Genomic analysis

Question 1

What is Sanger sequencing?

Answer 1

• Flourescent nucleotides, add one at a time, flash, rinse, repeat

Question 2

What is shotgun sequencing?

Answer 2

• Take larger sequence, digest it to small pieces then sequence shorter strands
• Computationally overlap-link reads to generate read on larger sequence

Question 3

What is Illumina sequencing?

Answer 3

• Makes use of polonies

- Read length 200bp

Question 4

What is immobilised DNA Polymerase (PacBio) sequencing? (Read length and error)

Answer 4

• Attach Polymerase to well with camera taking photos of modified nucleotides
• Read length as long as Polymerase travels(~15-60kb)
• High error rates

Question 5

What is Nanopore sequencing?

Answer 5

• Attach Polymerase to membrane
• Slowly pull DNA through via charge gradient
• Measure current from oligos forced off

Question 6

What are SNPs?

Answer 6

• Single nucleotide polymorphisms

- Identify point deviations that contribute to diseases/phenotypes

Question 7

What are GWAS?

Answer 7

• Genome wide association studies

- How many SNPs make small contributions to disease

Question 8

What kind of SNPs are commonly associated with diseases?

Answer 8

• More likely to be regulatory than protein coding

Question 9

How can positive selection contribute to population changes?

Answer 9

• Selective sweep of advantageous mutations or elimination of ones near harmful mutations

Question 10

What are the evolutionary consequences of different copy numbers? Also how do you sequence them?

Answer 10

• Redundancy allow gene families to evolve and diversify
• Can alter gene dosage
• Can be observed via microarrays or long read sequencing

Question 11

How can gene copy number change?

Answer 11

• Unequal crossover, no bias
• Replication slippage, bias towards gain
• Selection against too long or short sequences, bias against gain

Question 12

How can microsatellites be pathogenic?

Answer 12

• Huntington’s disease is result of overly long polyQ strech in protein
• Can spread heterochromatic DNA to inactivate genes

Question 13

What types of (transmission) transposons exist?

Answer 13

• Retroviral
• replicative
• non-replicative
• can be both as non-replicative can be made replicative by strand invasion repair

Question 14

What are defence mechanisms against transposons?

Answer 14

• RNAi
• piRNA
• KRAB-ZFPs(methylation)

Question 15

What are the types of RNA-mediated transposons?

Answer 15

• Retroviral like elements
• Long interspersed nuclear elements(LINEs), most common L1
• Short interspersed nuclear elements(SINEs)
• SINEs resemble RNA Pol III transcripts
• SINEs depend on L1 reverse transcriptase

Question 16

What is the likely origin of spliceosomes

Answer 16

• self-splicing introns

Question 17

How can TEs be used to introduce foreign DNA into eukaryotes?

Answer 17

• transposases flanking a marker gene and a gene of interest
• More likely to insert into accessible DNA
• Also a method for introducing mutations
• Secondary mobilisation: if a P element lands near a gene the fly can be crossed with transposase to cause mutation

Question 18

How can CRISPR be used for regulating a gene?

Answer 18

• Replacing Cas9 nuclease with activator or repressor

- Induce point mutations by removing half of the nuclease