A COMPREHENSIVE STUDY OF CANDIDATE GENES IN TWO SIGNALLING PATHWAYS TO IDENTIFY GENETIC VARIANTS THAT REGULATE PLATELET RESPONSIVENESS TO COLLAGEN AND ADP
Abstract number: O-M-075
Earthrowl1 M., Eades1 T., Angenent1 W., Griffiths2 S., Akkerman3 J., Burke4 D., Coffey1 A.J., Deloukas1 P., Dudbridge2 F., Dunn1 R., Farndale4 R.W., Hoylaerts5 M., Hunt1 S., Koch6 K., Ranhanath1 V., Rice1 K., Stephens6 J., Goodall7 A., Ouwehand6 W.H., Watkins6 N.A., Rogers1 J.
11Human Genetics, Wellcome Trust Sanger Institute 22MRC Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom 33Department of Haematology, Universitair Medisch Centrum, Utrecht, Netherlands 44Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom 55Laboratory for Thrombosis Research, Katholieke Universiteit Leuven, Kortrijk, Belgium 66Department of Haematology, University of Cambridge, Cambridge 77Department of Cardiovascular Science, University of Leicester, Leicester, United Kingdom
How-to-cite Earthrowl M, Eades T, Angenent W, Griffiths S, Akkerman J, Burke D, Coffey AJ, Deloukas P, Dudbridge F, Dunn R, Farndale RW, Hoylaerts M, Hunt S, Koch K, Ranhanath V, Rice K, Stephens J, Goodall A, Ouwehand WH, Watkins NA, Rogers J. A COMPREHENSIVE STUDY OF CANDIDATE GENES IN TWO SIGNALLING PATHWAYS TO IDENTIFY GENETIC VARIANTS THAT REGULATE PLATELET RESPONSIVENESS TO COLLAGEN AND ADP. J Thromb Haemost 2007; 5 Supplement 2: O-M-075
Abstract
Introduction: We postulate that variation in platelet response has a genetic component. Single nucleotide polymorphisms (SNPs), the most common source of sequence variation, can have significant effects on protein function and transcription. Using comprehensive knowledge of the collagen-GPVI/FcRg chain and ADP-P2Y12 signalling pathways we aim to determine the effect of sequence variation in platelet genes on function.
Methods: 110 genes encoding proteins in the CRP and ADP signallomes were identified, primers designed to the 2315 exons in these genes and exons re-sequenced in 48 Caucasoid reference samples. For ITGB1, ITGA2, GP6 and CD109, highly conserved non-coding regions (HCNCRs), identified by comparative genomics, were also sequenced. Protein abundance was measured in 500 controls to determine how sequence variation affects protein levels.
Results: A total of 1949 SNPs were identified and a comparison with the dbSNP database showed we had doubled the total number of SNPs with a specific enrichment of SNPs with a MAF of 0.03 to 0.1. Of the 89 nsSNPs, several were predicted to have a deleterious effect on protein structure and function including two in TUBB1, a protein in which genetic variants have been associated with arterial thrombosis. No nsSNPs were found in several genes, including ILK and BCL2, suggesting that they are protected against potentially damaging sequence variation in this cohort. Finally, a core panel of 1536 tag-SNPs were selected for genotyping the 110 loci with an r2>0.9 in 750 controls and 250 patients with myocardial infarction in whom extensive platelet function data is available.
Conclusions: Exon re-sequencing enriches for SNPs with a low MAF and identifies novel nsSNPs. Genotyping tag-SNPs in these 110 loci will identify genetic variants that regulate platelet responses to agonist. Integration of this data with those from recent Genome-Wide Association studies will aid the identification of SNPs associated with increased risk of atherothrombosis.
