SAQ Flashcards
Which FOUR evolutionary processes are primarily responsible for the introduction, spread and maintenance of genomic variation?
→Mutation
→gene flow
→genetic drift
→selection
Name three examples of types of common genomic variation and the name of the mechanism which leads to the occurrence of this variation.
→Single nucleotide variant/polymorphism and mismatch repair
→microsatellite and polymerase slippage
→copy number variation and non-allelic homologous recombination
A base change can result in the introduction of a different amino acid into the protein or the introduction of a stop codon.
→Missense/non-synonymous
→ Nonsense
Compare the use of microsatellite markers and SNPs heterozygosity for GWAS
→ Microsatellite markers have higher heterozygosity than SNPs (average heterozygosity 0.76 and 0.37, respectively). → because microsatellites are highly polymorphic so can have many possible alleles.
→ SNPs are typically biallelic so will only have two possible bases.
Compare the use of microsatellite markers and SNPS average spacing for GWAS?
→ Microsatellite markers are relatively widely spaced, whilst SNPs are spaced much closer together.
→ Typically, genome-wide scans utilise ~400 microsatellite markers with an average spacing of ~9cM (or 5-6Mb). SNP-based genome-wide scans require 6,000-10,000 SNPs with a mean spacing of ~0.3cM (or ~200kb).
Compare the use of microsatellite markers and SNPS genotype methodology for GWAS?
→ Microsatellite markers are genotyped using labour-intensive PCR-based methodology with fluorescently-labelled primers →genotypes are manually assigned.
→ Genome-wide scan typically takes 2-3 months to complete.
→ SNP markers are genotyped using high-throughput microarray-based technology and
→ Genotypes are assigned automatically.
→ Data from a genome-wide scan will usually be returned within 1-2 months
Give TWO ways in which next generation sequencing differs from traditional Sanger sequencing?
→Analogue versus Digital readout
→Manual versus automated
→Sanger sequencing is one single read per sample, next generation sequencing is a consensus of many reads per sample. →Single reaction versus massively parallel sequencing.
→Very low throughput versus very high.
→Less than 1kb sequence per reaction versus whole genome.
→Individual reads long (up to 1kb) versus very short reads (up to 300bp).
State TWO possible methods we could use to shear patient DNA samples to begin DNA library construction
Enzymatically (enzyme), chemically or physically (sonication)
What are the advantages of whole-exome sequencing of patient DNA samples compared to whole genome sequencing?
Whole-exome sequencing is cheaper than whole genome sequencing
Whole-exome sequencing is efficient as we are focusing on the coding portion (‘exome’) of the genome (1-2% of the genome) and most known pathogenic mutations are in the exome (~85%).
Give short description of PCR
Exponential amplification of a DNA fragment of known sequence
How many SNAP markers does a typical GWAS use?
700
What is x-activation an example of?
Epigenetic change
In polymorphism, what is the percentage frequency of a single base change?
10%
What is an advantage of Illumina Next Gen Sequence?
Massively parallel
What is a characteristic of a useful genetic marker
Randomly distributed across the genome
