
authors.lastname: Chiquette
authors.forename: Rachel
authors.initials: R
authors.lastname: Laframboise
authors.forename: Jean
authors.initials: J
authors.lastname: Lépine
authors.forename: Bernard
authors.initials: B
authors.lastname: Lespérance
authors.forename: Geneviève
authors.initials: G
authors.lastname: Ouellette
authors.forename: Roxane
authors.initials: R
authors.lastname: Pichette
authors.forename: Marie
authors.initials: M
authors.lastname: Plante
authors.forename: Sean V
authors.initials: SV
authors.lastname: Tavtigian
authors.forename: Jacques
authors.initials: J
authors.lastname: Simard
mesh_terms: D000328:Adult; D000368:Aged; D017398:Alternative Splicing; D064007:Ataxia Telangiectasia Mutated Proteins; D001483:Base Sequence; D001943:Breast Neoplasms / Q000208:ethnology / Q000235:genetics*; D018797:Cell Cycle Proteins / Q000235:genetics*; D016384:Consensus Sequence; D004247:DNA / Q000235:genetics; D004252:DNA Mutational Analysis; D004273:DNA, Neoplasm / Q000235:genetics*; D005006:Ethnicity / Q000235:genetics; D005091:Exons / Q000235:genetics; D005260:Female; D005602:France / Q000208:ethnology; D020022:Genetic Predisposition to Disease; D018095:Germ-Line Mutation; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium; D008875:Middle Aged; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins / Q000235:genetics*; D009386:Neoplastic Syndromes, Hereditary / Q000208:ethnology / Q000235:genetics*; D010051:Ovarian Neoplasms / Q000208:ethnology / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017346:Protein Serine-Threonine Kinases / Q000235:genetics*; D011792:Quebec / Q000453:epidemiology; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D012334:RNA, Neoplasm / Q000096:biosynthesis / Q000235:genetics; D012306:Risk; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion
chemical_list: D018797:Cell Cycle Proteins; D004273:DNA, Neoplasm; D009363:Neoplasm Proteins; D012333:RNA, Messenger; D012334:RNA, Neoplasm; D004247:DNA; C576597:ATR protein, human; D064007:Ataxia Telangiectasia Mutated Proteins; D017346:Protein Serine-Threonine Kinases