6, 7, 9 Population/Thalassemia Genetics & Genetic Tests

Quantitative vs binary trait

• A gene that impacts something on a range(how tall you grow, as an example) vs a gene that decides whether or not you have something(eg. cystic fibrosis, yes or no)

Pleiotropic effect

• When one gene has effects on multiple, seemingly unrelated things

In this locus on two homologous chromosomes, what is the SNP, and what is this person’s genotype?

acgCtaga

acgGtaga

The SNP is “single nucleotide polymorphism, aka a spot where the nucleotide isn’t the same in all people. This person’s genotype would be C/G

What is genotype vs allele frequency? Use the former acgCtaga example, and say 72 people were surveyed, with 20 people being C/C, 35 people being C/G, and 17 people being G/G

• Genotype frequency is how many people have that specific combination: So in our example, genotype frequency would be C/C 20/72 or 0.28, C/G being 35/72 or 0.48, and G/G being 17/72 or 0.24.

• Allele frequency is how often each allele appears, so not as a pair, just individually. So in this example, the 20 people with C/C would give 40 C alleles, and the 35 people with C/G also give another 35, ending up with 75. Meanwhile, the 17 people who are G/G give 34 G alleles and the 35 people with C/G give 35 G alleles, so 69 alleles in total. Frequencies are then 0.52 for C, and 0.48 for G.

In that last example, which one is the major allele, and why?

• The major allele is the one that’s more frequently found, so in that case, it would be C.

In terms of math, what notations can we give these alleles, use the same example.

• We can use p and q, so for example, freq(C) = 0.52 and freq(G) = 0.48, and so p+q=1

Hardy Weinberg Equation

• The equation

• The meaning

• The purpose

• p² + 2pq + q² = 1

• It’s saying that in a population, the genotype frequency should be based on three possibilities. Getting p and p, getting one p and one q, or getting q and q.

• It serves as a baseline for what a population should be if there are no mutations, no migration, no natural selection, and there is random mating and a large population size

What is

AE Bart’s

EF Bart’s

AE Bart’s CS

1. AE Bart’s: Hb A + Hb E and Hb Bart’s present, meaning there has to be one Hb E allele to make Hb E and one normal beta allele to make Hb A, but there is also enough alpha deficiency to make Hb Bart’s. How do we get this? Hb H along with Hb E/Beta

2. EF Bart’s: Hb E + Hb F + Hb Bart’s, meaning there’s no normal beta since we can’t make HbA, and there’s also enough alpha deficiency to make Hb Bart’s. How do we get this? Hb H along with Hb E/Hb E

3. AE Bart’s CS: Same as the first one, one normal beta and one Hb E allele, hence the production of both Hb A and Hb E, but also enough hemoglobin deficiency to make Hb Bart’s. How do we get this? Hb H CS with Hb E/Beta

What are the 4 danger thalassemia conditions we want to avoid?

1. Hb Bart’s

2. Beta thalassemia major

3. Beta-thal/Hb E

4. HbH

How do we avoid these danger conditions?

1. Screen for beta thal: To avoid a child unluckily getting the damaged Beta from both carrier parents → Beta thal major

2. Screen for alpha thal 1: To avoid a child unluckily getting the damaged chromosome from both parents → Hb Bart or a alpha thal 1 carrier parent with a alpha thal 2 trait parent → HbH

3. Screen for homo HbE: To avoid a child unluckily getting the HbE with a parent who has beta thal trait → Beta-thal/Hb E disease

4. Screen for HbE: To avoid a child unluckily getting the HbE with a parent who has beta thal. trait → Beta thal/Hb E disease

1. Risk of I-1 being a carrier

2. Risk of II-1 being a carrier

3. Risk of II-3 being a carrier

4. Risk of II 1 having an affected child

5. Risk of II 2 having an affected child

1. Risk of I-1 being a carrier: 100% because there’s an affected offspring and since it’s a recessive condition that the parent himself doesn’t have, he must’ve passed it on for it to show up in the kid

2. Risk of II-1 being a carrier: 2/3 because a child of 2 carriers will have a 2/4 chance of being a carrier, but once we see the child and see that they aren’t sick, that rules out one of the 4 chances because the kid clearly isn’t sick, so it leaves 2/3

3. Risk of II-3 being a carrier: 1/2. This is still ½ because we don’t know the kid’s anything yet since they are still in the mother’s stomach

4. Risk of II 1 having an affected child: 2/3(chance that II-1 is a carrier) x 1/4(Chance the kid is affected) x Carrier frequency of that allele in the population

5. Risk of II 2 having an affected child: 1/2(chance that the kid is affected because since II-2 is sick, there’s a 100% chance she passes on the sick allele and a 50% chance it meets the recessive sick allele of a carrier) x carrier frequency(The chance the person she has a kid with will be a carrier for this specific thing)

Classic genotype phenotype concordance vs genetic heterogeneity vs phenotypic pleotropy

1. Classic genotype phenotype concordance: One gene causes one disease

2. Genetic heterogeneity: One disease caused by multiple genes

3. Phenotypic pleiotropy: One gene causes multiple diseases

What is called when we do a test on someone who already has signs/symptoms of a disease and we want to confirm/rule out causes?

• Diagnostic testing

What is carrier screening, prenatal testing, preimplantation genetic testing?

1. Carrier screening: Testing to see if we are a carrier of a recessive disease causing gene

2. Prenatal testing: Testing fetus during pregnancy to see if they have any abnormalities

3. Preimplantation genetic testing: Testing embryos before implantation(For couples w 2 or more miscarriages due to genetic abnormalities)

What is predictive testing?

A test to see if we will develop a condition in the future

• Presymptomatic: Test for a disease with high penetrance

• Predispositional: Test for a disease with low penetrance

What substance should we not use to collect fresh whole blood and why?

Heparin; interferes with PCR

Sanger Sequencing

• What is it

• Pros and cons

• A DNA test that utilizes ddNTPs, or nucleotides that end the polymerase ability to continue if they are added to the DNA chain. There will be millions of copies of our target sequence to be replicated, and a pool of dNTPs and ddNTPs, and on average, there should be copies where the DNA polymerase added a ddNTP at each position, so we then separate them by size and see what each base is in each spot

• Accurate and reliable but not sensitive to low frequency variations and slow

PCR

• What is it

• Pros and cons

• A DNA test that multiplies one copy of DNA until there are millions, and these copies can be used in Sanger Sequencing, infectious disease identification, forensics

• Sensitive and cheap but we can’t actually look at the sequence in detail itself unless we do a next step

MLPA

• What is it

• A test to see if any copy number variants(extra copies of/deletions of a gene) are present; it’s done by adding 2 probes that are supposed to be next to each other on a gene, and so they should find each other and bind, and then we do PCR to amplify these probes. We then look at how many copies were produced, if it’s proportional to a patient having 2 genes like normal, less(a deletion), or more(duplication)

Linkage Analysis

• What is it?

• A genetic testing process used to roughly identify where a disease causing gene is. Because areas close to each other on chromosomes usually travel together, we can look at many generations of a family members to see if the sick individuals have any shared sequences, and we can tell that that area might be the area that codes for the disease to happen

Inverse PCR

• What is it?

• A method where we cut out a region of DNA including a known region, and we turn the DNA into a circle, and use the primer to go OUTWARD and replicate that whole circle, and then amplify it. Now, we have the gene regions slightly up and downstream of the known region

NGS

• What is it?

• A DNA test that shreds the sample into millions of small fragments, amplifies each into a cluster (like PCR), then reads all clusters simultaneously by adding one fluorescently-tagged base at a time and imaging the whole surface after each cycle. The many short reads are then computationally overlapped and reassembled into the full sequence.