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My N=1 Experience

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12.04.25 …

Pioneer Session: "N=1: Pioneers of Self-Tracking“
Panel at the Genomes, Environment, and Traits Conference
Harvard Medical School
Title:My N=1 Experience
Cambridge, MA

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  • 1. My N=1 Experience Pioneer Session: "N=1: Pioneers of Self-Tracking“Panel at the Genomes, Environment, and Traits Conference Harvard Medical School Cambridge, MA April 25, 2012 Dr. Larry Smarr Director, 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 http://lsmarr.calit2.net
  • 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. I Reversed My Body’s Decline By Altering Nutrition and Exercise
  • 3. From Measuring Macro-Variablesto Measuring Your Internal Variables www.technologyreview.com/biomedicine/39636
  • 4. My Quarterly Blood Tests In Addition to Lipids: Only One Was Far Beyond Normal Limits• 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
  • 5. Natural Anti-Inflammation Can Be Much Larger Effect Than Antibiotic-Induced Inflammation Remission 27x Much of the Inflammation Drop Is Spontaneous 15x Antibiotics Antibiotics Normal Range CRP < 1 Demonstrates Value of Fine-Grained Time Series
  • 6. Frequent Stool Analysis Reveals Lactoferrin Spike to Active Crohn’s Disease (CD) Level Colonoscopy Typical May 2011 Normal Lactoferrin Level < 7 Lactoferrin Value for Active Crohn’s Colonoscopy May 2006 Colonoscopy Jan 2012 Colonoscopy December 2010 Colonoscopy and Biopsies Support CD Diagnosis
  • 7. Confirming the Crohn’s Hypothesis: Finding the “Smoking Gun” with MRI ImagingLiver 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 Diseased Sigmoid Colon Major Kink Sigmoid Colon Threading Iliac Arteries
  • 8. LS Sigmoid Colon Cross Sections Showing Inflamed Wall Jan 2012 MRI Enterography report: “long segment wall thickening in the proximal and mid portions of the sigmoid colon, extending over a segment of approximately 16 cm, with suggestion of intramural sinus tracts. Ulcerative Colitis isRestricted tothe Mucosa, while Crohns Disease Note Affects the Thickness Whole of Wall -Bowel Wall Normal is 3mm (like a Balloon) Source: L Smarr Using Calit2’s Jurgen Schultz Software
  • 9. 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
  • 10. 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
  • 11. Microbial MetagenomicsCan Diagnose Disease StatesFrom www.23andme.com Mutation in Interleukin-23 Receptor Gene—80% Higher Risk of Pro-inflammatory Immune Response IBD Patients Harbored, on Average, 25% Fewer SNPs Associated with CD Microbial Genes than the Individuals Not Suffering from IBD. 2009
  • 12. First Stage of Metagenomic Sequencing ofMy Gut Microbiome at J. Craig Venter Institute I Received a Disk Drive Last Week With 35 GB FASTQ Files Weizhong Li, UCSD NGS Pipeline: 230M Reads Only 0.2% Human Next: 10-100,000 cpu-hrs 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