Quantifying My Body in Health and Disease
One of the Calit2’s original interdisciplinary themes in 2000 was “Digitally Enabled Genomic Medicine,” which envisioned a future in which both the human genomics and wireless sensor “read out” of individuals would be routine, as they have come to be 20 years later. I decided that to better understand these evolving trends I should try to live as a Future Patient in what Lee Hood has termed Predictive, Preventive, Personalized and Participatory (P4) Medicine. I had my full human genome sequenced and became actively involved with quantifying the state of my body, creating multi-year time-series of over 150 biomarkers from my blood and stool, with the later revealing the dynamics of gut microbiome genomics. In addition, I became an early member of Harvard’s Personal Genome Project led by George Church and of Lee Hood’s Pioneer 100 Wellness Project. By 2011, using these time series, I discovered that I was chronically inflamed, caused by an autoimmune disease [inflammatory bowel disease (IBD)-colonic Crohn’s disease] that both my doctors and I were unaware I had. The progression of the disease caused massive dysbiosis in my gut microbiome and eventually a stricture in my sigmoid colon. My team has worked for several years with Rob Knight’s team to analyze my gut microbiome time-series, while I developed close collaborations with UCSD doctors in surgery, radiology, gastroenterology, and other specialties. My Calit2@UCSD software development team has developed interactive visualization tools and environments for analyzing large amounts of human-generated biomedical data, including most recently 3D visualizations of individual patients derived from MRI/CAT scans to personalize pre-planning of robotically-assisted surgery, which I was able to help prototype with a sigmoid resection in November 2016.