title: Functional and genomic approaches reveal an ancient CHEK2 allele associated with breast cancer in the Ashkenazi Jewish population.
abstract: Functional and genomic approaches can be integrated to screen efficiently for pathogenic alleles in founder populations. We applied such approaches to analysis of the cancer-associated cell cycle regulator CHEK2 in the Ashkenazi Jewish population. We first identified two extended haplotypes at CHEK2 that co-segregated with breast cancer in high-risk families. We sequenced CHEK2 in a case representing each haplotype and discovered two novel amino acid substitutions, CHEK2.S428F in the kinase domain and CHEK2.P85L in the N-terminal region. To assay these alleles for loss of CHEK2 function, we tested their capacity to complement Rad53 deletion in Saccharomyces cerevisiae. CHEK2.S428F failed to complement Rad53 and thus largely abrogates normal CHEK2 function, whereas CHEK2.P85L complemented Rad53 as well as did wild-type CHEK2. Epidemiologic analyses were concordant with the functional tests. Frequencies of CHEK2.S428F heterozygotes were 2.88% (47/1632) among female breast cancer patients not selected for family history or age at diagnosis and 1.37% (23/1673) among controls (OR=2.13, 95% CI [1.26, 3.69], P=0.004), whereas frequencies of CHEK2.P85L were 0.92% among cases and 0.83% among controls. On the basis of the experience of mothers, sisters and daughters of probands, breast cancer risk due to CHEK2.S428F was estimated as 0.17 (+/-0.08) by age 60. We conclude that CHEK2.S428F increases breast cancer risk approximately 2-fold among Ashkenazi Jewish women, whereas CHEK2.P85L is a neutral allele. In general, these results suggest that selecting probands with extended haplotypes that co-segregate with disease can improve the efficiency of resequencing efforts and that quantitative complementation tests in yeast can be used to evaluate variants in genes with highly conserved function.
authors.affiliation: Department of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195-7720, USA.
authors.forename: Avraham
authors.initials: A
authors.lastname: Shaag
authors.forename: Tom
authors.initials: T
authors.lastname: Walsh
authors.forename: Paul
authors.initials: P
authors.lastname: Renbaum
authors.forename: Tomas
authors.initials: T
authors.lastname: Kirchhoff
authors.forename: Khedoudja
authors.initials: K
authors.lastname: Nafa
authors.forename: Stacey
authors.initials: S
authors.lastname: Shiovitz
authors.forename: Jessica B
authors.initials: JB
authors.lastname: Mandell
authors.forename: Piri
authors.initials: P
authors.lastname: Welcsh
authors.forename: Ming K
authors.initials: MK
authors.lastname: Lee
authors.forename: Nathan
authors.initials: N
authors.lastname: Ellis
authors.forename: Kenneth
authors.initials: K
authors.lastname: Offit
authors.forename: Ephrat
authors.initials: E
authors.lastname: Levy-Lahad
authors.forename: Mary-Claire
authors.initials: MC
authors.lastname: King
mesh_terms: D019943:Amino Acid Substitution; D001943:Breast Neoplasms / Q000201:enzymology / Q000453:epidemiology / Q000235:genetics*; D018797:Cell Cycle Proteins / Q000235:genetics; D064447:Checkpoint Kinase 2; D005260:Female; D005787:Gene Frequency; D005816:Genetic Complementation Test; D020022:Genetic Predisposition to Disease; D006239:Haplotypes; D006579:Heterozygote; D006801:Humans; D007585:Jews; D008297:Male; D009154:Mutation / Q000235:genetics*; D017346:Protein Serine-Threonine Kinases / Q000172:deficiency / Q000235:genetics*; D012307:Risk Factors; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D017384:Sequence Deletion
chemical_list: D018797:Cell Cycle Proteins; D029701:Saccharomyces cerevisiae Proteins; D064447:Checkpoint Kinase 2; C578634:CHEK2 protein, human; D017346:Protein Serine-Threonine Kinases; C067022:RAD53 protein, S cerevisiae