Module 11

Question 1

NGS

Answer 1

allows MPS, cell free system (no vectors), read directly without CE, but they’re short reads

Question 2

SMRT

Answer 2

• Single molecule real time sequencing
• Wells with polymerase at bottom so DNA synthesized in well
• Phospho-labelled so cleaved after addition of each nucleotide

Question 3

Nanopore

Answer 3

Motor protein ratchets strand through pore then measures current changes

Question 4

Sequence assembly errors

Answer 4

• Mis-assemblies: incorrect GAPs, test with PCR amp
• Consensus errors: different than actual base at same position

Question 5

Tracks

Answer 5

Regions conserved across all strains/isolate

Question 6

Read cleaning

Answer 6

• Primer and adapter removal with bioinformatics
• Duplicate removal
• Contaminated read removal
• Low quality read removal

Question 7

Microbial forensic diagnostics

Answer 7

• Protein (pathogen surface): low sensitivity, low cost + fast
• Nucleic acid: high sensitivity, requires DNA extraction so + time, pathogens change, false +/-

Question 8

Molecular beacons

Answer 8

like qPCR but dye/reporter not cleaver, hybridization = higher signal

Question 9

Chip-based detection

Answer 9

VNTR + MLVA + SNP, many targets at once, compares hybridization intensity to ID, high cost/interpretation difficult because so many targets