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EMS > Lecture 12 - Genome variation > Flashcards

Lecture 12 - Genome variation Flashcards

1
Q

How many years ago was the human population in Africa 10,000?

A

60,000 - 90,000

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2
Q

What is population bottleneck?

A

Population bottleneck is an event that drastically reduces the size of a population: migration, environment changes, disease

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3
Q

What do genetic bottlenecks reduce?

A

Genetic Variation

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4
Q

What do mutations promote?

A

Diversity

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5
Q

How many base pairs do we have in our diploid genome?

A

We have a diploid genome of (2x) 3x109 base pairs

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6
Q

how many base pairs do any two people have different?

A

about 6 x 106 base pairs (0.1 of genome)

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7
Q

How many mutations are there in each diploid genome?

A

70

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8
Q

What do mutation rates increase with?

A

Rate increases with paternal age

Non-germline mutation rates up to 20 fold higher

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9
Q

How identical is the population?

A

99.9%

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10
Q

Origin of genetic variation?

A

Exogenous factors (radiation, chemicals – mostly somatic)
Endogenous factors
Segregation (Aneuploidies e.g. Downs syndrome, Edwards syndrome)
Recombination (translocations)
DNA replication errors (mispaired bases, slippage)
Inadequate DNA repair mechanisms (e.g. mismatch repair, base excision repair)

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11
Q

What are the two classes of genetic mutation?

A
  1. Variation that does not alter the DNA content (number of nucleotides remains unchanged)
  2. Variation that results in a net loss or gain of DNA sequence
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12
Q

Give examples of Variation that results in a net loss or gain of DNA sequence?

A

Can be large (whole chromosome) or small (single nucleotide)

Most DNA changes are small scale and have no obvious effect on phenotype – neutral variation

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13
Q

Give examples of Variation that does not alter the DNA content (number of nucleotides remains unchanged)

A

Single nucleotide replacements
- Balanced translocations and inversions

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14
Q

What percentage of our DNA is poorly conserved?

A

90%

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15
Q

what percentage of all variation is caused by single nucleotide variants?

A

90%

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16
Q

what percentage of all variation is caused by Indels (1-10)?

A

9%

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17
Q

what percentage of all variation is caused by Indels (11-100 nucleotides)?

A

0.9%

18
Q

what percentage of all variation is caused by CNVs >100 nucleotides?

A

0.1%

19
Q

What is classed as polymorphism?

A

More common that 0.01 (1%)

20
Q

What is classed as rare variant?

A

Less common than 0.01 (1%) =

21
Q

What are indels?

A

Indels = insertion or deletion of one or more nucleotides

22
Q

What are Single Nucleotide Polymorphisms (SNPs)?

A

DNA sequence variation occurring when a single nucleotide (A, G, C, T) in the genome differs between between members of a species or between paired chromosomes in an individual.

23
Q

How many of SNPs are identifed?

A

~175 million identified
(Predominantly diallelic)

24
Q

What is the minor allele frequency?

A

the frequency of the less common variant in a population

25
Q

Intronic variant characteristics?

A

Between genes or between exons
Do not affect resulting protein directly
Could affect regulation of transcription or splicing

26
Q

What is a missense variant?

A

An amino acid change
(nonsynonymous)

27
Q

What is a nonsense variant?

A

Change of amino acid to a stop codon, which leads to nonsense mediated mRNA decay or protein truncation

28
Q

What is a synonymous variant?

A

The codon sequence for the amino acid is changed but the same amino acid is still encoded for. E.g. GGC and GGU both code for Glycine

29
Q

What can simple repeats cause?

A

diseases such as Huntington’s disease, Fragile X syndrome etc.

30
Q

Simple repeats characteristics?

A
  • Repeat length polymorphisms
    • Thousands
    • Not evenly distributed
    • Highly polymorphic
    • Prone to slippage
31
Q

What percent of the human genome contributes to CNVs?

A

4.8-9.7% from 50 bp

32
Q

What are CNVs?

A

Copy number variation refers to a circumstance in which the number of copies of a specific segment of DNA varies among different individuals’ genomes. The individual variants may be short or include thousands of bases. These structural differences may have come about through duplications, deletions or other changes and can affect long stretches of DNA.

33
Q

What is the formation of CNVs caused by?

A

Nonallelic homologous recombination (NAHR) as the mechanism for recurrent genomic rearrangements.

34
Q

How are CNVs distrobuted?

A

CNVs are distributed unevenly in the genome

35
Q

What is the telomere-to-telomere consortium?

A

Filled in the missing 151 Mb of DNA using long read sequencing technologies
- Able to map the full genome

36
Q

What will happen to mutations that are strongly deleterious?

A

They will be quickly eliminated by natural selection

37
Q

Where is reduced diversity evident?

A

Reduced diversity is evident in regions of the genome that have undergone selective pressure or selective sweeps

38
Q

what is a high AMY1A copy number thought to be?

A

High AMY1A copy number is thought to be a beneficial adaptation that spread as human diets increasingly became rich in insoluble starch.

39
Q

Population Structure Facts:

A

Differences between human populations account for only a small fraction of total variance in allele frequencies
Individuals can be correctly assigned to their population using genetic variation data
Most (85%-90%) human genetic variation is found within populations and only an additional 10-15% of variation is found between them.
Even when the most distinct populations are considered and hundreds of loci are used, individuals are frequently more similar to members of other populations than to members of their own.

40
Q

What does Africa have much more variation?

A

Because they didn’t go through population bottleneck

EMS (54 decks)

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