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genomics notes > genome variation > Flashcards

genome variation Flashcards

1
Q

what are 2 levels of variations?

A
  1. major macro - level differences generally associated with disease (aneuploidy, translocations e.t.c)
  2. micro/molecular level ( point mutation and sickle cell anemia, 3bp deletion in CFTR)
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2
Q

What % of DNA is the same between 2 people?

A
  • 99.7% DNA is same between 2 ppl ( ~ 9 million bases are different)
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3
Q

Define single nucleotide polymorphism (SNP/SNV).

A
  • DNA sequence variation that occurs when a single nucleotide (ATCG) in a genome sequence is altered.
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4
Q

What is polymorphism?

A
  • variation in DNA sequence gene expressed in many allelic form.
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5
Q

What are micro - satellite (short tandem repeat).

A
  • 2 to 5 bases (di, tri, tetra , pent)
  • sequence doesn’t usually vary , length varies.
  • heterozygous bc of variability tandem repeat
  • multi- allelic
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6
Q

what causes short tandem repeat?

A
  • polymerase slipage of replicated strand

=> pause in polymerase during elongation , polymerase reanneals and bases can bind to wrong - non complementary.

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7
Q

What are 3 types of common genetic variants?

A

common = see a lot of these types of variants throughout the genome
1. single nucleotide polymorphisms (SNPs) ~ 17 million identified , ~ 3 million / genome

  1. micro-satellites/STRs ~ 3% of the genome
  2. copy number variants (CNVs) > 2000 identified ~ 100 per genome.
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8
Q

What has higher frequency in biallelic, minor or major allele?

A
  • minor allele is relatively high
    => population frequency
    => proportion of chromosomes that carry each allele in the population
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9
Q

how do we know what is normal and what is variant?

A
  • 4 anonymous individuals averaged out
  • if 1 individual has C in position 2 lets say and the other 3 have A
  • reference allele is A so anyone who doesn’t have A has minor allele/alternative
  • anyone who has A has major allele.
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10
Q

What is heterozygous allele?

A
  • each chromosome has 2 copies
  • the base in each position of the 2 chromosomes is same (homozygous)
  • however sometimes there is a different base (A instead of C ) then this position is heterozygous.
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11
Q

What are characteristics of single (SNV/ SNP)?

A
  • high frequency : 1 in every 300 nucleotides in reference genome
  • one individual : 1 in every 1000 bases
  • millions SNVs identified in human genomes
  • majority exomes
  • generated by mismatch repair during DNA replication.
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12
Q

Where does SNV happen?

A 
1.  gene: can lead to :
=> no amino acid change (synonymous) 
=> amino acid change (non-synonymous/ missense) 
=> stop codon (non-sense) 
=> splice site 
=> UTR (gene expression)
  1. promoter:
    => protein expression
  2. non - coding region
  3. without deleterious effect or population annihilation, SNVs do not disappear.
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13
Q

Give an example of a mutation that is both deleterious and beneficial.

A
  • sickle cell anemia
  • deleterious = sickle cell anemia
  • benefit = heterozygous advantage against malaria , this is why SCA allele is more common in African countries as malaria is a bigger issue (1 in 20 chromosomes) compared to the European countries 1 in 10, 000 chromosomes.
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14
Q

What is the genetic basis of sickle cell anemia?

A
  • single base change /point mutation
  • codon GAG => GTG
  • glutamic acid => valine
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15
Q

What minor allele frequency is needed for rare and common polymorphism/variant?

A
  • rare polymorphism = MAF 1-5%

- common polymorphism = MAF > 5%

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16
Q

What evolutionary forces create single nucleotide variation (SNV)?

A
  1. mutation = new alleles
  2. gene flow = migration introduce new variants into population
  3. genetic drift = random change in variant allele frequency between generations
  4. selection = non - random change in variant allele frequency between generation, driven by benefit or deleterious effect.
17
Q

Where do micro- setellites/ STRs occur?

A
  • part of 98% of genome not coding for protein
    => intronic or UTR : may affect hene expression
    => intergenic
  • EXONS
    => extra AAs in proteins
18
Q

What is an STRs expansion disorder?

A

=> Huntingtons disease
- mono genie disorder as tandem repeat is within exon, alters size of the genome region.

  • 35 repeats + = Huntington disease
  • autosomal dominant, one parent has it child has 50% chance of having it.
19
Q

How do tandem repeats vary?

A
  • the bases are the same/ sequence is the same but the number of repeats varies.
20
Q

How are lengths of micro satellites named?

A
  • Dinucleotides (CA)(CA)…

- Pentanucleotide (AGAAA) (AGAAA) …

21
Q

Why does slippage tend to occur in tandem repeats?

A
  • when there is a breakage and the bases are reattaching to complimentary bases they reattach in the wrong position as the sequence is repettive.
22
Q

Define locus.

A

unique position in the genome.

23
Q

Define allele.

A

particular form of a given position in the genome.

24
Q

Define single nucleotide variant (SNV).

A

a variant arising due to mismatch repair going wrong.

25
Q

Define micro satellite (short tandem repeats).

A

a variant arising due to polymerase slippage.

26
Q

Define copy number variant (CNV).

A
  • a variant arising due to non-allelic homologous recombination.
  • simplest type of copy number variation is the presence or absence of a gene (2, 1, 0)
  • duplication of genomic segment could result in diploid copy numbers of 2, 3, 4.
27
Q

Define polymorphism.

A

AKA variant

one or more variants of a particular DNA sequence.

28
Q

What are genetic variants used for?

A
  • can be used as gene markers to help find disease causing genes/mutations
    => linkage analysis (microsatellite, SNPs)
    => association analysis
    (SNPs, CNVs)
29
Q

what is the book analogy?

A 
whole book = genome
chapter = chromosome 
paragraph = CNV
sentence = STRs
letter = SNP

genomics notes (18 decks)

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