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Detection and frequency estimation of rare variants in pools of genomic DNA from large populations using mutational spectrometry |
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| Authors: | Li-Sucholeiki Xiao-Cheng Tomita-Mitchell Aoy Arnold Kevin Glassner Brian J Thompson Terri Murthy Jaitra V Berk Lori Lange Craig Leong-Morgenthaler Phaik-Mooi MacDougall Damien Munro John Cannon Donald Mistry Trupti Miller Art Deka Chiranjit Karger Barry Gillespie Kathleen M Ekstrøm Per O Todd John A Thilly William G |
| Institution: | aBeckman Coulter, Inc., 6-C Gill Street, Woburn, MA 01801, USA bInstitute of Pharmacology and Toxicology, University of Lausanne, Rue du Bugnon 27, 1005 Lausanne, Switzerland cDepartment of Chemistry, University of Tampa, 401 West Kennedy Boulevard, Tampa, FL 33606, USA dJuvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK eBarnett Institute and Department of Chemistry, Northeastern University, Boston, MA 02115, USA fDivision of Medicine, University of Bristol, Bristol, UK gDepartment of Surgical Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, N-0310 Oslo, Norway hBiological Engineering Division, Room 16-743, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA |
| 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. |
| Keywords: | Rare variants CTLA-4 Type 1 diabetes Genetic association Pooled DNA |
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