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HapMap and Association Studies for Complex Diseases Two Examples. Augustine Kong. Mapping of a susceptibility gene for Type 2 Diabetes . Also observed in Mexican Americans. Reynisdottir et al , AJHG 2003;73:323-35. Locus-wide association study. High density of markers – 10.5 Mb region
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Reynisdottir et al, AJHG 2003;73:323-35
(R2 = 0.95, P = 5.53×10-38)
adjustment gives a P of 7.7×10-15
Only one gene in the LD Block
TCF4 (official gene symbol: TCF7L2)
(with highest R2 among the Phase I SNPs)
Subsets: Iceland (331 patients, 320 controls) US (226 patients, 210 controls)
Further Search of the Causal Variant
risk of type 2 diabetes mellitus
Saturday Session #63
Struan F.A. Grant1, G. Thorleifsson1, I. Reynisdottir1, R. Benediktsson2,3, A. Manolescu1, J. Sainz1, H. Stefansson1, V. Emilsson1, A. Helgadottir1, U. Styrkarsdottir1, M.P. Reilly4, D.J. Rader4, Y. Bagger5, C. Christiansen5, V. Gudnason2, G. Sigurdsson2,3, U. Thorsteinsdottir1, J.R. Gulcher1, A. Kong1, K. Stefansson1
1) deCODE Genetics, Reykjavik, Iceland; 2) Icelandic Heart Association, Reykjavik, Iceland; 3) Landspitali-University Hospital, Reykjavik, Iceland; 4) University of Pennsylvania Health System, Philadelphia, USA; 5) Center for Clinical and Basic Research A/S, Ballerup, Denmark
Candidate Gene for Myocardial Infarction
Resides in one LD block where there is no other gene
10 SNPs from sequencing
capturing the haplotype diversity
LTA4H structure with exons shown as colored cylinders, and the position of all genotyped SNPs relative to exons shown as green lines. The SNPs and alleles defining HapK are SG12S16 (C) (positioned in NCBI human assembly build 34 on chr. 1294.896055 Mb), rs2660880 (G), rs6538697 (T), rs1978331 (A), rs17677715 (T), rs2247570 (T), rs2660898 (T), rs2540482 (C), rs2660845 (G), and rs2540475 (G), respectively. The relative position of SNPs typed in the HapMap project (Phase I, version 16c.1) are shown as grey lines.
Additional CVD – Peripheral vascular disease and/or Stroke
P-value of 0.0091 becomes 0.035 after adjusting for multiple haplotyes tested
Marginal significance and very modest risk. Needs replication!
a Additional CVD, Cleveland and Atlanta cohorts only; no information for Philadelphia
bP-values for replication are one-sided
Is this real or is this a consequence of some bias such as imperfect matching of
cases and controls? Note that frequency of HapK is substantially lower in the
African Americans compared to the European Americans.
--- all the three US cohorts
--- 364 Icelanders
--- 90 Nigerian Yorubans (HapMap)
--- 22.3% versus 19.9%
--- 20.0% versus 19.2%
admix adj: admixture adjustment using estimated European ancestry as covariate
b Cleveland and Atlanta cohorts only; information from Philadelphia not available
Note that for All MI, the RR confidence intervals for the European Americans
and African Americans do not overlap (P < 0.001)
--- requires further investigations
Poster # 962
Anna Helgadottir1, Andrei Manolescu1, Agnar Helgason1, Gudmar Thorleifsson1, Unnur Thorsteinsdottir1, Daniel F. Gudbjartsson1, Solveig Gretarsdottir1, Kristinn P. Magnusson1, Gudmundur Gudmundsson1, Andrew Hicks1, Thorlakur Jonsson1, Struan F. A. Grant1, Jesus Sainz1, Stephen J. O’Brien2, Sigurlaug Sveinbjornsdottir3, Einar M. Valdimarsson3, Stefan E. Matthiasson3, Allan I. Levey4, Gudmundur Thorgeirsson3, Jerome L. Abramson4, Murdach Reilly5, Viola Vaccarino4, Megan Wolfe5, Vilmundur Gudnason6, Arshed A. Quyyumi4, Eric J. Topol7, Daniel J. Rader5, Jeffrey R. Gulcher1, Hakon Hakonarson1,Augustine Kong1, Kari Stefansson1.
1deCODE genetics Inc, Reykjavik, Iceland
2Laboratory of Genomic Diversity, National Cancer Institute.
3National University Hospital, Reykjavik, Iceland
4Emory University School of Medicine, Atlanta, GA,USA
5University of Pennsylvania School of Medicine, Philadelphia, PA, USA
6Icelandic Heart Association, Reykjavik, Iceland
7Cleveland Clinic Foundation, Cleveland, OH, USA