Genetics of Type 2 Diabetes

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Genetics of Type 2 Diabetes
HUEC 7005 Molecular and Clinical Nutrition II.
August 28, 2008
Eric Ravussin Pennington Biomedical Research
Center. Ravusse_at_pbrc.edu
2
What is Diabetes Mellitus?

• Diabetes mellitus is a metabolic disorder
  characterized by high blood glucose levels
  resulting from defects in insulin secretion,
  insulin action or both. The chronic high blood
  glucose levels are associated with long-term
  tissue damage, dysfunction and failure of various
  organs especially the eyes, kidneys, nerves,
  heart and blood vessels.

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Diabetes Mellitus

• Over the years, better phenotyping (e.g.
  introduction of assay for insulin) and recently,
  genetic studies have shown that diabetes is a
  phenotypically and genetically heterogeneous
  disorder.

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Genetics of Diabetes Mellitus

• Monogenic forms (MODY)
• Inherit diabetes per se.
• Mutation in a single gene is sufficient to cause
  diabetes.
• Polygenic forms (Type 1 and Type 2 diabetes)
• Inherit susceptibility to diabetes.
• Diabetes develops in genetically susceptible
  individuals but only in the presence of
  nongenetic risk factors.

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Diabetes Mellitus in 2006
MODY 1 (HNF4a)
MODY 2 (Glucokinase)
MODY 3 (HNF1a)
MODY 4 (IPF1)
MODY 5 (HNF1b)
Type 1
Type 1
MODY 6 (Beta2/NeuroD)
Type 2
Type 2
Insulinopathies (Preproinsulin)
MIDD (Mitochonchrial DNA)
Syndromes of
Other
Other
extreme insulin (Insulin
resistance receptor)
FPLD (Lamin A/C)
CGL (g3-like protein, AGPAT2)
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Features of Monogenic Diabetes Syndromes

• Known (and predictable) mode of inheritance
• Rare (lt4 of all diabetes cases)
• Diabetes may be the predominant feature or part
  of a syndrome
• Gene defects influence diverse cellular functions
  all leading to a common outcome hyperglycemia
• Chronic complications occur as a result of
  hyperglycemia regardless of the primary (genetic)
  defect

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(MODY)
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NM
NN
NN
NN
NN
NN
NN
NN
N
M
N
M
N
M
N
N
N
N
N Normal Gene
M Mutant Gene
N
N
N
M
N
M
N
N
Nondiabetic
Diabetic
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Molecular Genetics of MODY

• Autosomal dominant
• Molecular genetic basis
• MODY 2 - Glucokinase (chr 7)
• MODY 1 - Hepatocyte nuclear factor 4 (HNF-4)(chr
  20)
• MODY 3 - HNF 1-alpha (chr 12)
• MODY 4 - Insulin Promoter Factor (IPF-1)(chr 13)
• MODY 5 - HNF 1-beta (chr 17)
• MODY 6 Beta2/NeuroD
• Others
• Different MODYs are discernible by glucose
  priming

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MODY - A Genetic Disorder of Glycolysis and Gene
Expression
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(Syndrome of extreme IR)
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NM
NN
NN
NM
N
N
N
M
N
N
N
M
N
M
N
M
N
M
N
N
N
N
N
N
MM
N
M
N
N
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Type A Syndrome of Extreme Insulin Resistance

• Autosomal recessive
• Insulin receptor gene mutations
• Heterozygotes - mild to moderate insulin
  resistance
• Other syndromes
• Type B syndrome - autoimmune (insulin receptor
  antibodies)

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(Mitochondrial DNA)
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(Familial Partial Lipoatrohic Diabetes)
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Familial Partial Lipoatrophic Diabetes (FPLD)

• Autosomal dominant
• Partial lipoatrophy (female gt male)
• Extreme insulin resistance/hyperinsulinemia
• Hypertriglyceridemia (fatty liver)
• Mutations in the lamin A/C gene

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(Type 1 DM)
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Type 1 Diabetes Mellitus (IDDM)

• Autoimmune destruction of islet B-cells
• Antibodies detected months/years prior to
  diabetes onset
• Immunogenetics - HLA DR3/DR4, CTLA4
• Other genes (insulin, IDDM3-n)
• Viral etiologies, toxins?

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HLA - A Major Type 1 Diabetes Susceptibility
Locus (Chromosome 6)
Chromosome 6
(831 ASPs)
Cox NJ et al. AJHG 69820-30, 2001
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Joint analysis of US/UK T1DM Linkage DataLoci
with suggestive or significant evidence for
linkage
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Pathophysiology of Type 1 Diabetes Mellitus
MA Atkinson and GS Eisenbarth (2001) Lancet
358221
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Subphenotypes
of Diabetes
2006
MODY 1
a
(HNF4
)
MODY 2
(Glucokinase)
MODY 3
a
(HNF1
)
MODY 4
(IPF1)
MODY 5
b
(HNF1
)
Type 1
Type 1
MODY 6
(Beta2/
NeuroD
)
Type 2
Type 2
Insulinopathies
(
Preproinsulin
)
MIDD
(
mitochonchrial
DNA)
Syndromes of
Other
Other
extreme insulin
(Insulin
resistance
receptor)
FPLD
(
lamin
A/C)
CGL
g
(
3
-
like protein, AGPAT2)
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Background - Type 2 Diabetes

• Prevalence of 5-10 in Caucasians
• Incidence increases with age
• Fifth leading killer in the U.S.
• Costs one in seven U.S. Health Care Dollars
• Pathophysiology
• Insulin Resistance
• B-cell Dysfunction

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Dr David Satcher, The Surgeon General of the
United States, December 2001

• "..overweight and obesity may soon cause as much
  preventable disease and death as cigarette
  smoking."

Overweight and Obesity Threatens U.S. Health
Gains' Press release from US Dept of Health and
Human Services, 13 December 2001
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We Are All Part of the Largest Clinical Research
Project in World History since WWII

• AIM Study the effect of caloric excess in the
  population

• STUDY POPULATION 250-300 million Americans

• EXPERIMENTAL DESIGN - Decrease physical
  activity by ubiquitous
  motorization and video monitors - Promotion of
  energy intake through aggressive advertising

• ENDPOINT Body mass index

• RESULTS See next

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Prevalence of Obesity among US Adults from 1989
1999 ( 30 lbs above normal)
20 30
10 20
5 10
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Many Survival Genes (Fat Storage Genes) Have
Evolved During Mankind History
Borrowed from R Unger
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Gene-environment interaction

• While genetic susceptibility is a prerequisite,
  environmental factors determine expression of
  type 2 diabetes
• Migrant studies
• Epidemics of type 2 diabetes
• Same genes different environments

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Prevalence of Type 2 Diabetes
in Pima Indians in Mexico and Arizona (Aged 20
years and over)
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Effects of Traditional and Western Environments
on Prevalence of Type 2 Diabetes in Pima Indians
in Mexico and the U.S.
Diabetes Care, Volume 29, August 2006, 1866-1871
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Effects of Traditional and Western Environments
on Prevalence of Type 2 Diabetes in Pima Indians
in Mexico and the U.S.
Moderate/Heavy Physical Activity Hours/week
Obesity Prevalence ()
Diabetes Care, Volume 29, August 2006, 1866-1871
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Genetic Distance Between the US and Mexican Pimas
Diabetes Care 29 2006, 1866-1871
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Medical Complications of Obesity
Pulmonary disease Abnormal PFTs Obstructive
sleep apnea Hypoventilation syndrome
Stroke
Cataracts
Liver disease Steatosis NASH Cirrhosis
Coronary heart disease
Diabetes
Dyslipidemia
Hypertension
Gall bladder disease
Gynecological abnormalities Abnormal
menses Infertility PCOS
Cancer Breast, uterus, cervix Colon, esophagus,
pancreas Kidney Prostate
Osteoarthritis
Skin
Phlebitis
Gout
Borrowed from S. Klein
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The Darkening Scene of Diabetes Mellitus in the
US
1990
2000
Marx. Science, Vol 29626 April 2002
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Presidential Public Policy Meeting
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Total Federal Spending for Medicare and Medicaid
under Assumptions about the Health Cost Growth
Differential
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GLOBAL PROJECTIONS FOR THE DIABETES EPIDEMIC
1995-2010
26.5 32.9 24
14.2 17.5 23
84.5 132.3 57
9.4 14.1 50
1.0 1.3 33
15.6 22.5 44
World 2000 151 million 2010 221
million Increase 46
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Metabolic Predictors of Type 2 Diabetes Mellitus

• Obesity
• Insulin Resistance
• Abnormal Insulin Secretion
• Excess Glucose Production

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8 Year Cumulative Incidence () of Type 2
Diabetes in Pima Indians317 NGT/62 Diabetics
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7-year Cumulative Incidence of T2DM in 108 Pimas
Initially NGT
Weyer et al., Diabetologia, 2000
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Genes
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Type 2 Diabetes Evidence for a Genetic Basis

• Familial clustering
• Twin studies
• Population studies

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Familial Risk of DiseaseLambda coefficient
?R KR / K

• KR prevalence of disease / trait among
  relatives of an affected proband
• K prevalence of disease / trait in general
  population

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Familial Risk Level for Selected Conditions (l )
Cystic Fibrosis 500 Type 1 Diabetes 15 Type
2 Diabetes 3 Obesity 3 to 6
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Type 2 Diabetes Mellitus

• Much Effort, No Real Smoking Guns but a Few
  Recent New Genes underlying T2DM predisposition

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Genetic Studies of Diabetes Mellitus - Candidate
Genes and Genome Scans

• Genome-wide scans for linkage analyses (LOD
  scores) have been disappointing
• Studies of candidate genes examine known
  proteins, pathways and mechanisms implicated in
  the regulation of blood glucose levels (some
  success storries)
• Genome-wide associations studies (GWAS) may
  reveal new and unanticipated proteins, pathways
  and mechanisms (many recent papers 19 potential
  genes)

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Genetics of Typical Obesity and Type 2
Diabetes A complex interaction between genetic
susceptibility and environment
Aging
Relative Contribution
Environment
Genetic Susceptibility

• Polygenic the effect of any single gene may be
  modest
• Genetic heterogeneity between and within
  populations

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Gene effects

• Major a single gene that has a measurable
  effect on a trait
• Oligogenic several genes, each having
  measurable effects on a trait
• Polygenic many genes each of small effect,
  measurable influence on trait only in aggregate
  (additive)
• Pleiotropicc a gene that effects multiple
  traits
• Other Effects include environmental, GxG and GxE
  interactions/correlations

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Polygenes
Oligogenes
Genes
Complex Phenotype
Gene X Gene
Gene X Environment
Environmental Factors
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What Are the Odds of Finding Disease Genes?
46 Chromosomes
10,000 Phone books
About 40,000 genes
15 Million pages
3 Billion base pairs (chemical building blocks)
6 Billion names
Mutation (alteration) in one (or a few) base
pairs
Misspelling in one (or a few) names
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The Old Order Amish

• Genetically homogeneous closed founder population
• Western/Central European in origin
• Very large extended pedigrees who are
  geographically localized
• Extensive records (Fisher Book, AGD)
• Pedigree errors and/or non-paternity are minimal

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Diabetes in the Amish
Prevalence in siblings of DM probands
ls

9/34
26.5



3.28
13/187
7.0
Prevalence of DM in population
95CI 1.58-6.80
Adjusted for age be the Mantel-Haenszel procedure
Hsueh (2000) Diabetes Care
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Ascertainment The Amish Family Diabetes Study

• Amish Diabetes Research Clinic opened 2/95
• Diabetic proband with age of onset 35 - 65 years
• All willing 1st and 2nd degree relatives
• Phenotypes (medical and family history,
  questionnaires, anthropometry, fat mass, blood
  pressure, 3 hour oral 75 gm oGTT, hemoglobin A1c,
  fasting lipids, leptin)

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The Amish Family Diabetes Study (AFDS)

• 953 Subjects in one large extended pedigree
• Mean Age 46.9 years (range 18 - 93)
• BMI 27.2 4.9 kg/m2
• Average sibship size 4.5 (range 1-16)
• Affected 109 subjects with type 2 diabetes
• 160 subjects with IGT/IFG
• Recruitment is ongoing (n 1400)

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Clinical Characteristics of AFDS
p lt 0.05 p lt 0.001 versus euglycemic Hsueh
(2000) Diabetes Care
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Chromosome 1 Type 2 Diabetes Linkage
Hsueh (2003) Diabetes
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Linkage Disequilibrium

• Definition the nonrandom assortment of alleles
• Marker alleles in LD with disease alleles can be
  used to map the a disease causing gene

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Chromosome 1 Positional Cloning Consortium
French and U.K. Caucasians
Population Amish Pima Utah Caucasian French
Caucasian U.K. Caucasian
LOD 2.88 2.5 2.96 3.04 2.5
Peak Signal D1S2715 D1S1677 ApoA2 ApoA2 -
D1S484 APOA2
Utah Caucasians
Case-control Association analysis
Pima
Number of Meiotic Steps
Amish
Median Length of Shared Segment
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Genome Scans for Type 2 Diabetes and Related
Traits

• Australia - Indigenous Australians
• Canada - First Nation - Oji-Cree
• French Canadians (Heritage)
• China - Southern Han (2), Northern Han (in
  progress)
• France
• Finland - Botnia, FUSION (2)
• Germany (in progress)
• Iceland
• Israel - Ashkenazi Jewish
• Italy - Sardinia (in progress), Rome (in
  progress)
• Japan - Eastern Japan (2)
• Kosrae, Federated States of Micronesia

• Mauritius - Indo-Maritian
• Nigeria - (in progress)
• United Kingdom - Warren 2
• United States
• African American -GENNID, Jackson
• American Indian - Pima
• European American - GENNID, Utah Caucasians,
  Rochester, Framingham
• Japanese American - GENNID
• Mexican American - Starr County (2), San Antonio,
  GENNID
• Old Order Amish

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Molecular Basis of Type 2 Diabetes Candidate
Gene Approaches
Phenotype
Genotype
Trp64Arg ADRB3
Obesity
Pro12Ala PPARG
Insulin Action
Typical Type 2 DM
Ala54Thr FABP2
Lys121Gln PC1
Gly971Arg IRS1
CNS/ Behavioral
b -Cell
PPP1R3
Others
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The PPARg Gene (Chr 3p25)
g 1
g 3
g 2
g 4
Phe388Leu
Val290Met
Pro467Leu
Pro115Gln

• A few rare mutations cause obesity, insulin
  resistance, hypertension or lipodystrophy

• Ala12 is common in many populations
• Functionally has decreased activity
• - Ala12 , a thrifty allele - increased insulin
  sensitivity
• - obesity/weight gain
• - protection from diabetes

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Frequency of Pro12Ala PPARg2
Allele Frequency
Predicted Genotype Frequencies
Population
Pro/Pro
Pro/Ala
Ala/Ala
Caucasian (Finland) Caucasian (Denmark) Caucasian
(Australia) Mexican Americans Caucasian
(Germany) Caucasian (U.S.) Caucasian
(Sweden) Caucasian (U.K.) Caucasian
(French) Caucasian (Italy) Pima
Indians Samoans Korean Chinese Japanese Nauruans A
frican Americans
0.19 0.15 0.13 0.12 0.12 0.11 0.11 0.11 0.11 0.10
0.09 0.08 0.04 0.04 0.03 0.02 0.02
65.6 72.3 75.7 77.4 77.4 79.2 29.2 79.2 79.2 81.0
82.8 84.6 92.2 92.2 94.1 96.0 96.0
30.8 25.4 22.6 21.2 21.2 19.6 19.6 19.6 19.6 18.0
16.4 14.8 7.7 7.6 5.8 4.0 4.0
3.6 2.3 1.7 1.4 1.4 1.2 1.2 1.2 1.2 1.0 0.8 0.6 0.
2 0.2 0.09 0.04 0.04
 
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Ala12 PPARg Has Enhanced Insulin Sensitivity in
vivo Stumvoll, et al (2001) Diabetes
Hyperinsulinemic-euglycemic Clamp
Glucose utilization
Glycerol appearance
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ITT during low (left) and high (right) fat diet
PPARg Heterozygous Mouse Knockout (homozygous is
lethal) Have Increased Insulin Sensitivity
Kubota et al. (1999) Mol Cell
Fasting glucose (left) and insulin (right) on
high fat diet
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Pro12Ala PPARg2 and Insulin Sensitivity in Pima
Indians Baier, et al (2003) Diabetes
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Ala12 PPARg2 Decreases Risk of T2DM
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Meta-analysis of Pro12Ala PPARg2 and
T2DMAltshuler et al. (2000) Nat Genet
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Proposed Mechanism of Pro12Ala PPARg2 Effects in
Humans
Insulin Sensitivity
Protection from Type 2 Diabetes
Ala12 PPARg2
86
Genes Associated with T2DM
Gene Chr. Calpain-10 2q Insulin receptor
2qsubstrate Intestinal FABP 4q Glucokinase 7p
(MODY 2) Insulin receptor 10p Insulin 11p Hepato
cyte nuclear 12factor 1d (MODY3)
Gene Chr. Insulin promoter 13qfactor 1 (MODY
4) Glucagon receptor 17q gene Hepatocyte
nuclear 17cen-qfactor 1b (MODY 5) Glycogen
synthase 19q Hepatocyte nuclear 20qfactor 4a
(MODY 1) Mitochondrial genes mt DNA
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The genetic origin of phenotypic variation
Gene X
Regulatory Element
Exon
Exon
Exon
Gene product X
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The origin of discrete variation
Variation in the coding region may have no effect
or result in the lose of a functional gene
product.
Regulatory Element
Exon
Exon
Exon
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The origin of continuous variation
Variation in the coding region may affect a
structural aspect of the gene product or produce
a variant of the product
Regulatory Element
Exon
Exon
Exon
vs.
90
The origin of continuous variation
Variation in regulatory elements can produce
quantitative variation in the expression of a
gene product
Regulatory Element
Exon
Exon
Exon
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The origin of continuous variation
Gene X1
Gene X
Regulatory Element
Exon
Exon
Exon
It is also possible that variation in an upstream
regulatory gene can lead to quantitative
variation in the expression of the gene product
of a structural gene.
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A Genome-wide Association Study Identifies Novel
Risk Loci for Type 2 Diabetes Sladek R, Rocheleau
G, Rung J, Dina C, Shen L, Serre D, Boutin P,
Vincent D, Belisle A, Hadjadj S, Balkau B, Heude
B, Charpentier G, Hudson TJ, Montpetit A,
Pshezhetsky AV, Prentki M, Posner BI, Balding DJ,
Meyre D, Polychronakos C, Froguel P Nature. 2007
Feb 22445(7130)881-5. Epub 2007 Feb 11
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Type 2 Diabetes Confirmed Loci
Sladek et al, Nature, 2007
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Results from T2DM Genome-wide Association Studies
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The Genes Responsible for the Co-Variation
between Obesity and Diabetes Remain Unknown

• Mixed results have been obtained with a few
  genes ADRB3, ENPP1, FTO, TNMD, PPARA, PPARD,
  PPARG, etc.
• Disease-gene identification through GWAS and
  computational methods has yielded a number of new
  candidates that have not been fully tested yet,
  including CDKAL1, CDKN2B, CPE, FLJ39370, HHEX,
  HNF4A, IGF2BP2, KCNJ5, KCNJ11, LPL, NCOR2, PCK1,
  SCARB1, SLC30A8, TCF1, TCF7L2, etc.

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Type 2 Diabetes Genes
Polygenic
From Robert Sladek, McGill University and Genome
Quebec
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The Challenge
Identification of Functional Gene Variants
FINISH
START
vs.
Observable Phenotypic Variation
A T C C T G T A
Proline
vs.