The Ten Year     Calit2 Path Forward• A Ten-Year Vision of Digital Transformation   – Affiliated Academic Units   – Calit2...
Where I Believe We are Headed: Predictive,    Personalized, Preventive, & Participatory Medicine                          ...
Calit2 Has Been Had a Vision of  “the Digital Transformation of Health” for a Decade                                      ...
The Calit2 Vision of Digitally Enabled Genomic Medicine                 is an Emerging Reality                            ...
Lifechips--Merging Two Major Industries:        Microelectronic Chips & Life SciencesLifeChips: the merging of two major i...
SMART:        Social Mobile Approach to Reduce Weight• Leveraging social networks, social media, mobile phones, and  the w...
CitiSense –UCSD NSF Grant for Fine-GrainedEnvironmental Sensing Using Cell Phones                                         ...
By Measuring the State of My Body and “Tuning” It  Using Nutrition and Exercise, I Became Healthier                       ...
Wireless MonitoringHelps Drive Exercise Goals
Quantifying My Sleep Pattern Using a Zeo “LifeChip” -      Surprisingly About Half My Sleep is REM!           REM is Norma...
Combining the Wireless Internet, Body Sensors, Smart Phones,      and Social Networks to Drive Healthier Lifestyles
From One to a Billion Data Points Defining Me:The Exponential Rise in Body Data in Just One Decade!                       ...
From Measuring Macro-Variablesto Measuring Your Internal Variables  www.technologyreview.com/biomedicine/39636
Putting Your Heart On-line
I Have Greatly Lowered My Body’s Inflammation      From Food By Increasing Omega-3s                             “Silent In...
I Track 100 Variables in Blood Tests                     Done Quarterly to Annually•   Electrolytes                       ...
But, In Spite of My High Levels of Omega-3s,My Blood Measurements Revealed Chronic Inflammation           Episodic Peaks i...
By Quantifying Stool Measurements Over TimeI Discovered Source of Inflammation Was Likely in Colon                        ...
Putting Multiple Biomarker Time Series Together,Gives an Quantitative Readout of Health or Disease    Green : Inside Range...
Confirming the IBD (Crohn’s) Hypothesis:         Finding the “Smoking Gun” with MRI Imaging      Liver                    ...
Putting Your Organs On-line•   Videos of Me Giving Tours of My Insides:    – http://www.youtube.com/watch?v=9c4DtJ_L_Ps   ...
Why Did I Have an Autoimmune Disease like IBD?      Despite decades of research,     the etiology of Crohns disease       ...
I Wondered if Crohn’s is an Autoimmune Disease,  Did I Have a Personal Genomic Polymorphism?            From www.23andme.c...
I Tracked My Innate Immune SystemBy Measuring Lysozyme From Stool Samples Over TimeMy Immune System Seems to Be Fighting B...
Your Human Cells are Only 10% of Your Superorganism:   How Can We Track the 90% which are Microbes?                      1...
Determining My Gut Microbes  and Their Time Variation                  Shipped Stool Sample                   December 28,...
Almost All Abundant Species (≥1%) in Healthy Subjects           Are Severely Depleted in LS Gut       1/35                ...
LS Abundant Microbe Species (≥1%) AreDominated by Rare Species in Healthy Subjects                                      Nu...
Principal Component AnalysisOn Microbial Species Abundance
Next Step: Use Microarray to      Measure Time Series of Microbial Diversity                      www.secondgenome.com    ...
Metabolomics Can DifferentiateIleum vs. Colon Inflammation in Crohn’s Disease                                             ...
Integrative Personal Omics ProfilingReveals Details of Clinical Onset of Viruses and Diabetes                             ...
Publically Sharing Your Genome and Medical Records:               Is it Crazy or the Future?   I Have Been Accepted by PGP...
Crowd-Sourcing Health StudiesIs Rapidly Growing With More Open Health Data
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The Ten Year Calit2 Path Forward

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12.09.12
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VC Roundtable
Title: The Ten Year Calit2 Path Forward
La Jolla, CA

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The Ten Year Calit2 Path Forward

  1. 1. The Ten Year Calit2 Path Forward• A Ten-Year Vision of Digital Transformation – Affiliated Academic Units – Calit2 News and Videos• This Talk Focuses in on: – The Digital Transformation of Health www.calit2.net/research/index.php
  2. 2. Where I Believe We are Headed: Predictive, Personalized, Preventive, & Participatory Medicine I am Leroy Hood’s Lab Rat! Using a “LifeChip” Quantify ~2500 Blood Proteins,50 Each from 50 Organs or Cell Types from a Single Drop of Blood To Create a Time Series www.newsweek.com/2009/06/26/a-doctor-s-vision-of-the-future-of-medicine.html
  3. 3. Calit2 Has Been Had a Vision of “the Digital Transformation of Health” for a Decade www.bodymedia.com• Next Step—Putting You On-Line! – Wireless Internet Transmission – Key Metabolic and Physical Variables – Model -- Dozens of Processors and 60 Sensors / Actuators Inside of our Cars• Post-Genomic Individualized Medicine – Combine – Genetic Code – Body Data Flow – Use Powerful AI Data Mining Techniques The Content of This Slide from 2001 Larry Smarr Calit2 Talk on Digitally Enabled Genomic Medicine
  4. 4. The Calit2 Vision of Digitally Enabled Genomic Medicine is an Emerging Reality 4 July/August 2011 February 2012
  5. 5. Lifechips--Merging Two Major Industries: Microelectronic Chips & Life SciencesLifeChips: the merging of two major industries, themicroelectronic chip industry with the life science industry65 UCI Faculty LifeChips medical devices
  6. 6. SMART: Social Mobile Approach to Reduce Weight• Leveraging social networks, social media, mobile phones, and the web for weight loss among 18-35 year old young adults – Funded with a 5-year grant from NHLBI/NIH Source: Kevin Patrick, UCSD SOM & Calit2
  7. 7. CitiSense –UCSD NSF Grant for Fine-GrainedEnvironmental Sensing Using Cell Phones Seacoast Sci. 4oz 30 compounds Intel MSP sense co co W ntr ntr “d i “dis iibu Cii Ct s bu play play tiiS L te te Seens nse ”” e C/A S EPA ret ret diis ds r r trii tr b iiev ev bu ee ute F te CitiSense Team discover PI: Bill Griswold Ingolf Krueger Tajana Simunic Rosing Sanjoy Dasgupta Hovav Shacham Kevin Patrick Integrate Into a “LifeChip”
  8. 8. By Measuring the State of My Body and “Tuning” It Using Nutrition and Exercise, I Became Healthier 1999 2010 2000Age Age 51 61 I Arrived in La Jolla in 2000 After 20 Years in the Midwest and Discovered I was Pre-Diabetic
  9. 9. Wireless MonitoringHelps Drive Exercise Goals
  10. 10. Quantifying My Sleep Pattern Using a Zeo “LifeChip” - Surprisingly About Half My Sleep is REM! REM is Normally 20% of Sleep An Infant Typically Mine is Between 45-65% of Sleep Has 50% REM
  11. 11. Combining the Wireless Internet, Body Sensors, Smart Phones, and Social Networks to Drive Healthier Lifestyles
  12. 12. 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 Images Improving Body SNPs Million: My DNA SNPs, Zeo, FitBit Discovering Disease Blood Variables One: Hundred: My Blood Variables Weight Weight My
  13. 13. From Measuring Macro-Variablesto Measuring Your Internal Variables www.technologyreview.com/biomedicine/39636
  14. 14. Putting Your Heart On-line
  15. 15. I Have Greatly Lowered My Body’s Inflammation From Food By Increasing Omega-3s “Silent Inflammation” Chronically Ill I take 6 Fish Oil American Pills Per Day Average “Healthy” American Blood Ratio of Omega 6 to Omega 3 Ideal Range My Range Range Source: Barry Sears My Tests by www.yourfuturehealth.com
  16. 16. I Track 100 Variables in Blood Tests Done Quarterly to Annually• Electrolytes • Liver – Sodium, Potassium, Calcium, – GGTP, SGOT, SGPT, LDH, Total Magnesium, Phosphorus, Boron, Direct Bilirubin, Chlorine, CO2 Alkaline Phosphatase• Micronutrients • Thyroid – Arsenic, Chromium, Cobalt, – T3 Uptake, T4, Free Thyroxine Copper, Iron, Manganese, Index, FT4, 2nd Gen TSH Molybdenum, Selenium, Zinc • Blood Cells• Blood Sugar Cycle – Complete Blood Cell Count – Glucose, Insulin, A1C Hemoglobin – Red Blood Cell Subtypes• Cardio Risk – White Blood Cell Subtypes – Complex Reactive Protein • Cancer Screen – Homocysteine – CEA, Total PSA, % Free PSA• Kidneys – CA-19-9 – Bun, Creatinine, Uric Acid • Vitamins & Antioxidant Screen• Protein – Vit D, E; Selenium, ALA, coQ10, – Total Protein, Albumin, Globulin Glutathione, Total Antioxidant Fn. Only One of These Was Far Out of Normal Range
  17. 17. But, In Spite of My High Levels of Omega-3s,My Blood Measurements Revealed Chronic Inflammation Episodic Peaks in Inflammation 27x Followed by Spontaneous Drop 15x Antibiotics 5x Antibiotics Normal Range CRP < 1 Complex Reactive Protein (CRP) is a Blood Biomarker for Detecting Presence of Inflammation
  18. 18. By Quantifying Stool Measurements Over TimeI Discovered Source of Inflammation Was Likely in Colon 124x Upper Limit Typical Lactoferrin Value for Stool Samples Analyzed Active by www.yourfuturehealth.com IBD Normal Range <7.3 µg/mL Lactoferrin is a Sensitive and Specific Biomarker for Detecting Presence of Inflammatory Bowel Disease (IBD)
  19. 19. Putting Multiple Biomarker Time Series Together,Gives an Quantitative Readout of Health or Disease Green : Inside Range Orange: 1-10x Over Red: 10-100x Over Purple: >100x Over Source: Calit2 Future Health Expedition Team
  20. 20. Confirming the IBD (Crohn’s) Hypothesis: Finding the “Smoking Gun” with MRI Imaging Liver I Obtained the MRI Slices Transverse Colon From UCSD Medical Services and Converted to Interactive 3D Working With Small Intestine Calit2 Staff & DeskVOX Software Descending Colon MRI Jan 2012Cross Section Diseased Sigmoid Colon Major Kink Sigmoid Colon Threading Iliac Arteries
  21. 21. Putting Your Organs On-line• Videos of Me Giving Tours of My Insides: – http://www.youtube.com/watch?v=9c4DtJ_L_Ps – www.theatlantic.com/magazine/archive/2012/07/the-measured-man/309018/ Photo & DeskVOX Software Courtesy of Jurgen Schulze, Calit2
  22. 22. Why Did I Have an Autoimmune Disease like IBD? Despite decades of research, the etiology of Crohns disease remains unknown. Its pathogenesis may involve a complex interplay between host genetics, immune dysfunction, and microbial or environmental factors. --The Role of Microbes in Crohns Disease So I Set Out to Quantify All Three! Paul B. Eckburg & David A. Relman Clin Infect Dis. 44:256-262 (2007) 
  23. 23. I Wondered if Crohn’s is an Autoimmune Disease, Did I Have a Personal Genomic Polymorphism? From www.23andme.com Polymorphism in Interleukin-23 Receptor Gene — 80% Higher Risk ATG16L1 of Pro-inflammatory Immune Response IRGM NOD2 SNPs Associated with CD
  24. 24. I Tracked My Innate Immune SystemBy Measuring Lysozyme From Stool Samples Over TimeMy Immune System Seems to Be Fighting Bacteria Episodically 2x Upper Limit Normal Values from www.yourfuturehealth.com stool test Lysozyme is an Enzyme of the Innate Immune System that Attacks Bacterial Cell Walls
  25. 25. Your Human Cells are Only 10% of Your Superorganism: How Can We Track the 90% which are Microbes? 16 = All 4 at Full Strength Antibiotics Antibiotics Stool But Cultured Bacteria Are a Small Fraction of Total Values From www.yourfuturehealth.com stool test
  26. 26. Determining My Gut Microbes and Their Time Variation Shipped Stool Sample December 28, 2011 I 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 Per Person Analyzed!
  27. 27. Almost All Abundant Species (≥1%) in Healthy Subjects Are Severely Depleted in LS Gut 1/35 Numbers Over Bars Represent Ratio of LS to Healthy Abundance 1/15 1/8 1/18 1/3 1/3 1/7 1/25 1.1 1/12 1/9 1/6 1/62 1/15 1/22 1/65 1/39
  28. 28. LS Abundant Microbe Species (≥1%) AreDominated by Rare Species in Healthy Subjects Numbers Over Bars Represent 214x Ratio of LS to Healthy Abundance 58x 1/8x 254x 1/3x 1/3x 43x 17x 2x 2x 1x
  29. 29. Principal Component AnalysisOn Microbial Species Abundance
  30. 30. Next Step: Use Microarray to Measure Time Series of Microbial Diversity www.secondgenome.com “Second Genome has developed a sensitive, flexible and robust platform for the identification of microbiome-based signatures for the rapid identification of microbial gut health biomarkers.” DNA microarray that can identify, within hours, over 50,000 different microbesLBL’s Gary Andersenand his PhyloChip
  31. 31. Metabolomics Can DifferentiateIleum vs. Colon Inflammation in Crohn’s Disease blue   N= Ileum (ICD)  red     N= Colon (CCD) green N= Healthy Jansson, et al. PLOS ONE, July 2009 | Volume 4 | Issue 7 | e6386
  32. 32. Integrative Personal Omics ProfilingReveals Details of Clinical Onset of Viruses and Diabetes Cell 148, 1293–1307, March 16, 2012 • Michael Snyder, Chair of Genomics Stanford Univ. • Genome 140x Coverage • Blood Tests 20 Times in 14 Months – tracked nearly 20,000 distinct transcripts coding for 12,000 genes – measured the relative levels of more than 6,000 proteins and 1,000 metabolites in Snyders blood
  33. 33. Publically Sharing Your Genome and Medical Records: Is it Crazy or the Future? I Have Been Accepted by PGP and Spoke at GET 2012
  34. 34. Crowd-Sourcing Health StudiesIs Rapidly Growing With More Open Health Data
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