Genomes & Sequencing Flashcards

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1
Q

What are transposons & how do they work?

A

Jumping genes
Can replicate & insert into other parts of the genome.
Some transpose via mRNA (retrotransposon) eg LINES

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2
Q

Who discovered transposons & when?

A

Discovered by Barbara McClintock in 1940s from maize.

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3
Q

Give the 2 categories of transposons.

A

DNA transposons
-form most of the mobile elements in bacteria
-can also occur in eukaryotes
Retrotransposons
-form most of the mobile units in eukaryotes

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4
Q

How are genomes sequenced?

A

Very small fragments

Sequences assembled in silico by bioinformatics

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5
Q

Give the features of 1st generation sequencing.

A

amplify DNA via PCR or cloning

  • in vitro DNA synthesis
  • base specific chain-terminating inhibitors
  • typical length of sequences <1000 bases
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6
Q

Give the features of 2nd generation sequencing.

A

amplify DNA through multiple PCR ‘clusters’ on a glass slide

  • massive parallel in vitro DNA synthesis
  • typical length of sequences 75-300 bases
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7
Q

Give the features of 3rd generation sequencing.

A

amplify DNA not needed

  • a strand of DNA is passed through a nanopore. The current is changed as the bases G, A, T & C pass through the pore in different combinations
  • typical length of sequences 10s of Kbs of fragments bases
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8
Q

Monozygotic twins have no genomic differences, but have a few…

A

epigenetic differences.

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9
Q

Give the types of genetic variation.

A
  • single nucleotide polymorphisms (SNPs)
  • indels (insertions & deletions)
  • copy number variations (CNVs)
  • structural rearrangements
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10
Q

Give the definition of an allele.

A

Broad term used to describe alternative forms of a heritable trait.

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11
Q

Give the definition of a polymorphism.

A

Variation within a population of a given trait.

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12
Q

What is an SNP & its significance in the human genome?

A
  • differences at a single nucleotide
  • Dr James Watson’s genome contained 3.3 million SNPs relative to the human genome project reference, ~0.1% of the genome differed
  • approx. 10 million common SNPs in humans
  • SNP rate versus chimpanzee ~1%
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13
Q

What is an indel & its significance in the human genome?

A
  • insertion or deletion of 1 or a few nucleotides
  • ~4 x 105 indel polymorphisms identified in human genome, ~30% of these are tandem repeat expansion polymorphisms
  • can be analysed by PCR & gel electrophoresis
  • short tandem repeats are multi-allelic
  • used in genetic profiling
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14
Q

Give the phenotypic effects of genetic variation.

A
  • intergenic region has often no phenotypic effect

- non-coding regulatory regions may have effects on gene expression

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