Nanopore sequencing Flashcards
What is second generation sequencing?
Illumina. Sequencing by synthesis and fluorescently labelled dNTP.
What is first generation sequencing?
Sanger sequencing. Chain determination. DNA polymerase incorporates both normal dNTPs and the chain determining ddNTPs into growing DNA strands. When a ddNTP is incorporated the extension of that strand stops. Separated with capillary electrophoresis. Fluorescent label on each terminating nucleotide is read.
What is capillary electrophoresis?
Negatively charged DNA moves through a thin capillary filled with gel.
How many base pairs can the sequencing methods code?
Sanger 800, NGS 300-400.
What is third generation sequencing?
Oxford nanopore tech. Native DNA/RNA is passed through a nanopore. The current that typifies unique sequence of bases is recorded. Different bases disrupt the current and give out a different graph reading.
What are the challenges of CNS tumours?
Leading cause of cancer death for people under 40 years. Over 12,000 new brain tumours each year in UK. Only 15% of people with the most common brain tumours are alive 5 years after diagnosis.
Why look at molecules of brain tumours over morphology?
Tumours that look the same can behave differently. Tumours that look very different are actually the same. Many tumour entities do not have distinctive morphological features.
Why does correct diagnosis of brain tumours matter?
Can’t achieve diagnosis, oncological decisions, grade can change, surgical decisions, MDTs are inefficient, difficult psychologically.
How does nanopore sequence diagnose tumours?
Methylation-based classification and copy number variations.
What is the current NHS testing model?
7 days- sample transport, 14 days- batch processing 21 days- methylation array 28 days- report.
How does robin work?
Ultrafast sequencing. Receipt of sample. 30 mins DNA extraction, 30-90mins library preparation, 90- 2 hours start sequencing, 2 hours- 24 hours intraop classification.
How could the ROBIN model be developed?
Incorporate other specification molecular changes and train our own models to report on the data to clinicians in a straight forward way.
