Download - GenomeQuest -- The Bioinformatics Bottleneck
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The Bioinformatics Bottleneck
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% Time Spent on NGS Lifecycle*
* source: IlluminaConnect Presentation
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% Cost Breakdown*
* source: IlluminaConnect Presentation
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Why not?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
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“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
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“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
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“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
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Questions for the Bioinformaticist
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Have you ever compared two different mapping algorithms?
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Have you written a program to simulate reads and error rates?
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Have you ever written a parser to work with a BAM/SAM, BLAST, GFF, or FASTA file?
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Have you ever installed a genome browser onto a UNIX machine?
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Do people come to your office and ask you to write PERL scripts to transform format A into format B?
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Have you compared the Broad’s SNP-calling pipeline to BGI’s?
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Do you scan the literature looking for new alignment algorithms?
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Ever built up a data center to back up NGS data?
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Ever provisioned any hardware on Amazon’s EC2?
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You’re doing the same thing as all of your competitors.
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What Pharma Researchers
Tell Me
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“I’ve been waiting 4 months for my bioinformatics team to do my NGS analysis.”
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“I can’t easily share and collaborate with these large data volumes.”
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“When I finally get my data back I can’t interact with it.”
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“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.
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“My bioinfo support team is getting better at handling one exome, but I’m sequencing 1000 exomes this month.
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“I guess my only hope is to learn UNIX?”
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What the Industry is doing
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Provocation
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Develop, Communicate, and Roll-out Corporate Strategy
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Stop Building Better Mousetraps
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Stop building data centers
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Read This Book.
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Budget Realistically.
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Empower your departments and be there to support them with agility.
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Know What Business You’re In
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The Bioinformatics Bottleneck