Genome Organization and Variation Flashcards Preview

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Flashcards in Genome Organization and Variation Deck (33)
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1
Q

When you compare an individual’s genome to a reference genome…

A

Individuals have 3-4 million single nucleotide changes

2
Q

Single Nucleotide Variants (SNVs)

A

refer to any single nucleotide change in the genome

3
Q

Functional SNV

A

leads to amino acid change (affect protein function)

4
Q

Missense variants

A

change of an amino acid

5
Q

non-sense variants

A

change an amino acid to a stop codon

6
Q

Stop loss variants

A

lead to loss of the stop codon

7
Q

T or F: There are functional variants that disrupt a splice site

A

TRUE

8
Q

Non-functional SNV

A

no amino acid change (no effect on protein functions)

9
Q

Silent variants (non-functional)

A

change a nucleotide but not the amino acid

10
Q

Intronic variants (non-functional)

A

Introns

11
Q

Intergenic variants (non-functional)

A

between genes

12
Q

SNPs (single nucleotide polymorphism) definition

A

polymorphisms that occur in at least 1% of the population (more common than SNV)

13
Q

Mutation

A

change in genome more rare than SNP;

usually refer to a change which results in a phenotype

14
Q

Small insertions or deletions of up to 20-30 bases are called:

A

Indels (insertion/deletion);

vary in size, multiples of three are most common since they do not disrupt the reading frame

15
Q

Short Tandem Repeats (microsatellites)

A

2-12 nucleotides that can be present in 10-100 copies; more common than SNPs

16
Q

There are a lot of variations in the number of repeats of microsatellites due to:

A

errors during replication when polymerase slips

17
Q

T or F: Microsatellites can be used in forensics and linkage studies?

A

TRUE

18
Q

Transposons and retrotransposons are…

A

mobile DNA sequences

19
Q

Retrotransposons definition

A

copied into an RNA intermediate before they are reverse transcribed and inserted into the genome

20
Q

LINE (long interspersed repetitive elements)

A

encode the elements necessary for retrotransposons to make copies and insert into the genome;
17% of genome

21
Q

SINEs (short interspersed repetitive elements)

A

10% of genome;
300 bp long;
from retrotransposons

22
Q

LTRs (long terminal repeats)

A

several kilo bases in size and represent around 8% of genome;
from retrotransposon

23
Q

Retrotransposons/transposons pose a risk because…

A

can replicate and insert into the genome in places that cause harm

24
Q

Copy number variants (CNVs)

A

deletions or duplications of part of the genome that can range from 100 bp to an entire arm of a chromosome;
can be found at higher resolution than karyotyping

25
Q

Although inversions and translocations are large structural variations, they…

A

DO NOT AFFECT COPY NUMBER OF GENES

26
Q

Inversions definition

A

pieces of DNA that invert in the genome often due to recombination between repeats

27
Q

Translocations

A

exchanges of DNA between chromosomes

28
Q

______ can be used to map and find mutations that cause disease

A

Variants

29
Q

2 types of genetic mapping

A
  • map based strategy which uses a set of markers spread throughout the genome
  • direct approach of looking at the causal variants through genome or exam sequencing
30
Q

Linkage Studies

A

Use micro satellites;
DNA from family and sequences of 300-400 micro satellites are compared between affected and unaffected family members;
microsats that are more prevalent in the affected than unaffected are close enough to the disease allele that recombination has not occurred between them;
evaluation of microsats in the area can narrow down the portion of the genome containing the disease allele further

31
Q

Linkage Studies are successful at …

A

Identifying rare, inherited variants which are associated with severe disease in families

32
Q

GWAS (genome-wide association studies)

A

Genetic mapping using SNPs;
Advantage to GWAS is that studies can include populations and not just families;
must be large sample size and well defined phenotype

33
Q

Genome sequencing

A

Identify causal variants directly;
does not limit the type of variation that an be detected or inheritance pattern that can be studied;
Challenging to interpret large amounts of data