Linkage, Association, and Type 2 Diabetes Susceptibility. Karen Mohlke, Ph.D. Department of Genetics University of North Carolina - Chapel Hill

Transcription

1 Linkage, Association, and Type 2 Diabetes Susceptibility Karen Mohlke, Ph.D. Department of enetics University of North Carolina - Chapel Hill

2 Increasing prevalence of diabetes % % % % % World 2010: 221 million Increase +46% % Adapted from Zimmet et al (2001) Nature 414:782

3 Diabetes: a disorder of glucose metabolism Saltiel and Kahn (2001) Nature 414:799

4 Characteristics of complex traits Many genes Environmental role Incomplete penetrance Phenocopy Continuous phenotype

5 Contributions to a complex trait % risk to individual major gene a minor gene a minor gene b minor gene c exposure a exposure b % risk to individual

6 enetics of type 2 diabetes mellitus Concordance rates in MZ twins are approximately double those in DZ twins Relative risk to siblings/parents/offspring compared to population ~3.5

7 Contributions to type 2 diabetes PPAR KCNJ11 IRS1 CAPN10? minor gene? minor gene obesity sedentary lifestyle? exposure? exposure population risk

8 Diabetes: a disorder of glucose metabolism Saltiel and Kahn (2001) Nature 414:799

9 The FUSION Study Design Finland-United States Investigation of NIDDM enetics Linkage study using 2 or more affected siblings Association study using one sibling per family, spouses and elderly controls Additional relatives collected to determine haplotypes and some phenotypes

10 FUSION samples Linkage F1 Type 2 Diabetes cases: 1129 F2 Type 2 Diabetes cases: 580 Association F1 T2D cases: 532 F2 T2D cases: 263 Spouse controls: 190 Elderly controls: 225 At-risk offspring:

11 All subjects Phenotypic traits studied Fasting glucose, insulin Body mass index, weight, waist-to-hip ratio Lipids, blood pressure, pulse Free fatty acids Affecteds only Fasting C-peptide (insulin) Insulin secretion = fasting C-peptide/fasting glucose Unaffecteds only Oral glucose tolerance test (OTT) Frequently-sampled intravenous glucose-tolerance test (FSIT)

12 Linkage analysis Fine mapping with SNPs Association identified Extent of association determined Functional effect tested Causative variant identified

13 Linkage in affected sibling pairs alleles shared 0 1 2

14 enome scan linkage results X hosh (2000) AJH 67:1174 Silander (2004) Diabetes 53:821

15 Initial evidence for chr20q linkage Study Population LOD cm Trait Zouali (1997) French Caucasian Early-onset T2D Ji (1997); Klupa (2000) US Caucasian Middle-age-onset T2D Bowden (1997) US Caucasian T2D+diabetic nephropathy NPL scores converted to LOD scores cm positions adjusted to Marshfield genetic map

16 Evidence for chr20q T2D linkage Study Population Score cm Trait Zouali 1997 French Caucasian 1.31 MLS 51 T2D Permutt 2001 Ashkenazim 2.05 NPL 51 T2D Love-regory 2004 Ashkenazim 2.01 MLS 51 T2D diagnosis>35yrs Iwasaki Japanese 1.99 MLS 56 T2D Mori 2002 Japanese 2.32 MLS 62 Lean T2D Mori 2002 Japanese 1.67 MLS 62 T2D Bowden 1997 US Caucasian 1.48 MLS 66 T2D+nephropathy Vionnet 2000 French Caucasian 1.72 MLS 66 Large T2D families hosh 00; Silander 2004 Finnish Caucasian 2.48 MLS 66 T2D Ji 1997; Klupa 2000 US Caucasian 5.32 NPL 75 Middle-age-onset T2D Luo 2001 Han Chinese 1.52 NPL 75 T2D Rotimi 2004 West African 1.80 MLS 76 T2D Zouali 1997 French Caucasian 2.34 MLS 82 Early onset T2D Rotimi 2004 West African 2.63 MLS 93 T2D

17 Maximum LOD score enome scan linkage results: chr LOD = 2.48 at 70 cm F1 F2 F1+F Map position (cm)

18 Association analysis 400 controls 400 cases 5% variant nucleotide 15% variant nucleotide

19 enotyping of DNA pools F1 cases Elderly controls Mohlke et al. (2002) PNAS 99:16928

20 Screen for association using DNA pools 4 HNF4A X F1 vs EC F1&F2 vs EC&SP -log 10 (P-value) Position (kilobases)

21 Hepatocyte Nuclear Factor 4 Alpha

22 HNF4A in MODY1 Maturity onset diabetes of the young Autosomal dominant early-onset diabetes Defective glucose-induced insulin secretion MODY1 mutations: Missense, nonsense, frameshift, insertion Translocation between P2 and P1 promoters Likely MODY mechanism: haploinsufficiency Possible T2D mechanism?

23 Diabetes: a disorder of glucose metabolism Saltiel and Kahn (2001) Nature 414:799

24 Hepatocyte Nuclear Factor 4 Alpha Expressed: liver, pancreas, kidney, intestine Developmentally regulated Several splice variants Part of a complex transcriptional network Many downstream targets Odom (2004) Science 303: % of actively transcribed genes in liver 43% of actively transcribed genes in islets

25 Evidence for association near HNF4A P2 P1 3 rs log 10 (P-value) 2 1 rs Position (kilobases)

26 Linkage disequilibrium (LD) near HNF4A P2 P1 1 Cases Controls D Position (kilobases)

27 Hepatocyte Nuclear Factor 4 Alpha

28 3 Confirmed association with T2D in Ashkenazim P2 P1 -log 10 (P-value) Position (kilobases)

29 Minor allele frequency Confirmed association with T2D in Ashkenazim (rs ) Finns p=.011 and OR=1.33 Ashkenazim p=.006 and OR= cases controls cases controls

30 Evidence for association of HNF4A P2 SNPs in other populations Study Population Samples Result Silander et al Finnish 795 cases, 414 controls P=.011, OR=1.33 Love-regory et al Israel Ashkenazi Jewish 275 cases, 342 controls P=.008, OR=1.45 Weedon et al United Kingdom Caucasian 2004 cases, 1635 controls, 509 trio families P=.02, OR=1.15 Damcott et al Amish 137 T2D+139 IT, 342 NT individuals T2D+IT v. NT: Trend toward association, P=.07, OR=1.35 Winckler et al Swedish, Finnish and Canadian 1721 T2D+IT, 1692 NT individuals 1-tail P=.05, OR=1.11 Winckler et al North American and Polish 2235 T2D+IT, 2235 NT individuals OR=.88

31 Maximum LOD score Role of linkage detecting association HNF4A F1 F2 F1+F Map position (cm)

32 HNF4A SNPs associated with diabetes-related quantitative traits Insulin response Insulin to glucose Sensitivity 2.5 P =.022 P = x 10-2 *pmol*l -1 *8min *min -1 *pmol -1 *l AA A n= AA A

33 Evidence for association near HNF4A P2 P1 3 -log 10 (P-value) Position (kilobases)

34 HNF4A haplotypes associated with T2D Case Freq Control Freq Odds ratio P- value A C T C A

35 HNF4A haplotypes associated with T2D T T C C T C C T C A A C T C A C T C A C T C A T A C T A T C A P- value Odds ratio Control Freq Case Freq

36 Prior evidence for HNF4A in T2D Rare mutations in T2D: T110I reduces transactivation Ek (2005) JCEM in press V393I reduces transactivation Hani (1998) JCI 101:521 Deletion of Sp1 site in P1 promoter Price (2000) Dbtlg 43:364 V255M reduces transactivation Lausen (2000) NAR 28:430 Navas (1999) Diabetes 48:1459 Common protective haplotype Barroso (2003) PLoS Bio 1:41 P2 P1

37 Hepatocyte Nuclear Factor 4 Alpha Next steps: Altered expression in high vs low-risk alleles? Location of conserved functional elements? Functional consequences of altered P2 expression?

38 HNF4A Summary Common, noncoding HNF4A SNPs near P2 promoter associated with T2D in Finns Apparent confirmation in other populations Region of extensive linkage disequilibrium Confirmed T2D-associated SNPs span ~15 kb SNPs with similar effect could be located >100 kb away Association with decreased insulin secretion Unclear how many causative alleles exist

39 Haplotype Map (HapMap) individuals from 4 populations Caucasian, Yoruba, Japanese, Chinese March 2005 genotype data available: >1 million SNPs on 270 individuals mid genotype data expected: >5 million SNPs

40

41 Haploview

42 Contributions to type 2 diabetes PPAR KCNJ11 IRS1 CAPN10 HNF4A?? minor gene? minor gene obesity sedentary lifestyle? exposure population risk

43 Acknowledgments UNC Chapel Hill Li Qin NHRI / NIH Francis Collins Lori Bonnycastle Peter Chines Michael Erdos Erin Peck Kaisa Silander National Public Health Institute, Helsinki Jaakko Tuomilehto Timo Valle University of Michigan Michael Boehnke William Duren Tasha Fingerlin Anne Jackson Mingyao Li Laura Scott Andrew Skol Cristen Willer U Southern California Richard Bergman Tom Buchanan Richard Watanabe Washington University Alan Permutt Ben laser Latisha Love-regory Jiyan Ma Brian Suarez Jon Wasson Sanger Institute Panos Deloukas Sarah Hunt eorge Stavrides