Study designs for genetic studies of complex disease Flashcards
How identical are unrelated humans?
The sequences of unrelated humans are 99.9% identical.
What are the differences between unrelated humans mostly down to?
Single nucleotide polymorphisms (SNPs)
What are SNPs?
Single base changes, different alleles present at these positions.
What other variations cause differences between humans along with SNP?
Deletions
Inversions
Differences in number of repeats.
What kinds of differences in number of repeats are there?
CNV
STR
What are CNVs?
Copy number variants.
What are copy number variants?
Structural genetic variation that involves a gain or loss of DNA segments.
What are STRs?
Short Tandem Repeats
What are Short tandem repeats often referred to as?
Microsatellites
What are short tandem repeats?
Short repeated sequences of DNA (2–6 bp)
What is the function of short tandem repeats?
The number of repeat units is different in individuals, this allows indentification.
What is a locus?
Genetic position for 2 specific allels.
Why do individuals possess different alleles at certain loci?
Because each sequence is inherited from each parent.
What is the genotype at the locus?
Combination of the alleles they possess.
According to mendelian inheritance what is the probability that an allele is passed from a parent to an offsping?
0.5
What was incorrect about Mendel’s views on inheritance?
Alleles at different loci inherited independently of one another.
What does the inheritance of one gene with another depend on?
How close the loci of the genes is on the DNA strand.
What is a phenotype?
Characteristic or trait that results from having a specific genotype.
What is a disease loci?
Loci where there is a particular allele that increases
disease risk.
What is the correspondence between genotype and phenotype in Simple Mendelian or monogenic disorders?
Close correspondence.
What is penetrance?
Probability of being diseased, given genotype.
What is the genotype relative risk (GRR)?
The relative risk is the ratio of the disease risk for individuals with one specific genetic and environmental profile, to the disease risk for those at a reference level.
What is penetrance for Simple Mendelian or monogenic disorders?
Complete
What does complete penetrance mean for genotype relative risk?
The chances of getting the disease is 1 or 0 depending on the alleles inherited from parents.
What is the penetrance for complex diseases?
Incomplete penetrance
What does incomplete penetrance mean for genotype relative risk?
Probabilistic rather than deterministic relationship between genotype and phenotype, the GRR is not defined by 1 or 0.
During dominant Mendelian disorders, how is transmission shown from parent to child?
More than one generation is always affected, no skipping.
1 in 2 offspring affected on average
During recessive Mendelian disorders, how is transmission shown from parent to child?
Approximately 1 in 4 offspring affected
Often occur in consanguineous pedigrees.
What does consanguineous mean?
Relating to or denoting people descended from the same ancestor.
What is the definition of a complex disease?
A disease where one or more alleles acting alone or in concert increase or reduce the risk of developing a trait
What is the inheritance pattern for complex disease?
They don’t show a clear inheritance pattern for a disease gene since other genetic or environmental factors can be involved.
Results in reduced penetrance.
Mendelian diseases are often the result of what molecular change?
A mutation in the coding region of a gene, that results in a severe alteration of function when translated to protein.
Complex diseases are often the result of what molecular change?
Correspond to mutations that result in less severe alteration of function
Including mutations in regulatory (non-coding) regions, that may alter the expression of nearby genes.
Define PEDIGREE.
The recorded ancestry or lineage of a person or family.
What is the difference between a mutation in the coding and non-coding areas of the genome?
Coding DNA mutations have a direct effect on function whereas nearby non-coding DNA only increases the risk of change in function.
What kinds of techniques can be used to study pedigrees and the genetic cause of a disease?
Study of model organisms – through breeding experiments or CRISPR/Cas9 gene knockouts
Functional experiments in different human or animal cell
What is the purpose of segregation analysis?
Can be used to fit a mathematical model to the pattern of inheritance seen in a family.
What kind of patterns can be discovered using segregation analysis?
To estimate the parameters that best explain the inheritance pattern seen
Allows fitting of more complicated oligogenic models.
What kinds of parameters can be used to explain an inheritance pattern?
Gene Frequencies
Penetrance
Shared environmental effects
Why is the inclusion of oligogenic models through Segregation analysis important?
Including one or more major genes
Possibly operating against a polygenic background
Possibly subject to environmental effects
What are twin studies?
Compare concordance in disease status in a large sample of monozygotic (MZ) and dizygotic (DZ) twins.
What are monozygotic twins?
Basically genetically identical.
What are dizygotic twins?
Only half of genetic material shared, basically siblings.
What is recurrence risk?
Chance or possibility that a disease, especially an inherited one, will occur again in a family.
What is recurrence risk denoted by?
KR.
What is R in KR?
R takes different values according to the relationship we are interested in.
What is Ks?
KS is the risk of disease for a sibling of an affected individual.
What is KO?
Is the risk for the offspring of an affected individual.
What is KMz?
The risk for a monozygotic twin of an affected individual.
What is the recurrence risk ratio?
Relative to the background
population risk K.
What does it mean if the sibling relative risk (lambda R)?
A sibling of an affected person has three times the population risk.
Why do siblings have a higher risk of recurrence than the population?
Increased risk due to shared genetic factors but they also share many environmental factors.
What is the goal of parametric linkage analysis?
Identifying determinants of disease.
How are parametric linkage analysis experiments carried out?
Gather a small set of large families each containing a
number of affected individuals
Obtain DNA from all.
Use a genotyping technique to measure each individual’s two alleles (genotype) at one or more loci.
Fit a mathematical model modelling the co-segregation of disease phenotype and at genetic ‘marker’ loci.
What is tested for during linkage analysis?
Testing the hypothesis that a particular locus that we have genotyped is linked (lies close) to a locus that causes the disease.
What information do we gain from linkage analysis?
If the disease is recessive, we know all affected individuals must have two copies of the disease allele so their parents must each have at least one copy of the
disease allele, therefore we can investigate the co-transmission of marker and disease allele in the family.
How successful of a strategy is linkage analysis in localising disease alleles for monogenic disorders?
Highly sucessful.
How successful of a strategy is linkage analysis in localising disease alleles for complex disorders?
Less successful due to complex inheritance.
What is the role of
Determine whether members of a family with “similar” traits tend to inherit genetic material in common from their common ancestors.
What is the role of association analysis?
Determine whether a particular measured genetic variant (allele) influences the risk of developing disease
What could association analysis indicate?
Direct casual relationship
Indirect relationship.
What does a direct causal relationship allow us to investigate further?
Possible mechanisms and pathways in disease progression.
What is an indirect relationship?
Correlation between the test variant and the causal variant known as linkage disequilibrium (LD).
What is the importance of finding an indirect relationship?
Helps us localise the causal variant, and narrow the genomic region identified by linkage studies.
How are case/control studies of unrelated individuals set up?
Collect sample of affected (case) and unaffected (control) individuals
Compare the distribution of genotypes seen in the affected
individuals with that seen in controls
Examine the association between alleles present at a genetic locus and presence/absence of disease
How are diseased samples collected?
Collected in hospitals or clinics
Additional family members
Permission to contact extended family.
Where do control samples come from?
As part of a birth cohort
Population-based cohort
Blood donors
‘Bring a neighbour/friend’ (of the cases)
What are the candidate gene studies?
Focus on just one or a few genes of interest based on their known
biological function.
Can use targeted sequencing or SNP-based genotyping
What are genome-wide studies?
Allows you to carry out a ‘hypothesis-free’ investigation
Microarray-based SNP
genotyping
Sparse panels of 4000-10000 SNPs.
What is a hypothesis-free approach?
Don’t need to have any prior reason to focus on specific genes or genetic variants.
How do we find the correlation between phenotypes and genotypes during GWAS?
At each measured locus (SNP) carry out a χ2 (or other) test of association between genotype and phenotype
What are the disadvantages of using GWAS?
We don’t know the functional (causal) variant,
The causal variant may well not even have been genotyped
SNPs identified through GWAS generally have effects that are not very ‘important’.
The SNPs identified do not have strong predictive value
What are CRISPR/cas9 gene knockout experiments?
A single guide RNA (SRNA) guides easy to precise location in the host genome, where it creates a double stranded break (DSB) in the genomic DNA this can remove or add markers/genes through non-homologous recombination, this can give genomic stability.
What is heteroplasmy?
Presence of more than one type of organellar genome within a cell or a whole individual.
What is Microarray-based SNP genotyping?
Hybridization of fragment single-stranded DNA to array containing hundreds of thousands of unique nucleotide probe sequences.
Each probe is designed to bind to a target DNA sub sequence.
What are the features of autosomal dominant inheritance patterns?
Only one copy of a gene needed for the individual to be affected.
Even heterozygous are affected.
Each child has 50% chance of inheritance if one parent is heterozygous.
What are the features of autosomal recessive inheritance patterns?
2 alleles needed for individuals to be affected
25% of being affected if both parent heterozygous
50% chance to be a carrier
What are the features of X-linked inheritance patterns?
Pathogenic variant is carried on the X-chromosomes
Men only have 1 X-chromosome so more likely to be affected
Women are often asymptomatic carriers.
What are the features of Y-linked inheritance patterns?
Can only be passed from fathers to sons
What are the features of
Mitochondrial inheritance patterns?
Involves genes in mtDNA during early development.
Egg gamete gives the baby the mitochondria.
Only passed from Mother’s to their baby but can affect boys & girls.
Mother can be asymptotic carrier as the genes could be mosaic.
What are the features of De Novo inheritance patterns?
Present for the first time in a child, not inherited.
This can then be passed on to the next generation.
