Genome Variation

Question 1

What is a locus?

Answer 1

unique position in genome

single base to entire genomic region

Question 2

What is an allele?

Answer 2

particular form of a specific locus

Single base to entire genomic region

Question 3

What is the genotype?

Answer 3

The genetic makeup of an individual
An individual has 2 alleles for any autosomal locus
(heterozygous/homozygous)

Question 4

What does it mean to be biallelic?

Answer 4

2 possible alleles

Question 5

What does triallelic mean?

Answer 5

3 possible alleles

Question 6

If there are >3 possible alleles what term do we use to describe the genotype?

Answer 6

multiallelic

Question 7

How is the presence of an allele expressed in a population?

Answer 7

For a popn, presence of an allele is expressed as a freqy or %
Two popns of same species need not have same freqy at same locus

Question 8

Describe the gross structure of the human genome

Answer 8

Gross structure – 23 pairs chromosomes

Question 9

Describe the molecular structure of the human genome

Answer 9

Molecular structure – DNA sequence
3 billion bases (3000Mb)
~20,000 genes

Question 10

How much of the human genome makes up the exome?

Answer 10

~2% genome codes for protein = exome

Question 11

What type of genome variations cause disease?

Answer 11

Major macro-level differences generally associated with disease (aneuploidy, translocations, etc)

Question 12

What do micro/molecular level genome variations cause?

Answer 12

Micro / molecular-level pathogenic difference sometimes associated with disease (point mutation and SCA, 3bp deletion in CFTR)

Question 13

Give examples of micro / molecular-level variations

Answer 13

Coding variants that affect traits (height, hair colour, intelligence, etc)

Question 14

On average how much of our DNA differs from one another?

Answer 14

~99.7% same DNA between any 2 people (i.e. ~9 million bases different)

Question 15

What is defined as polymorphic?

Answer 15

Any position in the genome that varies between individuals is considered polymorphic = a variant

Question 16

What is the reference allele?

Answer 16

Refers to the base that is found in the reference genome

Since reference is just somebody’s genome, it is not always the major allele

Question 17

What is the major allele?

Answer 17

the most common allele for a given SNP

Question 18

What is the minor allele?

Answer 18

the less common allele for a SNP

Question 19

What is the minor allele frequency (MAF)?

Answer 19

frequency at which the second most common allele occurs in a given population

Question 20

What was the human genome mapping project?

Answer 20

1993 - 2001

4 anonymous individuals averaged out

Question 21

What is an SNP?

Answer 21

A SNP is a change in a single base

Question 22

How common are SNPs?

Answer 22

High frequency: 1 every 300 nucleotides in reference genome
One individual: 1 every 1000 bases
~17 million SNVs identified in human genomes

Question 23

Where are SNPs found?

Answer 23

Majority not in exome

Question 24

how are SNPs formed?

Answer 24

Generated by mismatch repair during DNA replication (mitosis)
Although there are mismatch repair mechanisms which should correct these mistakes, some don’t get corrected and we end up with a SNP

Question 25

How does DNA replication normally occur?

Answer 25

During DNA replication the two strands separate and used as templates to synthesise complementary strands => should end up with two identical copies

Question 26

How does a mismatch form during replication?

Answer 26

When synthesising the new strand, an incorrect base is incorporated instead Mismatch repair mechanism will identify the mistake and correct it so the bases are a standard Watson-Crick base pair or it might not...

Question 27

What is the consequence of a persistent mismatch?

Answer 27

If this change occurs in the gametes and isn’t deleterious then it will get passed onto the next generation As time goes on it can spread through the population.

Question 28

Where in a gene may a SNV be found?

Answer 28

``` No amino acid change (synonymous) Amino acid change (non-synonymous/missense) Stop codon (nonsense) Splice sit UTR (gene expression) ```

Question 29

Where else in DNA are SNVs found?

Answer 29

Promoter - Protein expression | Non-coding Region

Question 30

When do SNVs not appear?

Answer 30

Without a deleterious effect /population annihilation => SNV doesn’t disappear

Question 31

What is a missense point mutation?

Answer 31

A point mutation where a single nucleotide change results in a codon that codes for a different amino acid > type of nonsynonymous substitution

Question 32

Give an example of a disease associated with missense mutation

Answer 32

Sicke cell anaemia codon GAG -> GTG Glutamic acid -> Valine

Question 33

How common is the SCA point mutation across the globe?

Answer 33

Point mutation very rare in white European population Relatively common in black African population Estimated frequency of SCA variant allele: European = 0.02%, i.e. 2 in every 10,000 chromosomes African = 4.5%, i.e. ~1 in every 20 chromosomes

Question 34

Why is the SCA point mutation more prevalent in Black African populations?

Answer 34

Beneficial in places where malaria is rife (heterozygote advantage)

Question 35

How do we define a polymorphism?

Answer 35

If minor allele freqy >1% (i.e. at least 1 in every 100 chromosomes has non-reference allele) = polymorphism Rare polymorphism: MAF 1-5% Common polymorphism: MAF >5%

Question 36

Outline the features of a variant

Answer 36

Safer to use term variant - All variants start off rare - Evoly forces affect whether or not a variant remains rare - Rare variant may be damaging and/or recent

Question 37

How does mutation affect evolution?

Answer 37

New allele arises, we now have a Variant

Question 38

What is gene flow?

Answer 38

Migration leading to introduction of that variant into another population

Question 39

What is genetic drift?

Answer 39

Random change in variant allele frequency between generations

Question 40

What is natural selection?

Answer 40

Non-random change in variant allele frequency between generations because presence of one allele/genotype is pathogenic (negative selection) or beneficial (positive selection)

Question 41

How do we identify if a natural genetic variant is neutral?

Answer 41

By asking the following questions: Where are they? In a gene? Not in a gene? What sort of gene? Key developmental gene, e.g. HOXD1 Pigmentation, e.g. MC1R Not straightforward Depends on the type of variant (lots of variants in every gene –some pathogenic, some not; depends on the environment)

Question 42

Summarise SNVs

Answer 42

Millions in genome A position in genome at which the base can vary Can be anywhere in the genome (genic or non-genic) May do nothing, may affect a trait, may be associated with disorder Generally bi-allelic Due to mutation and mismatch repair These are base substitutions When pathogenic, may call point mutations

Question 43

What is a microsatellite?

Answer 43

a set of short repeated DNA sequences at a particular locus on a chromosome, which vary in number in different individuals and so can be used for genetic fingerprinting

Question 44

what is a STR?

Answer 44

a short tandem repeat is a micrsatellite Can be variation in number of repeats between people Reference often smallest allele but a range is often quoted

Question 45

What is polymerase slippage?

Answer 45

when the polymerase slips from the template strand during replication (error in DNA replication causing microsatellite expansion)

Question 46

what is the consequence of polymerase slippage?

Answer 46

Polymerase slippage causes the new strand to unpair (release) from the template strand, and is the main reason for codon expansion

Question 47

Using the huntingtin gene to describe how polymerase slippage causes expansion

Answer 47

1. Slip occurs at codon repeat region of Huntigntin gene 2. New strand has many identical codon copies to choose from when trying to reattach 3. New strand may reattach to template at wrong copy, (usually 1 away from the copy that was adjacent to the polymerase before it slipped) 4. Forms a bubble of unpaired bases, representing expansion of new strand 5. Once DNA replication is complete, an unknown mechanism allows template strand to realign with new strand and bring bases from the bubble back into line with the template strand => forms complementary base pairs The brand new double helix of DNA contains more CAGs in the repeat region of the Huntington gene than existed before. Polymerase slippage has caused expansion

Question 48

Where in the genome are microsatellites found?

Answer 48

Part of the 98% of the genome not coding for protein - Intronic or UTR: may affect gene expression - Intergenic Exonic - Extra amino acids in protein - pathogenic example?

Question 49

Outline the features of expansion disorders

Answer 49

Expansion disorders, e.g. Huntington’s = trinucleotide repeat expansion disorder, basically a “bad” microsatellite ``` 1000s in genome Repeat units Varying numbers of repeats Alters actual size of that region of the genome Multiallelic Can be anywhere in genome May do nothing…. ```

Question 50

What is a CNV?

Answer 50

A copy number variation (CNV) is when the number of copies of a particular gene varies from one individual to the next

Question 51

What is the reference number of a CNV?

Answer 51

Reference copy number = 1

Question 52

What is the simplest type of Copy number variation?

Answer 52

The simplest type of copy number variation is the presence or absence of a gene. An individual’s genome could therefore contain two, one, or zero copies

Question 53

What causes multiple copies of a variation?

Answer 53

Duplication of a genomic segment | could result in diploid copy numbers of two, three, or four.

Question 54

What is the result of allelic recombination during meiosis?

Answer 54

Allelic recombination is good! – shuffling of alleles | But non-allelic recombination results in duplication/deletion and copy number change

Question 55

Outline the features of CNVs

Answer 55

``` Intergenic But – quite large (>1kb) so often affect one or more genes (parts of genes) ~12% genome = CNV >2000 identified 1kb-5000kb ```

Question 56

Give examples of pathogenic CNVs

Answer 56

Microdeletion disorders, e.g. diGeorge syndrome

Question 57

Outline types of common genetic variants

Answer 57

Single Nucleotide Polymorphisms (SNPs) ~17 million identified; ~3 million/genome Microsatellites ~3% of the genome Copy Number Variants (CNVs) >2000 identified; ~100 per genome Remember – everyone “has” every variant, what may differ between individuals is the genotype

Question 58

How do we determine if biallelic variants are common?

Answer 58

If biallelic: high frequency of the minor allele Population frequency i.e. proportion of chromosomes that carry each allele in the population

Question 59

How do we assess multiallelic variants being common?

Answer 59

Compare with translocations or aneuploidies – we don’t see thousands or millions of those because they’re generally damaging

Question 60

How commonly do variants associate with disease?

Answer 60

Most common variants not causing Mendelian, monogenic disorders. Majority are probably neutral (particularly intergenic variants). BUT! May well impact upon complex, non-Mendelian disorders and undoubtedly contribute to general individual variation (personality, sporting ability, looks etc)

Question 61

List a few traits / non-mendelian disorders variants contribute to

Answer 61

``` Height Allergies Haemochromatosis Type 1 and Type 2 diabetes Alzheimer’s Anxiety Dyslexia Memory Sexual desire Aging Nicotine dependance Faithfulness Age-related hearing loss Gout Sciatica Sense of smell HIV susceptibility Anti-social behaviour ```

Question 62

What are the effects of variants?

Answer 62

Can be beneficial Can be pathogenic Most are neutral Are these of any use? Yes, can be used as markers to help find disease-causing genes and mutations Autozygosity mapping & linkage studies (Microsatellites, SNPs) Association analysis (SNPs, CNVs)