The Bioinformatics Bottleneck
% Time Spent on NGS Lifecycle* * source: IlluminaConnect Presentation
% Cost Breakdown* * source: IlluminaConnect Presentation
 
Why not? p-values   diagnostics   translational medicine   1000 genomes   clinical   personalized medicine   inheritance p...
“ I want to outsource  the elements of our research pipeline that are  pre-competitive .” - VP Research, unnamed Top 10 ph...
“ We need to be  innovative straight across the company .” - CEO, Unnamed Top 5 pharma “ We don’t have a genomics strategy...
“ We want to  keep our intellectual property safe  and secure.” - Chief Counsel, Top 10 pharma “ Over  50% of our company ...
Questions for the Bioinformaticist
Have you ever  compared  two different  mapping algorithms ?
Have you written a program to  simulate reads and error rates ?
Have you ever  written a parser  to work with a BAM/SAM, BLAST, GFF, or FASTA file?
Have you ever  installed a genome browser  onto a UNIX machine?
Do people come to your office and ask you to write PERL scripts to  transform format A into format B ?
Have you  compared  the  Broad’s  SNP-calling pipeline to  BGI’s ?
Do you  scan the literature  looking for  new alignment algorithms ?
Ever built up a data center to  back up NGS data ?
Ever provisioned any hardware on Amazon’s  EC2 ?
You’re doing the same thing as all of your competitors.
 
What Pharma Researchers Tell Me
“ I’ve been waiting  4 months  for my bioinformatics team to do my NGS analysis.”
“ I can’t easily share and collaborate with these large data volumes.”
“ When I finally get my data back I  can’t interact with it .”
“ NGS could be used today  in drug rescue but we’re working on a  corporate IT strategy  that will take  12 months  to sha...
“ My bioinfo support team is getting better at handling one exome, but I’m  sequencing 1000 exomes  this month.
“ I guess my only hope is to  learn UNIX ?”
What the Industry is doing
 
 
 
 
Provocation
Develop, Communicate, and Roll-out Corporate Strategy
Stop Building Better Mousetraps
Stop building data centers
Read This Book.
Budget Realistically.
Empower your departments and be there to support them with agility.
Know What Business You’re In
The Bioinformatics Bottleneck
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GenomeQuest -- The Bioinformatics Bottleneck

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The Pistoia Alliance Conference in April 2011 included a series of 10-minute "lightning talks" from vendors about what they think pharma will look like in 2020. This presentation was delivered by Richard Resnick of GenomeQuest (and yes, this 41 slide talk was over in just 8 minutes!)

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GenomeQuest -- The Bioinformatics Bottleneck

  1. 1. The Bioinformatics Bottleneck
  2. 2. % Time Spent on NGS Lifecycle* * source: IlluminaConnect Presentation
  3. 3. % Cost Breakdown* * source: IlluminaConnect Presentation
  4. 5. Why not? p-values diagnostics translational medicine 1000 genomes clinical personalized medicine inheritance patterns pathology my genome ms cure population study biological significance genomic medicine cancer genomics pharmacogenomics HIPPA compliance
  5. 6. “ I want to outsource the elements of our research pipeline that are pre-competitive .” - VP Research, unnamed Top 10 pharma “ We’ve decided to build our own internal pipeline for managing sequence data.” - Director of Bioinformatics, same company
  6. 7. “ We need to be innovative straight across the company .” - CEO, Unnamed Top 5 pharma “ We don’t have a genomics strategy .” - Director of Bioinformatics, same company “ Collaborations to rescue drugs using genomics are a key strategy for us this year.” - VP Translational Medicine, same company
  7. 8. “ We want to keep our intellectual property safe and secure.” - Chief Counsel, Top 10 pharma “ Over 50% of our company compares proprietary sequences directly against the open, unsecured NCBI website.” - Director of Bioinformatics, same company
  8. 9. Questions for the Bioinformaticist
  9. 10. Have you ever compared two different mapping algorithms ?
  10. 11. Have you written a program to simulate reads and error rates ?
  11. 12. Have you ever written a parser to work with a BAM/SAM, BLAST, GFF, or FASTA file?
  12. 13. Have you ever installed a genome browser onto a UNIX machine?
  13. 14. Do people come to your office and ask you to write PERL scripts to transform format A into format B ?
  14. 15. Have you compared the Broad’s SNP-calling pipeline to BGI’s ?
  15. 16. Do you scan the literature looking for new alignment algorithms ?
  16. 17. Ever built up a data center to back up NGS data ?
  17. 18. Ever provisioned any hardware on Amazon’s EC2 ?
  18. 19. You’re doing the same thing as all of your competitors.
  19. 21. What Pharma Researchers Tell Me
  20. 22. “ I’ve been waiting 4 months for my bioinformatics team to do my NGS analysis.”
  21. 23. “ I can’t easily share and collaborate with these large data volumes.”
  22. 24. “ When I finally get my data back I can’t interact with it .”
  23. 25. “ NGS could be used today in drug rescue but we’re working on a corporate IT strategy that will take 12 months to shake out.
  24. 26. “ My bioinfo support team is getting better at handling one exome, but I’m sequencing 1000 exomes this month.
  25. 27. “ I guess my only hope is to learn UNIX ?”
  26. 28. What the Industry is doing
  27. 33. Provocation
  28. 34. Develop, Communicate, and Roll-out Corporate Strategy
  29. 35. Stop Building Better Mousetraps
  30. 36. Stop building data centers
  31. 37. Read This Book.
  32. 38. Budget Realistically.
  33. 39. Empower your departments and be there to support them with agility.
  34. 40. Know What Business You’re In
  35. 41. The Bioinformatics Bottleneck
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