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.


  • 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.]


  • 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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