The Contribution of Genetic Changes to Human Disease Flashcards
How do genomes compare between indiv?
- genomes unique to each person but overall v.sim + small % varies
- some of variation is common, some rare, some unique to our families and each of us
What does the genomes of each indiv consist of?
each have 1 mat + 1 pat genome - shuffled versions of our parents genomes
What makes our genome unique?
Combo of variation patterns (alleles)
What is DNA variant/variation?
Specific sites (locus(i)) within genome at which 2/more versions (alleles) may be present
What is polymorphism?
Common DNA variant
What is a mutation?
Pathogenic DNA variant/process through which new DNA variant may arise (de novo)
How does a DNA variant arise?
Through process of mutation which is constantly occuring
What causes variation in genome?
Mutation events occurring over 1000s of yrs
What is the role of selection?
Determines what variant remains in pop i.e. if trait has less -ve/more +ve phenotypic consequences - more likely to inc freq in pop
What mixture will be contained in our genome?
Old mutation events not -vely selected that are likely to be common in pop + more recent mutation events that gen variants unique to ourselves + specific parts of our bodies (somatic)
List ways DNA Sequences can vary?
- Single nucleotide sub
- Deletion
- Insertion
- Translocation
What is single nucleotide sub?
Straight sub of 1 base for another
How can single nucleotide sub be subdivided?
- Transition
2. Transversion
What is a transition?
Sub which conserves base chem
What is a transversion?
Sub which changes base chem e.g. go from purine to py + vice versa
Why are transitions roughly 2x common as transversions?
Although there’s 2x as many poss transversions as transitions, transitions more common as easier to go from same base chem than a diff one
What is a deletion?
Loss of single base/continuous block of seq
What is an insertion?
Insertion of single base/continuous block of seq between 2 prev adj bases
What is tandem dup?
Special case of an insertion where inserted material identical to adj sequence
- can be 3bp/repeat/microsatellite repeat expansion
What is an inversion?
- Block of seq is inverted - bc of nature of DNA pairing, inverted seq replaced with its rev compliment
- as DNA double stranded, seq gets inverted also + placed back into DNA strand
What is a translocation?
DNA exchanged between chr
How many bp can be involved in del, ins, tandem dup + inv?
Single base to sev milli bases in size
As rearrangements are often imperfect, what can happen as a result?
seq at ends of blocks may also be disrupted
Why might inv/translocations be benign?
if breakpoints don’t disrupt genes e.g. in non-coding region of genome - not much of an effect
Where do DNA variants occur?
Throughout our genomes
What types of consequences can DNA variants have?
Some have functional (post phenotypic) consequence
Others are benign - changing seq has no effect on biology/phenotype
What is functional consequence of a variant defined by?
effect it has on functional regions of genome i.e. changing seq will have detrimental consequences which leads to functional then phenotypic consequences
What do almost all disease causing variants directly affect?
Functional parts of known genes
What do most known functional parts of genes depend critically on and what is the result of this?
Nucleotide seq and is therefore sensitive to variation
What are the diff parts of a gene?
- upstream ass site
- promoter
- 5’ UTR
- initiation codon
- coding region
- splice donor site
- splice acceptor site
- splice branch site
- intron (cryptic splice)
- stop codon
- 3’ UTR
- polyadenylation site
How do the effects of coding region single nucleotide sub vary?
Can be silent, missense/nonsense sub
What is a silent sub and its effect?
- single bp sub but result is it still codes for same aa
- not affect protein directly but may affect splicing
What is a missense sub and its effect?
- single bp sub causes single aa change
- may be neutral/harmful effect resulting in gain or direct/indirect loss of function
What is a nonsense sub and its effect?
- single bp sub causes stop codon
- cause premature termination of reading frame resulting in truncated protein/NMD (nonsense mediated decay = mech in cell detects early stop codon and degrades protein being made)
What are the effects of small rearrangements e.g. del, ins, dup, inv?
effects confined to single exon of gene
Which effect of a variant is the most important?
Effect on reading frame
What is the result if bp ins/del is multiple of 3?
Don’t get frame shift
What do variants in all known splice recognition elements cause?
- Disruption of splicing process
- some exonic variants (ESEs) important for correct splicing to occur
- results depend on rel strength of elements, severity of change and proximity of alt options
What are the commonest consequences of variants in splice recognition elements?
- exon skipping = no splicing for certain exon
- use of cryptic splice sites (in exon/intron) - if seq damaged, nearby alt version used
- intron retention (small introns only) - if intron not spliced out, it’s retained
- combos of above
What do sizes of rearrangements form?
Continuum from 1bp to whole chr
What is the result of large rearrangements of 1/more exons of a gene if exon is multiple of 3?
Can get full length of transcript as won’t disrupt reading frame but if not, can disrupt
If an exon is 30bp and is dup, how man aa does it encode and what is the effect?
- encodes 10 aa
- dup adds just 10 aa - less disruptive than if its not 30bp
What is the effect of large rearrangements such as inversion on an exon?
- disrupts seq for splicing as they’ll be in wrong orientation and therefore exon is removed
What is the critical determinant of effect of large rearrangements?
- whether/not removal/insertion of exon (s) affects reading frame
What accounts for the vast majority of reported functional variants?
- small rearrangements (del, ins, dup, inv)
- large rearrangements of 1/more exons of a gene, del, dup and inv
What can also be pot sites of functional variation and why are they rarely described?
- variants in promoters
- variants in UTRs
- variants in polyadenylation signals
Why might variants in promoters be rare?
- promoters may be rel insensitive to variantion
What is effect of variants in promoters?
- can result in tissue/stage specific phenotype (if it promotes expression of gene in particular tissue/stage in dev) which can lead to phenotype
Why might variants be found in UTRs and which ones?
- some UTRs more highly conserved than coding regions
- v. few confirmed pathogenic variants e.g. myotonic dystrophy, fukuyama muscular dystrophy
Why might functions of variants in UTRs be poorly understood?
- transcript stability
- subcellular location
What effects does variants in polyadenylation signals cause?
- few characterised variants result in dec transcript levels
- ev from yeast that NMD pathway involved
Which terms classify mutations based on their behaviour in various genetic situations?
- loss of function: amorph + hypomorph
- gain of function: hypermorph, antimorph, neomorphic
What is an amorph?
variant that causes complete loss of gene function e.g. truncated gene
What is a hypomorph?
variant that causes partial loss of gene function e.g. by sub where protein works but not as well
What is a hypermorph?
variant that causes inc in normal gene function e.g. variant disrupts enz but its now more active as a result
What is an antimorph?
- dom alleles that act in opposition to normal gene activity e.g. protein that forms disomer
- mutations in 1 copy of gene - when dimers form, some have mutated copy which disrupts normal copy
What is a neomorphic variant?
- variant that causes dom gain of gene function that’s diff from normal function
What happens as a result of loss of function variation?
- protein product fails to perform its normal function
What causes loss of function variation?
- little/no protein produced (e.g. whole genome del, nonsense variant resulting in NMD
- mutation makes protein unstable/inappropriately targeted and is degraded (e.g. in frame del causing misfolding)
- residue/domain essential for function is missing/critically altered (missense variant in enz active site)
Why is loss of function variation usually rec?
- presence of 2nd, normal allele can usually rescue phenotype resulting in normal heterozygotes
In what ways can loss of function alleles exhibit dom form of inheritance?
- haploinsufficiency
- dom -ve effect
- somatic second hits
What is haploinsufficiency?
org so sensitive to levels of protein that 50% of dec in quantity causes noticeable phenotype
What is dom -ve effect?
- formation of homomultimeric complexes means that not only does protein lose its function but it disrupts function of its normal counterpart
What are somatic second hits?
- org largely normal but somatic 2nd mutations give rare clones of null cells which are defective
- rec at cellular level but dom inherited in families
- indiv inherits loss of function copy of gene and somatic 2nd mutation hits 2nd copy of gene
e. g. predis of BRCA to breast cancer + 2nd hit causes disease to manifest
What happens in gain of function variation?
- rather than lose its principal function, protein may become less specific in its normal function/even acquire novel function
In what ways can gain of function alleles exhibit dom form of inheritance?
- loss of regulation
- novel function
What is loss of regulation?
- activity of protein (enz etc) loses its spacial/temporal specificity
- may be due to loss of regulatory region/mislocation in cell
- variant in inhib domain - constitutive activity (dom) or variant in active domain - loss of function (rec)
What is novel function?
- protein has novel effect which is not characteristic of normal product
- common novel function is formation if insol aggregates
- e.g. HD + triplet repeat expansion due to mutation of huntingtin which forms aggregates which is basically new function of protein but has detrimental effect
What was identified as cause of infantile onset epilepsy in Amish?
- identified on chr 2, homozygosity in affected indiv
- in SIAT9 gene, affected indiv homo have C to T sub for stop codon
- SIAT9 encodes GM3 synthase - critical in syn of a + b series gangliosides
- mutation identified predicted to lead to loss of function of GM3 syn - don’t get gangliosides which leads to seizures
How did carriers compare to affected in Amish case?
- carriers have 1 copy of arg + stop codon
- measurement of levels of gangliosides of affected indiv homo for disease causing variant confirmed complete lack of a + b series gangliosides
- measurement in carrier parents hetero for disease causing variant demonstrated normal levels of a + b
- demonstrated that 1 normal copy of gene is OK but no normal copies resulted in loss of a + b series and epileptic phenotype
What did profiles between carriers and affected show?
- parents have wild type and mutated copy (50% normal activity of gene and protein but prfiles are same as control therefore 50% of enz sufficient for pathway to work
- affected had no GM3 peaka and therefore no gangliosides
- higher peaks also as lactosyl cermaide goes down other pathways due to no GM3 syn
- lac cer also builds up which may be whats actually causing seizues
What do certain bio biases mean?
- Certain types of mutation events more freq
What do consequences of variation depend on?
- pos of variation wrt functional seq
What is functional consequence of disease causing variants?
- leads to phenotypic effect
