Be Your Own Health Detective


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Invited Talk
Personalized Life Extension Conference
Title: Be Your Own Health Detective
San Francisco, CA

Published in: Health & Medicine
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Be Your Own Health Detective

  1. 1. Be Your Own Health Detective Invited Talk Personalized Life Extension Conference San Francisco, CA March 31, 2012 Dr. Larry SmarrDirector, California Institute for Telecommunications and Information Technology Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD Follow me at
  2. 2. I am the Digitally-Enabled “Patient of the Future”: Measuring the State of Your Body and “Tuning” It 1999 2010 2000Age Age51 61 I Arrived in La Jolla in 2000 After 20 Years in the Midwest and Discovered I was Pre-Diabetic
  3. 3. From Measuring Macro-Variablesto Measuring Your Internal Variables
  4. 4. From One to a Billion Data Points Defining Me:The Exponential Rise in Body Data in Just One Decade! Billion: MyFull Genome Full DNA, MRI/CT Images SNPs Million: My DNA SNPs, Zeo, FitBit Blood Variables One: Hundred: My Blood Variables Weight Weight My
  5. 5. Tracking and Reducing Inflammation is Critical to Your Health 2004
  6. 6. I Have Greatly Lowered My Body’s Inflammation From Food By Increasing Omega-3s Ratio of AA/EPA “Silent Inflammation” Chronically Ill I take 6 Fish Oil American Pills Per Day Average “Healthy” American Ideal Range My Range Range Source: Barry Sears My Tests by
  7. 7. Blood Tests I Do Quarterly to Annually In Addition to Lipids• 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. I Track Over 100 Blood Variables Over Time
  8. 8. But, In Spite of My High Levels of Omega-3s,Blood & Stool Measurement Show Chronic Inflammation Stool Tests by Graph From Oct 2010 Talk at This Conference Colonoscopy May 2006 “Mild Inflammation of ? Colonic Muscosa” hsCRP Good Range Lactoferrin Good Range High CRP Drives Arterial Plaque Formation
  9. 9. Measuring Stool and Blood Markers RevealedEpisodic Inflammation Peaks of CRP and Lactoferrin Stool Tests by Colonoscopy December 2010 “Significant Peaks 25-30x Normal Inflammation of Sigmoid Colon” Colonoscopy May 2006 “Mild Inflammation of Colonic Muscosa” hsCRP Good Range Lactoferrin Good Range Colonoscopy Revealed Inflamed Pseudopolyp In Sigmoid Colon, Colon Otherwise Fine
  10. 10. High Lactoferrin Biomarker Led Me to Hypothesis I Had Inflammatory Bowel Disease (IBD) IBD is an Autoimmune Disease Which Comes in Two Subtypes: Crohn’s and Ulcerative Colitis Scand J Gastroenterol. 42, 1440-4 (2007) My Values 2009-10 Inflammatory Bowel Disease Affects Over One Million Americans
  11. 11. Latest Data Point Reveals Lactoferrin Spike to Active Crohn’s Disease (CD) Level Colonoscopy Typical May 2011 Lactoferrin Value for Active Crohn’s Colonoscopy May 2006 Colonoscopy Jan 2012 Colonoscopy December 2010Box Shows Previous Size of Graph Colonoscopy and Biopsies Support CD Diagnosis
  12. 12. Confirming the Crohn’s Hypothesis: Finding the “Smoking Gun” with MRI ImagingLiver Transverse Colon I Obtained the MRI Slices From UCSD Medical Services and Converted to Interactive 3D Working With Calit2 Staff and Software Small Intestine Descending Colon Diseased Sigmoid Colon Major Kink Sigmoid Colon Threading Iliac Arteries
  13. 13. Front and Back View of LS Diseased Sigmoid ColonFront of Sigmoid Back of Sigmoid
  14. 14. LS Sigmoid Colon Cross Sections Showing Inflamed Wall Ulcerative Colitis isRestricted tothe Mucosa, while Crohns Disease Affects the WholeBowel Wall Note Thickness of Wall - Normal is 3mm (like a Balloon)
  15. 15. LS Sigmoid Colon Cross Sections Showing Inflamed Wall Note Small Opening In Colon
  16. 16. Exploring My Internal Organs in the Calit2Virtual Reality CAVE Using DeskVOX Software Photo & DeskVOX Software Courtesy of Jurgen Schulze, Calit2
  17. 17. Autoimmune Diseases Effect 5-8% of Americans• Crohn’s Disease Despite decades of research, the etiology of Crohns disease• Ulcerative Colitis remains unknown.• Rheumatoid Arthritis Its pathogenesis may involve a complex interplay between• Multiple Sclerosis host genetics,• Psoriasis immune dysfunction,• Type 1 Diabetes, and microbial or environmental factors.• Ankylosing Spondylitis --The Role of Microbes in Crohns Disease Paul B. Eckburg & David A. Relman• Lupus Erythematosus Clin Infect Dis. 44:256-262 (2007)• Plus Over 70 Others The National Institute of Allergy and Infectious Diseases (NIAID)
  18. 18. Single Nucleotide Polymorphisms (SNPs) Make Up About 90% of All Human Genetic VariationPerson A SNPs Occur Every 100 to 300 Bases Along Human DNAPerson B Tracks One Million SNPs
  19. 19. I Wondered if Crohn’s is an Autoimmune Disease, Did I Have a Personal Genomic Polymorphism? From Polymorphism in Interleukin-23 Receptor Gene — 80% Higher Risk ATG16L1 of Pro-inflammatory Immune Response IRGM NOD2 SNPs Associated with CD
  20. 20. You are a Superorganism:Your Body Has Ten Microbes for Every Human Cell! Firmicutes Are the Dominant Phyla in the Human Microbiome Science v.330, p. 1619 (2010)
  21. 21. Except for E. Coli, My “Good” Cultured Gut Bacteria Collapsed After Antibiotics 16 = All 4 at Full Strength Antibiotics Antibiotics ? Antibiotics: Levaquin & Metronidaloze Values From stool test
  22. 22. My Cultured “Bad” Dysbiotic Bacteria Have Been Flourishing But Most Gut Bacteria Can Not Be Cultured AntibioticsAntibiotics
  23. 23. The Gut Microbiome Has Been Mapped in the Last Five Years Using Genome Sequencing“A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms.” 395 Phylotypes Firmicutes Bacteroidetes “Diversity of the Human Intestinal Microbial Flora” Paul B. Eckburg, et al Science 308, 1635-8 (2005)
  24. 24. Crohn’s Disease Patients Have Number of Firmicute Gut Microbe Species Reduced by Over 2/3! Healthy Gut MicrobesActinobacteria 7 Bacteroidetes Proteobacteria Firmicutes 33 5 43 IBD Gut MicrobesActinobacteria 7 Bacteroidetes Proteobacteria Firmicutes 33 5 13 The Missing Firmicutes Inhibit Pro-Inflammation Manichanh, et al, Gut 2006;55:205–211
  25. 25. Can Increasing Use of Antibiotics and Western Diet Be Causing Increase in IBD? “Importantly, changes in diet, use of antibiotics,… have likely modified intestinal microbial communities and contributed to the increased prevalence of IBD during the past century.” Nature Reviews Immunology 9, 313-323 (2009)
  26. 26. Next Step: Use Microarray to Measure Time Series of Microbial Diversity “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
  27. 27. First Stage of Metagenomic Sequencing ofMy Gut Microbiome at J. Craig Venter Institute I Will be Receiving a Disk Drive Next Month With 30-50 GigaBytes Gel Image of Extract from Smarr Sample-Next is Library Construction Manny Torralba, Project Lead - Human Genomic Medicine J Craig Venter Institute January 25, 2012
  28. 28. Sadly, Because of the Colon Wall InflammationI Have Taken 1 Month Antibiotics & 2 Months Prednisone 27x Much of the Inflammation Drop Is Spontaneous 15x Antibiotics Antibiotics Normal Range CRP < 1 However, Stool Calprotectin Inflammation Biomarker Doubled During the Last Month!
  29. 29. Evidence for the Efficacy of Probiotics is IBD is Mixed - More Clinical Research Needed“...there is virtually no evidence of probiotic efficacy in Crohn’s disease.”
  30. 30. I Take a Probiotic “Cocktail” to Enhance Microbial Diversity-48 Species of Bacteria• Genera Covered: • Genera Covered: – Azospirillum – Lactococcus – Azotobacter – Leuconostoc – Bacillus – Myrothecium – Bacteriodes – Pediococcus – Bifidobacteria – Phanerochaete – Brevibacterium – Pseudomonas – Kurtha – Streptococcus – Lactobacillus – Streptomyces
  31. 31. Fecal Transplants May Be a Radical New Treatment for IBD The Advantage: A Mature Biochemically- Integrated Microbial Ecology is Transferred, In Contrast to a Collection of Individual Microbial Species Dr. Alexander Khoruts, NY Times as in Not FDA Approved; Very Few Doctors Performing Procedure; Essential No Clinical Trials So Far; But, Encouraging Results…
  32. 32. Publically Sharing Your Genome and Medical Records: Is it Crazy or the Future? I Have Been Accepted by PGP and Will Speak at GET 2012: My Full Genome (6 Billion Bases) Will Be Sequenced This Year
  33. 33. From “How Do You Feel?”,to “What Are Your Numbers?” Where’s There’s Data There’s Hope