MUS2046 Genetics in Medicine Finding disease genes Cathryn
Lewis Professor of Genetic Epidemiology and Statistics
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Introduction to genetics: 1 DNA structure
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www.onlineeducation.net/dna Introduction to genetics: 2 DNA
sequence
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What makes us different? These differences control our hair
colour, our height, and the diseases we will get Introduction to
genetics: 3 DNA differences
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Complex disease: contributions from genetic and environmental
factors Gene4 Env4 Env3 Env2 Env4 Disease Env1 Gene8 Gene7 Gene6
Gene5 Gene4 Gene3 Gene2 Gene1 Examples: asthma, breast cancer,
heart disease, autism, arthritis, migraine, obesity, diabetes,
stroke Most diseases that have a major economic, social and health
burden
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Complex Diseases Raised risk in families But increase in risk
may be slight compared with population risk Can be measured by the
sibling relative risk No clear mode of inheritance Multiple genes
Environmental effects Gene-gene, gene-environment interactions
Examples Inflammatory bowel disease, multiple sclerosis,
depression, asthma, rheumatoid arthritis, diabetes, heart
disease,.... Most diseases that have a considerable public health
impact
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Genetic Association Study A genetic association study tests
whether the presence of a specific genetic variant correlates with
a trait of interest (such as risk of disease) A SNP has two
alleles: C, T Each individual has a genotype at this SNP CC, CT or
TT
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Genetic variation: Single nucleotide polymorphism (SNP) Alleles
A and C are present in the population Genotype : carried by an
individual, on paternal and maternal inherited
chromosomes....TGGACCTGCA........TGGACATGCA........TGGACCTGCA........TGGACATGCA........TGGACATGCA........TGGACCTGCA....
Genotype: AA ACCC
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Genetic Association Study A genetic association study tests
whether the presence of a specific genetic variant correlates with
a trait of interest (e.g. presence/absence of disease)
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Identifying SNPs that increase risk of disease Cases affected
with disease Controls not affected with disease Genotype SNP with
A, C alleles: AAACCC More AC and CC genotypes in cases than in
controls Indicates that carrying C allele increases risk of
disease
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Case control studies Compare frequency of SNP alleles or
genotypes in a series of cases and controls Cases Diagnosed with
disease Ascertainment - through hospital or community? Define
criteria for inclusion in study Controls Unaffected with disease
(supernormal controls) Randomly ascertained (e.g. blood donors)
Both types of controls are valid Important to match cases and
controls on genetic ancestry if not, genetic differences between
cases and controls may reflect their ancestry, not their disease
status
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Association of PTPN22 mutation with rheumatoid arthritis (RA)
Steer et al., Arthritis Rheum, 2005 RA is a complex disease with a
sibling relative risk of approximately 3, and a strong HLA effect
PTPN22 encodes a protein tyrosine phosphatase which interacts with
the negative regulatory kinase Csk to inhibit T cell signalling and
activation The R620W mutation was shown in other studies to
increase risk of RA Association study of R620W performed in London
RA patients 302 RA cases (hospital-ascertained) and 374 controls,
all of European ancestry
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Association of PTPN22 mutation with RA Significant difference
in allele frequency (p=3 x 10 -5 ) 17.2 (3.8-77.8) 1.7 (1.2 2.5)
1Odds ratio (95% CI) 15.9%12 4% 72 24% 218 72% Cases (n=302) 8.4%1
0.3% 61 16% 312 83% Controls (n=374) Freq. of T allele TTCTCC Odds
ratio of CT genotype compared to CC genotype = 312 x 72 / (218 x
61)
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Association of PTPN22 mutation with RA 17.2 (3.8-77.8) 2.05
(1.47- 2.88) 1Allelic Odds ratio (95% CI) 15.9%12 4% 96 16% 508 84%
Cases (n=302) 8.4%1 0.3% 63 8% 685 92% Controls (n=374) Freq. of T
alleleTTTC Odds ratios for genotypes CC, CT, TT are 1, r, r 2 Here,
OR for CC 1 (baseline), OR for CT=2.05, OR for TT = 4.02
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Rheumatoid arthritis: contributions from genetic and
environmental factors STAT4 TRAF1 PTPN22 Gene4 ? Sex Age Env4
Rheumatoid arthritis Smoking HLA TNFAIP3 CD40 CTLA4 Other genes Now
over 100 genes identified that are associated with rheumatoid
arthrtis
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Genome-wide association studies (GWAS) SNP chips from Illumina
and Affymetrix will genotype up to 1 million SNPs across the genome
Capture most of the variation across the genome
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WTCCC (2007) Nature 447: 661-78
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Steps in WGA study Design study Collect samples Define
phenotypes Type DNA on whole-genome panel Quality Control (QC)
SNP-by-SNP analysis Interpret results Replicate, perform
meta-analysis
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GWAS analysis methods SNP-by-SNP analysis against phenotype
Analysis of genotype counts Regression analysis of quantitative
trait Logistic regression of case-control status on SNP genotype,
ancestry covariates, phenotypic covariates, environmental
factors.... Problems of multiple testing with 500K SNPs