Genomes & Sequencing Flashcards
What are transposons & how do they work?
Jumping genes
Can replicate & insert into other parts of the genome.
Some transpose via mRNA (retrotransposon) eg LINES
Who discovered transposons & when?
Discovered by Barbara McClintock in 1940s from maize.
Give the 2 categories of transposons.
DNA transposons
-form most of the mobile elements in bacteria
-can also occur in eukaryotes
Retrotransposons
-form most of the mobile units in eukaryotes
How are genomes sequenced?
Very small fragments
Sequences assembled in silico by bioinformatics
Give the features of 1st generation sequencing.
amplify DNA via PCR or cloning
- in vitro DNA synthesis
- base specific chain-terminating inhibitors
- typical length of sequences <1000 bases
Give the features of 2nd generation sequencing.
amplify DNA through multiple PCR ‘clusters’ on a glass slide
- massive parallel in vitro DNA synthesis
- typical length of sequences 75-300 bases
Give the features of 3rd generation sequencing.
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
Monozygotic twins have no genomic differences, but have a few…
epigenetic differences.
Give the types of genetic variation.
- single nucleotide polymorphisms (SNPs)
- indels (insertions & deletions)
- copy number variations (CNVs)
- structural rearrangements
Give the definition of an allele.
Broad term used to describe alternative forms of a heritable trait.
Give the definition of a polymorphism.
Variation within a population of a given trait.
What is an SNP & its significance in the human genome?
- 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%
What is an indel & its significance in the human genome?
- 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
Give the phenotypic effects of genetic variation.
- intergenic region has often no phenotypic effect
- non-coding regulatory regions may have effects on gene expression