Key Numbers

Question 1

What it is

Answer 1

% to know

Question 2

The 1000 genome project made it possible to examine ____% share variants

Answer 2

99.5%

Question 3

Unrelated individuals would have __ - __ shared variants

Answer 3

5%-10%

Question 4

Comparing individuals would eliminate __-__ and comparing three individuals would eliminate __ -__ of all collected variants

Answer 4

90-95%

92-99.75%

Question 5

Related individuals would still be useful. Comparing two individuals __, three individuals __ and four individuals will eliminate __ of the observed variants (if genetic relatedness is 50%)

Answer 5

50%

75%

87.5%

Question 6

Variants in the common category (>_%) are ancient and considered benign

Answer 6

5%

Question 7

The threshold frequency for MAF is _% for recessive variants and _% for dominant variants in the human population

Answer 7

5%

1%

Question 8

Researchers suggest _% frq in the human population as the cutoff for dominant variants and _% frq for recessive variants

Answer 8

1%

5%

Question 9

Each personal genome possesses a large number of variants, of which __% (10 years ago) or __% (according to 1000 genome project) are shared with others in the human population

Answer 9

80%

99.5

Question 10

Rare mutations constantly arise, but most of the new rare mutations are discarded by evolutionary forces. >_% common variants, therefore represent benign, neutral, or beneficial variants

Answer 10

5%

Question 11

The average length of shared haplotype between parents and offsprings would be __-__% of chromosome size

Answer 11

30-50%

Question 12

Scale of GWAS: requires thousands of individuals for _% variants and > million for __% (rare) variants to be scanned, considering the # of individuals homozygous for the variant

Answer 12

5%

0.5%

Question 13

Global average variant frequency (up to __% as f2 from 5000 haploid genome equivalents) for precise MAF calculation

Answer 13

0.04%

Question 14

How many severe/non-functional variants are in our genome?

_____-______ known severe variants are present in every individual.

These variants are most likely present in heterozygous form (e.g., Ref/Var); therefore, Individuals perform normal functions.

Answer 14

150-200 known severe variants are present in every individual.

• As we get older, those heterozygous variants may become homozygous by spontaneous mutations (i.e. environmental mutagens like UV light)
• This is one major route of developing late-onset cancers.

Question 15

Of the 4-5 million variants in a genome, _____% are shared throughout the population, and _____% are in the non-shared category.

Answer 15

Of the 4-5 million variants in a genome, 99.5% are shared throughout the population, and 0.5% are in the non-shared category.

Question 16

About ______ of random SNPs produce amino acid changes.

Answer 16

About half of random SNPs produce amino acid changes.

Question 17

Re-sequencing is highly reproducible by high-depth sequencing (~ ___X)

Answer 17

Re-sequencing is highly reproducible by high-depth sequencing (~ 40X)

Question 18

Minimal ____X coverage necessary for making reliable genotype calls (diploid)

Answer 18

Minimal 10X coverage necessary for making reliable genotype calls (diploid)

Question 19

Comparing two related individuals (siblings) that have ____% shared variants would eliminate ____% of the variants.

Answer 19

Comparing two related individuals (siblings) that have 50% shared variants would eliminate 50% of the variants.

Question 20

Comparing 3 related individuals (siblings) that have ____% shared variants would eliminate ____% of the variants.

Answer 20

Comparing 3 related individuals (siblings) that have 50% shared variants would eliminate 75% of the variants.

Question 21

Comparing 4 related individuals (siblings) that have ____% shared variants would eliminate ____% of the variants.

Answer 21

Comparing 4 related individuals (siblings) that have 50% shared variants would eliminate 87.5% of the variants.

Question 22

Comparing 2 unrelated related individuals that have ___%-___% shared variants would eliminate ___%-___% of the variants.

Answer 22

Comparing 2 unrelated related individuals that have 5%-10% shared variants would eliminate 90%-95% of the variants.

Question 23

Comparing 3 unrelated related individuals that have ___%-___% shared variants would eliminate ___%-___% of the variants.

Answer 23

Comparing 3 unrelated related individuals that have 5%-10% shared variants would eliminate 99%-99.75% of the variants.