The document discusses the challenges faced in bioinformatics, particularly in the context of next-generation sequencing (NGS) and the inefficiencies in the research pipeline reported by pharmaceutical companies. It highlights the need for innovation, collaboration, and improved corporate strategies to address issues like data sharing and analysis delays. The document advocates for a shift from merely enhancing existing infrastructure to empowering departments with agile support and realistic budgeting.

1. The Bioinformatics Bottleneck

2. % Time Spent on NGS Lifecycle* * source: IlluminaConnect Presentation

3. % Cost Breakdown* * source: IlluminaConnect Presentation

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

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

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

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

9. Questions for the Bioinformaticist

10. Have you ever compared two different mapping algorithms ?

11. Have you written a program to simulate reads and error rates ?

12. Have you ever written a parser to work with a BAM/SAM, BLAST, GFF, or FASTA file?

13. Have you ever installed a genome browser onto a UNIX machine?

14. Do people come to your office and ask you to write PERL scripts to transform format A into format B ?

15. Have you compared the Broad’s SNP-calling pipeline to BGI’s ?

16. Do you scan the literature looking for new alignment algorithms ?

17. Ever built up a data center to back up NGS data ?

18. Ever provisioned any hardware on Amazon’s EC2 ?

19. You’re doing the same thing as all of your competitors.

21. What Pharma Researchers Tell Me

22. “ I’ve been waiting 4 months for my bioinformatics team to do my NGS analysis.”

23. “ I can’t easily share and collaborate with these large data volumes.”

24. “ When I finally get my data back I can’t interact with it .”

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.

26. “ My bioinfo support team is getting better at handling one exome, but I’m sequencing 1000 exomes this month.

27. “ I guess my only hope is to learn UNIX ?”

28. What the Industry is doing

33. Provocation

34. Develop, Communicate, and Roll-out Corporate Strategy

35. Stop Building Better Mousetraps

36. Stop building data centers

37. Read This Book.

38. Budget Realistically.

39. Empower your departments and be there to support them with agility.

40. Know What Business You’re In

41. The Bioinformatics Bottleneck