AGBT talk:David R. Bently – Illumina

Title: Evolving technology for clinical sequencing

[no blogging of clinical data – the rest is fair game. good policy.]

Review of sequencing technology, and intresting point that we’re now running towards smaller system for faster runs with smaller number of reads, which will lead to clinical or diagnostic use.

Improvements:

  • increase cluster density
  • minimise gc bias
  • increase ata yeld
  • increase flowcell area
  • increase chemistry
  • [more]

Increased representation of GC-rich features – much improved representation with new chemistry.  Slide showing same region over time, goes from gaps to complete coverage.

unique paired read alignment also makes a big impact, particularly with paired ends.

Contrast of HiSeq to MiSeq.  Usual things – push button, all on board, etc etc…  [different clients for each tool set, I would think.]  Run time 10 Days @600Gb vs 1Gb@ less than one day.

All methods are interchangeable between platforms.

Power of deep sequencing.  With sufficiently deep sequencing, it’s easy to see minor variants… (1.47% detectable in a 750k depth???  [That just sounds odd… maybe I got it wrong.])

Covering Chronic Lmphocytic Leukaemia (CLL)  example [- will not blog this part.]

  • New Bayesian caller: HYRAX
  • indels/SV de novo assembled with GROUPER
  • CNVs use recursive partitioning….[using the software published by Sergii Ivankhno, which I totally did not understand last night.]

Conclusion:

  • First description of progression of CLL
  • Limited number of NS mutations and CNV occur
  • Candidates involved in regulation of innate immune response and cancer progression
  • relapse drivers are actually present in pre-treatement samples
  • profiling identifies mutations eradicated by or resistant to treatment
  • Quantification of mutational burden by deep sequencing reveals clusters.

Spectrum of seuqencing:  Targetted test <===> Whole Genomes.

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