title: Detection and frequency estimation of rare variants in pools of genomic DNA from large populations using mutational spectrometry.
abstract: DNA variants underlying the inheritance of risk for common diseases are expected to have a wide range of population allele frequencies. The detection and scoring of the rare alleles (at frequencies of <0.01) presents significant practical problems, including the requirement for large sample sizes and the limitations inherent in current methodologies for allele discrimination. In the present report, we have applied mutational spectrometry based on constant denaturing capillary electrophoresis (CDCE) to DNA pools from large populations in order to improve the prospects of testing the role of rare variants in common diseases on a large scale. We conducted a pilot study of the cytotoxic T lymphocyte-associated antigen-4 gene (CTLA4) in type 1 diabetes (T1D). A total of 1228 bp, comprising 98% of the CTLA4 coding sequence, all adjacent intronic mRNA splice sites, and a 3' UTR sequence were scanned for unknown point mutations in pools of genomic DNA from a control population of 10,464 young American adults and two T1D populations, one American (1799 individuals) and one from the United Kingdom (2102 individuals). The data suggest that it is unlikely that rare variants in the scanned regions of CTLA4 represent a significant proportion of T1D risk and illustrate that CDCE-based mutational spectrometry of DNA pools offers a feasible and cost-effective means of testing the role of rare variants in susceptibility to common diseases.
authors.affiliation: Beckman Coulter, Inc., 6-C Gill Street, Woburn, MA 01801, USA.
authors.forename: Xiao-Cheng
authors.initials: XC
authors.lastname: Li-Sucholeiki
authors.forename: Aoy
authors.initials: A
authors.lastname: Tomita-Mitchell
authors.forename: Kevin
authors.initials: K
authors.lastname: Arnold
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Glassner
authors.forename: Terri
authors.initials: T
authors.lastname: Thompson
authors.forename: Jaitra V
authors.initials: JV
authors.lastname: Murthy
authors.forename: Lori
authors.initials: L
authors.lastname: Berk
authors.forename: Craig
authors.initials: C
authors.lastname: Lange
authors.forename: Phaik-Mooi
authors.initials: PM
authors.lastname: Leong-Morgenthaler
authors.forename: Damien
authors.initials: D
authors.lastname: MacDougall
authors.forename: John
authors.initials: J
authors.lastname: Munro
authors.forename: Donald
authors.initials: D
authors.lastname: Cannon
authors.forename: Trupti
authors.initials: T
authors.lastname: Mistry
authors.forename: Art
authors.initials: A
authors.lastname: Miller
authors.forename: Chiranjit
authors.initials: C
authors.lastname: Deka
authors.forename: Barry
authors.initials: B
authors.lastname: Karger
authors.forename: Kathleen M
authors.initials: KM
authors.lastname: Gillespie
authors.forename: Per O
authors.initials: PO
authors.lastname: Ekstrøm
authors.forename: John A
authors.initials: JA
authors.lastname: Todd
authors.forename: William G
authors.initials: WG
authors.lastname: Thilly
mesh_terms: D000328:Adult; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D017931:DNA Primers; D019075:Electrophoresis, Capillary; D005828:Genetics, Population; D006801:Humans; D016133:Polymerase Chain Reaction
chemical_list: D017931:DNA Primers; D004247:DNA