Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Genomics > Genome Variation > Flashcards

Genome Variation Flashcards

1
Q

How big is the human genome?

A

3 billion bases
About 20,000 genes
About 2% of the genome codes for protein = exome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are major macro-level differences associated with? Examples

A

Associated with disease (aneuploidy, translocations etc)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are micro or molecular level pathogenic differences associated with? Examples

A

Sometimes associated with disease (point mutation and SCA, 3bp deletion in CFTR)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What do coding variants effect?

A

Effect traits such as height, hair colour, intelligence etc

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is a variant?

A

Any position in the genome that varies between individuals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Homozygous

A

Same alleles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Heterozygous

A

Different alleles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Reference allele

A

What you would expect the base to be at a particular position on the chromosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Usefulness of the human genome mapping

A

Enabled us to base all our assumptions of what we expect given positions on the genome to be hence the reference alleles.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is an SNP?

A

A change in a single base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How many SNPs are there when comparing the human genome?

A

Approx. once every 300 bases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

In an individual, how many SNPs are there per base?

A

1 every 1000 bases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How many SNVs have been identified in the human genome?

A

About 17 million

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How does a SNP occur?

A

Typically caused by faulty replication of DNA during mitosis. There is a mismatch repair mechanisms that should correct these mistakes, some don’t get corrected and end up as a SNP.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How does the mismatch repair system work?

A

Repair the parental strand and not the new strand resulting in the T being changed for a C. This will result in variation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is the polymerase slippage event?

A
  • The polymerase in the template strand during replication slips.
  • It causes the new strand to unpair (release) from the template strand.
  • If occurs in the codon repeat region, then the new strand will reattach to the template strand and it will have many identical copies of the codon to choose from.
  • With so many identical codon copies to reattach to, the new strand may reattach to the template at the wrong copy.
  • The new strand forms a bubble of unpaired bases, which represents the expansion of the new strand.
  • The template strand will realign with the new strand and bring the bases from the bubble back into line with the template strand.
  • The brand new double helix of DNA contains more CAGs in the repeat region.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Where are SNPs located/

A

In the 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
- Less likely to have a detrimental effect

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Why do SNPs not disappear?

A

Without a deleterious effect or population annihilation, they remain.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Describe the distribution of the SCA variant allele in the european population

A

0.02% - 2 in every 10,000 chromosomes

Point mutation very rare in white European population

20
Q

Describe the distribution of the SCA variant allele in the african population

A

4.5% - about 1 in every 20 chromosomes

But, relatively common in black African population

21
Q

What is the heterozygous advantage of SCA?

A

Beneficial in places where malaria is rife

22
Q

What is a minor allele frequency?

A

Frequency is greater than 1 then in at least 1 in every 100 chromosomes has non-reference allele

23
Q

Describe the MAF levels in rare and common polymorphisms

A

Rare - MAF 1-5%

Common - MAF > 5%

24
Q

What affects whether a variant remains rare?

A
  • All variants start off rare (via the mismatch repair system).
  • Evolutionary forces affect whether or not a variant remains rare.
  • Rare variants may be damaging and/or recent,
  • However, some minor allele frequencies may have just occurred therefore using the 1% measure may also be accurate to distinguish between a mutation and a polymorphism.
25
Q

What are the evolutionary forces that affect SNVs?

A
  • Mutations: New allele arises, now 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.
    - Pathogenic (negative selection)
    • Beneficial (positive selection)
26
Q

What do genetic variants most likely cause?

A

Most likely cause a detrimental effect if they are in a gene especially in a key developmental gene.

27
Q

What is a microsatellite?

A

A short repeating sequence in the DNA unit.

28
Q

Where are microsatellites located?

A
  • Part of the 98% of genome not coding for protein
    - Intronic or UTR: may affect gene expression
    - Intergenic
  • Exonic
    • Extra amino acids in protein
    • Expanison disorders e.g. Huntington’s = trinucleotide repeat expanison disorder
29
Q

What is a copy number variant?

A

Large sections of the genome are repeated and the number of repeats in the genome varies between individuals

30
Q

What is the simplest type of a copy number variation?

A

The presence or absence of a gene.

31
Q

What can a duplication of a genomic segment result in?

A

It could result in diploid copy numbers of two, three, or four.

32
Q

How does the duplication or deletion of loci on chromosomes occur?

A

It occurs via non-allelic homologous recombination.

33
Q

How does non-allelic homologous recombination occur?

A

This is due to misaligned crossover driven by sequence similarity due to viral/bacterial genomes which have incorporated during evolution.

34
Q

Where are CNVs located?

A
  • Intergenic
  • Often affect one or more genes (parts of genes)
  • About 12% of genome is CNV
35
Q

Give an example where the CNV is pathogenic?

A

In microdeletion disorders e.g. DiGeorge syndrome

36
Q

Give some types of common genetic variant

A
  • SNP: 17 million identified - about 3 million/genome
  • Microsatellites: about 3% of the genome
  • Copy number variants: about 2000 identified
37
Q

What do most common variants cause?

A

Probably neutral (particularly intergenic variants). Most common variants do not cause mendelian, monogenic disorders.

38
Q

What are the effects of variants?

A
  • Can be beneficial
  • Can be pathogenic
  • Most are neutral
  • Used as markers to help find disease-causing genes and mutations.
39
Q

Give examples of tests that can be used to find diseases and mutations

A

Autozygosity mapping and linkage studies - microsatellites, SNPs

Association analysis - SNPs and CNVs

40
Q

Locus

A

Unique position in genome

41
Q

Allele

A

Particular form of a specific locus

42
Q

Biallelic

A

2 possible alleles

43
Q

Triallelic

A

3 possible alleles

44
Q

Multiallelic

A

> 3 alleles

45
Q

Genotype

A

An individual has 2 alleles for any autosomal locus (heterozygous/homozygous)

Genomics (19 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions