L14 Human Genetics Flashcards
benefits of identifying a disease gene
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)
whats an example of genetic testing done on newborns
blood spot test
used for sickle cell disease, hypothyroidism, CF
what are the 2 therapies for CF
Orkambi
and
Kaftrio
amyloid hypothesis
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
what is the key process to go from disease to gene
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
for pedigree symbols see onenote
:) also includes ways to determine autosomal recessive or dominant etc etc
what might cause complications in producing a family pedigree
> 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
how do we overcome the problem of genetic heterogeneity in family pedigrees
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)
what are 2 key features of DNA markers in humans
polymorphic - variable and must be 2 or more alleles present in the population
easy to assay - so easy to distinguish from each other
2 types of DNA markers
short tandem repeats (STRs)
single nucleotide polymorphism (SNPs)
what is a short tandem repeat (or microsatellite repeats)
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
what is a minisatellite repeat
longer repeats (more than 10 nucleotides)
how do we distinguish these STRs in forensic analysis
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
in an STR DNA profile, what does 1 peak mean and what does 2 peaks mean
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)
what is single nucleotide polymorphism
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
how do we use linkage analysis with SNPs
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
how do we genotype the SNPs
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
finally, positional cloning: how do we acc locate the position of the affected gene in the region of the chromosome
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
what is another method of sequencing DNA to identify the affected gene
next generation sequencing - NGS
what is NGS and the 2 types
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
how to use NGS to detect affected genes
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)
how is NGS useful in detecting de novo mutations
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
waht is 100,000 genome project
sequenced genome of people with unknown genetic disease or cancer
were able to identify many genetic diagnosises by identifying the disease
