>> HELLO, EVERYONE, IT'S MY PLEASURE TO INTRODUCE OUR WALS SPEAKER DR. GEORGE CHURCH. NORMALLY THIS WOULD BE DONE BY SOMEBODY LIKE DR. COLLINS, BUT HE IS OTHERWISE OCCUPIED TODAY AND COULDN'T ATTEND, SO I WILL BE INTRODUCING DR. CHURCH. IF ANYONE HAS LOOKED AT HIS RESUME, IT'S VERY IMPRESSIVE, BECAUSE I'M SURE YOU WOULD RATHER HEAR WHAT HE IS GOING TO TALK ABOUT, I WILL KEEP MY COMMENTS BRIEF. HE WENT TO DUKE UNIVERSITY WHERE HE RECEIVED DEGREES IN CHEMISTRY AND ZOOLOGY AND THEN WENT ON TO GET HIS PH.D. AT HARVARD AND BUY NO CHEMISTRY AND MOLECULAR BUYIOLOGY. HE IS CURRENTLY A PROFESSOR OF GENETICS AND DIRECTOR OF THE CENTER OF COMPUTATIONAL GENETICS. WHILE HE WAS ON HIS EDUCATIONAL MATH, HE HAD A NUMBER OF ADVANCES RELATED COMPUTATIONAL BIOLOGY AND GENETICS INCLUDING THE DEVELOPMENT OF CRYSTAL SOFTWARE THAT LED TO FIRST RYE RESOLUTION RNA STRUCTURE AND THE DEVELOPMENT OF THE FIRST AUTOMATED DNA SEQUENCING. HE ALSO HELPED DEVELOP THE FIRST DIRECT GENOME SEQUENCING METHODS. HE HAS BEEN INSTRUMENTAL IN VARIOUS ASPECTS OF THE HUMAN GENOME PROJECT, AND IN THE USE OF MOLECULAR MULTIPLEXING FOR HIGH THROUGHPUT BIOLOGICAL ASSAYS. HE HAS BEEN A MAJOR PLAYER IN THE FIELD OF SYNTHETIC BIOLOGY AND IN THE PUSH FOR PERSONAL GENOMICS. HE HAS A HUGE LIST OF PUBLICATIONS, VERY HIGH QUALITY PUBLICATIONS, AND THE MOST RECENT ONES, I THINK, REFLECT HIS FOCUS ON USING GENOMIC APPLICATIONS TO CREATE HIGH THROUGHPUT TECHNOLOGY TO MAKE PERSONAL GENOMICS A REALITY, AND THE USE OF PERSONAL GENOMICS IN MEDICAL ADVANCEMENT. I SUSPECT THAT'S WHAT HE WILL BE TALKING ABOUT TODAY, AND SO WITH NO FURTHER ADIEU, DR. CHURCH. [APPLAUSE] >> THANK YOU VERY MUCH FOR THAT INTRODUCTION AND FOR EVERYBODY HERE, I HAVE SOME OLD FRIENDS I HAVE SEEN ALREADY. THIS IS MY THANK YOU SLIDE. IT ALSO ACKNOWLEDGES RELATIONSHIPS THAT I HAVE WITH SOME GOVERNMENT AND COMMERCIAL COLLABORATORS OF VARIOUS SORTS AND FUNDING AGENCIES. I'M VERY GRATEFUL TO THESE AND GRATEFUL TO THE GRADUATE STUDENTS AND POST DOCS AS WELL. THE LONG TITLE WAS REALLY JUST KIND OF TO EMPHASIZE THAT WE ARE TRYING TO DEVELOP BASIC ENABLING TECHNOLOGY THAT WE THINK MIGHT ALREADY OR SOME DAY IMPACT ALL OF THE NATIONAL INSTITUTES, AND THEY HAVE IMPACTED US IN VARIOUS WAYS AS WELL, VERY POSITIVELY. SO THANK YOU TO THEM AS WELL. I ALSO WANT TO GET OUT OF THE WAY, YOU KNOW, ANOTHER EMBARRASSING FACT, WHICH WE STILL HAVEN'T SEQUENCED ANY HUMAN GEE NOMES IN THEIR ENTIRETY, THERE IS STILL ABOUT 5% MISSING AND IT'S NOT A TRIVIAL 5% EITHER AT LEAST IT MAY NOT BE IN THAT HERE IS AN EXAMPLE OF AN ASSOCIATION WITH MULTIPLE SCLEROSIS THAT'S SITTING IN ONE OF THE BILLINGEST GAPS IN THE GO GENE GENE NOME, ONE OF THE 300 GAPS AND THIS HAS POTENTIALLY VERY SIGNIFICANT GENETIC ASSOCIATION. NOW, I DON'T THINK I NEED TO TELL YOU THAT WE HAVE RECENTLY BROUGHT DOWN THE COST OF SEQUENCING BY ABOUT A MILLION FOLD, AND THE COMMENT BACK IS THEY WOULD LIKE SOME MORE. WE WOULD LIKE SOME MORE, THANK YOU. SO HOW DID WE DO THIS? HOW DID WE HAVE THE DIGESTIVE CAPABILITIES AND EXACTLY WHAT ARE WE DOING WITH THIS THAT'S USEFUL? THIS COMES DOWN TO THE OBVIOUS INHURT RITED GENETIC TESTS WHICH BUILD A STRONG HISTORY OF MEDICAL GENETICS. THERE IS NEW METHODS THAT ARE MUCH MORE FEASIBLE NOW WHICH LOOKS FOR DEKNOW VO MUTATIONS, DIFFERENCES BETWEEN THE CHILD AND THE PARENTS. AND THIS ALLOWS US TO EXTEND MEDICAL GENETICS BEYOND CASES WHERE THE USUAL CASE WHERE YOU HAVE -- REQUIRE MEDICAL HISTORY WHICH MAY NOT HAPPEN IN THE CASE OF ADOPTION AND NEW COME COMBINATION WHERE YOU ARE THE FIRST PERSON IN YOUR FAMILY AND THIS IS A VERY IMPORTANT MEDICAL EXTENSION OF MEDICAL GENETICS. THE VERY OBVIOUS ONCO GENOMICS, PERSONALIZED GENOMIC MEDICINE IS PRACTICES AND PHARMACOGENETICS THAT EXTEND BEYOND CANCER, CHEMOTHERAPIES AND SORTS, WE CAN NOW DO STRUCTURAL CHROMOSOME VARIATIONS, QUANTITYTATION OF RNA, CHROME MAT CONTINUE, METHALLATION OF DNA AND CHROME MAT IN. MICROBEALL AND IMMUNE SYSTEM, WE CAN DO IN C2 SEQUENCING. WE CAN LOOK FOR VERY, VERY RARE CELLS AND IN A CERTAIN SENSE THERE IS THIS FEELING THAT WE ARE REPLACING THE HIGH THROUGHPUT CHIPS PATHOLOGY AND CYTOLOGY PRACTICE THAT HAS BEEN IN PLACE FOR QUITE AWHILE. AS AN EXAMPLE OF THIS, I HAVE CHOSEN FOUR ARTICLES -- I COULD HAVE CHOSEN MANY OTHERS INCLUDING SOME INTERMURAL SUCCESS HERE AT NIH WHERE COHORTS AS SMALL AS ONE, YOU KNOW, IN THE RANGE OF ONE TO TWENTY, NOT THE GIGANTIC COHORTS WE HAVE COME TO THINK ABOUT FOR MODERN GENETICS BUT THESE SMALL COHORTS ARE YIELDING VERY EXCITING, VERY MEDICALLY CAUSEITIVE AND SIGNIFICANT ALLELES WITH AS LITTLE AS 10 GENE NOMES PRODUCING 22 ALLELES INCLUDING CONFIRMATORY SEQUENCING VERY TARGETED IN INDIVIDUAL ALLELES OR GENES. SO, BY GENE NOMES, I MEAN GENE NOMES OR X ONLIES. JIM LUFSKI WHO IS AUTHOR AND RESEARCH SUBJECT FOR A NEUROPATHY THAT WAS PUBLISHED AND HEATHER AND LOGAN MADISON ARE ADULT CHILDREN IN A FAMILY THAT WERE ALL FOUR MEMBERS WERE SEQUENCED, AND IS THAT LED TO NOT ONE NEW ALLELE, BUT FOUR NEW ALLELES, TWO COMPOUND HETERO SKY GOATS PRODUCING TWO DIFFERENT SYNDROMIC -- THEY ARE FORTUNATE TO HAVE TWO RECESSIVE COMBINATIONS FOR TWO DIFFERENT DISEASES. AND THE LIST GOES ON. SOME OF THESE WERE DONE BY JASON DRURY, WHO IS -- WAS A GRADUATE STUDENT M.D. AND POST DOC IN MY LABORATORY AND IS A PROFESSOR IN SEATTLE. THE COST NOW FOR AN X SOME WHICH IS 1% OF THE GENE NOME IS $4,000 AND THE PRICE FOR A GENOME IS AROUND $7,000. AND THE DISTANCE BETWEEN RESEARCH AND PRACTICE IS GETTING VERY, VERY SMALL, PERHAPS CLOSE TO ZERO. IN THIS ANECDOTE, AND IT IS JUST AN ANECDOTE REPORTED IN NATURE NOT TOO LONG AGO WHERE A CHILD AT THE AGE OF THREE HAD MORE THAN 100 SEPARATE SURGERIES ALREADY BEFORE HIS FOURTH BIRTHDAY. OBVIOUSLY DIAGNOSIS WAS NOT GOING WELL, PERFECTLY, AND SO THEY IN DISPRAITION DID SEQUENCING AND THIS CHANGED THEIR VIEWPOINT FROM IT BEING AN INTESTINAL PROBLEM WITH THESE MULTIPLE INTESTINAL LESIONS TO SOMETHING THAT WAS IMMUNE SYSTEM DYSFUNCTION DUE TO APOPTOCIC GENE XAIP SO THEY DID A BONE MARROW TRANSPLANT WHICH HAD IMPACT IN A COUPLE OF WEEKS AND THE CHILD HAS BEEN FINE EVER SINCE. GENERALIZING THIS BEYOND ANECDOTES AND FOCUSING ON MEDICAL GENETICS, NOT DIRECT CON STOOPER GENETICS WHICH I WON'T TALK ABOUT, BUT REAL MEDICAL GENETICS, HERE NOW OVER 2200 GENES WHICH IS CONSIDERED HIGHLY ACTIONABLE. IT MAY NOT BE THE PERFECT TOUR, BUT THERE ARE MEDICAL DEVICES, TREATMENTS, THERAPIES OF VARIOUS SORTS FOR THE 2200 GENES AND IT'S BETTER TO KNOW WHAT YOU ARE DEALING WITH THAN MERELY KNOWING THE SYMPTOMS. AN EARLY SUCCESS IS ONE ABOUT 40 GENES WHICH ARE ROUTINELY ANALYZED, USUALLY BY ENZYME ASSAYS FROM A HEEL PRICK OF BLOOD FROM 4 MILLION INFANTS PER YEAR IN THE UNITED STATES ALONE. AND THEN ONE OF THE FIRST AND FOREMOST OF THE TWO GENES ONE AND TWO IN THE EARLY 90s ESTABLISHED AS DNA SEQUENCING BASED TEST AND THESE HAVE BEEN EXTREMELY HEARTILY EMBRACED BY THE COMMUNITY AND THEY HAVE CONTINUED TO INCREASE QUITE STEADILY DURING THE ERA OF THE GENOME PROJECT AND BEYOND TO 2200 PLUS GENE GENES. EVEN THOSE ARE HIGHLY PREDICTABLE AND ACTIONABLE IT DOESN'T MEAN EVERYTHING ABOUT GENOMICS IS AND IT DOESN'T MEAN OUR FAILURES IN CASES WHERE BIOLOGY LESS PREDICTIVE, DOES IT SOUNCOULDN'T AS A FAILURE. THERE IS A WORK IN PROGRESS. WE ARE NOT SAYING WE ARE GOING DIRECTLY FROM YOUR PERSONAL GENOME WITH THREE MILLION DIFFERENCES BETWEEN YOU AND THE REFERENCE SEQUENCE DIRECTLY TO TRAITS. THAT'S NOT THE IDEA. THE IDEA IS ENVIRONMENTS IS SAY BIG COMPONENT AND THE REVOLUTION AND IS SEQUENCING IS PARTIALLY SPILLING OVER INTO ENVIRONMENTAL MEASURES AS YOU WILL SEE MOMENTARILY, PLUS ALL OF THE ELECTRONIC SOPHISTICATION WE HAVE IS BEGINNING TO HAVE IMPACT IN TERMS OF STANDARDIZATION AND REPORTING OF ENVIRONMENTAL COMPONENTS. I AM GOING TO MENTION THIS SORT OF IN THE CONTEXT OF THE PERSONAL GENOME PROJECT WHICH STARTED ACCIDENTALLY IN AN LC COMPONENT, A ONE PAGE LC COMPONENT IN A 2003 GRANT TO NIH, BUT IT NOW INCLUDEDS CENTERS IN FOUR CITIES AND THREE COUNTRIES, AND THE IDEA IS TO MEASURE THESE ENVIRONMENTAL COMPONENTS OR CAPTURE THEM FROM MEDICAL RECORDS, ELECTRONIC MEDICAL RECORDS, PERSONALLY CONTROLLED HEALTH RECORDS. AND MEASURE THE INTERMEDIATES TO THE EXTENT POSSIBLE OF GOING THROUGH EPI GENETICS, SO FORTH, EITHER DIRECTLY FROM CELL SAMPLES OR VIA REPROGRAMMED STEM CELLS, I WILL SHOW YOU THAT NOW, THIS PROJECT IS BASED ENTIRELILY ON INDIVIDUALS WILLING TO HAVE THEIR GENOMIC DATA, CELL DATA, AND EXTENSIVE TRAIT DATA WHICH I HAVE MENTIONED, IN AN OPEN ACCESS, CREATIVE COMMON ZERO FORMAT AS OPEN AS YOU CAN GET, REALLY. AND THEY ARE NOW OVER 13,000 VOLUNTEERS THAT ARE REGISTERED INTERNATIONALLY. OVER 2,000 HAVE ACHIEVED 100% ON ENTRANCE EXAM. THIS IS A DEVIATION FROM STANDARD PRACTICE OF GIVING A CONSENTING FIVE TO TWENTY PAGE CONSENT FORM THAT MOST PEOPLE DON'T READ AND POST PRINCIPLE INVESTIGATORS ARE AWARE THEY ARE NOT READING THEM, AND WE HAVE OVER A THOUSAND OF THEM HAVE THEIR MEDICAL RECORDS ON LINE, AND SIX COUNTRIES. THIS IS MEANT TO BE AN ICON FOR HOW IMPORTANT IT IS TO EMBRACE OUTLIARS, NOT JUST TO LOOK IN THE MIDDLE BUT LOOK AT THE HIGH DEVIANTS. THIS IS NOT INTRASPECIES BUT INTERSPECIES DEVIATION, BUT IT'S TO SAY WE WANT TO EMBRACE THESE OUTLIERS IN A VARIOUS RIGHT OF WAYS. AND THIS HAPPENS TO BE A DATABASE, AN AGING DATABASE THAT PEDRO DEMAGOLIS PUT TOGETHER OVER THE YEARS, MANY OF THEM IN MY LABORATORY, AND WE ARE IN THE PROCESS OF SEQUENCING OF THESE OUTLIERS THAT HAVE, FOR EXAMPLE -- WHICH LIVES ABOUT TEN TIMES LONGER THAN ITS CLOSE RODENT COUSIN AND CAPUCHA. N MONKEY, THE BOW HEAD WHALE LIVES UP TO 200 YEARS AND THIS CLAM LIVES 4 O 00 YEARS AND HERE IS A HUMAN CELEBRATING HER 121st BIRTH OKAY AND I INSEARLY HELP THAT MANY OF US CAN DO LIKEWISE. RIGHT NOW, THESE ARE OUTLIERS. THE OLDEST, AND WE INTEND TO GET -- WE ARE LOOKING VERY MUCH AT OLDER FAMILIES, FAMILY MEMBERS THAT -- THIS IS OUR OLDEST COMPLETE GENOME SEQUENCE SO FAR IN THE PERSONAL GENOME PROJECT, AND AS FAR AS I KNOW INTERNATIONALLY HE IS OF AFRICAN-AMERICAN AN SETTRY SO HE SAYS SICKLE CELL TRAIT. IT HASN'T PUT TOO MUCH OF A CRIMP IN THE LIFE SPAN EVEN THOUGH IT IS ONE OF THE FEW THINGS THE U.S. MILITARY DIAGNOSES BECAUSE PRESUMABLY HIGH ALTITUDE IMPLICATIONS AT ONE POINT THEY FELT WAS SIGNIFICANT. AND I WANT TO POINT OUT THIS RESOURCE, PERSONAL GENOMES.ORG WHERE WE ARE BUILDING COMMUNITY RESOURCES FOR ANNOTATION OF THIS CONNECTION BETWEEN GENES, ENVIRONMENTS AND TRAITS, BUT AUTOMATIC AND MANUAL CURATION TO YOU CAN GO AS WELL AS YOU CAN FROM GENES IN THE ENVIRONMENT TO TRAITS IN A WAY THAT THE COMMUNITY CAN CRITIQUE RATHER THAN SOME PROPRIETARY SYSTEM WHICH IS MORE DIFFICULT TO CRITIQUE. THIS IS SORT OF A WIKI PEDIA TYPE OF MODEL BUT WITH SLIGHTLY HIGHER ACCOUNT ACCOUNT FOR THE INDIVIDUALS -- ACCOUNTABILITY FOR THE INDIVIDUALS EDITING IT. THE KIND OF MOTIVATION FOR THAT REPORT WAS WHEN YOU PUT DATA IN A PUBLIC DOMAIN, THEN IT'S POSSIBLE, IN FACT, LIKELY, THAT THE INDIVIDUALS WILL GET ACCESS TO THEIR OWN DATA AND YOU HAVE THE CHOICE OF LETTING THEM GO OFF AND INTERPRETING THEIR DATA WITH THEIR OWN COMPUTER PROGRAMS OR SOMETHING, SOME FLY BY NIGHT OPERATION THEY FIND ON THE INTERNET OR WE CAN BUILD A COMMUNITY WHERE WE CAN CRITIQUE THE PROCESS BY WHICH PEOPLE ANALYZE THEIR FULL GENE NOME FEE SENSES OR PAR THAT GENOME SEQUENCES. THIS IS AN EXAMPLE OF THE ONE OF THE GRAY ZONES. THIS IS NOT ONE OF OUR EASIEST CASES, THIS IS ONE OF OUR MOST DIFFICULT CASES WHERE PGP NUMBER 6 WAS FOUND TO HAVE A PARTICULAR ALLELE AN ALNONE IN THE MI2 GENE WHICH IS ONE OF THE MANY GENES INVOLVED IN HYPER-TROPIC CARDIOMYOPATHY, MANY ALLELES AND GENES ARE ESTABLISHED FOR THIS DISEASE AND IT IS A VERY IMPORTANT AND INTERESTING DIAGNOSTIC SITUATION BECAUSE THIS IS NOT PART OF STANDARD MEDICAL CARE. YOU DON'T NORMALLY GET DIAGNOSED FOR HYPERTROPHIC CARDIOMYOPATHY OR TESTED FOR IT UNLESS YOU HAVE FAMILY HISTORY, BUT IT IS SOMETHING THAT CAN HAPPEN VERY SWIFTLY RATHER THAN THE LONG-TERM WARNING YOU MIGHT GET FORAGE THOROUGH SCLEROSIS WHERE YOU MIGHT GET ATHEROSCLEROSIS WHERE YOU GET TIRED GOING UPSTAIRS THIS CAN HIT ATHLETES VERY SUDDENLY AND CAUSE DEATH WITHOUT WARNING. THERE WAS ONLY ONE CASE IN THE LITERATURE OF THIS EXACT ALLELE IN THIS GENE AND WE FELT THIS WAS INSUFFICIENT TO GET TOO WORKED UP ABOUT IT EVEN THOUGH THIS PERSON HAD THE SAME ALLELE. WE WANTED TO AVOID THE INCIDENTAL LOME, BUT THE PHYSICIANS THAT ARE PART OF THE PERSONAL GENE NOME PROJECT FELT THAT IF WE ASKED AROUND WE WOULD FIND ADDITIONAL DATA HIDING IN PEOPLE'S FILING CABINETS, COMPANIES AND CLINICS AND INVESTIGATORS, AND SURE ENOUGH, WE DID ASK AROUND AND DID FIND MANY MORE CASES OF THIS A13P ALLELE, MANY OF WHICH WERE AFFECTED WITH HYPERTROPHIC CARDIOMYOPATHY AT RELATIVELY EARLY ON SET. SO WE FELT THIS WASN'T PERFECT, BUT IT WAS ENOUGH TO RECOMMEND TO THIS INDIVIDUAL TO GET AN ECHOCARDIOGRAM LOOKING FOR AN INCREASED THICKENING OF THE VENTRICULAR WALL, AND SINCE IT'S UNCERTAIN WHEN THE AGE OF ON SET WOULD BE, TO DO THAT EVERY TWO YEARS. THAT'S WHAT HE DID. THIS IS KIND OF A DRIVE SLIDE, BUT IT'S TO TELL YOU THAT THERE ARE MANY USES OF THE PERSONAL GENOME PROJECT DATA AS WELL AS TISSUES ALREADY. THESE WERE PUBLISHED IN DECENT JOURNALS RANGING FROM SEQUENCING ITSELF TO ANALYSIS OF METHALLATION, AND MICROBE BEEALL DIVERSITY, HYPERMUTABILITY AND STEM CELLS. WHY IS IT THAT WE CAN DO ALL OF THESE APPLICATIONS, THAT WE CAN SEQUENCE ALL OF THESE INDIVIDUALS AND ANIMALS SUDDENLY, AND PART OF IT IS KIND OF A STANDARD MOORE'S LAW CURVE WHERE WE GET A FACTOR OF 1.5 FOLD EXPONENTIAL, PRETTY FAST ONE EVER SINCE I WAS A TEENAGER BASICALLY FOR A COMPUTERS AND FOR DNA SEQUENCING. BUT THEN WHAT HAPPENED IS SORT OF ABOUT THE TIME THE GENOME PROJECT WAS BEING DECLARED A VICTORY, IT SLOPED TO FACTORS OF 10 PER YEAR RESULTING IN THE MILLION FOLD EFFECT. I DON'T THINK WE WILL GET A FACTOR OF TEN THIS YEAR UNFORTUNATELY, BUT IT IS STILL GOING TO BE STRIKING EXPONENTIAL FOR LONGER AND WE ARE IN THE RANGE OF A THOUSAND DOLLARS COST TO AROUND $7,000 PRICE, AND THAT'S WHAT YOU WOULD ACTUALLY HAVE TO PAY IN FAIRLY LARGE BULK PROJECTS. AND THE REASON THAT THIS HAS HAPPENED IN PART IS BECAUSE OF THE BREAKING OF A MONOPOLY THAT EXISTED DURING THE GENOME PROJECT WHICH I THINK MANY OF US FOUND QUITE FRUSTRATING AND MAYBE WE HAVE OVERCOMPENSATED BY HAVING 22 DIFFERENT TECHNOLOGIES, ALL OF THEM DIFFERENT FROM THE ONE THAT PRODUCED THE DRAFT SEQUENCE, AND MY GROUP AND I ARE INVOLVED IN ALMOST ALL OF THESE, ABOUT 18 OF THEM AND IN A BOX HERE ARE THE SIX THAT HAVE BEEN ON THE MARKET AVAILABLE FOR ABOUT TWO YEARS, AT LEAST TWO YEARS NOW, SOME OF THEM LONGER, AND THERE ARE A COUPLE MORE COMING SOON THAT I WILL MENTION. AND I DON'T NECESSARILY SEE THIS AS A STRICT DARWINIAN SITUATION WHERE THERE IS ONLY ONE WINNER. I THINK THERE ARE THESE SEVEN DIFFERENT NICHES, YOU KNOW, THE CHEAPEST FOR BASE PAIR, THE CHEAPEST INSTRUMENT, LONG READS, DEALING WITH REPEAT, SPEED, PORTABILITY AND SO FORTH. I THINK THESE NICHES MAY BE DOMINATED BY ONE MACHINE OR THERE MAY SH SEVEN DIFFERENT OR A VARIETY. I WILL WALK YOU THROUGH THREE BRIEFLY JUST TO GIVE YOU A FEELING FOR HOW IT IS WE GO ABOUT THINKING ABOUT INVENTING, YOU KNOW, 20 NEW TECHNOLOGIES AND OPTIMIZING THEM AND BRINGING THEM INTO THE MARKET. AND THIS IS ONE THAT ACTUALLY REPRESENTS QUITE A FEW OF THEM THAT WERE IN THAT BOX, AND SO FLUORESCENT STATE, MANY OF THEM ARE FLUORESCENT STATE, THEY INVOLVE SMALL AMPLIFICATIONS OR SINGLE MOLECULES WITH SEQUENCING BY SYNTHESIS WHICH IS SEQUENCING BY LIE GAS OR PLUMERASE. ONE IS PLACING SINGLE MOLECULES OR SLIGHTLY AMPLIFIED FROM A SINGLE MOLECULE IN A RANDOM GRID OR IN THIS CASE AN ACTUALLY ORDERED GRID, THIS IS COMPLETE GENOMICS, AND THEN FOR EACH OF THESE SINGLE MOLECULES, WHICH CONTAINS SYNTHETIC DNA IN YELLOW, AND UNKNOWN GENOMIC DNA IN GREEN IS EXTENDING FROM THE KNOWN REGIONS INTO THE UNKNOWN WITH EITHER PLUMBER AS OR LIE GAS WITH FLUORESCENTLY LABELED FOUR COLORS REPRESENTING TYPICALLY ABOUT ONE BASE AT A TIME. BUT BILLIONS OF THESE SIMULTANEOUSLY. SO YOU CAN HAVE FAIRLY TYPICAL TO HAVE A BILLION OF THESE READS GOING ON SIMULTANEOUSLY IN A RUN. SO THIS IS NOW MY BEAUTIFUL INTERACTION BETWEEN SINGLE MOLECULES AND MICRO FABRICATION AND SINGLE MOLECULES ARE AMPLIFIED JUST ENOUGH SO THEY COMPLETELY COVER THIS 200 TO 300 NANO METER.OF POSITIVE CHARGE AND WE CALL THIS POLLINATE EXCLUSION PRINCIPLE. THIS IS INTENDED SO THAT ONE MOLECULE WILL BIND THERE AND YOU GET THE MORAL EQUIVALENT OF CLONALITY WITHOUT DOING STANDARD CLONING. AND THIS SHOWS HOW THE GRID IS REALLY CLONAL WHEN WE DO ONE ROUND OF SEE AGAINING WHERE WE GET AC CS AND T'S THE FOUR COLORS IT'S VERY CLEAR, YOU HAVE VERY LITTLE OVERLAP OF COLORS. AND YOU SEE THE DIFFERENCE BETWEEN THE GRID AND THE SQUARE GRID AND THE RANDOM DISTRIBUTION WE HAD IN THE EARLY DAYS IN THE LATE 90s AND EARLY 2000S WHERE WE WOULD RANDOMLY DISTRIBUTE THESE CLUSTERS OR SINGLE MOLECULES. YOU GET A FACTOR OF FIVE OR SO DUE TO THE DIFFERENCE IN THE PLUS ON DISTRIBUTION WHERE THESE BLACK REGIONS ARE GENERALLY NOT USEFUL, PLUS WE HAVE NOW IMPROVED THE DENSITY BECAUSE IT'S A SQUARE GRID, YOU CAN GET ALIGNMENT WITH THE DIGITAL CAMERA, AND YOU CAN GET ANOTHER FACTOR, YOU CAN -- INSTEAD OF GETTING 25 PIXELS PER BASE PERIOD, YOU CAN GET AS LITTLE AS ONE OR TWO PIXELS PER TEMPLATE. THAT'S ANOTHER FACTOR OF TEN OR MORE. SO THAT'S ONE EXAMPLE. THIS IS CHARACTERISTIC OF ALL OF THE ONES THAT HAVE BEEN AVAILABLE FOR THE LAST TWO YEARS. THERE IS, YOU KNOW -- I WILL SHOW YOU TWO EXAMPLES WHICH ARE NOT QUITE AS REDUCED TO PRACTICE AS THAT. THIS IS -- WHICH IS A VARIATION ON THE PYROSEQUENCING METHOD WHERE YOU ARE DESECTING THIS REACTION OF MULTIPLE MOLECULES, WHERE THE TRIPHOSPHATES REACT WITH A PRIMER REPRESENTED BY THE OH, 3 PRIME OH TO RELEASE PYROPHOSPHATE AND PRO TONS IN THIS REACTION. IN THE 454 ROASH METHOD YOU DETECT PYROPHOSPHATE BY ENIS DISCIPLE REACTIONS THAT RESULT IN BUY NO LOOM NECESSARY SENSE. AND IN THIS YOU -- BUT IN BOTH CASES WHETHER A CAMERA OR AN ARRAY, YOU BASICALLY HAVE A MICRO FABRICATED CHIP THAT EITHER DETECTS PROTONS OR FAUX PHOTONS. THE THING IN COMMON WITH THE 454, IS WHEN YOU HAVE A RUN UP BASIS, YOU TYPICALLY HAVE TO MEASURE THE HEIGHT, THE INTEGRATED INTENSITY OF THE PHOTONS OR THE PROTONS COMING THROUGH HERE, AND THAT CAN LEAD TO AMBIGUITY WHEN YOU HAVE VERY LONG HOME MOO POLYMER RUNS. THIS IS PROBABLY THE MOST MINIATURE AND THE LEAST EXPENSIVE STARTING INSTRUMENT. AND WE WILL COME BACK IN A MINUTE. >> THIS IS FARTHER IN THE FUTURE, IT'S ALSO PRETTY FAR IN THE PAST. THIS IS ONE OF THE FIRST SEQUENCING METHODS MY LABORATORY WORKED ON IN COLLABORATION WITH OTHERS AND IT WAS BEAUTIFULLY REDUCED PARTIALLY TO PRACTICE HERE BY HIGGEN DAILY AND HIS CO-WORKERS WHERE THEY SHOWED -- THIS IS ACTUAL PYCOAMPER CURRENT GOING THROUGH ONE OF THESE HIGHLY MODIFIED SINGLE MOLECULES WHERE YOU CAN SEE THE EFFECT OF PUTTING IN A CC'S OR T'S THROUGH MON MERES BY DISCRETE AMOUNTS HERE COLOR CODED WITH C AS BLUE, AND THAT'S -- AND YOU CAN SEE IT DROPPING DOWN INTO THE BLUE, WHATEVER YOU THROW A C THROUGH AND C'S AND A'S HAVING DISCREET LEVELS WHICH ARE REPRESENTED HERE WHERE YOU CAN SEE VERY LITTLE OVERLAP IN THE CHARACTERISTIC CORE CURRENT FOR DETECTING THESE MONO NUCLEOTIDES. THERE IS A VARIATION WHICH USES POLLY NUCLEOTIDES WHICH IS SENSITIVE TO MONO NUCLEOTIDES AND IT'S AN OPEN QUESTION OF WHICH IS GOING TO WIN, MONO NUCLEOTIDES EMBEDDED IN POLYMER OR BROKEN FREE. SO THE POINT IS THIS IS NOT COMPLETE PIE IN THE SKY, AND IT'S QUITE EXCITING. NOW, HOW DO WE EVALUATE THIS? ONE OF THE THINGS WE NEED TO EVALUATE IS ERRORS IN THROUGHPUT. SO JUST TO PUT THIS IN PERSPECTIVE, THESE TWO SEQUENCING BY LIGATION METHODS, THE APPLIED BIOSYSTEMS LATEST MODEL HAS ON THE ORDER OF A BILLION READS FOR INSTRUMENTS AND THE TWO THAT ARE JUST COMING AROUND THE CORNER RIGHT NOW ARE IN A WAY MUCH LOWER NUMBER OF TEMPLATE MOLECULES BUT THEY ARE READING FASTER. SO THESE ARE NOT IN THE BILLIONS, BUT IN THE HUNDREDS OF THOUSANDS, IF NOT 100,000 OR LESS AND THEY HAVE A MUCH HIGHER ERROR RATE, AS SHY AS 15% RELATIVE TO 0.1% YOU CAN GET FROM THE DUAL NUCLEOTIDE CODING YOU GET. HERE IS AN INTERESTING EXAMPLE SHOWING IN THE APPLIED BIOSYSTEM HOW YOU CAN GET SLIGHT NOTICEABLE DECREASED IN THE RAW DATA QUALITY. THIS IS FOR THE TWO BASE HE ENCODING THEY TYPICALLY USE. THIS IS AROUND TEN TO THE MINUS THREE RAW ERROR RATE AND THAT CAN, WITH CONSENSUS, ALL OF THESE CAN BE IMPROVED SORT OF TOWARDS THE TEN TO THE MINUS SIX ERROR RATE THAT PEOPLE HAVE COME TO EXPECT NOW. THAT'S ALL VERY COOL TECHNOLOGY, BUT, AND THE BIG BUT IS THAT IF YOU HAVE A PHONE, WHETHER IT'S A LAND LINE OR A CELL PHONE OR A COMPUTER NETWORK, AND YOU ARE THE ONLY ONE ON IT, IT'S NOT -- THAT'S NOT REALLY GREAT. AND THE QUESTION IS HOW MUCH SHARING DO WE NEED IN ORDER TO GET THE AWESOME POWER OF GENES ENVIRONMENTS AND TRAITS. >> AS I HAVE SAID, I'M INSPIRED BY WICKKY PEDIA WHICH ONE WOULD HAVE AS ONE OF THE WORST POSSIBLE EDITORIAL POLICIES WHERE YOU LET ANONYMOUS INDIVIDUALS BE EDITORS WORLDWIDE, BUT IT IS A REMARKABLE RESOURCE AND SOMETHING WE SHOULD STUDY. SO YOU CAN ASK WHO SHOULD HAVE ACCESS TO THE GENES, TRAITS AND ENVIRONMENT DATA. SHOULD IT BE ONLY THE EXPERTS, THE ONES THAT WROTE THE GRANT AND COLLECTED THE DATA AND THEIR CLOSE COLLEAGUES? AND I WOULD SAY WE DON'T KNOW WHO IS GOING TO MAKE THE BREAK THROUGHS. IT COULD BE, YOU KNOW, REAL OUTSIDERS THAT, AND HERE ARE SOME OF MY HEROES THAT REALLY ARE ONLY INSIDERS IN THE SENSE THAT THEIR FAMILY IS AFFECTED BY THESE VARIOUS DISEASES. HERE IS ONE THAT WAS IMMORTALIZED BY HOLLYWOOD IN LORENZO'S OIL, AND THIS IS THE REAL DORN ANY WITH HIS SON AND THIS IS -- WHO TOLD ME IN AN EMAIL RECENTLY THAT HE FIGURED OUT WHAT HIS DAUGHTER HAS. IT WAS AN UNKNOWN DISEASE, BUT, AGAIN, HE IS DOING THIS MORE AS AN INDIVIDUAL THEN AS A MEMBER OF AN INSIDER TEAM. K COMP ALL WAS AN UNDERGRADUATE IN ONE OF MY CLASSES AND WELL AFTER SHE WAS OUT OF THE CLASS SHE WENT OFF AND STARTED STUDYING HER OWN GENOMICS BECAUSE OF HEME MA CHROME TO SIS THAT WAS IN HER FAMILY. AND -- HAS THIS WEB SITE WHERE PEOPLE REVEAL QUITE A BIT ABOUT THEIR NEUROPSYCHIATRIC, THEIR SEXUALLY TRANSMITTED DISEASES AND A NUMBER OF THINGS THAT YOU WOULD CONSIDER STIGMATIZING, BUT THEY ARE OPEN ABOUT IT AND THEY FIND VALUE, BOTH MEDICAL, SCIENTIFIC AND SOCIAL FROM THIS EXERCISE. >> NOW, WE HAVE A BIG, IN OUR PROJECT AND IN MANY OTHER PROJECTS THIS EMPHASIS ON ENVIRONMENTAL, AND THE IDEA OF GENETICS IS IN PART TO HELP US STRATIFIED AND SEGMENT DISEASES THAT LOOK LIKE THEY ARE HOMOGENOUS, AND THAT HELPS US UNDERSTAND THE ENVIRONMENT. THE IDEA IS WE ARE NOT SAYING HERE IS YOUR GENOME, YOUR GENOMIC DESTINY, GET USED TO IT. IT'S MORE A MATTER OF HOW CAN WE FIND PEOPLE WHO HAVE ALREADY OR HOW CAN WE -- AVOIDED THEIR GENETIC DESTINY BY CHANGING THEIR ENVIRONMENT. HERE IS AN EXAMPLE OF PKU WHICH IS 100 PREDICTIVE AND YOU COULD CONSIDER IT 100% GENETIC PRIOR TO BEING ABLE TO CIG NOSE IT, IT WOULD HAVE -- DIAGNOSE IT, IT WOULD HAVE RESULT IN MENTAL RETARDATION WITH CLOSE TO 100% CERTAINTY BUT NOW IT IS 100% ENVIRONMENTAL BECAUSE YOU CAN AVOID DIETARY -- NOT A TRIVIAL EXERCISE BUT YOU CAN DO IT FOR YOUR CHILDREN IF THEY ARE HOME MOO DISIEG GUS, AND BCR ONE AND TWO THAT I HAVE ALREADY MENTIONED, THE COMMON ACTION, MEDICAL ACTION IS THERE IS BILATERAL MASTECTOMY AND OVAR ET CETERA MY, WHICH YOU CLEARLY DON'T WANT TO TAKE LIGHTLY BUT IT IS VERY COMMON ACTION, AND CONSIDERED QUITE IMPORTANT. NOW, THAT IS A PRE-EXISTING, PREDISPOSITION TO CANCER IS PART OF IT. THE INHERITED PART OF CANCER. IN ADDITION THERE IS A SO MATTIC COMPONENT AND I DON'T NEED TO TELL THIS AUDIENCE ABOUT, A MULTISTEP PROCESS BY WHICH YOU GO FROM POSSIBLY SOME INHURTED PREDISPOSITION PLUS POSSIBLE ENVIRONMENTAL COMPONENTS, AND SO FORTH, AND THEN FINALLY YOU CAN GET A SET OF MUTATIONS THAT ONCE YOU UNDERGO CHEMOTHERAPY OR CANCER THERAPY BECOME RESISTANT. HERE IS AN EXAMPLE OF SOMETHING I THINK IS QUITE IMPORTANT GOING FORWARD IS OUR ABILITY TO CATCH RARE CELLS. SO IN GREEN ARE CELLS THAT WE CAN GENE ONLYICALLY DETERMINE IN A CERTAIN SENSE IN C2 IN THAT EACH OF THOSE GREEN DOLTS REPRESENTS A SINGLE CELL AND WE ARE ANALYZING IT'S CERTAINLY THE COMBINATION OF INHERITED, SOME ATTIC, AND CANCER CAUSING MUTATIONS AND MUTATIONS WHERE WE KNOW THE IMPACT ON THE BINDING OF A DRUG MOLECULE WHERE THESE MUTATIONS, THE STRUCTURE IS KNOWN AND THE MECHANISM BY WHICH YOU GET DRUG RESISTANCE IS KNOWN. SO YOU CAN TRACK THIS AT THE SINGLE CELL LEVEL AND THE IDEA WOULD BE TO DETECT THIS AS EARLY AS POSSIBLE AND AS RARE A CELL AS POSSIBLE AS LONG AS YOU ARE NOT CREATING FALSE POSITIVES IN THE PROCESS. SO THAT'S AN EXAMPLE OF WHERE WE WOULD LIKE TO GO WITH SEQUENCING WHICH IS TOWARDS C2 SEE SEQUENCING AND QUESTION WILL COME BACK TO THAT IN A MOMENT IT DEMONSTRATES THE ISSUE OF DRUG RESISTANCE WHICH CAN BE DUE TO THE POINT MUTATIONS IN THE TREATMENT OF BCR ABLE CIE NEIGHS, AND IN THIS CASE A MULTIDRUG RESISTANCE THAT OCCURS IN A MAJOR GLOBAL PATHOGEN, TUBERCULOSIS, THIS WAS DONE IN COMBINATION OF THE MURRAY LAB, AND MIKE STRONG WAS THE POST DOC IN MY LAB WHERE THE FULL GENE NOME SEQUENCE OF MANY STRAINS, THERE WAS EXTREME DRUG RESISTANCE OR MULTIDRUG RESISTANCE WERE COMPARED AND THIS CAN BE FIT ONTO THE STRUCTURES HOMOLOGOUS STRUCTURES OF SUCH STARINGETS AS GYR ACE AND -- AND EACH OF THESE CAN POTENTIALLY SUGGEST THE MECHANISM BY WHICH THESE POINT MUTATIONS CAUSE DRUG RESISTANCE. AND POSSIBLY NEW CLASSES OF DRUGS THAT COULD BE USED IN COMBINATION TO NIP OFF THIS MULTIDRUG RESISTANCE ISSUE. >> NOW, THIS ILLUSTRATES A PARTICULAR VIEW ON MICRO BIOMIX. WHERE WE ARE NOT SEQUENCING THE ENTIRE GENOME OF ALL OF THE MICRO ORGANISMS, FUNCTIONAL, BACTERIAL, VIRAL AND SO FORTH THAT EXIST IN ABUNDANCE, IN EVERY HUMAN BEING, BUT WE ARE TARGETING A TINY FRACTION OF IT, NOT EVEN SMALLER THAN THE FRACTION THAT WE TARGETED, WHICH IS 0.01% OR SO WHERE WE ARE SPECIFICALLY LOOKING AT DRUG RESISTANCE AND PATHOGEN ISTY ALLELES. THIS IS NOT JUST GENES, BUT IT COULD BE AS LITTLE AS A BASE PAIR. SO SOMETIMES, OR VERY OFTEN, JUST KNOWING WHAT ORGANISM YOU ARE DEALING WITH IS INSUFFICIENT. YOU NEED TO KNOW HOW MANY ANTIBIOTICS, AND WE WOULD LIKE TO MAKE THIS AS HIGH THROUGHPUT AS POSSIBLE. IN THE PROCESS OF STUDYING PERSONAL GENOME VOLUNTEERS OVER THE COURSE OF A LONG TIME SERIOUS, OVER THE COURSE OF A YEAR OR SO AND LOOKING AT ENVIRONMENTAL SAMPLES, -- IS NOW AT WASHINGTON UNIVERSITY AND MORTON SUMMER WHO IS IN COPENHAGEN AS A PROFESSOR STUMBLED UPON THIS PHENOMENON THAT WE PUBLISHED THAT WE FOUND MULTIP.M. YLA, DIFFERENT PHYLA COULD BE FOUND TO HAVE MEMBERS THAT COULD NOT ONLY BE RESIS ANTED TO 50 TIMES NORMAL CLINICAL DOSES, NOT JUST TO ONE ANTIBIOTIC BUT TO ALL 18 CLASSES OF ANTIBIOTICS THAT WE TESTED AND NOT ONLY RESISTANT TO THOSE LEVELS BUT SUBSISTING ON THEM AS THEIR SOLE SOURCE OF CARBON. SO THIS IS AN INTERESTING ANECDOTE BUT IT ILLUSTRATES THE MOST GENERAL TOPIC THAT WE WANT TO BE ABLE TO MONITOR IN A ROUTINE MANNER SUBSETS OF THE MICROBUY ONLY IS THAT ARE MEDICALLY RELEVANT SO WE ARE NOT SURPRISED AND THIS COULD BE INTEGRATED WITH OTHER ASPECTS OF EPIDEMIOLOGY OR OR PERSONAL GENOME PROJECT. IT ALSO ILLUSTRATED THAT, OKAY, DOING DIRECT MICROBIAL GENOMICS IS IMPORTANT IN CASES WHERE YOU ARE IN A BIG RUSH OR LOOKING AT DRUG RESISTANCE. THE ALTERNATIVE IS LOOKING AT IMMUNE RESPONSE TO MICRO ORGANISMS AND THIS IS COMMONLY PRACTICED IN DIAGNOSTICS FOR HIV AND TUBERCULOSIS. CONTINUESICALLY THAT RESPONSE WON'T TELL YOU WHETHER YOU HAD AN IMMUNE RESPONSE TO A DRUG RESISTANT OR MULTIDRUG RESISTANCE ORGANISM SO THESE ARE COMPLIMENTARY APPROACHES. I WANT TO PURSUE FOR A FEW SLIDES HOW WE WOULD GENERALIZE THE SINGLE PURPOSE IMSMIEWN IMIMMUNE TESTS THAT HAVE BEEN OF GREAT DIAGNOSTIC SIGNIFICANCE. SO HOW WOULD WE -- AXIS, AND SO THIS IS A PROJECT THAT WOULD HAVE BEEN RIDICULOUS A FEW YEARS AGO, BUT BECAUSE SEQUENCING IS A MILLION TIMES CHEAPER, IT'S ONLY MILDLY RIDICULOUS, WHICH IS SEQUENCING THE ENTIRETY OF THE IMMUNE RESPONSE AND THE T AND D CELL RECEPTORS TO ANSWER A VARIETY OF HUMAN IMMUNE SYSTEM QUESTIONS, AND OTHER ORGANISMS AS WELL. WE DID THIS IN COLLABORATION WITH MIKE GAGENHOME AT ROASH, WHO IS NO LONGER AT ROASH, AND THE IDEA IS, AND IT SHOULD BE PROBABLY OBVIOUS HERE IS THAT THE HUMAN GENOME, OR AT LEAST MOST OF THEM HAVE 46P REGIONS, 23D'S AND 6J'S AND WE CAN RECOMBINE IN EVERY POSSIBLE COMBINATION PRODUCING 2 MILLIONS RECOME MIN ANTS, BUT IN ADDITION TO THAT 2 MILLION YOU HAVE THE N REGIONS WHICH ARE MEDIATED AND THEY BASICALLY CAN GREATLY EXPAND AND INSERT LONG SOURCES OF NUCLEOTIDE THAT DOESN'T EXIST ANYWHERE IN THE GENOME, IT DOESN'T EXIST IN THE BIOSPHERE, IN FACT. SO WE ARE DOING THIS IN THE CONTEXT OF A TIME SERIES ACTION EXPERIMENT, NORMAL ADULT VACCINES IN PERSONAL GENOME PROJECT VOLUNTEERS, MAINLY HEPATITIS AND SEASONAL INFLUENZA VACCINES AND WHEN YOU EXPECT IS THAT YOU HAVE TRACE AMOUNTS IN BLUE OF D CELLS RESPONSIVE TO ANY PARTICULAR ANTIGEN THAT THEY HAVE NEVER SEEN BEFORE AND THEN AFTER VACCINATION OR INFECTION YOU GET MAYBE A THOUSAND FOLD RESPONSE AND AN ABUNDANCE OF THAT, OF CELLS REACT ANT TO THAT ANTY AGAIN AND THEN WITH A BOOSTER OR REEXPOSURE YOU GET ADDITIONAL RESPONSE, MAYBE ANOTHER THOUSAND FOLD. SO WE WANTED TO SEE THIS IN A TIME SERIES, AND ANALYZE IT AS YOU WILL SEE IN A MOMENT. HERE IS -- THIS IS -- AND THEY -- THIS IS SHOWING THE N REGION I WAS TALKING ABOUT EARLIER, WHERE YOU HAVE THE CDR3, WHICH IS ONE OF THE MAJOR HYPER-VARIABLE REGIONS FLANKED BY V AND J AND IN THE MIDDLE IS D WHICH WITH SHRINK TO ZERO, YOU CAN BASICALLY ELIMINATE THE D REGION DURING THE RECOME NATION PROCESS OR EXPAND IT TO GET AS LARGE AS 140. SO YOU HAVE THIS RANGE OF 0 TO 140. THIS IS MOSTLY DENOVO, AND THIS IS A LOGARITHMIC Y AXIS AND YOU CAN SEE THIS INTERESTING DISTRIBUTION WITH THESE SPIKES, AND THESE SPIKES IS BECAUSE THERE IS ALREADY, EVEN BEFORE THE SYSTEM DECIDES WHAT ANTIGENS ARE STIMULATING IT, THERE IS SELECTION FOR FULL LENGTH IN FRAME RECOME MINNATION, SO ONLY ONE IN THREE OF THE RECOME INATION REPRODUCES A FULL LENGTH HEAVY CHAIN, SO THAT ONE OUT OF THREE IS HE HIGHLY ENRICHED BY A LOG OR TWO. AND IN DARK BLUE IS ACTUALLY ALL OF THE DATA THAT EXISTED PRIOR TO THIS PROJECT IN THE DATABASE AND IN LIGHT BLUE IT'S A FEW TIME POINTS FROM ONE INDIVIDUAL FROM THESE TIMED SERIES TO GIVE YOU THE IDEA OF THE AWESOME POWER OF SEQUENCING. >> SO THIS IS ONE OF THE MANY COMPUTATIONAL TOOLS THAT WE EMPLOY ON THIS WHERE WE ARE LOOKING AT A TIMED SERIES OVER A THREE-YEAR PERIOD FOR THIS INDIVIDUAL WHERE WE HAVE RESET THE ZERO POINT IS ONE OF THE VACCINATION DAYS, AND HERE IS 14 DAYS BEFORE, AND HERE IS ACTUALLY ONE HOUR AFTERWARD, AND THREE DAYS, AND SEVEN TO TWENTY ONE DAYS IS WHERE WE EXPECT AND FIND ANTIBODIES WHICH SEEM TO BE RESPONSIVE TO THE ANTIGEN, IN THIS CASE, INFLUENZA, AND IN THIS CASE BECAUSE IT'S HIGH THROUGHPUT SEQUENCING, WE HAD TO TAKE THE SEQUENCE AND USE HIGH THROUGHPUT SYNTHESIS TO SYNTHESIZE THESE ANT BOTIES AND THEN DO MINING ASSAYS. SO THAT'S EXAMPLES OF SEMI EPI GENOMIC PHENOMENON, THE IMMUNE RESPONSE, THE ENVIRONMENT. ANOTHER CRITICAL COMPONENT OF THE EPI GENOME IS YOUR RNA AND CHROME MAT CONTINUE. AND IN DISTINCTION FROM YOUR GENOMIC Z NA WHICH YOU CAN GET FROM A CELL IN YOUR BODY, THESE EPI GENETIC MEASUREMENTS HAVE TO BE DONE FROM THE CORRECT CELL AND IF YOU WANT TO BE COMPREHENSIVE THEY HAVE TO BE DONE FROM EVERY CELL IN YOUR BODY AND DOING EVERY CELL IN YOUR BODY IS NOT SCALABLE OR EMBRACEABLE BY THE VOLUNTEERS. SO INSTEAD, WHAT WE DO IS OUR BEST EFFORT SO FAR AND MAY BE SOMETHING THAT MAY TURN OUT TO BE QUITE USEFUL, IS WE ESTABLISHED STEM CELLS FOR EACH OF THE VOLUNTEERS, AND WE HAVE PUBLISHED QUITE A FEW PAPERS ON THESE PARTICULAR STEM CELL LINES. AND HERE IS SOME EXAMPLES FROM DIFFERENTIATION IN SARA TOMORROW MAS, ALL OF THE MAJOR LYNN CADGES, EPITHELIUM, BONE, EP DETERMINE, BEATING CARDIAC TISSUE AND IN IN THIS CASE HEPATIC TISSUE, AND YOU CAN SEE NOT ONLY HISTOLOGICAL AND RNA EXPERIMENTS BUT PROTEIN LEVEL VARIATION FROM INDIVIDUAL VARIATION THAT MAY OR MAY NOT BE PREDICTABLE FROM THE GENOME BY ITSELF AND EVEN ACTIVITY LEVELS THROUGH SIGH TO CHROME P450'S WERE DISCUSSED IN THIS, IN ONE OF THESE PAPERS. TO TAKE THIS TO THE NEXT LEVEL, WE WOULD REALLY LIKE TO BE DOING IN C2 ANALYSIS WHERE WE CAN DISTINGUISH THE TWO ALLELES OR AT LEAST QUANTITATE THE OVERALL RNA LEVEL AS YOU WOULD IN RNA SEQUENCING. RNA SEQUENCING IS SAY GOOD QUANTITATIVE METHOD THAT ALLOWS YOU TO LOOK AT ALTERNATE SPLICING FOR ALL OF THE GENES THAT ARE EXPRESSED IN A GIVEN CELL SAMPLE, AND IN C2 HAS THE AWESOME POWER OF BEING ABLE TO LOOK AT INDIVIDUAL CELLS IN THEIR CONTEXT MAKING COMPLICATED CELLULAR CONTACT, AND INDEED MAKING INTERESTING SUBCELLULAR COMPONENTS, SUBCELLULAR LOCALIZATION OF TRANSCRIPTS AND PROTEIN. SO AS A PRECEDENT FOR THIS, THIS IS WORK WE DID, NOW, ALMOST FIVE YEARS AGO WHERE WE DID C2 SEQUENCING IN A SMALL SUBCELLULAR COMPONENT WHICH IS A CHROMOSOME AND THE ORIGINAL RATIONAL WAS FOR DOING TYPING, HERE YOU CAN DO HAPLO TYPING IF YOU HAVE A TRIO BUT THERE ARE MANY CASES WHERE YOU DON'T NECESSARILY HAVE THE TRIO OR WHERE THE TYPING GETS SCRAMBLED BY REARRANGEMENTS, AND ANY WAY, IN THIS CASE, WE VALIDATED IT USING CAREFULLY CHOSEN HOME MOO HOMOZYGOUS ALL ALONG THE FATHER, THE MOTHER AND THE, LET'S SEE, THE SON, AND WE CAN ACTUALLY PHASE WITHOUT NEEDING THE TRIO, BASED ON SINGLE MOLECULEDY SOLUTION, WE CAN SAVE TIP TO TIP THE ENTIRE 103 MEGA BASES DOING MULTIPLE ROUNDS OF LOCAL SEQUENCING FOR SHORT READS, IN THIS CASE, ONE BASE THERE WHERE YOU CAN SEE A T AT ONE END OF THE CHROMOSOME AND A T AT THE OTHER END OF THE CHROM CHROMOSOME TEND TO COME TOGETHER DUE TO INHERITANCE FROM THE MOTHER OR A C AND ANOTHER C IS FROM THE FATHER. AND THIS IS AN EXAMPLE OF INVITETO SEQUENCING OF SORTS BUT WE WOULD LIKE TO AND ARE MOVING TOWARDS APPLYING THIS TO RNA'S WHICH ARE PRESENT IN HIGHER ABUNDANCE THAN THE CHROMOSOMAL DNA, AND HERE IS AN EXAMPLE FROM SOME WORK THAT WE DID TO JOHN AUKEN, AND CHRIS McCALL, WHERE WE ARE ONLY LOOKING AT A FEW -- IT'S KIND OF AS TYPICAL, WE ARE ONLY DOING A FEW -- THREE DIFFERENT MOLECULES WITH THREE DIFFERENT CHLOROFORS AT A TIME MAYBE FOUR OR FIVE OR SO IF POSSIBLE, BUT IF YOU TREAT THIS AS A NEXT GENERATION SEQUENCING EXPERIMENT WHERE YOU CAN DO IT OVER AND OVER, YOU CAN SEE WHERE WE ARE GOING WITH THIS INCYTO, WE ARE SHOWING THE POWER OF USING WITH COMPUTATIONAL METHODS TO BE ABLE TO AUTOMATICALLY ANALYZE UP TO 140 DIFFERENT MORE F LOGICAL WITH COMPUTATIONAL ANALYSIS. I WANT TO END ON GENERALIZING THIS ISSUE OF IMAGING AS A PHENOTYPE THAT WE NEED IN THESE LARGE COHORTS THAT ARE INTENDED TO BE HIGHLY INTEGRATED WHERE WE HAVE MULTIPLE DATA TYPES OPENLY AVAILABLE FOR PEOPLE TO DEVELOP STANDARDS AND TO DEVELOP INTEGRATIVE TOOLS. SO HERE IS A COMPLETELY DIFFERENT LEVEL OF IMAGING, RANDY BROCKNER HAD A GRANT TO DO MAGNETIC RESONANCE IMAGING LOOKING FOR VARIATION IN HUMAN POPULATIONS, AND LOOKING AT THINGS LIKE LATTERRALTY, AND AGE, SEX, AND GENETIC VARIATION. SO HE TOOK ADVANTAGE OF THE PGP COHORT AND JUST ADDED THIS AS ANOTHER TRAIT TO OUR LIST, AND HE GOT THE BENEFIT OF THE RESEARCH SUBJECTS, AND YOU CAN SEE HERE ARE SOME VARIATIONS THAT YOU SEE FROM THE CNF PAPER DUE TO AGE AND SEX AND THEY ARE JUST BEGINNING TO FIGURE OUT SOME INTERESTING GENETIC CORRELATES. KIN KNOCK YAM MA HAD INTERESTING BEHAVIOR ON COGNITIVE TESTS SO RANDY NOT ONLY MEASURES THE MRI BUT BEHAVIOR AND COGNITIVE TESTS AND THE GENETICS AND KEN IS INTERESTED IN PROSOPAK KNOX LIA WHICH IS SOMETHING THAT AFFECTS 5% OF THE POPULATION HAS DIFFICULTY RECOGNIZING HUMAN FACES. THEY CAN RECOGNIZE ALMOST ANYTHING ELSE, VERY INTELLIGENT AND SO FORTH BUT THIS PARTICULAR TISSUES ANS HE IS INTERESTED IN BEHAVIOR AND COGNITIVE TESTS IN GENERAL. AND HE HAS AN ADDICTIVE WEB SITE CALLED TEST MY BROTHER-IN-LAW.ORG WHICH I THINK NOW MORE THAN 50,000 PEOPLE HAVE TESTED THEIR BRAIN. AND GENERALIZING THIS EVEN FURTHER, THE IDEA IS NOT TO BE HAVING ONE COHORT FOR ONE SPECIFIC TRAIT THAT MIGHT INTERACT WITH A WHOLE VARIETY OF OTHER TRAITS AND ENVIRONMENTAL COMPONENTS, YOU HAVE TO TRY TO MAKE IT LOW COST AND HIGH QUALITY. A LARYNXER COHORT WHERE YOU HAVE INVESTED ENOUGH THAT EACH ADDITIONAL TRAIT YOU GET IS BUILDING ON TOP OF THE OTHER ONES YOU HAVE AND YOU CAN RECONTACT THIS COHORT AND THESE PEOPLE ARE AMAZINGLY ENTHUSIASTIC, AT LEAST SO FAR, AND JUST TO GIVE YOU A FEELING OF ONE OTHER WAY OF LOOKING AT IT, WE CAN LOOK AT IT AS DISEASES HERE IN BRACKETS OR TREATMENTS, WHICH COULD BE EITHER MEDICAL DEVICES OR DRUGS OR, YOU KNOW, OVER-THE-COUNTER TREATMENTS, SO FORTH, AND IT'S KIND OF HERE ORGANIZED BY GEO GRAPHIC LOCATION ON THE BODY, THIS PARTICULAR PERSON IS NOT A PGP VOLUNTEER. HE WAS ACTUALLY A MEDICAL VOLUNTEER. HE DID GET ELECTROENCEPHALOGRAM DURING HIS LIFETIME AND DONATED HIS BRAIN FOR ANATOMICAL RESEARCH AFTERWARD. AND BUT YOU GET THE IDEA IS THAT WE ARE TRYING TO ENGAGE THE COMMUNITY OF PHENOTYPE COLLECTION, THIS IS NOT JUST US, THIS IS -- THEY ARE ENABLED IN SOME WAY BY HAVING A COHORT THAT THEY CAN CALL UPON AND THEY DON'T HAVE TO NECESSARILY DO THE GENOME FEE SENSE OR IF THEY SEE SOMEONE OR SOMEONE SEES A PHENOTYPE THEY ARE INTERESTED IN. IT'S ALREADY ON THE WEB SITE THAT HASN'T BEEN SEQUENCED THEN THEY CAN TARGET THAT FOR PRIORITY SEQUENCING. YOU HAVE ALREADY SEEN THIS. I WANTED TO USE THIS AS A SUMMARY SLIDE AND OPEN IT FOR QUESTIONS. WE ARE NOT GOING FROM GENOME TO TRAIT, BUT WE CONSIDER REDUCING THE COST OF COLLECTING ALL OF THESE OTHER ENVIRONMENTAL COMPONENTS, SOME OF WHICH ARE GENOMIC THEMSELVES OR IN SOME OTHER WAY BEING INCREASINGLY WELL CAPTURED BY SOMETIMES PEOPLE JUST DOING MORE AND MORE MONITORING OF THEMSELVES. IT COULD BE THE NEXT APPLICATION OF CONSUMER ELECTRONICS IS SELF MONITORING. AND WE ARE TRYING TO CAPTURE THIS FLOW. MORE AND MORE PEOPLE ARE COMING TO US WHO HAVE ALREADY DONE THEIR GENOME SEQUENCE ON THEIR OWN DIME SO THIS COULD BE A VERY COST EFFECTIVE COHORT AND PROJECT, WE HOPE. SO PERIOD, FULL STOP. HAPPY TO ANSWER QUESTIONS. [APPLAUSE]. >> HI, GEORGE, BURT GOLD NCI. I'M GLAD THAT YOU MENTIONED SICK WILL SELL TRAIT CASE, THE SORT OF HIGH ALTITUDE SICKNESS REPORT FROM THE 1970s, I THINK IT WAS IN PASSING BECAUSE IT KIND OF PROVIDES THE REAL PROBLEM OF PHENOTYPING. I THINK IT'S NOW THE YEAR 2010, IT'S LIKE 40 YEARS OR SO AFTER THAT NE NEW ENGLAND JOURNAL OF MEDICINE REPORT, AND I DON'T THINK WE KNOW A LOT MORE ABOUT THE PHENOTYPE OF SICK WILL CELL TRAIT THAN FROM THAT 40-YEAR-OLD REPORT IN PEOPLE AND YET THE ARMY, AS YOU POINTED OUT OR THE MILITARY WANTS TO KNOW ABOUT THAT TRAIT. SO CAN YOU GIVE US SOME OF YOU ARE INSIGHT ABOUT HOW WE CAN KNOW MORE ABOUT THAT TRAIT AND MODIFY OUR GENES? >> LET ME GENERALIZE THAT A LITTLE BIT. THE QUESTION IS WHAT HOPE IS THERE FOR EXPANDING ON A VARIETY OF TRAITS. I MEAN, REALLY, I THINK THE NEXT BIG PUSH THAT WE ALL HAVE TO FOCUS ON IS ON TRAITS BECAUSE GENETICS IS GETTING QUITE INEXPENSIVE, I DON'T MEAN TO UNDERSTATE IT. AND OUR ABILITY TO GET HIGHLY PREDICTIVE, HIGHLY MEDICAL ACTIONABLE ALLELES IS REALLY DEPENDENT UPON BREAKING UP THESE BUCKETS OF, YOU KNOW, THESE VERY LARGE BUCKETS THAT CONTAIN A LARGE TRAIT LIKE DEATH OR CANCER OR, YOU KNOW, SOMETHING THAT'S TOO LARGE, BREAKING UP INTO SMALLER ONES AND THEN YOU CAN ACTUALLY FIND THE CAUSE OF ALLELES EFFECTIVELY. THAT SAID, SO THERE ARE TWO THINGS I THINK ARE BIG BREAK THROUGHS. ONE IS THIS DECREASE IN COST OF THE DEVICES YOU CAN PUT ON YOUR BODY OR PUT IN YOUR ENVIRONMENT, SO FORTH, THAT WILL HELP US MEASURE. AND PROBABLY THEY WILL BE INCREASING ADOPTION OF THIS AS WELL CELL PHONES. INITIALLY IT WILL START WITH WEALTHY PEOPLE AND WORK ITS WAY DOWN. AND THE SECOND THING IS AN INCREASED WILLINGNESS OF PHYSICIANS TO RUN DIAGNOSTICS WHICH HAVE MULTIPLE MODALITIES IN THEM. I THINK THERE WAS A GREAT FEAR OF THAT UNTIL RECENTLY AND IT'S STARTING TO DESOLVE AND WE WILL HAVE TO WAIT AND SEE TO WHAT EXTENT. SO IT'S THE INDIVIDUAL TAKING CHARGE AND VARIOUS CLINICAL RESOURCES COLLECTING MORE DATA. AND THEN THE ISSUE BECOMES SHARING. BECAUSE IF THIS IS SHARED VERY FREELY, IT GOES A LITTLE FASTER THAN IF IT'S PUT INTO SILOS THAT ARE PROPRIETARY OR OTHERWISE INACCESSIBLE TO CREATIVE INDIVIDUALS. >> IF THERE IS NO FURTHER QUESTIONS, DON'T FORGET THERE IS A RECEPTION AFTER THIS TALK AT THE ATRIUM, IN THIS BUILDING AND JOIN ME IN THANKING DR. CHURCH FOR HIS TIME. [APPLAUSE] (CONCLUDED AT 3:59).