Metagenomics talk from uBiome's Jessica Richman


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Jessica Richman addressed the Singularity University Executive Program in May 2013, and talked about the metagenomics work at the new company uBiome.

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  • 1977, the Commodore PET 2001, including either 4 KB (the 2001-4) for $795 or, later, 8 KB (2001-8) of 8-bit RAM. an iPhone has 8 million times more memory$795 in 1977 is $2800 in 2010 dollarsSo, 3 times as expensive and 8 million times less capacity.After receiving your sample, lab professionals extract DNA from cells in your saliva. Your DNA is then chopped up into shorter strands and copied many times via a process called amplification. Next, your DNA is washed over a small microchip-like device that contains short strands of synthetic DNA. The synthetic DNA fragments latch onto the pieces of your DNA that are a complementary match. Then a laser-scanning step reveals which strands of synthetic DNA are stuck to your DNA to determine your genotype. The chip used in our process is the Illumina HumanHap550+ BeadChip, which reads more than 550,000 SNPs (single nucleotide polymorphisms) plus a 23andMe custom-designed set that analyzes more than 30,000 additional SNPs. What this means is that the laboratory process reads nearly 600,000 data points on your genome. Find out more about our genotyping process.
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  • Metagenomics talk from uBiome's Jessica Richman

    1. 1. Sequencing the human microbiomewith citizen science
    2. 2. Exponential changes in understanding• About us• What is the microbiome?• Next generation sequencing• What is citizen science?• New kinds of partnerships between industry,academia, and the public• Solving the world’s problems and affectingthe lives of a billion people in a positive way(Singularity!)
    3. 3. $350,000 in crowdfundingOver 2,500 participants  4,500 samples  40 countriesLargest citizen science crowdfunding project in historyTop 15 on Indiegogo crowdfunding platformFeatured in Wired, Scientific American, MIT TechnologyReview, ABC News, MSNBC, dozens of others
    4. 4. Jessica Richman• Started and sold her first companybefore university• Co-founder international onlineprogram for women• Graduate Fellowship at Oxford• DPhil in progress, mathematicalsociology at Oxford• BS, Economics and interdisciplinaryengineering, StanfordZachary Apte, PhD• Founded synthetic biologycompany based on microfluidicsinvention, funded by DOE• Inventor of statistical measure ofintracellular organization• Built international open scienceweb platform• PhD, Biophysics, UCSF• BS, Physics, Hampshire CollegeWill Ludington, PhD• NSF Graduate ResearchFellowship• Extensive work in bioinformatics,biophysics, ecology andmicroecology• Created Ecological ManagementPlan for Palmyra Atoll• PhD, Biochemistry, UCSF• BS, Biological Sciences, StanfordAbout usEntrepreneur  MathematicalSociologist  Study DesignBiophysicist  Entrepreneur Inventor  Developer  StatisticsBiochemist  MicrobiologistEcologist  Bioinformatics
    5. 5. What is the microbiome?
    6. 6. The end of the germ theoryof the disease• Microscope as enabling technology• Culture-based research• Next generation sequencing changesEVERYTHING
    7. 7. $795 in1977(=$2,800 incurrent $)Accelerating technology &plummeting costNextGenerationSequencing
    8. 8. HGP - Research Funding ($mm)HGP - Company Market Cap ($bn)HGP and HMPHGP1990 – Launch of Human Genome Project1997 – E Coli genome sequenced2001 – First draft of human genome2003 – Human Genome Project completedHMP2007 – Launch of Human Microbiome Project2010 – First microbiome-funded IBD paperpublished in Gastroenterology2012 – Human Microbiome Project completedThe per‐base cost of DNA sequencinghas plummeted by ~100,000‐fold overthe past decade, far outpacing Moore’sLaw of technological advance in thesemiconductor industry.Eric Lander, MIT Broad InstituteHMP - Research Funding ($mm)Year 1 Year 20 Year 1 Year 5HMP – CompanyFunding ($mm)
    9. 9. Ecosystem, like the rainforest
    10. 10. What is affected by the microbiome?Gut microbiome• Weight loss• Low carb diet?• Alcohol, caffeine• Inflammatory Bowel Disease (IBD)• Antibiotics• Cancer, anxiety, depressionOther microbiomes• Chronic sinusitis• Penis microbiome and bacterial vaginosis, and HIVtransmission
    11. 11. What can we learn from themicrobiome?• Mouse studies and obesity• Targeted probiotics• Fecal transplants and synthetic stool(RePOOPulate)• Soil and water• Commercial products
    12. 12. What problems can this solve?PersonalizedMedicineClinicalTrialsWeightLossAutism/Mood/BehaviorCrohn’sand IBDQuantifiedSelf
    13. 13. What diet will help me lose weight?I have IBD, what might help me with my symptoms?How do I know?What elements of my diet are most important tomaintaining a healthy microbiome?Sinusitis, vaginosis, smelly feet, smelly people?
    14. 14. Citizen Science
    15. 15. What do participants have access to?State of the Art DNA sequencingIllumina Hi-SeqPatent-pending quality control andbioinformatics technologiesWE BUILT A WORLD CLASS LAB FOR$10,000$89 easy-to-use collection kit for consumersHealth metadata surveyFive collection sites  infinity16S sequencing  full sequencingInteractive, gamified websiteIn the lab For the user
    16. 16. What’s in your microbiome?
    17. 17. Who can get involved?• Aligning incentives with citizen science• Next generation sequencing is allowing usto directly connect researchers, industry,citizens and their microbiome.• Partnerships with organizations benefit all
    18. 18. Questions people ask• Data ownership• Privacy• Regulation• IRBPlatform for collaboration
    19. 19. The future• DIY clinical trials• Anecdotes become data• New ways to do product development• Bacteria as biosensors• Personalized medicinePlatform for collaboration
    20. 20. Contact me•• 415-275-2461Platform for collaboration