Human Genome variation

Question 1

How many pairs of chromosomes do we have (gross structure)?

Answer 1

23

Question 2

How big is the human genome?

Answer 2

• 3 billion bases (3000Mb)
• ~20,000 genes
• ~2% genome codes for protein = exome

Question 3

What are Major macro-level differences?

Answer 3

• Major macro-level differences generally associated with disease (aneuploidy, translocations, etc) (not common)

Question 4

Whar are micro or molecular-level pathogenic differences?

Answer 4

• Also micro or molecular-level pathogenic difference sometimes associated with disease (point mutation and SCA, 3bp deletion in CFTR)

Question 5

Give some examples of Coding variants that effect traits

Answer 5

• height
• hair colour
• intelligence

Question 6

What is a variant?

Answer 6

• ~99.7% DNA same between any 2 people (i.e. ~9 million bases different)
• Any position in the genome that varies between individuals is considered polymorphic = a variant

Question 7

Define “common” in terms of genomics

Answer 7

• The frequency of the minor allele is relatively high in the population frequency and proportion of chromosomes that carry each allele in the population
• Or multiallelic

Question 8

What are 2 of the same and different alleles called?

Answer 8

• 2 same alleles = homozygous

* 2 different alleles = heterozygous

Question 9

What is a gene reference?

Answer 9

A gene reference is the most common allele in the population

Question 10

What is Single Nucleotide Variant (SNV)/Polymorphism (SNP)?

Answer 10

A single base change

Question 11

Describe the frequency of an SNV

Where are they mostly found?

How are they generated?

Answer 11

• High frequency: 1 every 300 nucleotides in reference genome
• One individual: 1 every 1000 bases
• Millions SNVs identified in human genomes
• Majority not in exome
• Generated by mismatch repair during DNA replication

Question 12

Describe the process of DNA replication and incorporate a SNP

Answer 12

• DNA is unwound by helicase
• DNA polymerase is used to generate new daughter strands based on parental template strands
• The bases are complementary AT and CG
• Repair mechanisms in place
• This diagram shows how DNA replicates and how it corrects itself if there is a mismatch. This produces variation. A single nucleotide variant. This is shown in read. We have introduced a variant into a population

Question 13

What is biallelic?

Answer 13

2 alleles present

Question 14

Where may a single nucleotide variant be found?

Answer 14

Gene:
•	No amino acid change (synonymous)
•	Amino acid change (non-synonymous/missense)
•	Stop codon (nonsense)
•	Splice site
•	UTR (gene expression)

Promoter:
• Protein expression

• Non-coding region:
• Without a deleterious effect or population annihilation, SNVs do not disappear

Question 15

Give an example of a single nucleotide variant

Answer 15

On image

Question 16

What is a polymorphism?

What percentage is a rare polymorphism, common and mutation?

What is a better description of one?

Answer 16

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%
Less than 1% is a mutation

Polymorphism is used to describe a single nucleotide variant that doesn’t have a bad effect, so use variant INSTEAD.

Question 17

What causes single nucleotide variants?

Answer 17

Mutation
New allele arises, we now have a Variant

Gene flow
Migration leading to introduction of that variant into another population

Genetic drift
Random change in variant allele frequency between generations

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

Question 18

What are microsatellites?

Another name for them?

Answer 18

Repetitive bases

Also known as a short tandem repeat

Question 19

Name the 6 types of microsateliltes

Answer 19

On image pg 5

Question 20

How does the formation of microsatellites happen?

Answer 20

• Errors in DNA replication
• The polymerase stutters and causes repeat sequences. It will cause gaps in other words, bases will shift back to other bases leaving some unpaired bases.
• To fix this, it has to re-anneal back to the parental strand. It looks for complementary bases. It causes a gap in the parental strand and adds some bases

On image

Question 21

Where are Microsatellites found?

Answer 21

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

Question 22

Read summary of microsatellites

Answer 22

• 1000s in genome
• Repeat units
• Varying numbers of repeats
• Alters actual size of that region of the genome
• Multiallelic
• Can be anywhere in genome

Question 23

What is “Copy number of variants”?

Answer 23

Copy number of variants >2000 identified – 100 per genome

• An entire chunk of bases may be repeated, as shown below.

Question 24

How does copy number variation occur?

Answer 24

Non-allelic homologous recombination in meiosis

Question 25

Describe the extent of copy number variations

Answer 25

CNVs may be….

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

Question 26

What are the effects of copy number variants?

Answer 26

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 27

What are the variant effects?

Answer 27

• 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)