Lecture 13: Genetic Mapping & Complex Traits Flashcards
(32 cards)
list the challenges in mapping complex traits
- incomplete penetrance
- phenocopy
- locus heterogeneity
- polygenic determination
incomplete penetrance
an individual carrying the disease genotype may not express the disease phenotype
give an example of incomplete penetrance
only 66% of individuals with a mutant BRCA1 allele will develop cancer by the age of 55
phenocopy
disease phenotype can be expressed by an individual who does not have the disease genotype, caused by environmental conditions
give an example of phenocopy
3% of women still develop breast cancer by age 55 from somatic mutations in the breast cells themselves
locus heterogeneity
mutations in more than one locus cause the same phenotype in different families: different disease genotypes are responsible for the same phenotype
give an example of locus heterogeneity
BRCA1 (chromosome 17) and BRCA2 (chromosome 13) both predispose to breast cancer
polygenic determiantion
mutant alleles at more than one locus influence expression of the disease phenotype in a single individual
define Quantitative Trait Loci (QTL)
loci that influence quantitative traits
a quantitative effect can be attributed to
2 or more important genes
how are QTLs identified?
- using genetic mapping and association of molecular markers with the trait
- statistical methods allow the identification of more than one QTL at a time
state the 5 steps that are carried out in order to dissect QTLs
- make an informative cross between individuals which differ at the trait(s) of interest. This step creates a population with a range of phenotypes that can be studied.
- determine the frequency distribution in the F2. This step shows how variable the trait is and suggests how many genes may be involved (more genes = smoother distribution).
- use molecular markers to genotype the individuals, attempting to find markers that co-segregate within the trait.
- use a statistical method to determine if markers are co-segregating (associating) with the trait or not.
- plot the degree of association (LOD score) on a linkage map. This tells you where in the genome the important genes affecting the trait are located.
RFLP as a molecular marker
RFLP - Restriction Fragment Length Polymorphism
- a type of molecular marker based on SNPs
- if one allele has a restriction site, the enzyme cuts there
- if the other allele lacks the site, it produces fragments of different lengths.
- these fragment patterns are detected using gel electrophoresis and probes.
STR analysis as a molecular marker
STRs - Short Tandem Repeats
- alleles vary in the number of STRs that they contain
- electrophoresis can be used to separate different alleles based on size
describe how different alleles will move through an electrophoresis gel
- longest/heaviest alleles move the least, whereas shorter/lighter alleles move the most
- when a sequence of DNA is cut by a restriction enzyme, the resulting fragments will result in different bands based on their size
if there is no association between a particular genotype and the phenotype of interest, what will we notice in the experimental results?
we will notice that the phenotype does not change with different genotypes - different sized parents overlap in terms of the alleles being studied
if there is an association between a particular genotype and the phenotype of interest, what will we notice in the experimental results?
we will notice that the phenotype does change with different genotypes - different sized parents have different (combinations of) alleles
odds ratio =
probability of linkage/probability of no linkage
LOD =
log (OR)
what is the LOD?
the log of the probability/likelihood of co-segregation of trait and alleles at a locus being due to chance
if the LOD = 3,
p = 0.001 likelihood of association due to chance (ie there is a 99.9% chance that the association is REAL)
in terms of LOD, what does the threshold value represent?
The threshold value represents the minimum LOD score required to declare a statistically significant association between the marker and the trait.
what do we do once the QTL have been identified?
molecular techniques - fine mapping - can be employed to narrow the QTL down to candidate genes
RILs
Recombinant Inbred Lines:
- Generated by crossing two genetically distinct parents (that differ in the trait), then selfing or sibling-mating for many generations.
- Each line becomes homozygous but carries a unique combination of parental segments.
- This allows for mapping of QTLs with increased precision by comparing many recombinant genotypes with their phenotype.
