1. Sequence recognition P(M|s) = P(M)* P(s|M) / P(s) (Bayes' theorem)
(from Apr 12 ppt)
Recognition question - What is the probability that the sequence s is from the start site model M ?
P(M|s) = P(M)* P(s|M) / P(s)
(Bayes' theorem)
P(M) and P(s) are prior probabilities and P(M|s) is posterior probability.

2. Trait prediction P(M|s) = P(M)* [P(s|M) / P(s)]
Probability of trait M given sequence s
P(M|s) = P(M)* [P(s|M) / P(s)]
Posterior = Prior * [standardized likelihood]
Probability predicts unknown outcomes based on known parameters. Likelihood estimates unknown parameters based on known outcomes.

3. Trait prediction Monogenic: 1 = 1E-4 *[7E-2 /7E-7]
Probability of trait M given sequence s
P(M|s) = P(M)* [P(s|M) / P(s)]
Monogenic: 1 = 1E-4 *[7E-2 /7E-7]
“Monogenic forms of obesity at present account for approximately 7% of children with severe, young-onset obesity (3), but as this severity of obesity is only seen in <0.01% of the population .. 66% of the U.S. population had a BMI ≥ 25 kg/m2 and 32% were obese .. FTO: The 16% of adults who are homozygous for the risk allele weighed about 3 kilograms more and had a
1.67-fold increased risk of obesity” .
--Frayling et al. Science 12 April 2007
FTO: 1.67*0.32 = .32 * [ .265/.16]

4. Trait prediction given diploid s
A likely scenario: Not in OMIM & heterozygous
P(deleterious | s) e.g. polyphen
P(dominant | s)
P(epistatic | s)

5. OMIM stats Dominant= 4170, recessive 3674 hits Autosomal X-Linked
Autosomal
X-Linked
Y-Linked
Mitochondrial
Total
Gene with known sequence
10812
500 48 37
11397
Known sequence & phenotype
351 31
382
Phenotype, molecular basis known
1892
176 2 26
2096
Phenotype, molecular basis unknown
1423
133 4
1560
Suspected mendelian
Phenotypes
2000
144
2146
16478
984 56 63
17581
Dominant= 4170, recessive 3674 hits

6. Genotype % chances if a subject has one copy of a (co)dominant allele "Aa" & most people are "aa".
Family Risks

7. Genotype % chances if a subject has 2 copies of a (co)dominant allele "AA" & most people are "aa".
Family Risks

8. Hardy–Weinberg equilibrium
Assumptions:
Diploid
Trait is autosomal
Is sexually reproducing, either monoecious or dioecious
Discrete generations
Random mating within a single population
Population size sufficiently large so to minimize effect of genetic drift
No selection, mutation, migration

9. PhenotypeGenetics allele interactions, epistasis