Leveraging Biomedical Big Data: Quantified Self & Beyond

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  1. 1. Leveraging Biomedical Big Data: Quantified Self & BeyondInvited TalkFutureMedSingularity UniversityNASA Ames CampusFebruary 5, 2013 Dr. Larry SmarrDirector, California Institute for Telecommunications and InformationTechnology Harry E. Gruber Professor, Dept. of Computer Science and Engineering1 Jacobs School of Engineering, UCSD
  2. 2. Where I Believe We are Headed: Predictive,Personalized, Preventive, & Participatory MedicineI am Leroy Hoods Lab Rat! www.newsweek.com/2009/06/26/a-doctor-s-vision-of-the-future-of-medicine.html
  3. 3. I Arrived in La Jolla in 2000of My Body andin the Midwest By Measuring the State After 20 Years Tuning It Using Nutrition and Exercise, Ithe Obesity Trend and Decided to Move Against Became Healthier Age AgeAge4151 6119992010 2000 19991989I Reversed My Bodys Decline ByQuantifying and Altering Nutrition and Exercisehttp://lsmarr.calit2.net/repository/LS_reading_recommendations_FiRe_2011.pdf
  4. 4. From Measuring Macro-Variablesto Measuring Your Internal Variableswww.technologyreview.com/biomedicine/39636
  5. 5. From One to a Billion Data Points Defining Me:The Exponential Rise in Body Data in Just One Decade! Billion:Microbial Genome My Full DNA,MRI/CT ImagesImproving BodySNPsMillion: My DNA SNPs, Zeo, FitBit Discovering DiseaseBlood Variables One:Hundred: My Blood Variables Weight WeightMy
  6. 6. Visualizing Time Series of150 LS Blood and Stool Variables, Each Over 5 Years Calit2 64 megapixel VROOM
  7. 7. Only One of My Blood MeasurementsWas Far Out of Range--Indicating Chronic Inflammation Episodic Peaks in Inflammation27x Followed by Spontaneous Drop 15xAntibiotics5x AntibioticsNormal Range CRP < 1 Complex Reactive Protein (CRP) is a Blood Biomarker for Detecting Presence of Inflammation
  8. 8. By Quantifying Stool Measurements Over TimeI Discovered Source of Inflammation Was Likely in Colon124x Upper Limit Typical LactoferrinValue for Stool Samples AnalyzedActiveby www.yourfuturehealth.comIBDNormal Range 100x Over Source: Calit2 Future Health Expedition Team
  9. 21. Four Immune Biomarkers Over Time Compared with Four Signs/SymptomsHere Immune biomarkers are normalized 0 to 1,with 1 being the highest value in five yearsSource: Photo of Calit2 64-megapixel VROOM
  10. 22. Intense Scientific Research is Underwayon Understanding the Human Microbiome June 8, 2012 June 14, 2012
  11. 23. Microbes are 90% of Your Cells-So I Set Outto Determine My Gut Microbes & Their Time VariationShipped Stool Sample December 28, 2011I Received a Disk Drive April 3, 2012 With 35 GB FASTQ Files Weizhong Li, UCSD NGS Pipeline:230M Reads Only 0.2% Human Required 1/2 cpu-yr at SDSCPer Person Analyzed!
  12. 24. Phyla Gut Microbial Abundance: LS, Crohns, UC, and Healthy Subjects Source: Weizhong Li, UCSD; Calit2 FuturePatient ExpeditionLS Crohns UlcerativeHealthyColitisToward NoninvasiveMicrobial Ecology Diagnostics
  13. 25. LS Gut Microbe Species 12/28/11 (red) compared to Average of Healthy Subjects (blue)Derived from metagenomic sequencing of LS stool sample.Each species is a bar, height is logarithmic abundance,species are divided into microbial phyla Source: Photo of Calit2 64-megapixel VROOM
  14. 26. Top 20 Most Abundant Microbial Species In LS vs. Healthy Subject152xNumber Above LS Blue Bar is Multiple of LS Abundance 765x Compared to Average 148x Healthy AbundancePer Species849x 483x220x201x169x 522xSource: Sequencing JCVI; Analysis Weizhong Li, UCSD LS December 28, 2012 Stool Sample
  15. 27. 200 LS Gut Microbe Species at 3 Times12/28/11, 4/3/12, 8/7/12Red is at Highest Value of CRPBlue is the Day After End of Antibiotic/Prednisone TherapyGreen is Four Months LaterSource: Photo of Calit2 64-megapixel VROOM
  16. 28. Closeup of Uncommon LS Microbes12/28/11 Stool SampleTwo separate45xresearch teamsReduced have found strikingly highBy8%90x concentrationsTherapyIncreasedReduced of Fusobacteriumin tumor samplesByBycollected fromTherapy Therapy colorectal cancerpatients.October 18, 2011
  17. 29. From Current IBD Therapies to Novel Systems Approaches Current Therapies Diet Probiotics Drugs Surgery Emerging Directions Microbiome Transfer Synthetic Microbiomes Ecological Gardening Targeted Bacteriophage
  18. 30. From Warto GardeningI would like to lose the language of warfare, said Julie Segre, a senior investigator atthe National Human Genome Research Institute.It does a disservice to all the bacteriathat have co-evolved with usand are maintaining the health of our bodies.
  19. 31. From the Single Bad Microbe Medical Targetto the Microbiome Ecology Paradigm Sci Transl Med 4, 137rv5 (2012);Science 336, 1255 (2012) Problem of Alternative Stable States In Ecological System Dynamics
  20. 32. Next Decade Will See New Microbiome Gardening Tools August 7, 2012Journal of Nanotechnology (2012)
  21. 33. Startups Are Enabling Genomic Sequencingof Your Microbiome http://ubiome.com/
  22. 34. DIY Systems Biology -Toward P4 Healthcare Over 1000 Downloads So Far Download pdfs from Journal:http://onlinelibrary.wiley.com/doi/10.1002/biot.201100495/full