What is genetic association?
- presence of an allele at a higher frequency in unrelated subjects with a particular trait, compared to those that do not have the trait.
- if we substitute the word disease for trait this is how we determine whether variants in the genome are associated with a disease (cases)
What are some examples of case -control in genetic studies?
=> cases are subjects with disease of interest, eg. obesity, schizophrenia, hypertension
=> definition of the disease must be applied in a rigorous and consistent way
=> controls must be as well matched as possible for non-disease traits
=> such as age, ethnicity, location, sex
What are stages of case control genetic study to identify disease genes?
- measure genetic loci of interest (affected cases)
- statistical analysis to determine which genetic loci are associated with disease
- identify genes /genomic regions
Case control genetic study must have:
- large numbers of well defined cases (10 000s)
- equal numbers of matched controls
- reliable genotyping technology (SNP microarrays)
- standard statistical analysis (PLNK)
- positive association should be replicated
what are genetic markers?
- individuals in a population are genetically far more diverse than individuals in a single family
- to capture this genetic diversity we need reliable genetic markers
- genetic markers are alleles that we can genotype and asses whether they are associated with disease.
What is an ideal genetic marker?
- polymorphic
- randomly distributed across the genome
- fixed location in genome
- frequent in genome
- frequent in population
- stable with time
- easy to assay (genotype)
what are SNP generated by?
- mismatch repair during mitosis, mismatch
- 12 million common SNPs identified in human genome
- common in the genome ~ 1/300 nucleotides
Where are SNPs located?
- Gene (coding region)
- no AAs change (synomous)
- AAs change (non- synonymous)
- new stop codon (nonsense) - gene (non coding region)
- promoter = mRNA and protein level changed
- terminator = mRNA and protein level changed
- splice site = altered mRNA, altered protein - intergenic region (98% of genome)
What do minor and major allele add up to?
Minor allele frequency + major allele frequency = 1.
- common diseases are likely to be caused by common variants
- SNPs with MAF >0.05 (5%) are usually used in association studies – GWAS
What do genome wide association study (GWAS) do?
- look for association between disease and alleles of each marker - chi -squared test
- by genotyping markers across the whole genome (using SNP microarrays)
- look for association between disease and alleles of each marker- chi squared test
- positive association is at p<5x10-8 (multiple testing correction)
How do you plot GWAS results?
- GWAS results are presented in Manahattan plot
- the peak association often does not identify the gene causing the disease, it identifies the genomic region associated with the disease and this is usually smaller than 100kb
- all data is plotted typically for >1M SNPs
- x axis is position of the SNP on the chromosome
- y axis is -log10 (p value) of association
What was the first GWAS study published?
- WTCCC
- manhattan plots if association of SNP markers with 7 diseases
- green peaks indicate significant p values
how did GWAS develop over the years?
- started around 2006
- each different colour represents different disease.
- got bigger over the years
- as meta analysis happens and results are pooled the number of results for different traits increases
- the empty areas are centromeres
What are problems with GWAS?
- GWAS has identified associations that are statistically strong and reproducible
- however, their contribution to the genetic component of disease is estimated to be low (<5%)
=>why?
-many common SNPs of very small effect - rare SNPS
-copy number variation
-epigenetic variation
Why is increasing obesity a problem?
leads to many medical complications such as:
- pulmonary disease
- non alcoholic fatty liver disease
- cancer
- gall bladder disease
- gynecologic abnormalities …
How do twin studies show obesity to have a strong genetic link?
- twin studies
- monozygotic twins (share both genes and environment)
- dizygotic twins share the environment only
- concordance of similarity between two monozygotic twins demonstrates genetic effect (70 -80% of body shape is genetically determined)
- adoption studies (share genes but not environment , 30-40% similarity)
- family studies 40-60%
- evidence for genetics > environment
What are features of large scale meta analysis on obesity?
- BMI meta-analysis ~ 322K subjects
-97 BMI- associated loci - 125 separate studies
->600 authors and >2000 collaborators
=> novel loci = red
=> known loci = blue
What does obesity GWAS result venn diagram show?
- some traits overlap
- gives idea of interrelationship of different traits
What is linkage disequilibrium (LD)
When two alleles are inherited together more often than expected due to chance
This is usually because they are close together in the genome
Alleles that are physically close together (within 100kbs) are rarely separated by recombination so genetic marker is found in disease allele.
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DNA hybridisation26
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PCR and diagnostics23
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molecular evolution32
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genome structure42
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genome variation29
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inheritance pattern16
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enzyme and restriction mapping20
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recombinant DNA5
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microarrays and next generation sequencing33
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metagenome23
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mitochondrial genome32
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Epigenome22
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mapping mandelian disease13
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Genetics of common diseases19
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DNA sequencing0
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linkage analysis35
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association analysis19
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functional genome20
