Genetics 2 Flashcards
how much of the genome consists of exons and is therefore translated?
2-3%
what does the other 97-98% of the genome do?
regulation of genes
spaces the genes out - insulating the genes from promotors
provides substrate to expand genome/add genes
how are large changes in DNA analysed?
array comparative genetic hybridisation looks for deletions/duplications
chromosome/karyotype analysis looks for balanced rearrangements
how are smaller changes in DNA analysed?
PCR and sanger sequencing
next generation sequencing
mutation vs polymorphism?
mutation = genetic variation that causes disease polymorphism = genetic variation that is prevalent in the population and not in itself disease causing
how does PCR work?
select one small piece of the genome from patient and makes lots of copies of the short stretch of the genome using taq polymerase and a primer so that it can be analysed and sequenced properly
what are the steps in PCR?
denature the DNA with heat
cool the strand so primers can bind to the DNA template
raise the temperature again so taq polymerase can bind and extend the primers and synthesize new strands
results visualised via gel electrophoresis or sequencing
what happens if there is a mutation in the promotor region?
no, or reduced transcription and therefore no or reduced protein
what happens if a mutation is between intron and exon causing alteration in splice consensus?
splicing and transcription is altered (e.g an exon is missing as its been wrongly spliced out) causing abnormal or absent protein
what does a mutation in base sequence forming a new stop codon cause?
short or absent protein
what does a mutation in base sequence altering amino acid sequence cause?
different or non-functioning protein
missence mutation?
base is swapped for another one
deletion in frame vs deletion out of frame?
in frame = deletion of number of base pairs divisible by 3 (whole codons deleted)
out of frame = number of bases not divisible by 3 deleted so all codons are altered
triplet expansion?
repeat of a codon
at what stage in reproduction can a new mutation occur that is not present in the parents?
gametogenesis (formation of gamete within the parent)
can have a post-zygotic mutation causing the child to be mosaic
what happens to child if one parent is mosaic?
if gamete is from mutated cell population then the mutation passes to the zygote and all of the childs cell then possess the mutation
overview of whole genome sequencing in NGS?
extracted gDNA > gDNA is fragmented into a library of small segments that are each sequenced in parallel > individual sequence reads are reassembled by aligning to a reference genome > the whole genome sequence is derived from the consensus of aligned reads
how are mutations detected in the whole genome in NGS?
alignment of multiple short reads shows that there is a different base in half the reads since half the reads come from a variant allele which contains either a polymorphism or a disease causing mutation
what is the catch with NGS?
most people have around 3,000,000 polymorphisms (changes from normal sequence) but only one mutation causing the genetic disease
questions to ask to help determine where genetic change is polymorphism or disease causing mutation?
is it de-novo
is it in the right gene
has it been reported before (as a polymorphism or in the same phenotype meaning it may be causative)
what does the change do to the gene’s protein
how are the detected genetic changes filtered in NGS?
check if the change is known to be a polymorphism
(left with 1000s)
check if the change affects the gene’s function
(left with 100s)
check if it is in a gene that explains the phenotype in the patient
(should hopefully be left with 1)
what is penetrance?
likelihood of having a disease if you have the mutation
100% penetrance = if you have the mutation you will definitely have the disease
what is a mendelian disorder?
disease that segregates in families in the manner predicted by mendels laws
(basically a disease that is predominantly caused by a change in a single gene - high penetrance)
types of mendelian inheritance?
autosomal dominant
autosomal recessive
X linked
mitochondrial
features of AD inheritance?
only need one copy to cause disease
disease seen in all generations but disease severity can vary
50% risk in child if parent is affected
can different mutations in the same gene cause the same disease?
yes
and vice versa - same disease can be caused by mutations in one of several genes
features of autosomal recessive inheritance?
often only seen in one generation
1 in 4 risk in child if parent affected
increased likelihood if parents are related
relevance of y chromosome in disease?
basically irrelevant
describe X linked inheritance
gene fault present on X chromosome
can only be passed on by females
females with the gene fault are carriers (as they also have one normal X chromosome from father)
males with the gene fault are affected (as they don’t have another X chromosome)
rate of transmission of X linked recessive disorder if mother is carrier?
half of male children will be affected
half of female children will be carriers
rate of transmission of x linked recessive disorder if father is affected?
all male children will be normal (can only pass Y on to sons so no male to male transmission)
all female children will be carriers (can only pass on X to daughters)
why may a female carrier of X linked disease show mild symptoms?
X inactivation
only one X chromosome is active in each cell so if normal X chromosome is inactivated then the cell will be faulty
methods of X inactivation?
XIST gene at Xq13 is needed for X inactivation
methylation is one mechanism for X inactivation
when can X inactivation be skewed?
occurs when one X chromosome carries a lethal mutation
mutation in one XIST gene
balanced X autosome translocations
can happen by chance
impact of skewed X inactivation?
can knock out working X chromosome in all cells so every cell is affected by faulty gene
causes of common vs rare genetic diseases?
common = combination of lots of gene changes and environment rare = single genetic change and very small impact of environment
what are single nucleotide polymorphisms and how common are they?
alterations in DNA sequence that generally are not in themselves disease causing
usually found every 100-300 base pairs so people have around 3,000,000 each
effects of polymorphism in promotor region?
less transcription > reduced mRNA > less protein
types of genetic variations other than single nucleotide polymorphisms?
copy number variations (extra or missing stretches of DNA)
sizes ranges from few bases to millions
deletions or duplications
what concept links genetics of rare and common disease?
penetrance
mendelian disorders = high penetrance and small environmental contribution
multifactorial disease = genetic change is just another risk factors and low penetrance
mutation/polymorphism frequency in common vs rare diseases?
common = higher frequency (but lower penetrance)
how much of the genome is shared in mono vs dizygotic twins?
mono = 100% dizygotic = 50%
what is the P value in a statistical test?
probability that the data you see has happened by chance
e.g P value of 0.05 = there’s a 1 in 20 chance that the data you see has happened by chance
how do you know which gene to look at?
test whole genome and analyse as many polymorphisms as you can
work out which ones are significant
example of a null allele polymorphism?
filaggrin deficiency
