Genetics 2

Question 1

how much of the genome consists of exons and is therefore translated?

Answer 1

2-3%

Question 2

what does the other 97-98% of the genome do?

Answer 2

regulation of genes
spaces the genes out - insulating the genes from promotors
provides substrate to expand genome/add genes

Question 3

how are large changes in DNA analysed?

Answer 3

array comparative genetic hybridisation looks for deletions/duplications
chromosome/karyotype analysis looks for balanced rearrangements

Question 4

how are smaller changes in DNA analysed?

Answer 4

PCR and sanger sequencing

next generation sequencing

Question 5

mutation vs polymorphism?

Answer 5

mutation = genetic variation that causes disease
polymorphism = genetic variation that is prevalent in the population and not in itself disease causing

Question 6

how does PCR work?

Answer 6

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

Question 7

what are the steps in PCR?

Answer 7

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

Question 8

what happens if there is a mutation in the promotor region?

Answer 8

no, or reduced transcription and therefore no or reduced protein

Question 9

what happens if a mutation is between intron and exon causing alteration in splice consensus?

Answer 9

splicing and transcription is altered (e.g an exon is missing as its been wrongly spliced out) causing abnormal or absent protein

Question 10

what does a mutation in base sequence forming a new stop codon cause?

Answer 10

short or absent protein

Question 11

what does a mutation in base sequence altering amino acid sequence cause?

Answer 11

different or non-functioning protein

Question 12

missence mutation?

Answer 12

base is swapped for another one

Question 13

deletion in frame vs deletion out of frame?

Answer 13

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

Question 14

triplet expansion?

Answer 14

repeat of a codon

Question 15

at what stage in reproduction can a new mutation occur that is not present in the parents?

Answer 15

gametogenesis (formation of gamete within the parent)

can have a post-zygotic mutation causing the child to be mosaic

Question 16

what happens to child if one parent is mosaic?

Answer 16

if gamete is from mutated cell population then the mutation passes to the zygote and all of the childs cell then possess the mutation

Question 17

overview of whole genome sequencing in NGS?

Answer 17

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

Question 18

how are mutations detected in the whole genome in NGS?

Answer 18

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

Question 19

what is the catch with NGS?

Answer 19

most people have around 3,000,000 polymorphisms (changes from normal sequence) but only one mutation causing the genetic disease

Question 20

questions to ask to help determine where genetic change is polymorphism or disease causing mutation?

Answer 20

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

Question 21

how are the detected genetic changes filtered in NGS?

Answer 21

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)

Question 22

what is penetrance?

Answer 22

likelihood of having a disease if you have the mutation

100% penetrance = if you have the mutation you will definitely have the disease

Question 23

what is a mendelian disorder?

Answer 23

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)

Question 24

types of mendelian inheritance?

Answer 24

autosomal dominant
autosomal recessive
X linked
mitochondrial

Question 25

features of AD inheritance?

Answer 25

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

Question 26

can different mutations in the same gene cause the same disease?

Answer 26

yes | and vice versa - same disease can be caused by mutations in one of several genes

Question 27

features of autosomal recessive inheritance?

Answer 27

often only seen in one generation 1 in 4 risk in child if parent affected increased likelihood if parents are related

Question 28

relevance of y chromosome in disease?

Answer 28

basically irrelevant

Question 29

describe X linked inheritance

Answer 29

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)

Question 30

rate of transmission of X linked recessive disorder if mother is carrier?

Answer 30

half of male children will be affected | half of female children will be carriers

Question 31

rate of transmission of x linked recessive disorder if father is affected?

Answer 31

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)

Question 32

why may a female carrier of X linked disease show mild symptoms?

Answer 32

X inactivation | only one X chromosome is active in each cell so if normal X chromosome is inactivated then the cell will be faulty

Question 33

methods of X inactivation?

Answer 33

XIST gene at Xq13 is needed for X inactivation | methylation is one mechanism for X inactivation

Question 34

when can X inactivation be skewed?

Answer 34

occurs when one X chromosome carries a lethal mutation mutation in one XIST gene balanced X autosome translocations can happen by chance

Question 35

impact of skewed X inactivation?

Answer 35

can knock out working X chromosome in all cells so every cell is affected by faulty gene

Question 36

causes of common vs rare genetic diseases?

Answer 36

``` common = combination of lots of gene changes and environment rare = single genetic change and very small impact of environment ```

Question 37

what are single nucleotide polymorphisms and how common are they?

Answer 37

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

Question 38

effects of polymorphism in promotor region?

Answer 38

less transcription > reduced mRNA > less protein

Question 39

types of genetic variations other than single nucleotide polymorphisms?

Answer 39

copy number variations (extra or missing stretches of DNA) sizes ranges from few bases to millions deletions or duplications

Question 40

what concept links genetics of rare and common disease?

Answer 40

penetrance mendelian disorders = high penetrance and small environmental contribution multifactorial disease = genetic change is just another risk factors and low penetrance

Question 41

mutation/polymorphism frequency in common vs rare diseases?

Answer 41

common = higher frequency (but lower penetrance)

Question 42

how much of the genome is shared in mono vs dizygotic twins?

Answer 42

``` mono = 100% dizygotic = 50% ```

Question 43

what is the P value in a statistical test?

Answer 43

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

Question 44

how do you know which gene to look at?

Answer 44

test whole genome and analyse as many polymorphisms as you can work out which ones are significant

Question 45

example of a null allele polymorphism?

Answer 45

filaggrin deficiency