L14 Human Genetics

Question 1

benefits of identifying a disease gene

Answer 1

can develop genetic testing

or new therapies - e.g.drugs

and genes involved in these rare diseases can give insight into more common sporadic diseases (e.g. familial hypercholesterolemia was the first thing that told us that cholesterol is bad for heart)

Question 2

whats an example of genetic testing done on newborns

Answer 2

blood spot test
used for sickle cell disease, hypothyroidism, CF

Question 3

what are the 2 therapies for CF

Answer 3

Orkambi
and
Kaftrio

Question 4

amyloid hypothesis

Answer 4

research into a genetic basis of alzhiemrs
usually its said to be fully sporadic
theres a protein that appears in alzheimers
called amyloid
and they didnt know if that was a cause or effect of alzheimers

but then discovered that gene codes for amyloid in people with alzheimers

Question 5

what is the key process to go from disease to gene

Answer 5

pedigree analysis
- investigate the occurrence of the disease in families to determine the type of disease mutation

linkage analysis
- evidence of genetic lnkage between disease gene and genetic markers
- map the gene precisely (determines the region on the chromosome)

positional cloning of the disease gene
- select “candidate gene” in region of the chromosome
- look for disease associated mutations in each candidate gene

Question 6

for pedigree symbols see onenote

Answer 6

:) also includes ways to determine autosomal recessive or dominant etc etc

Question 7

what might cause complications in producing a family pedigree

Answer 7

> incomplete penetrance and/or variable expressivity
- so might not be able to see the pehnotype

> delayed onset
- e.g. breast cancer

> genetic heterogeneity
- mutations in different genes will give same disease
- e.g. at least 3 genes cause familial early-onset alzheimers

> can’t be 100% sure who the dad is lol
missatributed paternity

Question 8

how do we overcome the problem of genetic heterogeneity in family pedigrees

Answer 8

could look at genetically homogenous populations

e.g. icelanders (few people living there, and theyre all kinda related), mormons (big families, detailed records, small population of people)

Question 9

what are 2 key features of DNA markers in humans

Answer 9

polymorphic - variable and must be 2 or more alleles present in the population

easy to assay - so easy to distinguish from each other

Question 10

2 types of DNA markers

Answer 10

short tandem repeats (STRs)

single nucleotide polymorphism (SNPs)

Question 11

what is a short tandem repeat (or microsatellite repeats)

Answer 11

tadnem = one in front of the other

basically its repeats of short sequences (~2-4 nucleotides)
usually in non coding sequences

so its just bits of repeated DNA sequences

Question 12

what is a minisatellite repeat

Answer 12

longer repeats (more than 10 nucleotides)

Question 13

how do we distinguish these STRs in forensic analysis

Answer 13

using PCR

so can amplify small parts of DNA to make more DNA via PCR

then run it out via electrophoresis to give a DNA profile

see onenote for example of a dna profile

Question 14

in an STR DNA profile, what does 1 peak mean and what does 2 peaks mean

Answer 14

2 = heterozygous, so have 2 variants for the allele of the STR (one might be shroter than the other, showing that one of the alleles has less number of repeats in the STR)

1 = homozygous (both alleles have same number of STR repeats, so during the PCR they aren’t represented as 2 diff things)

Question 15

what is single nucleotide polymorphism

Answer 15

base differences in sequences of DNA

so if u compared the sequence of any 2 humans, one base diff occurs in every 1000 nucleotides

most of these are in non coding DNA too

this is the most common type of polymorphism in the human genome (~10million common SNPs, so once every 300bp)
so we utilise it for DNA marking

Question 16

how do we use linkage analysis with SNPs

Answer 16

if a mutation occurs in a location with SNPs

and the mutation is passed down through many generations

the SNP closest to the muation will have linkage with it, so it prevails through generations alongside mutation

but the other SNPs might have crossing over or something that causes their linkage to decay over time

see onenote

Question 17

how do we genotype the SNPs

Answer 17

via GeneChips

so it allows 0.5-1 million SNPs to be genotyped

so do it on an individual in a family pedigree

and each SNP that is detected is tested for linkage with the disease phenotype

so can identify several SNPs in a region of the genome where the gene must be located

see onenote xoxo

Question 18

finally, positional cloning: how do we acc locate the position of the affected gene in the region of the chromosome

Answer 18

after identifying the SNPs, we know the location in the genome that is linked with the disease

to identify the candidate gene, must inspect the sequence of affected and unaffected individuals

obvs affected individual will show a mutation in the sequence in a certain gene compared to the unaffected

Question 19

what is another method of sequencing DNA to identify the affected gene

Answer 19

next generation sequencing - NGS

Question 20

what is NGS and the 2 types

Answer 20

just another way to sequence the genome and is cheaper and faster

whole genome sequence (WGS)

or

whole exomes (WES)
- just sequencing the exons
- even cheaper

Question 21

how to use NGS to detect affected genes

Answer 21

sequence the genome or exome depending on how stingy u are ig
from unaffected and affected individual

identify any rare variants that only the affected people share
and any potentially causative variants (so any mutation that could cause the disease:
- could be easy to detect e.g. a mutation that causes a change in amino acid sequence
- or could be hard to detect e.g. a mutations that causes a change in a control region of gene that determines expression level)

identify functional consequences of the potential variants(e.g. LOF mutation or something)

Question 22

how is NGS useful in detecting de novo mutations

Answer 22

de novo = mutation in a child that must’ve occured in egg or sperm cuz it doesn’t exist in the parents

can sequence genome of parents and child

each child has ~50-60 mutations that aren’t present in mum or dad, most of these are in non-functional regions

use same method to find the affected gene

Question 23

waht is 100,000 genome project

Answer 23

sequenced genome of people with unknown genetic disease or cancer

were able to identify many genetic diagnosises by identifying the disease