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Flashcards in Key Numbers Deck (23)
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1
Q

What it is

A

% to know

2
Q

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

A

99.5%

3
Q

Unrelated individuals would have __ - __ shared variants

A

5%-10%

4
Q

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

A

90-95%

92-99.75%

5
Q

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%)

A

50%

75%

87.5%

6
Q

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

A

5%

7
Q

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

A

5%

1%

8
Q

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

A

1%

5%

9
Q

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

A

80%

99.5

10
Q

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

A

5%

11
Q

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

A

30-50%

12
Q

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

A

5%

0.5%

13
Q

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

A

0.04%

14
Q

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.

A

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.
15
Q

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

A

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.

16
Q

About ______ of random SNPs produce amino acid changes.

A

About half of random SNPs produce amino acid changes.

17
Q

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

A

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

18
Q

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

A

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

19
Q

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

A

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

20
Q

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

A

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

21
Q

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

A

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

22
Q

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

A

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

23
Q

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

A

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