Genome variation Flashcards
What is karyotyping?
the process of sorting chromosomes into their matched pairs
an important technique for investigating chromosomal disorders
What are Macro-level differences in genome generally associated with?
Generally associated with disease:
- aneuploidy
- translocations
What are Micro or molecular differences in genome sometimes associated with?
Sometimes associated with disease:
- point mutation causing sickle cell anaemia
- 3bp deletion in CFTR
Which regions of a genome affect trait?
Exome region (about 2% of the genome)
the small proportion of variation accounts for all the genetic difference that then leads to phenotypic differences (the results in phenotype that we get is a combination of DNA and the environment, not solely DNA variation)
What is a polymorphism?
position on the genome that varies between individuals (a variant)
What is a reference sequence?
consensus sequence that tells us what we expect to see in the genome
this is used to determine whether there are any genetic variants (polymorphisms)
What are Single Nucleotide Variants (SNVs)/Polymorphism (SNP)?
Substitution of a single nucleotide at a specific position in the genome.
High in frequency and occurs 1 in 300 nucleotides in reference genome
Bi-allelic
In every individual, occurs once in every 1000 bases (1kb)
How are SNVs/SNPs generated?
During mismatch repair during DNA replication:
1) Mismatch during DNA replication
2) DNA mismatch repair system should excise out the base that doesn’t belong there
3) Instead, it incorrectly excises out the wrong base, resulting in genetic variation
Where are the majority of SNPs?
Not in the exome
Why are the majority of SNPs not in the exome?
because exome has strong selective pressure to not incoporate mutations which will lead to detriment in individuals
Describe the function of the selective pressure in the exome.
high selective pressure in the exome keeps the variation relatively low in comparison to the non-coding regions of the genome
HOWEVER, there still is variation in the exome causing for the variations amongst individuals (e.g. hair colour, height, intelligence, etc)
Where are SNVs found?
Gene >no amino acid change (synonymous) >amino acid change (non-synonymous/missense) >stop codon (nonsense) >splice site >UTR (gene expression)
Promoter
> affects protein expression
Non-Coding Region
>if in non-coding region, less likely to have a detrimental effect
What is the only way SNVs disappear?
If they have a deleterious effect or population annihilation.
Without a deleterious effect or population annihilation, SNVs do not disappear
What is sickle cell anaemia caused by?
Single nucleotide variant (point mutation: non-synonymous/missense) changing the base sequence and therefore the amino acid sequence.
GAG → GTG
Glutamic Acid → Valine
What is the Link between sickle cell anaemia and malaria?
Individuals who are heterozygous for SCA have some protective advantage against malaria. As a result, the frequencies of sickle cell carriers are high in malaria-endemic areas
SCA point mutation is therefore very rare in white European population (0.02%), but relatively common in black African population (4.5%)
When is an SNV described as a polymorphism or a mutation?
SNV is described as a:
- polymorphism if minor allele frequency is >1%
- mutation if minor allele frequency is <1%
HOWEVER, this doesn’t always hold true:
- rare polymorphism: MAF 1-5%
- common polymorphism: MAF>5%
What do SNVs arise from?
All SNVs arise from a mutation and so are rare to begin with
How do SNVs spread throughout the population?
through reproduction and migration unless there is negative selection pressure against these variants
What is positive pressure selection?
genotypes that result in a beneficial trait that increases fitness are chosen FOR
What is negative pressure selection?
genotypes that result in a disadvantageous trait that reduces fitness are chosen AGAINST
What are SNVs called when proven to be pathogenic?
Point mutations
Describe how evolution is tied with SNVs.
1) New allele arises from mutation, causing a variant
2) Gene flow through reproduction and migration leading to introduction of that variant into another population
3) Genetic drift as there is a random change in variant allele frequency between generation
4) Selection: non-random change in variant allele frequency between generations because presence of one allele/genotype is pathogenic (negative selection) or beneficial (positive selection)
What are Microsatellites (short tandem repeats)?
repetitive DNA units typically 2-5 nucleotides in length, which directly affect the physical length of the genome
unlike SNVs which are bi-allelic, micro-satellites are tri-allelic
Why do microsatellites arise?
due to a problem in DNA replication (Polymerase Slippage):
1) DNA Polymerase pauses to proofread, and elongating strand becomes disengaged from template
2) Elongating strand needs to re-anneal to template so polymerase can continue adding specific nucleotides, but because template strand consists of repetitive sequences, elongating strand re-anneals to incorrect base pairs because they are all identical
3) This causes a bubble of unpaired bases
4) DNA Repair Mechanism adds two extra bases into the parental strand and elongation therefore continues
Where does polymerase slippage occur?
only in sections of DNA with repeated patterns of bases and cannot occur in DNA without repeating patterns of bases
Where are microsatellites found?
May be part of 98% of the genome not coding for a protein:
- Intronic or UTR: may affect gene expression
- Intergenic
May also be exonic
>causes extra amino acids in protein and results in expansion disorders such as Huntington’s= trinucleotide repeat expansion disorder
What characteristic do STRs have that allows them to be used for identification of an individual?
Each STR is highly polymorphic
How is PCR used to amplify STRs?
unique primers flanking each STR allow specific PCR amplification of the two STR alleles at a given locus
How do STRs identify an individual in the UK database?
A panel of 10 STRs that are used in the UK are amplified and are sorted by size (gel electrophoresis) and the repeat number is thus determined.
This gives a pattern of 20 numbers along with a gender identifier, and this gives a uniqueness (frequency) of 1 in 1 billion.
What is a copy number variant (CNV)?
a polymorphism in which the number of repeats of a DNA sequence at a location varies from person to person
What is the simplest type of CNV?
presence or absence of a gene
-individual’s genome could therefore contain 2 (one on each homologous chromosome), 1 or 0 copies
What is a CNV caused by?
CNV is caused by non-allelic homologous recombination in meiosis
>allelic recombination is good because it increases genetic variation, however non-allelic recombination results in duplication/deletion and copy number change, impacting future generation
What is Non allelic homologous recombination?
a form of homologous recombination that occurs between two lengths of DNA that have high sequence similarity, but are not alleles
When are CNVs pathogenic?
CNVs are pathogenic in microdeletion disorders e.g. diGeorge syndrome
What are the effects of most common variants?
Most common variants don’t cause Mendelian monogenic disorders and the majority are probably neutral (particularly intergenic variants)
BUT, they may well impact upon non-Mendelian disorders and undoubtedly contribute to general individual variation (e.g. personality, sporting ability, looks, etc)
Variants therefore can be:
- beneficial
- pathogenic
- neutral
Give clinical uses of variants.
Used as markers to help find disease-causing genes and mutations:
- Autozygosity Mapping and Linkage Studies (microsatellites, SNPs)
- Association Analysis (SNPs, CNVs)
