Genetic Variation I

Question 1

What percent of protein-coding genes are polymorphic?

Answer 1

33%

Additional nucleotide diversity in introns, regulatory sequences, and flanking sequences

Question 2

What percentage of total genetic variation is found within populations?

Answer 2

~85%

Question 3

What causes genetic variation in humans?

Answer 3

Changes to base sequence in 2 categories:

Do not affect DNA content (Number of nucleotides unchanged and insteadbases are replaced or translocated/inverted)

Causes a net gain/loss of DNA sequence (changes in copy number of DNA sequence or abnormal chromosome segregation; deletions or insertions of single nucleotides or short sequences of Mb DNA)

Question 4

Do all DNA changes affect phenotype?

Answer 4

Most DNA changes are on small scale so they may or may not effect phenotype

Question 5

What are DNA variants caused by?

Answer 5

Mutations resulting in alternative forms of DNA

Question 6

What is a polymorphism?

Answer 6

For any locus, if more than one DNA variant is common in the population (Pr>0.01) it is called a polymorphism.

If Pr<0.01 it is a rare variant

Question 7

Where does knowledge of DNA variants come from?

Answer 7

From analysing DNA from complete genome sequencing of multiple individuals

Question 8

Where is most genetic variation located?

Answer 8

In non-coding regions of the human genome.

Question 9

What are single nucleotide polymorphisms (SNPs) and variants (SNVs)?

Answer 9

Most common variation due to single nucleotide substitution:

Type of variant produces single nucleotide variants and if 2 or more alternative DNA variants exceed frequency of 0.01 in population it is called a single nucleotide polymorphism (SNP)

Question 10

What is the “major allele”?

Answer 10

The allele that is more common in a population. Different populations can have different alleles as the “major allele”.

Question 11

Why are SNVs not considered random?

Answer 11

Different regions have different mutation rates

mtDNA higher than nuclear

C-T substitutions are most common

Question 12

What do alternative SNPs tell us about evolutionary ancestry?

Answer 12

Alternative SNPs mark alternative ancestral chromosome segments common in present day population

Question 13

What do SNPs do to overall function of DNA?

Answer 13

They can cause gain or loss of restriction enzyme sites leading to (RFLP) Restriction fragment length polymorphism

Question 14

What do indels create?

Answer 14

Copy number variations.

Heterozygous deletion of a single nucleotide at a defined position on a chromosome has one copy of that nucleotide instead of 2.

Question 15

What does modern convention describe indels as?

Answer 15

Deletions/insertions up to 50 nucleotides long

Question 16

What is a change in copy number of a sequence described as?

Answer 16

Change in copy number of sequences resulting in larger deletions/insertions (>100 nucleotides)

Question 17

How common are indels?

Answer 17

1/10th of single nucleotide substitution

Question 18

What are the types of tandom repeat structures in DNA?

Answer 18

Satellite DNA

Minisatellite DNA

Microsatellite DNA

Question 19

What are satellite DNA structures?

Answer 19

length = 20kb to many 100s kb; located at centromeres, heterochromatic regions

Question 20

What are minisatellite DNA strucutures?

Answer 20

length - 100 bp to 20 kb; located primarily on telomeres and subtelomeric regions

Question 21

What are microsatellite DNA structures?

Answer 21

Length - fewer than 100 bp located widely throughout euchromatin

Question 22

How stable are repeat sequences?

Answer 22

Variants differ in number of repeats

Question 23

What causes variation in copy number?

Answer 23

Replication slippage or unequal crossover

Question 24

How do microsatellites differ in population genomics to SNPs?

Answer 24

Microsatellites have multiple alleles unlike SNPs that only have 2 alleles

Question 25

How does slippage cause insertion?

Answer 25

Repeat loops out and so the replication creates an extra repeat in its place due to it not aligning perfectly with the template strand.

Opposite occurs for deletions (Template strand loops out)

Question 26

How can unequal crossing over result in additional repeats of a sequence?

Answer 26

Misaligned chromatids on homologous chromosomes can be on homologous chromosomes and when recombination occurs there is an extra few base sequences added to the end of the repeat sequences resulting in expansion of repeat length.

Question 27

What are microsatellite markers used for? How are they used?

Answer 27

They are used to track inheritance of different chromosomes in a family.

Primers are added to flank each region before PCR is used to amplify these regions.

Then length is determined by the longest sequences via sequencing capillary column.

Question 28

What do peaks on a gene scan (after sample is run through a sequencing capillary column) tell us about the gene?

Answer 28

The size of the repeats and their frequency. This is more informative than SNPs for distinguishing between individuals or following chromsome segments through pedigrees

Question 29

How important was the human genome project to understanding microsatellites?

Answer 29

Early years Human Genome Project largely devoted to defining and mapping microsatellites. 150000 identified.

Question 30

What are the limitations to using repeats over SNPs?

Answer 30

Repeat sequencing is much harder to automate than SNPs.

Question 31

Where does DNA variation come from?

Answer 31

Some arise from errors in DNA replication or recombination

Errors in chromosome segregation results in abnormal gametes with fewer or more chromosomes than normal

Various natural errors give rise to altered copy numbers of specific sequence within a DNA strand. Crossover errors

Various endogenous/exogenous sources can cause damage to DNA by altering chemical structure

Question 32

What large-scale changes are important for genetic variation?

Answer 32

Balanced Structural Variation

Unbalances Structural Variants

Question 33

What is balanced structural variation?

Answer 33

DNA variants have same DNA content but differ in some DNA sequences are located in different positions of the genome. Chromosomes break and fragments are incorrectly rejoined without loss or gain of DNA (inversions and translocation0

Question 34

What is unbalanced structural variation?

Answer 34

DNA variants differ in DNA content. Rare case where person gained/lost chromosomal region, often results in disease.

Also includes commonly occurring copy number variation, variants differ in number of copies of moderately long to very long DNA sequence. Some CNVs contribute to disease and others are normal

Question 35

What is the most common type of genetic variation?

Answer 35

SNPs (75% of DNA changes are SNPs)

Question 36

How many SNPs are there in a human genome?

Answer 36

38 million (1 per 100)

Vast majority are rare in any population

Most people would be homozygous for any SNP loci.

Personal sequencing - SNVs between maternal/paternal = 1 per 1000 bps.

Structural variations = 1/4 of mutational events dominated by CNV

Question 37

What is the human genome project good for?

Answer 37

For consensus, not good for individual differences. Not good for genetic variation.

Question 38

What are the steps that took place historically to come up with variant maps?

Answer 38

Human genome project

Identifying of genetic variants (anonymous with respect to traits)

Assay genetic variants (verify polymorphisms, catalogue corrections amongst sites, anonymous with respect to traits) [hapmap project]

Question 39

How were SNPs found and understood?

Answer 39

SNPs were first discovered (goal was to identify 300k SNPs and to determine the allele frequency of SNPs)

Then SNPS were characterised

Question 40

What reference genome was used for SNPs?

Answer 40

Human Genome Project