1000 Genome Slidedeck

Question 1

Long haplotypes= what type of frequency

Answer 1

low

Question 2

Length of a haplotype that a mutations is present on is proportional to

Answer 2

how old the mutation is
Recent=long=low frequency

Question 3

why was wide and shallow coverage done in the 1000 genome project?

Answer 3

Wide=more people and more data
having more people means more variation in data and allows for the identification of common variants

Question 4

Why was exon sequencing used in 1000 Genome project

Answer 4

sequencing is expensive
exons are the coding region so to find meaningful variants it would make sense to use the coding region

Question 5

average distance of nucleotides between variants

Answer 5

number of variants over total space

Question 6

Which would produce more accurate variable calls, low coverage WGS, or high coverage exome?

Answer 6

Snip chips are more accurate so variant calls

Question 7

Pros of WGS

Answer 7

errors become big with little data

Question 8

Pros of high coverage exomes

Answer 8

average of 80x

Question 9

cons of high coverage exome

Answer 9

more expensive

Question 10

Pros of SNP

Answer 10

high confidence and cheap

Question 11

Why did the 1000 genomes project summarize variant sites with 0,1, and 2

Answer 11

Diploid=2 chromosomes
AA=0
AB=1
BB=2

Question 12

Why is the evidence for a single genotype typically weak in low coverage regions

Answer 12

can be a sequencing error
not enough data to confirm

Question 13

How can we address the problem of evidence being weak in low coverage regions

Answer 13

sequencing using SNP chips

Question 14

type of variation we didn’t talk about

Answer 14

structural

Question 15

what is another name given to regions of low complexitity

Answer 15

repetitive regions

Question 16

What technology is used to help with repetitive regions

Answer 16

longer reads that can map out more unique data

Question 17

Accessible genome

Answer 17

the fraction of the reference genome in which short-read data can lead to reliable variant discovery

Question 18

Accessible genome percentage went from 85% to

Answer 18

94% now

Question 19

why would individual calls be more accurate at common variants than at low frequency variants

Answer 19

common variants have more data and are more likely to be true than to be a sequencing error

Question 20

variation among samples in genotype accuracy is primarily driven by sequencing depth- why is this true

Answer 20

more data=less sequencing errors
allows you to determine what are the variants

Question 21

Moderate to high frequency variants tend to be

Answer 21

old

Question 22

low frequency variants tend to be

Answer 22

new

Question 23

New mutation equation

Answer 23

1/2N

Question 24

Lower frequency variants are

Answer 24

population dependent- show up in one population and have not spread to others

Question 25

Why would we expect many low frequency variants

Answer 25

different environments and more people is what gets new variants

Question 26

What would you expect for a population that is contracting

Answer 26

less new variants, more variants at a higher frequency

Question 27

Are all variants equally important?

Answer 27

NO

Question 28

Wobble

Answer 28

third base on codon is changed

Question 29

Synonymous

Answer 29

same amino acid is coded for

Question 30

nonsynonymous

Answer 30

different amino acid is coded for

Question 31

How do you know if an individual has more or less variants than expected

Answer 31

Intron vs. exon placement of variation
wobble
nonsense
synonymous
nonsynonymous

Question 32

How is it that we can have an average 150 broken genes but still be normal

Answer 32

It depends on other genes or factors
environment also plays a role

Question 33

Everyone carries

Answer 33

bad variants

Question 34

Lots of variants in regulatory regions. Why

Question 35

Why would regulatory sequence tolerate deleterious variations?

Question 36

What is the primary reason to do imputation

Answer 36

fine mapping existing association signals and detecting new associations

can fill in missing stuff and find variants

Question 37

Rare variants need to be evaluated using

Answer 37

the correct null distribution