>> GOOD AFTERNOON, EVERYONE. THANKS FOR COMING TO THIS WEEK'S NEUROSCIENCE SEMINAR SERIES TALK WHICH IS DELIVERED BY PROFESSOR DANIEL GESCHWIND AND IT'S ENTITLED INTEGRATIVE GENOMICS IN NEUROPSYCHIATRIC DISORDERS. IT'S A PLEASURE FOR ME TO TALK ABOUT HIS WORK WITH ALZHEIMERS. HE OBTAINED HIS AB DEGREE IN MDPh D AT YALE AND COMPLETED INTERNSHIP RESIDENCY AT POST DOCKETSERAL FELLOWSHIP AT UCLA AND JOINED IN 1997 FACULTY THERE. HE IS THE GORDON McDONALD GENOMICS PROFESSOR AND PSYCHIATRICCATE THE HARVARD PROGRAM SCHOOL OF MEDICINE AND HE DIRECTS THE PROGRAM THERE AND THE CENTER FOR AUTISM AND RESEARCH TREATMENT AND THE CENTER FOR GENETICS AT UCLA, HIS LABORATORY USES FUNCTIONAL GENOMIC AND ANIMAL MODELS IN AND BIOSTATISTICS TO DRIVE INTEREST THE BIOLOGY OF NEUROPSYCHIATRIC CONDITIONS AT BOTH ENDS OF THE LIFE SPAN AND THIS WORK IS TOUCH OFFICE OF DIVERSITY DEEP ASPECTS OF BASIC SCIENCE ENCOMPASSING AND THE EVOLUTION OF GENE EXPRESSION IN BRAIN CROSS-SPECIES WORK. HE'S RECEIVED SEVERAL AWARDS IN THE DENNY BROWN SCHOLAR AWARD FROM THE NEUROLOGICAL ASSOCIATION IN 2004, THE SCIENTIFIC SERVICE AWARD FROM AUTISM SPEAKS IN 2008 AND THE WAYNE PRIZE FROM THE BRAIN AND BEHAVIOR FOUNDATION IN 2012. INDUCTED INTO THE INSTITUTES OF MEDICINE AND ACADEMIES IN 2011 AND A MEMBER OF THE NEUROSCE FORUP AND ON TOP OF ALL THIS I CAN SAY FROM A PERSONAL PERSPECTIVE THAT HE IS AN INSPIRING MENTOR AND THE FEW MOTHER-IN-LAWS I SPENT SHOWED ME THE EXTENT TO WHICH HE ELICITS DEEP GENUINE RESPECT AND ADMIRATION FROM THE LAB HE LEADS. AND I AM ABSOLUTELY DELIGHTED WE GET A CHANCE TO HEAR HIM SPEAK TODAY. >> SO AS SOUC WITH A LITTLE BIT, TOO KIND BUT IT IS REALLY GREAT TO BE HERE. OUR LAB IS WORKING ON AUTISM WE'RE WORKING ON A COUPLE OF OTHER NEUROGENRATIVE DISORDS BUT WE'VE BEEN HIGHLY FOCUSED ON AUTISM AND WE'RE TRYING TO YOU KNOW, YOU CAN DECIDE WHETHER SUCCESSFULLY OR NOT, SPAN THE GAMUT IF WE'RE GOING TO STUDY A DISORDER, WE CAN'T JUST BE AN ANIMAL MODEL OR IMAGING LAB WHERE A LAB THAT COLLABORATES WITH OTHER PEOPLE. WE TRY TO FIND THE GENES AND THEN MOVE TO THERAPY AND THAT INVOLVES A LOT OF ANIMAL MODEL WORK WHICH I'LL NOT GOING TO TALK ABOUT TODAY. I WILL FOCUS 1 TOPIC INSTEAD IN THINKING ABOUT HOW TO MOVE GENETIC INFORMATION AND GENETICS AND FUNCTIONAL GENOMICS TO A MORE CO HERE EPT NOTION OF DISEASE. --CO HERENT NOTION OF DISEASE. MY CONFLICT OF INTEREST, I'M A PAID CONSULTANT FOR SYNAPDX CORP WHICH IS GEEPING BIOMARKERS FOR AUTISM, I WON'T REFLECT ON THAT TAD BUT IT'S IMPORTANT TO MENTION FOR CONFLICT OF INT. AND I WILL TALK ABOUT, I WILL TALK ABOUT A BRIEF, HOPEFULLY FOR YOUR SAKE, GENETIC WHO IS HAVEN'T BEEN FOLLOWING THE FIELD SO THAT WE'RE ON THE SAME PAGE AND THEN I'LL DISCUSS WORK WE'VE BEEN DOING THAT I CALL INTEGRATIVE GENOMICS BUT INVOLVES NETWORK BIOLOGY TO ASK IF THERE'S CONVERGENCE IN AUTISM AS WELL AS CAN WE USE THIS INTEGRATIVE GENOMIC TO TAKE THE NEXT STEPS IN BIOLOGY. SO, AGAIN, THE CRITICAL, IF YOU DON'T LISTEN TO ANYTHING ELSE OR I PUT YOU TO SLEEP DURING LUNCH TIME, AUTISM HAS GENETIC AND ENVIRONMENTAL FACTORS. VERY SAFE HERITABILITY ESTIMATE IS AROUND 70% WHICH IS QUITE HIGH FOR NEUROPSYCHIATRIC CONDITIONS. THERE ARE MANY GENETIC MODELS AND HIGH HETEROGENEITY, THAT'S BECAUSE DOZENS OF GENES IATED WELL OVER A HUNDRED BUT NO GENE ACCOUNTS FOR MORE THAN 1%. SO IF YOU HAVE A HUNDRED KIDS WITH AUTISM AND THEY HAVE GENETIC FORMS, YOU HAVE A HUNDRED DIFFERENT TYPES OF AUTISM. ANOTHER CRITICAL ISSUE IS THAT IT OVERLAPS WITH OTHER NEURODEVELOPMENTAL DISORDERS SO JUST TO ILLUSTRATE THIS IN A VERY GROSS WAY, 1 COULD SAY THAT NOW WITH DSM 5 THIS, IS A SLIGHTLY OLD SLIDE, I STILL HAVE A STRONG CONCEPTUAL NOTION THAT LANGUAGE IS PART OF AUTISM. EVEN THOUGH IN THE NEW DSM 5, IT IS ESSENTIALLY, YOU HAVE TO HAVE DEFINITES IN SOCIAL COGNITION AND SOCIAL RELATEDNESS AND RESTRICTIVE REPETITIVE BEHAVIOR AND THE LANGUAGE PART HAS BEEN TAKEN OUT AND KIND OF SUBSERVED TO BE, YOU NOTE WHETHER THERE'S LANGUAGE DELAY OR LANGUAGE PROBLEMS BUT IT'S NOT CORE TO THE DIAGNOSIS ANYMORE. AND SO, YOU KNOW IT'S BEEN NOTED FOR DECADES THAT MANY INTELLECTUAL DISABILITY SYNDROMES HAVE A HIGH PREVALENCE--PREDISPOSE TO AUTISM THERE,'S AN OVERLAP, 1 COULD SAY WITH AN AUTISM ABOUT 30% OF THE KIDS HAVE INTELLECTUAL DISABILITY. AND THEN THERE'S SEIZURES AND ESY OCCUR AND MAYBE AGAIN, IT DEPENDS ON THE COHORT, BUT 5-15% OF KIDS. SO THERE IS THIS KIND OF NOTION THAT THERE ARE OVERLAPPING POTENTIAL RISKS WITH THESE OTHER DISORDERS AND 1 OF THE CRITICAL THINGS HAS BEEN TO TRY TO SEPARATE AUTISM AND INTELLECTUAL DISABILITY AND I'LL TALK ABOUT THAT A BIT LATER. SO THERE ARE MANY GENES FOR ESTIMATES AND I'LL DISCUSS IT BRIEFLY, A THOUSAND OR SO GENES THAT MIGHT CONTRIBUTE TO AUTISM, MANY GEBETTIC MODELS, I'LL DISCUSS THAT AS LIT'S NOT A MENDELIAN DISORDER, NOT A COMPLEX ORDER AND AS I SAID NO MAJ OR GENES ACCOUNT FOR 1% AND I KEEP HAMMER TAG IN AND YOU'LL SEE WHY AS I GET INTO THE MEAT OF MY TALK. JUST IN CASE--YEAH. SO THIS IS A TABLE FROM A CHAPTER THAT BRETT ABRAMSON AND I WROTE A FEW YEARS AGO AND NOT MUCH HAS CHANGE FRIDAY THE MAIN POINTS I'LL MAKE HERE AND WE WERE LISTING THE COPY NUMBER VALID AND RELIABLEIANTS OTHERS SYNDROMES AND GENETIC MUTATION SYNDROMES, MEDICAL GENETIC SYNDROMES ASSOCIATE WIDE AUTISM. SO THERE ARE A LOT OF THEM, MANY OF THEM ARE JUST NAMED INSTEAD OF BY A PERSON, MORE MODERN 1S ARE NAMED BY THE ACTUAL GENOMIC INTERVAL. AND I WANT TO MAKE 2 MAJOR POINTS HERE, AGAIN, CAN YOU SEE THAT WITH THESE SYNDROMES, NONE ACCOUNT FOR MORE THAN 1% OF AUTISM. FRAGILE X, PEOPLE HAVE CLAIMED 3% BUT I'VE NEVER SEEN THAT IN ANY COHORT THAT'S BEEN ASCERTAIN IN AN ACADEMIC MEDICAL CENTER OR OTHERWISE FOR GENETICS, IT'S AROUND 1% OR SO AND AUTOMOBILE COMMON 1 IS THE 15 Q DUPLICATION INHERITED FROM THE MOTHER, THAT'S ABOUT 1%. SO AGAIN NO MAJOR AUTISM CAUSE, A LOT OF DIFFERENT 1S. AND THE PROPORTION WITH AUTISM IN ANY OF THESE, VARIES. THAT IS THE PENETRANT VARIES FROM LOW, YOU KNOW 10% OR 5% TO HIGH WHERE YOU GET--IT'S REALLY UNCLEAR WHETHER IT'S 90% OR 80% BUT A LOT OF PEOPLE WITH THIS DUPLICATION SEEM TO HAVE AN AUTISM SPECTRUM DISORDER, THIS CORTICAL DISPLASSIA SYNDROME WITH CNT AND APT2, ABOUT 75% HAVE THE AUTISM DISORDER AND AND AGAIN THIS IS FROM ANOTHER REVIEW IN COGNITIVE SCIENCE SHOWING THAT IT'S NOT ONLY OUR--ARE THE CAUSES HETEROGENEOUS BUT THERE'S PLEOTROPY. IN OTHER WORDS YOU CAN HAVE A STRONG MAJ OR GENE DISORDER AND-MAJOR GENE DISORDER AND IT INCREASES RISK MAYBE 30-50 FOLD AND IT MIGHT DO THE SAME FOR SCHIZOPHRENIA, LIKE THE 22 Q OR HD EPILEPSY, ET CETERA, SO THERE'S AN OVERLAP IN A SINGLE GENE DISORD OF THE KIND OF AND DIAGNOSTIC CLICKICAL DIN CHROME THAT A PARENT HAS. AND AT SOME--THAT A PATIENT HAS. AT SOME LEVEL THIS, SHOULD NOT BE SURPRISING AT ALL. THIS IS THE RULE RATHER THAN THE EXCEPTION. IF YOU LOOK AT THE--FOR EXAMPLE, THE FRONTER TEMPORAL DEMENTIAS, IT USED TO BE CALLED PIXELS DISEASE, AND WITH THE DOMINANT MUTATIONS, THAT YOU'LL SEE A VARIETY OF PHENOTYPES EVEN WITHIN A FAMILY FROM CORTICAL BASAL DEGENERATION TO PROGRESSIVE SUPERNUCLEAR PALSY PLUS NEURON DISEASE, YOU HAVE PARIETAL LOBE BEING AFFECTED AND OTHERS AFFECTED AND SAME MUTATION. IT'S NOT SURPRISE THAT THIS TOPOLOGY OF THE DISORDER CAN EVEN VARY QUITE A BIT AND IT'S UNCLEAR WHAT OTHER GENETIC OR ENVIRONMENTAL OR EPIGENETIC FACTORS MIGHT BE MODIFYING BUT TT'S QUITE INTERESTING. SO LOCALIZED PROSTASTY OTHERS DISORDERS AND LIKE THE STORY, TIS IS NOT--THIS SHOULD NOT BE SURPRISING, IT JUST HAPPENS TO BE A FACT. SO, IN 2012, THERE WERE A FLEURY OF--FLURRY OF PAPERS, THERE WERE SEVERAL IDENTIFY MUTATIONS, AT THAT POINT GIVEN THE NUMBER SEQUENCED WAS SUFFICIENT TO HAVE STATISTICAL EVIDENCE THAT THAT RARE DE NOVO MUTATION CAUSED THE AUTISM. BUT IF YOU LOOK ON AVERAGE THESE RARE DE NOVO PROTEIN DISRUPTING MUTATIONS WHAT I MEAN BY RARE DE NOVO, LESS THAN 1%, NOT SEEN IN THE PARENT SOMATIC TISSUES SO IT'S A GERM LINE MUTATION, KIND OF LIKE A DOWNS SYNDROME AND IF YOU LOOKED AT THEM ON AGGREGATE, THESE RARE DE NOVO PROTEIN DISRUPTING MUTATIONS, WE ARE SEEING 6 TIMES MORE IN THE PROBANDS THAN IN UNAFFECTED SIBLINGS SO IT'S CLEAR THAT SOME OF THESE NOW THAT THOUSANDS OF PEOPLE HAVE BEEN SEQUENCED WITH THESE VARIANTS, SOME OF THAT WORKED ON THAT SOME OF THESE NEVER APPEAR IN CONTROL, SO THAT SOME OF THESE ARE CLEAR, YOU KNOW, VERY BIG OOSKTS, SIZE, GENES SO 1 OF THE ISSUES HAS BEEN TO SEPARATE THE WEED FROM THE CHAFF. HOW DO I ADENTIFY WHICH OF THESE, YOU KNOW RARE PROTEIN DISRUPTING MUTATION SYSTEM GOING TO TURN OUTS TO BE CAUSAL AND UNTIL YOU SEQUENCE 10S OF THOUSANDS OF PEOPLE, YOU MAY NOT SEE THE MUTATION MORE THAN ONCE OR TWICE, YOU MAY SEE IT TWICE AFTER YOU'VE GOTTEN TO 5000 CASES GIVEN THE RARITY OF THESE MUTATIONS. SO 1 OF THE KEY THING SYSTEM THAT IF YOU COMPILE ALL OF THE MUTATIONS IN THE 6 MOST FREQUENT GENES AND I COULD SAY WITH CERTAINTY THESE ARE RISK FACTORS FOR AUTISM NOW,--AND NOW THEY'RE ABOUT 25 GENES THAT HAVE BEEN OBSERVE SAID 2 OR 3 MORE TIMES IN AUTISM COHORTS THAT HAVE BEEN SEQUENCE THAD TOGETHER THEY ACCOUNT FOR LESS THAN 1% OF THE CASES. ANOTHER INTERESTING FINDINGS FROM THESE PAPERS WAS THAT 1 COULD MAKE AN ESTIMATE AND IT'S--IT HAS A HUGE CONFIDENCE BOUND AND WE DID IT AND THE BROKED GROUP DID IT AS WELL, MARK DALE TOW TRY TO GET A SENSE OF HOW MANY GENES ARE PREDICTED AND THE CONFIDENCE BOUNDS ARE AROUND A THOUSAND IN OUR COHORT BUT GO FROM 300 TO 1400 IN THE ORIGINAL PAPER MPLET NOW, WHEN WE LOOK NOW, YOU KNOW 2 YEARS LATER, WHAT LINE THE NUMBER OF YOU HADITATIONS, YOU KNOW WE SEQUENCE A NUMBER OF CASES NOW AND WE HAVE MORE MUTATIONS, IT REALLY--IT'S ON A LINE THAT LOOKS LIKE IT'S GOING TO A THOUSAND. SO AGAIN, WITH DOUBLE THE NUMBER OF CASES, WE'RE SAYING IT'S GOING TO BE OVER500 GENES WITH RARE DE NOVO MUTATIONS AND IT'S LIKELY TO BE CLOSE TO A THOUSAND. THAT'S PRETTY REMARKABLE IF THEY'RE AROUND 20,000 PROTEIN CODING GENES, ABOUT 5% OF THEM MT CONTRIBUTE TO SOMETHING LIKE AUTISM AND AGAIN AUTISM IS A BROAD SYNDROME. IT'S--JUST HAS TO INVOLVE SOCIAL COGNITION AND COMPETITIVE RESTRICTIVE BEHAVIOR AND THAT'S WHAT A LOT OF THE CHILD IS DOG IN THE EARLY DEVELOL STAGES. SO THERE'S A STRONG EFFECT OF PATERNAL AGE TO MUTATION RATE AND THIS HAS BEEN OBSERVED IN NUMEROUS STUDIES NOW AND SO, ROUGHLY THE RULE OF THUMB IS FOR EVERY DECADE, THERE'S ABOUT A THIRD-40--30-40 RISK OF DENOVAE MUTATION. SO THE DIFFERENCE BETWEEN NUMBER 25, AND 55 MIGHT BE A 3-4 FOLD INCREASE RISK SO IT CLEARLY CAN'T EXPLAIN ALL THE RISK FOR AUTISM. IF AUTISM IS OCCUR NOTHING ABOUT 1% OF PEOPLE, ROUGHLY, BUT, IT HAS A SMALL EFFECT, DOES THAT MAKE SENSE. SO, YOU KNOW, I'VE GONE THROUGH THE GENETICS VERY QUICKLY TO GET INTO MEAT BUT I WANTED TO GET ACROSS THE POINT OF HETEROGENEITY AND DIVERSITY AND I'LL SUMMARIZE THAT HERE BY SAYING IF YOU LOOK IN THE POPULATION, THIS IS A--THIS IS A REVIEW, A SHORT PERSPECTIVE THAT WAS WRITTEN BY JASON STEIN IN MY LAB, LOOKING AT A COUPLE OF PAPERS THAT CAME OUT IN NEURON THAT WERE LOOKING AT RARE RECESSIVE MUTATIONS, OBSERVED SO IF WE KIND OF ADD UP RATHER THAN THE PERCENTAGE. SO, A MUTATION--LIKE IF WE DO--LET'S AIAN CLINICAL STUDY WHERE I TAKE A HUNDRED PATIENTS THAT COME THROUGH UCLA AND I DO A MICROARRAY LOOKING FOR RARE DE NOVO COPY NUMBER VARIANTS, I'LL FIND A COPY NUMBER VARIANT 6-10% OF THOSE CASES THAT'S LIKELY TO BE CAUSAL BUT THERE'S A PENETRANCE ISSUE THERE AND SO IF YOU WANT TO UNDERSTAND THE% OF TOTESSAL GENETIC VARIANTS, EXPLAIN, DO YOU HAVE TO TAKE NOT JUST THE FREQUENCY OF THE MUTATION BUT IT'S PENETRANTS, IT'S RISK AND SO, THAT'S WHAT WE'VE DONE HERE IN TERMS OF LOOKING AT THE PERCENT VARIANTS EXPLAINED AND THESE ARE ESTIMATES BUT YOU CAN SEE THAT MOST OF IT IS UNEXPLAINED, STILL. THERE'S VERY INTERESTING PAPER BY BERNIE DEVLIN'S GROUP THAT I THINK FAIRLY CONVINCINGLY ASSERTS THAT 40-60% OF THE VARIATION WILL BE COMMON VARIATION INHERITED VARIATION BUT STILL HAS NOT BEEN IDENTIFIED AND THIS KIND OF RECESSIVE MODEL AND THESE RARE DE NOVO MUTATIONS ARE EASIER TO DETECT, THEY'RE THE LOW HANGING FRUIT WITH OUR TECHNOLOGY AND SO THEY COMBINED ACCOUNT FOR ABOUT 10% OF THE VARIANTS IN AUTISM AND IT'S POSSIBLE THEN, THAT MAYBE WE'LL DRAWING A LINE HERE AND THAL BE ACCOUNTING FOR THAT MUCH BUT I DON'T THINK THEY'RE GOING TO BE ACCOUNTING FOR HALF IN THE END. WE ESTIMATE AT LEAST 15% WILL BE CONTRIBUTESSED TO--BY RARE DE NOVO VARIATION AND COULD BE AS HIGH AS 25 OR 30% BUT I DON'T THINK MORE THAN THAT. SO TO SUMMARIZE IN THE POPULATION, COMMON VARIANTS HAVE SMALL EFFECT SIZES, AND 1 CAN DO THESE KIND OF AGGREGATE STUDIES TO ESTIMATE THAT. RARE DE NOVO VALID AND RELIABLEIABILITYS CANNOT LIKELY EXPLAIN THE HERITABILITY AND FAMILIESIAL OCCURRENCE RISK. ALL THE GENES FOR FINDING MANY OF THEM HAVE DE NOVO VARIANCE, THEY DON'T EXPLAIN THE 70% VARIABILITY, BECAUSE A DE NOVO IS LEAK A DOWNS SYNDROME, IT'S GENETIC BUT NOT INHERITED. BUT THERE IS A SIGNIFICANT ROLE FOR THESE AND LARGER EFFECTS AND MANY WITH INTERMEDIATE EFFECTS SIZES AND IDENTIFYING HERITABLE ARRAIATION IS--VERYIATION IS CRITICAL. SO 1 THE FIELD CAN COLLABORATE. IDENTIFY LARGE COHORTS, IDENTIFY GENES THAT CONTRIBUTE TO AUTISM IN 10-20% OF PARENTS VERSES ALMOST 010 YEARS AGO, SO IT'S BEEN ENORMOUS PROGRESS. THE ISSUE IS, IN AN INDIVIDUAL, THERE'S ISSUES OF REDUCED VARIABILITY PENETRANTS, AND VARIABLE EXPRESSIVITY SO WHAT DOES AUTISM LOOK LIKE IN AN INDIVIDUAL? AND THESE--THIS IS JUST FROM A REVIEW AND I JUST WANT TO MAKE THE POINT THAT WE DON'T KNOW THAT EXCEPT FOR VERY FEW CASES. THERE IS THIS MENDELIAN MODEL, THE CHILD WITH FRAGILE X, IT'S LIKELY THAT MOST OF THE RISK COMES FROM HAVING THAT MAJOR MENDELIAN MUTATION. BUT THE ONLY WAY TO EXPLAIN WHAT HAS BEEN OBSERVED CLINICALLY OVER THE LAST 2 DECK CHASED IS SH OLD AUTISTIC LIKE TRAITS, LANGUAGE DELAY, ISSUES WITH SOCIAL COGNITION, EVEN--EVEN MENTAL FLEXIBILITY ISSUES RELATED--YOU KNOW THAT COULD BE RELATED TO OCD BUT CERTAINLY RELATED TO THE RESTRICTIVE REPETITIVE BEHAVIOR OF AUTISM IS OBSERVED MUCH MORE THAN YOU WOULD EXPECT BY CHANCE IN THE FIRST DEGREE RELATIVES OF CHILDREN WITH AUTISM. EITHER IN THEIR PARENTS OR UNAFFECTED SIBLINGS SO TO BE ABLE TO EXPLAIN THAT, WE HAVE AND THE HERITABILITY WE HAVE TO HAVE OTHER MODELS, EITHER COMBINATION OF COMMON VALID AND RELIABLEIANTS THAT IS--COMBINATION OF COMMON VARIANTS AND SOMEONE WITH AUTISM MIGHT JUST HAVE A FEW OF VARIANTS, SUBTHRESHOLD. YOU COULD HAVE A MAJOR EFFECT, RARE VALID AND--VARIANT AND THAT WOULD EXPLAIN WHY SOMEBODY WITH 22 Q GETS SCHIZOPHRENIA OR PSYCHOSIS VERSES AUTISM, ET CETERA. BUT WE HAVE TO CONSIDER ALL OF THESE MODELS, IT'S NOT A 2 HIT MODEL THAT'S CONVENIENT BECAUSE IT'S A MODEL IN CANCER. IT'S GOING TO BE ALL OF THIS. AND DEFINING AUTISM IN AN INDIVIDUAL IS NOW POSSIBLE USING DENOME AND EXOME SEQUENING SO THE NEXT 5 YEARS WILL BE PRETTY INTERESTING IN TERMS OF UNDERSTANDING HOW THE RISK VARIANTS CONVERGE IN A PATIENT. BUT THE REAL QUESTION IN MY MIND AS A NEUROBIOLOGIST IS HOW CAN I USE THIS INFORMATION TO GAIN TRACTION, TERMS OF UNDERSTANDING HOW AUTISM UNFOLDS, WHAT THE MECHANISM OF DISEASE IS AND ASKING THE QUESTION, IF THERE ARE HANDLEDS OF DIFFERENT FORMS OF AUTISM, WHERE DO THEY CONVERGE BIOLOGICALLY. SO THIS IS JUST A--A MINOR THOUGHT EXPERIMENT FROM A NEUROLOGIC PERSPECTIVE BECAUSE AUTISM INVOLVES SPECIFIC PATTERNS OF BEHAVIOR AND DEVELOPMENT. AUTISM HAS TO CONVERGE AT THE LEVEL OF BRAIN REGIONS AND CIRCUITS THAT'S WHERE BEHAVIOR COMES FROM. YOU HAVE TO AFFECTS CIRCUITS INVOLVE INDEED SOCIAL COGNITION TDOESN'T MEAN YOU HAVE TO AFFECT THEM SPECIFICALLY, THERE'S NOTHING THAT SAYS IT HAS TO BE ONLY SOCIAL COGNITION BUT YOU HAVE TO AFFECT THOSE CIRCUITS SO THAT WILL BE FRONTAL STRIATAL, FRONTAL PARIETAL, COULD INVOLVE THE CEREBELLUM AS WELL, IT'S INVOLVED IN DEVELOPMENT OF FRONTAL CONNECTIONS AS L. BUT FROM A KIND OF MODERN THERAPEUTIC STANDPOINT, IDENTIFYING THESE BRAIN REG I DON'T KNOWS AND CIRCUIT SYSTEM INTERESTING AND IMPORTANT ESPECIALLY IN DETERMINING HOW AUTISM MIGHT DIFFER FROM INTELLECTUAL DISABILITY, SYICOSEIS, ET CETERA. BUT THE MAJOR QUESTION IF YOU'RE TRYING TO DEVELOP THERAPY SYSTEM HOW TO GENETIC VARIANTS CONVERGE ON MOLECULAR PATHWAYS OR BIOLOGICAL PATHWAYS AND THIS IS JUST A CARTOON SHOWING A FEW OF THESE KNOWN TO HIGHLY PENETRANT MUTATIONS AND WE KNOW THAT MANY OF THESE DON'T JUST AFFECT 1 BIOLOGICAL PATHS, THEY AFFECT MANY. SO NTSCMUTATIONS MIGHT AFFECT PATTERNING, WIRING, SYNAPTIC FUNCTION, ET CETERA. SO THIS WILL BE COMPLICATED AND 1 OF THE ISSUES IS THAT ARE THERE TIMES AND DEVELOPMENT, ARE THERE REGIONAL CIRCUITRY SPECIFIC NEURONS AND ARE THERE MOLECULAR PATHWAYS BE WHERE THESE MIGHT CONVERGE. SO OUR APPROACH HAS BEEN THIS NOTION OF A SYSTEMS BIOLOGY, I HAVE TO SAY THAT I DON'T THINK THAT WE'VE GOTTEN THERE YET BUT IT'S OUR GOAL. RIGHT NOW WHAT I'M GOING TO DESCRIBE TO SURVEYS USING TRANSCRIPT OHMICS, THIS LEVEL, GENE EXPRESSION DAT APHENOTYPE DATA AND TOPY NUMBER SEQUENCE DATA TOGETHER--COPY NUMBER SEQUENCE DATA TOGETHER TO IDENTIFY PATHWAYS BUT THE NOTION HERE IS THAT RATHER THAN TAKING A UNIDIMENSION AMILLIO APPROACH, WE CAN NOW LOOK AT--WE HAVE THE KIND OF MATHEMATICAL FORMULA AND WE CAN BEGIN TO COLLECT THE DATA IN A WAY THAT WILL ARK LOW US--ALLOW US TO INTEGRATE THESE LEVELS SIMULTANEOUSLY RATHER THAN CEREALLY. SO THAT'S BEEN OUR GOAL AND AGAIN I'M GOING TO TALK ABOUT GENE EXPRESSION DATA. AND AGAIN, THE NOTION IS, WE CAN STUDY HUMAN BRAIN BUT IN HUMAN BRAIN WE DON'T GET CAUSAL, IT'S VERY DIFFICULT TO INFER CAUSALITY SO WE NEED TO HAVE EITHER MODELS INVITRO, OR ANIMAL MODELS, TO REALLY TEST THE CAUSAL HYPOTHESIS HERE BUT WE ALSO NEED THE HUMAN TO ASK ABOUT THE RELEVANCE OF THESE. IS WHAT WE'RE FINDING HERE, EVEN PLAUSIBLE OR POSSIBLE BASED ON WHAT WE KNOW SO WHAT I WILL TALK ABOUT TODAY, I WILL SKIP LOT OF WORK WE'VE BEEN DOING ON MICE, FOCUS MOSTLY ON THE BRAIN AND PATIENT ISSUE AND AT THE END ON OUR WORK IN HUMAN NEUROPROGENITTORS AND HOW THIS SYSTEMS BIOLOGY OR NETWORK APPROACH CAN INFORM THAT. ONE OF THE ISSUES, THOSE WHO HAVE DONE GENE EXPRESSION PROBABLY KNOW AND IT'S A HEADACHE--LET'S PUT IT THIS WAY TO THOSE IN THE FIELD THAT IF YOU COMPARE ANY 2 STATES, DISEASE VERSES CONTROL, TREATED VERSES UNTREATED WITH SOME DRUG, YOU WILL FIND HUNDREDS OF GENES AND IF YOU DO THE EXPERIMENT WITH HIGH ENOUGH STATISTICAL PATTERN, YOU WILL FIND THOUSANDS THAT ARE DIFFERENT BETWEEN THE 2 CONDITIONS OR 3 CONDITIONS, WHATEVER YOU DECIDE TO DO. AND SO WE REALIZE THOSE QUITE EARLY ON, ABOUT 10 YEARS AGO AND STARTED TO WORK ON WAYS OF GAINING INSIGHT FROM THE SATA THAT WASN'T--DATA OF PRECONCEIVED NOTION OF WHAT WAS IMPORTANT. WE DIDN'T LOOK AT THE MOST HIGHLY EXPRESSED GENE. WE DEVELOP A NETWORK FRAMEWORK TO UNDERSTAND THIS AND I WON'T GO INTO TOO MUCH OF THE DETAIL OTHER THAN I WANT TO TELL YOU JUST 1 LITTLE LOS ANGELES HOLLYWOOD ANECDOTE, MAYBE TO WAKE YOU UP A LITTLE. IT'S AN ANALOGY WITH GOING FOR THE HIGHEST EXPRESSED GENE, NOT THAT ROOTS WRONG ALL THE TIME BUT IT CAN BE MISLEADING, WHO IS THE HIGHEST EXPRESSED ACTOR? WHO HAS DONE THE MOST FILM? S ANYBODY KNOW? >> SOMEBODY HAS TO YELL OUT. SAMUEL JACKSON 1 VOTE FOR SAMUEL JACKSON. ANYBODY ELSE OUT THERE? >> OKAY YOU'RE NOT EVEN IN THE SAME RIGHT BALL PARK IT'S A MALE PORN ACTOR THAT SHOULD GIVE YOU THE IDEA THAT--AND SO ... I'LL JUST LEAVE IT THERE. KD--SALLY[LAUGHTER] NOTHING MORE TOW SAY ON THAT. AND--MORE TO SAY ON THAT THAT'S NOT A PLUG ON THAT PART OF THE WORLD EITHER, AGAIN IF WE USE THAT SAME LODGE TOYING IDENTIFY THE HIGHEST EXPRESSED GENE, THAT'S THE HIGHEST EXPRESSED ACTOR. I HOPE NONE OF YOU KNOW THE NAME. ANYWAY. SO WITH ME COLLEAGUE STEVE HORBATH, WHO DEVELOPED THIS FOR ALL OF WHAT I WILL SHOW YOU, HE DEVELOPED AND DEVELOPED IN CO EXPRESSION ANALIS SIS AND IT DOES THIS. --ANALYSIS AND IT DOES THIS. IF YOU LOOK AT EXPRESSION OVER SAMPLES, YOU CANEE FROM THIS CARTOON THAT GENES CO VARY OVER THIS GROUP OF SAMPLES. ASSUME THIS IS 50 DIFFERENT BRAIN SAMPLES AND YOU CAN SEE THERE'S A GROUP--YOU CAN GROUP THEM BY THE EXTENT TO WHICH THEY CO VARY AND IF WE--IF WE CAN IDENTIFY GENES THAT CO VARY STRONGLY TOGETHER, WE CAN IDENTIFY THE NETWORK NEIGHBORHOODS AND THESE MODUSELESS OF HIGHLY CO EXPRESSED GENES SO EACH OF THESE COULD BE CONSIDERED A MODULE. SO IF WE USE CORRELATION, WE COULD IDENTIFY SUCH A MODULE AND THEN WE CAN ASK HOW IT THE MODULE RELATED TO ALL THE EXPERIMENTAL VARIABLES, ASPECTS OF CLINICAL FUNCTION, ET CETERA. THIS IS JUST 1 EXAMPLE WHERE IF WE DO A PRINCIPLE COMPONENT ANALYSIS OF WHOLE CORTICAL TISSUE, THE MODULES THAT WE IDENTIFY, LARGELY CORRESPOND TO SELL TYPES, TELLING US THAT THE MAJOR SOURCE OF VARIATION THAT'S CAUSING THIS VARIATION IS VARIATION BETWEEN INDIVIDUALS IN CELL TYPE COMPOSITION OF THE TISSUE. NOT SURPRI, BUT IT ENABLES US TO DO AN INSILLY CODISSECTION OF THE TISSUE WITHOUT DISSECTING IT. WITHIN THESE MODULES ANOTHER CRITICAL INSIGHT IS THAT WE IDENTIFY THE CORE HUB GENES, HIGHLY CONNECTED HUB GENES THAT ARE LIKELY CENTRAL TO THE PROCESS, I'M GOING TO TELL YOU NETWORK STRUCTURES ARE ROBUST AND PRODUCIBLE AND REFER YOU TO THE PAPERS, A GENES NETWORK POSITION IS BIOLOGICALLY MEANINGFULFUL, WHAT MODULE IT IS IN AND WITHIN THE MODULE WEES CAN IDENTIFY THE HUBS, WHERE IT IS SEN ILLEGALSENERALLITY AND IT SERVES AS A BASIS FOR IDENTIFICATION OF BIOLOGICALLY MEANINGFUL INSIDES. SO WE COPE PAIR MODULES BETWEEN CONTROL AND DISEASE, AND LOOK AT A GENES CONNECTIVITY WITHIN A MODULE AND LET'S SAY A MODULE AND PRESERVED IN MODULES AND CONTROLS, ARE THERE GENES THAT CHANGE POSITIONS STRONGLY. MAYBE THOSE ARE IMPORTANT. AND THEN GUILTY BY ASSOCITION. IF I HAVE A RIBOSOMAL MODULE OR YOU KNOW LIKE--IF I LOOK ACROSS SPECIES, ALL DIFFERENT SPECIES, I FIND THEM TO BASIC ELEMENTS OF CELLULAR FUNCTION AND WE'VE DONE THOSE EXPERIMENTS, AND WE CAN FIND GENES THAT ARE UNANNOTATED WESTBOUND A MODULE, AND WE CAN PROVE THAT IS A RIBOSOMAL GENE, ET CETERA. I WILL GIVE YOU AGAIN ANOTHER PIECE OF INSIGHT INTO THIS, HOPEFULLY IT'S A PIECE OF INSIGHT. LOOK AT THESE 2 GENES, THEY'RE NOT DIFFERENTIALLY EXPRESSED. SO GENE 1 BETWEEN THE CONTROL AND EXPERIMENT, AND GENE 2. HOWEVER, IF I LOOK AT AGAIN THEIR CORRELATION WITH EACH OTHER, FROM WHICH WE INFER CO REGULATION, WE CAN SEE THAT IN THE CONTROL GROUP, THESE 2 GENES ARE HIGHLY--SHOW A HIGHLY SIMILAR PATTERN OF VARIATION BUT NOT IN THE EXPERIMENTAL GROUPS. AND THERE ARE NUMEROUS REASON YES THAT COULD BE BUT WE SEE THIS OVER AND OVER AGAIN AND AGAIN THIS SHOWS YOU HOW LOOKING AT DATA IN A SLIGHTLY CURRENT WAY CAN GIVE YOU INSIGHT THAT YOU DON'T SEE FROM LOOKING AT THE DATA ON AGGREGATE. SOEE USE THIS KIND OF NETWORK, THE NOTION OF KIND OF CORRELATION, CO REGULATION TO DRIVE THESE MODULES, CENTSIALLY WITHOUT GOING INTO THE STATISTICS AND I'M HAPPY TO IN THE QUESTION PERIOD, WE CAN--IT'S ESSENTIALLY, ALTHOUGH ALTHOUGH NOT STRUCTURALLY CORRELATE WIDE THE DATA, BUT CORRELATE WIDE THE NEIGHBORS THEY'RE LIKELY TO BE CLOSE TO EACH OTHER IN NETWORK SPACE. WE LOOK AT THIS, THIS WAS ABOUT 4 YEARS AGO. AND WHAT WE HAD WERE ABOUT 20 BRAINS, 19 CASES AND SLIGHTLY FEWER CONTROLS FROM AUTISTIC INDIVIDUALS. NOW THERE ARE 50 CASES IN THE BRAIN BANK BUT WHEN WE LOOK AT RNA INTEGRITY, THE VAST MAJORITY WOULD NOT PASS OUR QUALITY CONTROL. SO WENNED UP WITH ABOUT 19 BRAINS AND A GOOD RNA AND WE TOOK FRONTAL AND TEMPORAL LOBE AND CEREBELLUM AND SAW CHANGES FEW CHANGES IN THE CEREBELLUM AND WE FOCUSED ON THE CORTEX AND THIS HAS BEEN PUBLISHED SO I WILL HIGHLIGHT THE FINDINGS. SHE WAS ABLING TO MODULATE M12 TO SYNAPTIC FUNCTION AT LARGE WITH ATBT 1, IT'S A SPLICING FACTOR AND THEN M16 UPREGULATION OF MICRO GLIAL AND ASTRO SIGHT GENES. THIS M16 CORRESPONDED TO WHAT WE SEE ACROSS NORMAL HUMAN CORTEX AS THE MICROGLIA AND ASTROCCTE MODULE. IT'S CORRESPONDING TO NORMAL GENES IN MICROGLIA AND THIS IS TING US THAT MICROGLEEL CELLSA AND ASTRO SIGHTS AND CORTEX IN WHICH THEY'RE 4 OR 5 STUDIES SHOWING THAT. SO ANOTHER THING YOU CAN SEE THIS, IS THE LIGAND GENE OF THE COMPONENT YOU CAN SEE THAT M12 IS DOWN AND ABOUT 2/3RDS TO 3-QUARTERS OF THE SUBJECTS AND M16 IS UP, AND ACTUALLY THE SAME 1S SO THAT THESE ARE HIGH LEE CORRELATED PROCESSES, ALMOST THE R-SQUARE IS ALMOST POINT SABBATH, SO REALLY HIGHLY CORRELATE WIDE EACH OTHER AND WE WERE ABLE THEN TO ASK A CAUSAL QUESTION. AS I MENTIONED TO YOU BEFORE, THE PROBLEM, 1 OF THE DIFFICULTIES OF GENE EXPRESON, ESPECIALLY IN POSTMORTEM IS THAT, WE DON'T KNOW WHETHER THESE CHANGES REFLECT A LIFETIME OF LIVE WITH AUTISM, MEDICATION, OTHER THINGS SO OF COURSE WE TRY TO--WE'VE TRIED TO RULE OUT OF CO VALID AND RELIABLE RELIABLE--CORVARIANTS OF AGE, SEIZURES THAT WE WERE ABLE TO BASED ON HISTORY BUT WE CAN'T ANSWER THE CAUSAL QUESTION, WHICH IS ARE THESE CAUSAL, RELATED TO THE ORBED LYING CAUSAL SYSTEM OR JUST REFLECT SOMEBODY LIVING WITH AUTISM FOR 10 OR 15 YEARS OR 3 YEARS. AND TAKEN--THEY'S WHAT HAPPENED TO THE--THAT'S WHAT HAPPENED TO THE BRAIN. NOW AT 1 CASE WE WERE HAPPY TO HAVE THIS. WHEN WE COULD IDENTIFY CAUSAL ANCHOR OR NOT, BECAUSE AS I TOLD YOU BEFORE IN 20 CASES OF AUTISM WE EXPECT 20 DIFFERENT GENETIC ORIGINAL ENVIRONMENTAL FORMS IT'S A HETERODISORDER, AND WHAT WE'RE SEEING HERE IS AT LEAST TO 3-QUARTERS OF CASES IS A COMMON MOLECULAR PATHOLOGY. WHICH I THINK WAS REALLY AMAZING AND TOTALLY UNEXPECTED BASED ON GENETICS AT LEAST IN OUR LAB. SO WHAT WE DID IS WE ASKED IF WE TREAT THESE MODULES LIKE PATHWAYS AND NOW ASK IF I TAKE THE DATA FROM PUB LIFT GWAS STUDIES IN AUTISM AND ASK: IS THERE ENRICHMENT OF GENES WITH LOWER P-VALUES, MORE THAN YOU PICTURE BY CHANCE IN EITHER OF THESE MODULES? WE FOUND, YES, IN THIS M12 THERE WAS A HIGHLY SIGNIFICANT CORRECTED ENRICHMENT FOR GENETIC ASSOCIATION SIGNALS. IN FACT, THERE WERE 4 OR 5 GENES THAT CAUSE SYNDROMIC ASD IN THIS AS WELL WHICH WAS SIGNIFICANT ENRICHMENT BASED ON THE NUMBER KNOWN AS THAT TIME. WHEREAS THERE WAS NO SIGNAL HERE. SO, OUR REASONING AT THAT TIME IS THEN, WE HAVE A CAUSAL GENETIC ANCHOR IN THIS MODULE, NO CAUSAL GENETIC ANCHOR IN THIS MODULE BUT THEY'RE CORRELATE WIDE EACH OTHER. SO OUR WORKING MODEL IS THAT THERE'S SYNAPTIC DYSFUNCTION AND THIS LEADS TO UPREGULATION OF THESE CELLS WHICH IS PROBABLY NOT INFLAMMATION IN THE WAY THAT WE THINK ABOUT PERIPHERAL INFLAMMATION BUT IT HAS TO DO WITH SYNAPTIC REMODELING AND SYNAPTIC DYSFUNCTION THAT MICROGLEEL CELLSA AND ASTRO CITES ARE KNOWN TO BE IN SYNAPTIC PLASTICITY SO WE THINK THAT'S WHAT'S REALLY HAPPENING HERE BUT WE CAN'T PROVE THIS, THIS IS THE MODEL. THE NOTION WOULD BE TO TRY TO FIND THIS IN ANIMAL MODELS, ET CETERA. SO NOW WE'VE DONE A REPLICATION, WE'VE USED THE SEEK WITH 1 TOTAL 13 BRAINS, AND DUPLICATION SYNDROME SO IT'S ABOUT HALF AUTISM AND ABOUT HALF CONTROL. THESE ARE MOSTLY ADULTS OR EVERYBODY IN HERE IS OVERAGE 10. SO FAR THAT WE'VE ANALYZED. BUT, I SHOULD TELL YOU, WE FIND THIS SAME PATTERN IN THE YOUNGER CASES AS WELL. WE JUST DON'T USE THEM IN THIS ANALYSIS BECAUSE WE DON'T HAVE THE AGE MATCH CONTROLS. SO WE USE NEXT GENERATION SEQUENCING, THESE ARE THE BASIC METHODS, NEAL P A RIGSHA, AND THE LAB HAVE BEEN LEADING THIS IN THE LAB. SO I WILL GIVE YOU PRELIMINARY. WE'VE DONE MORE BUT IT'S IN PROCESS. IF WE TAKE WANAGs OLD SAMLES, WE DON'T HAVE ALL OF THEM LEFT BECAUSE SOME OF THEM ARE USED AND THEN YOU READ IN NEW YORK TIMES THE HARVARD BRAIN BANK FOLDED, LOST SAMPLES, SO WE COULD BT GET ALL OF THEM BUT IF WE LOOK AT OUR OLD SAMPLE ON A MICROARRAY AND LOOK AT RNA SEEK, THIS IS ABOUT WHAT WE SEE AND THIS IS TYPICAL FOR RNA SEEK VERSES ARRAY. SO YOU GET A 50% OVERLAP OR YOU KNOW SOMETHING LIKE THAT AND THAT'S WHAT WE'RE--THIS IS ABOUT 30%, BUT FWE LOOK AT THE NEW RNA SEEK, THAT IS THE TOTALLY INDEPENDENT SAMPLES FROM IT, NOW, AND WHICH IS MORE SAMPLES AND HIGHER POWERED, WE GET A HIGHER OVERLAP NOTHER WORDS WE'RE ESSENTIALLY USING THE SAME PADERNS AND I--PATTERNS AND I CAN SHOW THIS IN A NUMBER OF DIFFERENT WAYS WE SAW BEFORE. WE ABLE TO REFINE THESE BETTER BECAUSE WITH THE SAMPLES WE CAN REFINE THE MODULES INTO--SO IN STED OF 2 MODULES WE HAVE 5 BUT THEY FALL WITHIN THOSE OLDER 2 LARGER MODULES. BUT WHAT'S REALLY AMAZING TO ME IS THAT 15 Q-DUPLICATION, WE HAVE 8 CASES WITH GOOD RNA SHOW ESSENTIALLY THE SAME PATTERNS IF WE USE THE MODEL, ABT COUNTS FOR AGE AND ALL OF THE--ALL OF THE CONFOUNDERS WERE WORRIED ABOUT, WE END UP WITH A .94 R-SQUARED WITH THE EXPRESSION WITH AUTISM CONTROL VERSES 15 Q CONTROL AND THE SIGNAL IS STRONGENER IN HOMOGEANIOUS GROUP. SO AGAIN, I THEN IS TELLING US THAT THE SIGNAL WE'RE SEEING IS NOT A RANDOM OUTCOME OF SOME ENVIRONMENTAL PROTEIN COMPLEX BATION OR SOMETHING LIKE THAT. WHATEVER WE'RE SEE NOTHING THESE ADULT SYSTEM DUE TO THEIR UNDERLYING AUTISM CAUSE, WHETHER IT BE ENVIRONMENTAL OR GENETIC, SO TO SUMMARIZE THERE'S A ROBUST GENE EXPRESSION PATTERN SHARED BY MORE THAN HALF THE CASES BY AUTISM, SHARED BY AT LEAST 1 MAJOR GENE FORM AND I SHOULD TELL YOU THAT IN NO WAY IS THIS--I WAS REALLY WORRIED THIS WAS ASSOCIATED WITH SEIZURES AND IT'S NOT IN THE 15 Q OR IT OUR GROUP. AND THIS PATTERN IS WHAT WE THINK OF DEFINING MOLECULAR PATHOLOGY OF AUTISM. SO WE HAVE THESE ISSUES WITH CAUSAL IS HOW GENETIC MUTATIONS THAT ARE OCCURRING CAUSE DISREPRESENTATION IN BRAIN DEVELOP AND WANT SUBSEQUENT FUNCTION AND CIRCUIT FUNCTION TO LEAD TO THIS PATHOLOGY AND AND THERE'S WAY LONG IF AND THERE'S A LONG ASK STARTING WITH THE GENETIC LESION AND FIGURING OUT HOW WE GET AND IT'S A START AND IT'S TELLING US THERE IS A GROUP OF AUTISTIC PATIENTS THAT SHARE COMMON MOLECULAR PATHOLOGY. SO AN ALTERNATIVE APPROACH AND I WILL SPEND MOST OF THE REST OF THE TIME TALKING ABOUT IS TO MATCH AUTISM RISK GENES NOW THE GENE SEQUENCE SUGGEST IDENTIFYING DOZENS AND DOZENS OF GENES 2 PATHWAYS. HOW DO WE DO THAT. HOW ARE THE SPECIFIC PROCESSES OR CIRCUITS. SO OUR THOUGHT PROCESS IS THIS: WE IDENTIFY REPRODUCIBLE ROBUST CO-EXPRESSION NETWORKS AND MODULES IN NORMAL HUMAN IN VIVO BRAIN DEVELOPMENT AND WE CAN DO THAT NOW BECAUSE THERE'S A BRAIN SPAN DATA SET AND OTHER DATA SETS WHERE PEOPLE PROFILE USING ARRAYS OR NASEEK FROM 8 WEEKS GESTATION FETAL CORTEX ALL THE WAY THROUGH ADULTHOOD AND WE USE THAT DATA TO SAY WHAT IS THE NORMAL TRAJECTORY OF DEVELOPMENT SO WE DOT PROPER CONTROLS, COEXPRESSION NETWORKS HELP PRIORITIZE VARIANTS, IN OTHER WORDS 1 OF THE THINGS I DIDN'T MENTION FROM THE SEQUENCING STUDIES THERE'S VERY SMALL 8 SIGNAL FOR VARIANTS THIS CHANGE ITS AMENEE ACID BUT DOESN'T KNOCK OUT THE PROTEIN. SO, CAN WE ACTUALLY DO SOMETHING TO HELP ENRICH FOR HERITABLE OR MISSENSE VALID AND RELIABLEIABILITIES AND CAN THEY--MISSENSE VARIANT AND CAN THEY PREDICT IN WHICH GENES WILL BE IN THE FUTURE SO IS THERE PREDICTIVE POWER? SO NEAL TOOK THE LIST OF AUTISM GENES FROM A WEB CURATED LIST. THIS INCLUDES A LOT OF CANDIDATE GENE COMMON VARIATION STUDIES. THE MODULE M12 THAT HAS A GENETIC SIGNAL THAT'S DOWN REGULATED IN AUTISM. WE WANTED TO COMPARE IT TO INTELLECTUAL DISABILITY BECAUSE THEY'RE OVER 400 FORMS OF IT AND DOMINANT AND RECESSIVE DOES THAT LOOK LIKE AUTISM OR NOT. AND THEN WE TOOK THE CURATED LOOSE OF RARE DE NOVO VARIANTS AND AFFECTED AND WE WANT TO MAP THEM TO DEVELOPMENT AND ANATOMICAL RELATIONSHIP. SO AGAIN WE CREATED A NORMAL BRAIN DEVELOPMENT NETWORK AND KEY ASK WHERE DO THE GENES FALL. ARE THEY RANDOM OR SPECIFIC TIME POINTS OR PROCESSES? AND THEN THERE'S LAMINAR DATA FROM THE ALAN INSTITUTE FROM A PROJECT WE DID WITH THEM ON MACAQUE ADULT PRIMATE AS WELL AS HUMAN FETAL LAYERS THAT JUST CAME OUT IN NATURE RECENTLY. AND THEY SHARED AS THEY ALWAYS DO, AGAIN A GREAT PLUG FOR WHAT THEY'RE DOING AND WHAT WE SHOULD ALL BE DOING IS THERE DATA WASOT WEB, A YEAR AGO, WAY BEFORE THESE PAPERS WERE PUBLISED SO THAT WE'RE ABLE TO USE IT. SO NEAL OOH DENTIFIED BETWEEN 12 AND 18 DEPENDING ON HOW YOU LOOK AT IT REPRODUCIBLE MODULES, ACROSS MULTIPLE DATA SETS SO THAT'S A CRITICAL THING. WE IDENTIFY A MODULE AND THEN WE TAKE OTHER PUBLISHED DATA AND WE SHOW THAT WE CAN SEE IT GAB AND AGAIN, WE DON'T WANT TO ADENTIFY RANDOM NOISE AND SO, YOU KNOW, THERE ARE OTHER THING QUEYS DO, WE KEPREMIER THE MODULES, ET CETERA. BUT THESE ARE SOLID MODULES OBSERVED OVER AND OVER AGAIN. THEY REFLECT TRUE BIOLOGICAL PROCESSES AND THESE ARE EXAMPLES OF THEM. THESE ARE 2 THAT M2 AND M3 THAT HAVE VERY HIGH, THIS IS THE IGANNA GENE OF THE MODULE SO IT'S SHOWING OVERTIME AND THIS IS THE 8 WEEKS GUESTATION, MONTHS, AFTER BIRTH, THE TRAJECTORY OF AVERAGE GENE EXPRESSION IN THAT MODULE SO THE AVERAGE GENE IN THIS MODULE IS NOT MUCH EXPRESSED AT 8 TO 10 WEEKS SO THAT'S WHEN THE CORTICO GENESIS BEGINS IN HUMANS. AND DURING THE BIRTH OF NEURONS AND THEIR MIGRATION, IT'S HIGH AND THEN IT GOES LOW. THIS 1 IS VERY HIGH EARLY, DROPS OFF AROUND 16 WEEKS SO IT'S LIKELY INVOLVED IN PROGENITOR PROLIFERATION AND THE KIND OF MAKING OF PROGENITORS THAT WILL FORM THE CO TEX AND WHAT'S SO INTERESTING IS THAT THIS MODULE IS ENRICHED IN TRANSCRIPTION FACTOR IS HISTONE CHROMATIN STRUCTURE AS IS THIS 1 REGULATION OF GENE EXPRESSION. SO THESE ARE--AND WE'LL GET TO THIS IN A SECOND. HERE IS MODULES THAT GO UP DURING DEVELOPMENT BUT THEY HAVE SLIGHTLY DIFFERENT TRAJECTORIES AGAIN THERE ARE 3 THAT ARE RELATED TO SYNAPSES THAT I WILL TALK ABOUT, M13 AND M16 AND M17. M16 GOES UP AROUND 12 WEEKS AND A LITTLE LATER THAT IS AN EARLIER TRAJECTORY WHERE THE M17 IS LATER AND IT'S INTERESTING BECAUSE ALTHOUGH THEY'RE ENRICHED AT THE BROAD GEOTERM NAILING FOR SYNAPTIC TRANSMISSION, THEY CONTAIN DIFFERENT GENES THIS IS A LOT OF GENES THAT ARE INVOLVED IN DEVELOPMENT OF SYNAPSES AND HOPE OPHILIC AND HETEROPHILIC CELL ADHESION AND CALCIUM DEPENDENT CELL ADHESION AND MIGRATION AND THIS IS REALLY A LOT OF GENES INVOLVED IN REGULATING ION CHANNELS AND NERVOUS TRANSMISSION. STHE WHAT YOU NEED, THIS SET UP A SYNAPSE AND THIS IS WHAT YOU NEED TO BEGIN TO HAVE SINCE APSE FUNCTIONING IN A WAY TO GIVE YOU AN IDEA OF A FEW OF THESE MODULES. SO THEN, THIS IS SHOWING WHAT A NETWORK DENDRITIC CELLOGRAM THIS, IS ALL THE GENES, MODULES ALL 18 IDENTIFY INDEED THE BRAIN SPAN DATA SET AND AND THEN WHAT NEIL DID IS HE BASICALLY ASKED, IF WE LOOK AT OUR CANDGAITIDATE GENE LIST, LOOK AT THE RARE DENOVAE VARIANTS IN AFFECTED VERSES THOSE IN SIBLING WHICH SHOULDN'T BE CAUSAL DO, THEY COALESCE IN ANY BIOLOGICAL PROCESSES AND THE ANSWER IS YES, THESE RARE DE NOVO VARIANTS THAT DISRUPT PROTEINS AS WELL AS MISSED SENSE ARE ARE ENRICH INDEED THE 2 EARLY CHROMATIN TRANSCRIPTION MODULES. BUT IMPORTANTLY, SILENT MUTATIONS FOUND IN AFFECTED AREN'T NOR ARE ANY OF THE VARIANTS IDENTIFY INDEED SIBLINGS. AGAIN A GOOD CONTROL. INTELLECTUAL DISABILITY GENES, THIS IS A LARGER LIST THAN ANY OF THESE, IT'S ABOUT 400 SOMETHING GENES, IT'S REALLY PRETTY EVENLY SPREAD ACROSS DEVELOPMENT THERE'S NO SIGNIFICANT ENRICHMENT SO HERE'S A PLACE WE'RE BEGIN SEE A SEPARATION BETWEEN WHAT MIGHT BE SPECIFIC FOR AUTISM AND WHAT MIGHT BE MORE GENERAL INTELLECTUAL DISACT. IT WAS INTERESTING IS THAT ASDM 12 ENRICH INDEED COMMON VARIANTS, AND THE SAFARI ASD LIST WHICH IS ALSO ENRICHED WHICH IS A LARGE NUMBER OF COMMON VARIANT GENE TODAYS ARE IN THESE MODULES. SO WE HAVE KIND OF 2 TRAJECTORIES, WHICH MAY BE WRONG BY THE WAY, 1 IS THAT WE HAVE THESE--YOU KNOW MOST OF THE REALLY SEVERE THIPGS THAT AFFECT TRANSCRIPTION IN CHROMATIN ARE THESE RARE DE NOVO PROTEIN DISRUPTING VARIANTS AND THEY'RE OCCURRING VERY EARLY, HENS, YOU KNOW IT'S A LITTLE TOP LOGICAL BUT THEY CAUSE THESE MORE SEVERE DE NOVO SYNDROMES AND THIS IS THE KIND OF IN GENERAL AGGREGATING THE LESS SEVERE RISK FACTORS IN SYNAPTIC DYSFUNCTION SO WHAT 1 OF THESE MIGHT LOOK LIKE IS THIS. THIS IS A MULTIDIMENSIONAL SCALING PLOT OF THESE M2 AND M3. THERE'S A LOT OF INTERESTING THINGS SO THERE'S MATH MEMBER FOR THOSE, 6 OR 7 OUT OF THE KNOWN TWEET MEMBERS OF THE BATH COMPLEX WHICH IS A CHROMATIN NEURAL AND DIFFERENTIATION PROCESS, ARE ACTUALLY SEEN IN MEAS MODULES AND HIT BY RARE DE NOVO VARIANTS. WE CAN THEN TAKE THOSE GENE EXPRESSION MODULES AND REDUCE THEM TO NONPROTEIN MODULES HERE THEY ARE DAPPLE. AND AND WHAT'S SUPERINTERESTING, IT BECOMES THE HUB OF THIS MODULE. WHAT'S INTERESTING IS AS WE PUBLISH THIS UNDER REVIEW, PAPER CAME OUT OF NATURE SHOWING THAT THE TOP O ISOMER ACE 1 IS RESPONSIBLE FOR THE TRANSCRIPTION OF GENES WHICH IS IN AUTISM. NOW THE FLAW WITH THE PAPER AND IF THEY CORRECT WITH WITH THE NMENT, IT'S NOT AUTISM GENES, JUST IN GENERAL BUT THE POINT HERE IS THAT HERE INDIRECT AND DIRECT WE CAN SAY THAT PERHAPS TOP O ISOMER ACE 1 AND THESE OTHER GENES MAY BE INTERACTING, GIVING US LAY PLACE TO LOOK AT TO ASK HOW THESE CHROMATIN MODIFYING GENES AND DRAINS SCRIPGZ FACTORS MAY BE INTERACTING WITH THE TRANSCRIPTIONAL APPARATUS TO CHANGE GENE EXPRESSION SO VERY SPECIFIC PROTEIN INTERACTIONS WE CAN BEGIN TO LOOK AT AND ASK IF THESE ARE DISRUPTED BY MUTATIONS, ET CETERA. IT'S A NICE STARTING PLACE. WE CAN ALSO USE THE STRATIFYING VARIANTS COULD WE AND WE CAN'T F. WE TOOK FROM ALL THE SEQUENCING STUDIES THE SILENT RARE DE NOVO VARIANTS, THE MISSING RARE DE NOVO VARIANTS, AND WE LOOK AT THEM, THEY'RE NOT DIFFERENT IN TERMS OF METRICOT Y-AXIS CALLED PROBABILITY OF HAPPEN LOW DEFICIENCY THAT MATT HURLS DEVELOPED SEVERAL YEARS AGO, IT'S BASED LARGELY ON 30-40 EVOLUTIONARY TAKEN--THEY RAM TERS, IT'S NOT THE BE ALL, END ALL BUT IT WAS INTERESTING TO ASK, OKAY, WE SEE NO DIFFERENCE IN THESE AND ACTUALLY IN THE PAPER THAT WE PUBLISHED WITH MATH STATES GROUP, STEPHAN SHOW THAD USING 6 MEASURES OF EVOLUTIONARY AND PROTEIN CONSERVATION, WE COULDN'T DISTINGUISH BETWEEN THE CALL CAUSE OF MUTATIONS AND THOSE THAT DON'T THIS IS A MORE DETAILED AND SOPHISTICATED WAY OF DOING THAT. HOWEVER, WITH THE M2 OR M3 THIS, THEIR IS A SIGNIFICANT INCREASE AND THERE IS A SIGNAL THERE SO THIS IS THE FIRST APPROXIMATION THESE ARE ENRICHING FROM MUTATIONS THAT ARE MORE LIKELY TO CAUSE HAPPEN LOW INSUFFICIENCY BASED ON BIOINFORMATIC PREDICTIONS. AND THIS IS LATERONCH O GENESIS OF SINAT I OBJECT FUNCTION AND ENRICH INDEED AUTISM AND IT LOOKED LIKE THEY WERE CROSSING AROUND 16 WEEKS AND WON GOING UP AND 1 GOING DOWN O WE'RE WONDER FIGURE THEY'RE TRANSCRIPTIONALLY REGULATED AND THE ANSWER IS USING BIOINFORMATICS WE CAN IDENTIFY A NUMBER OF THEM AND SOME OF THEM, I DRAW YOUR ATTENTION TO THE MAPS WHICH ARE HIGHLY ENRICHED IN BOTH M2 AND IN M17 KIND OF CONNECTING THESE 2 PROCESSES PRETTY CLEARLY. THIS IS SHOW THE DATA VALIDATING SOME OF THESE RELATIONSHIPS THAT ARE INFERRED BY THE BIOINFORMATIC ANALYSIS SO WE DO SEE AN ENRICHMENT OF TRANSCRIPTION REGULATORS THAT ARE COMMON TO THE EARLY ANDALATE PROCESS. SHOWING LINKING. WE ALSO ASKED ABOUT TRANSLATION AND FMRP, BOB DARNEL'S GROUP HAD DONE A BEAUTIFUL STUDY, HAD LED THE STUDY, DOING FMRP CLIP TO IDENTIFY FMRP RNA TARGETS WE LOOK AT ENRICHMENT, THEY'RE SIGNIFICANTLY RICH AND IN FACT, IN MIKE WIGLER'S PAPER THEY SHOWED AN RATIO OF 5 IN THEIR SEQUENCING DATA AND WE'RE SEEING ABOUT THE SAME SOMETHING IN THE SAME MAG FIELD FUNCTIONS FEUD BUT AGAIN IT'S CROSS THE MODULES TO CONNECTING MANY OF THESE ARE NOT KNOWN TO BE MIXED LEUKEMIA 5 AND 3. THESE ARE GENES THAT ARE NOT KNOWN TO BE CRIT INVOLVED IN THE NEURODEVELOPMENT BUT THIS IS TELLING US THEY CLEARLY ARE. SO, WE HAVE BOTH KIND OF--WE HAVE THE NETWORKS WE CAN--YOU KNOW COALESCE THEM DOWN TO PROTEIN LEVEL AND DEVELOP HYPOTHESIS AROUND THAT, SHOW HOW THEY MIGHT BE CO REGULATED, AGAIN STARTING TO UNDERSTAND THE NETWORK AND THE RELATIONSHIPS BETWEEN TRANSCRIPTIONAL AND TRANSLATIONAL CO REGULATION. WE CAN ALSO LOOK AT THE ANATOM AND I CAN CIRCUIT SPECIFICITY AND I WILL NOT SPEPPED TIME ON THIS BECAUSE I WANT TO GET TO MY LAST FEW SLIDES BUT, 1 OF THE POINTS HERE IS THAT WE LOOK AT LAMINAR ENRICHMENT AND LOOK AT THE MODULES THAT ARE ENRICH INDEED THE SUPERFICIAL LAYER OF THE CORTEX THIS, IS EXPRESSION IN LAYER 5 AND LAYER 6. THEY'RE NOT ENRICHED OVER RANDOM EXPECTATIONS BY PERMUTATION. THIS IS SHOWN AGAIN IN THE AGGREGATE Z SCORE, IF WE LOOK AT SAFARI ASD ONLY GENES ASDM GENES THEY SHOW A NONRANDOM SUPERFICIAL PATTERN AND THE PROTEIN DISRUPTING GENES. WE LOOK AT IDG GENES, INTELLECTUAL DISABILITY GENES THEY'RE LIGHTLY MORE ENRICH INDEED LAYER 5 AND 6. AND AGAIN JUST SHOWING SOME OF OUR FAVORITE GENES FOR THOSE WORKING ON MODELS FOR FOR WHO MIGHT WANT TO AND THESE ARE AUTISM AND SCHIZOPHRENIA RISK GENES AND SHOWING AT THEAT LAS PINTAS, LAMINAR PATTERN AND PRIMATES AND AGAIN VERY SUPERFICIAL FOR NEUREXPECTATIONSIN, A LITTLE SUPERFICIAL FOR FOX 1 AND CNATP 2, AND THE SCAFFOLDING MOLECULE IS NOT HIGHLY EXPRESS INDEED LAYER 5 OR 6, IT'S MUCH MORE URFICIAL AND HAS A SPECIFIC AREAIAL PATTERN IN CORTEX. WHEN THE LOOK AT A CARTOON OF THE SYNAPSE THIS, IS NOT THE SAME IN EVERY CELL AND EVERY AREA THIS, IS SHOWING THAT VERY CLEARLY. SO TO SUMMARIZE THIS PART, LOOK AT DEFERENTIAL EXPRESS FROM BRAIN, WE'RE ABLE TO DISTINCT WISH ID FROM AUTISM BY WAY OF TRANSCRIPTIONAL REGULATION AND SYNAPTIC DEVELOPMENT AND SHE THESE HAVE FUNDAMENTALLY TRANSLATIONAL RESEARCH CORRECTORYS SO--TRANSLATIONAL RESEARCH JECTORS AND SHOWN THERE WAS A COMPANION GROUP SO THEY'RE HARD TO COMPARE BUT THEY FOUND ENRICHMENT IN GLUTAMINERGIC NEURON AS DO WE AS WELL. SO TO SUMMARIZE, THE GENES CONVERGE ON PRENATAL DEVELOPMENTAL PROCESSES, TRANSCRIPTIONAL AND TRANSLATIONAL CO REGULATION LINCHED THEM, MULTIPLE ASD RISK GENE MODULES OR ENRICH INDEED GLUTEA MITTERGIC PROJECTION NEURONS AND THESE PATTERNS HIGHLIGHT FEATURES FROM THIS INTELLECTUAL DISABILITY SO I ASK THIS QUESTION BEFORE, ARE THE 5 NETWORK MODULES THAT ARE ENRICHED FOR CANDIDATE GENES PREDIE SO WE'VE NOW GONE ON 2 YEARS LATER, WE BEING THE COMMUNITY AND NOT ME, AND MIKE WEEINGLER SHARE WIDE ME THE LIST OF WHAT WE CONSIDER THE MOST COMMONLY IDENTIFIED RECURRENT DE NOVO VARIANT WHICH IS ARE NOW MORE THAN TWICE AS MAY BE AS WE HAD ORIGINALLY AND SO, IN THE INITIAL ANALYSIS THEY EACH HARBOR THEN AND THESE ARE 62 AND 2 AND ACTUALLY 12 OUT OF 26 THAT MIKE GAVE ME 46 ARE IN 1 OF THE 5 ASD MODULES, AND SMALL SOMEBODY, 14 OR 26 AND AND BRINGING HOME THE FACT THAT THERE IS SOMETHING BEING IN THESE MOLLULES THAT WILL ENRICH YOU AND TELLING OLES THAT WE HAVE IDENTIFIED AT LEAST AN INITIAL PLATFORM TO PRIORITIZE VARIANTS WITH. SO THE LAST COUPLE MIBUTES OF THE TALK--MINUTES OF TALK. I'VE BEEN TALKING FOR 50 MINUTES SO, I'LL JUST END IN 2 MINUTES THEN. I WANT TO TELL YOU ABOUT USING THIS FRAMEWORK TO MOVING TO BIOLOGICAL UNDERSTANDING SO WHAT WE'VE BEEN BEING ABOUT IS HOW TO TAKE THESE MUTATIONS AND TRY TO UNDERSTAND HOW THEY MIGHT CONVERGE IN WHAT THEY DO, THERE ARE A LOT OF DIFFERENT APPROACHES THAT ARE VALID. ONE OF THE APPROACHES THAT 2 POST DOCS IN THE LAB, LEWIS, RIGHT THERE, LEWIS AND JASON STEIN HAS BEEN DOING IS AUTISM IN A DISH AND AGAIN IT GETS TO THE ISSUE OF WE WANTED SOMETHING WITH HIGH HUMAN RELEVANCE AND GETTING HIGH MECHANISTIC INSIGHT AND THEN IN THE LONG RUN WE HAVE THE THROUGH PUT TO ACTUALLY DO SCREENING AND THAT COMES DOWN, SO THE NOTION IS YOU TAKE 20, 30, 40, 50, AUTISM RISK GENES, YOU NOW WITH THE ENGINEERING MAKE THE MUTATIONS IN THE CELLS AND IF THIS EARLY PHASE WHEN WE STARTED USING THIS SHRNAs TO KNOCK DOWN GENES THAT WERE RECESSIVE OR HAPPEN LO INSUFFICIENT WE CAN ASSESS MORROLOGY AND HIGH THROUGH PUT AND WE CAN LOOK AT TRANSCRIPTIONAL SIGNATURE AND WE CAN USE SOMETHING LIKE THE CONNECTSIVITY MAP FOR EXAMPLE TO SEE ARE THERE DRUGS THAT REVERSE THIS TRANSCRIPTIONAL SIGNATURE, ET CETERA. ARE THERE CONVERGENT PATHWAY FIST I TAKE 20 DIFFERENT MUSEUM TOGSES AND PUT THEM INTO THE THE-OVERLAPPING ON THE SAME GENETIC BACK GRABBED ON--BACK GROUPED ON A PRIMEY HUMAN PROGENTITTORS ON UNBIASED TRANSCRIPT OHMICS SO THEY'VE BEEN DOING THIS IS FETAL BRAIN AT UCLA, FRESH FETAL BRAIN FROM ABORTION, THE CORTEX IS DISASSOCIATED, NEUROSPHERES, ESTABLISH MONOLAYER CULTURES INDUCE NEURONAL DIFFERENTIATION 1 AT MORPHOLOGY, AT DIFFERENT TIME POINTS, TRANSCRIPT OHM, ET CETERA AND WE HAVE 150 DONORS. >> THE MAJOR QUESTION, WITH IPSCs IS WHAT ARE THESE CELLS? WHAT ARE THEY DOING? ARE THEY DIFFERENTIATING LIKE IN VIVO. DO THEY LOOK LIKE IN VIVO CORTEX OR ARE THEY SOMETHING ELSE? NOBODY'S ANSWERED THAT QUESTION SO AGAIN TO REMIND YOU, WE'RE LOOKING AT EMBRYONIC PERIODS AND WE'RE DIFAREN'TIATING THEM 8 OR 12 WEEKS SO WE EXPECT OUR NEURONS TO GET AROUND 24-26 WEEKS AND DURING THIS TIME WE HAVE A LOT OF MAJOR CORTICAL NEUROGENESIS ONGOING SO THE QUESTION IS, WHAT ARE WE GETTING? SO AGAIN WE USE THIS THE NONSUSTAN RESOURCE, PUBLISHED UING MICROARRAY IN NATURE. THESE ARE THE DIFFERENT STAGES SO 8--RIGHT AFTER BIRTH SO THE FETAL GOES FROM 1-7, LATE MIDFETAL IS 6 SO WHAT LOUIS AND JASON DID WAS DEVELOP A NUMBER OF QUANTITATIVE UNBIASED METHODS FOR ASKING. WHEN WE LOOK AT A DISH FROM 1 WEEK TO 12 WEEKS DO OUR NEUROBSESSIVES MATCH WHAT'S HAPPENING IN VIVO. SO THE ANSWER IS, THE TRANSITION THAT MAPS THE BEST IS 1-6. WHICH IS THIS MIDLATE FETAL WHICH IS WHAT WE EXPECTED. THIS IS A CARTOON THAT SHOWS OVERLAPPED IN THE UPREGULATED, YOU CAN SEE THAT'S THE STRONGEST SO WE'RE USING A RANK-RANK HYPER GEOMETRIC TEST AND AND I WON'T GO INTO TOO MUCH MORE DETAIL BUT THE CRITICAL ISSUE HERE IS THAT WE CAN SHOW VERY STRONG TRANSITION MAPPING. ONE OF THE ISSUE SYSTEM IF WE TOOK THE NEURONS THEY WOULD SHOW VERY HIGH TRANSITION MAPPING TOO, BECAUSE THEY DEVELOP ALL OF THESE SAME MACHINERY. SO THE QUESTION SCAN WE DO BET TORE IDENTIFY REGIONAL IDENTITY AND STAGE SO WE DEPRIVATIONED A MACHINE LEARNING, MULTILABEL, MULTICLASS MACHINE LEARNING, THAT WE CALL CONTEXT, CLASSIFICATION OF NEUROANATOMICAL EXPRESSION AND BIOTRANSCRIPT OHMICS. THE NOTION IS WE TOOK THE HUMAN BRAIN SAMPLES, USED TOXIC EFFECTS CLASSIFY THEM AND THEN WE APPLY THIS, TO IN 4 OTHER IN VIVO SAMPLES. AND SO WE CAN VALIDATE THIS USING OTHER IN VIVO DATA. AND SO WE CAN PREDICT THE PROBABILITY OF BELONGING TO A DEVELOPMENTAL PERIOD. SO HERE IT WOULD TELL US THAT THIS--YOU KNOW SAMPLE IS 5, THIS 1'S 6 AND A LITTLE 7, ET CETERA. AND WHAT YOU CAN SEE, IN GENERAL HERE, IS THAT IT'S REALLY GOOD FOR THE FETAL STAGE BECAUSE WE HAVE A LOT OF SAMPLES AND DISTINCTIONS ARE VERY CLEAR, AS YOU GET INTO THE DIFFERENCE BETWEEN A 10 AND A 20 YEAR-OLD AND A 20 AND 30 YEAR-OLD, THERE'S MORE THOUGHTS AND THAT'S WHERE SOME OF THE AIRS ARE, BUT IN GENERAL OUR PREDICTION ACCURACYS FOR PERIOD WERE OVER 80% AND AFRACKED OVER 90% AND FOR REGION EXTREMELY HIGH OVER 98%. SO WE CAN APPLY A SAMELE TRUE PERIOD, SAMPLELE PREDICTED DEVELOPMENTAL SAMPLE SO THE ACCURACY PLUS OR MINUS 1 PERIOD IS 84%. AND AGAIN FOR DISTINGUISHING EARLY FETAL, MIDFETAL, LATE FEEDAL, LATE CHILDHOOD, ADULT CHILDHOOD, BEING OLD IS 100%. BUT FOR ANY KIND EVER GIVER CLASS IT'S 84% AND IT'S VERY GOOD FOR REGION SHOWING CEREBELLUM VERSES CORTEX THERE. AND SO WE CAN DID THIS WITH THE INVITRO SOLES SO WE CAN SEE AT WEEK 1 OUR PROGENITORRING LOOK MOSTLY LIKE STAGE 1 AND A LITTLE BIT LIKE STAGE 5 AND THAT'S BECAUSE AGAIN WE'VE CULTURED FROM MIDGUESTATION FETUS OVER TIME, THESE NEURONS DON'T SURVIVE THESE PROGENITORS FORM YOU KNOW DEVELOP AND OVER 12 WEEKS WE GET THIS STAGE, 5, 6, NEWSPAPERONS. SO THIS IS 1 WAY OF THAT'S BASED ON IN VIVO VALIDATED DATA TELLING US THAT THIS IS WHAT WIRE GETTING. THAT KIND OF DEVELOPMENTAL TRAJECTORY, IT DOESN'T TELL WHAT DID YOU SAY BIOLOGICAL PROCESSES ARE PREEVERYBODIED SO WE CAN USE--PRESERVED SO WE CAN USE THE NETWORK SUMMARY SCORE OF WHAT IT PRESERVED VERSES IN VIVO MODULES SO WE'RE ASKING INVITRO, WHICH OF THESE MODULES CORRESPONDS TO AN IN VIVO. AND AGAIN THIS IS JUST THE GENE ONTOLOGY AND OCCASION TO TELL YOU THAT MANY OF THE PROCESSES WE'RE IDENTIFYING IN VIVO ARE PRESERVED INVITRO. IN FACT THIS TAN MODULE. THE HISTONE WILL BE IMPORTANT. WHAT'S INTERESTING IN SOME WAYS ARE THE IMMUNE MICROGLEA IS NOT PRESERVED AND WE DON'T HAVE MICROGLIA IN THESE CULTUR SO WE'RE HAPPY ABOUT THAT AND THIS 1'S INTERESTING, IT'S CALLED SYMMETRY AND IT TURNS OUT TO BE ENRICHED THAT ARE INVOLVED IN NODAL ASYMMETRY SO THESE AREN'T, BUT OUR NOTION IS THAT THESE PROVIDE US, THE 1S THAT ARE AREN'T PRESERVED, WITH THINGS THAT WE MIGHT NEED TO ADD OR MOVE THE CULTURES IN WHAT DIRECTION AND GIVES US THE GENES AND THE HUNS TO MOVE IT. --HUBS TO MOVE T. SO WE HAVE THESE STAGES PRESERVED. SO OUR NEXT QUESTION WAS HOW WELL ARE IPSC DERIVED NEURONS PRESERVED THIS IS IMPORTANT. WE HAVE THEM FROM 3 LABORATORIES, THIS IS A PUBLISHED DATA SET. THESE ARE NEUROPROGENITTORS, FROM 1 LAB AND THIS IS FROM ANOTHER LAB, AND I'LL TELL YOU THAT THEY'RE NOT AS WELL PRESERVED AS THE PRIMARY NEURAL PROGENITORS, BUT AT A NETWORK LEVEL, MANY OF THE MODULES ARE PRESERVED AND MANY OF THE PROCESSES ARE AND 1 EVER THE 1S THAT ISN'T IS THAT TAN MODULE WHICH I'LL SHOW YOU IN THE NEXT SLIDE IS THE 1 THAT'S ENRICHED FOR THE M2 AND M3 GENES, THE CHROMATIN GENES THAT WERE INTERESTING IN MODELING. SO IT WOULD BE VERY DIFFICULT TO MODEL THOSE MUTATIONS. SO PEOPLE MAKES CHD8 MUTATIONS IN IPSCs FROM THESE PATIENTS. THAT PROCESS, ACCORDING TO ALL OF OUR ANALYSIS IS NOT PRESERVED YET, IN MOST OF THE IPSC IN THESE 3 DIFFERENT LABS THAT WE'VE LOOKED AT. AND JUST TO SHOW YOU THESE ARE SOME OF THE COMPLEX MEMBERS AND MODIFYING GENES AND THEIR IN VIVO RELATIONSHIP TO THE MODULE LIGAND GENE AND THIS IS THEIR INVITRO AND WE CAN SEE STRONG CONSERVATION FOR MANY OF THEM, NOT ALL OF THEM. I WOULDN'T WANT TO MODEL THIS 1 INVITRO UNTIL I FIGURED WHY IT'S DOWN HERE BECAUSE IN VIVO VERY IMPORTANT IN THIS MODULE BUT INVITRO IT'S NOT EVEN REALLY EXPRESSED. SO THIS REALLY AGAIN TELLS US, THIS IS THE HNPs, THE PRIMARY PROGENITORS THIS, IS THE M2 CONTAINING MODULE AND THESE ARE THE IPSCs, ES DERIVED NEURONS, THIS MODULE, THIS PROCESS IN THREES CELLS SHOULD NOT AND CANNOT BE MODELS. SO THIS IS JUST GIVING OUR CURRENT DATA. SO TO END MY TALK, THESE HNPs ARE CORTICAL AND REPRESENT THE TRANSITION DURING 12 WEEKS OF DIFFERENTIATION, THE KNOWN FUNCTIONAL PROCESS OF THE NEUROGENESIS MIGRATION AND GLEEL CELLS O GENESIS ARE HIGHLY PRESERVED, THEY HAVE STRONG RACAPPITIULATION OF DEVELOP AND WANT THIS PROVIDES A FRAHM WORK FOR BETTER MATCHING OF IN VIVO DEVELOPMENT USING INVITRO SYSTEMS. WE CAN SEE HUGE VARIABILITY IN THESE 3 DIFFERENT LABS, IPS DERIVED NEURONS AND THEY'RE VERY VARIABLE, THAT'S KNOWN, BUT NOW WE A RUBRIC WE CAN USE TO DRIVE THEM TO LOOK MORE CORTICAL. SO LAST WE CAN USE USE THESE USING THE COB? A. NO, SIRRATIVEIT MAP OR THE LINK SPEEDS TO MAP IF WE HAVE A MEASURE OF EXPRESSION PROFILE WE CAN MAP THIS ON, BY PATTERN MATCHING TO DRUGS AND THAT'S 1 OF THE THINGS WE'RE INTERESTED IN DOING. AND THAT'S WHERE THIS WILL GO HOPEFULLY. BECAUSE--SO IN COP CLIEWGZ ALTHOUGH AUTISM IS HETEROGENEOUS WE CAN CAPITALIZE ON GENETIC FINDINGS AND THESE INTEGRATIVE APPROACHES TO IDENTIFY CONVERGENT PATHWAYS POTENTIALLY. OUR CURRENT WORKING MODELS IS WE OBSERVE SYNAPTIC FUNCTION AND MICROL CELLSA UPREGULATION. ASD RISK GENES SHOW ULATORY ORGANIZATIONS DEVELOPMENTAL TRAJECTORIES INDICATIVE OF BIOLOGY. NOT ALL BUT THERE IS SOME CONVERGENCE, EARLY TRANSCRIPTIONAL REGULATION AND EARLY SYNAPTIC FUNCTION DEVELOPMENT. ASD RISK GENES ARE EXPRESSED THROUGHOUT THE BRAIN AND ARE ENRICH INDEED SUBPLATE, CORTICAL PLATE AND FETAL BRAIN, AND CORDICLE LAYER NEURONS AND THIS IS INTERESTING TO ME BECAUSE THE NEUROPSYCHEICOLOGY AND IMAGE SUGGEST SUGGESTING LONG RANGE DIGS CONNECTION OF PRONTAL FROM POSTERIOR REGIONS. THERE'S LOT OF STUFF SUGJELLING THAT. AND--OF COWER THE CROSS COLOSSAL OR HEMISPHERIC CONNECTING NEURONS. AND AS I HOPE I SHOWED NUCLEOTIDES THE QUICK INTRODUCTION TO OUR PATTERN MAPPING STUFF, THAT THE NETWORK CONTEXT, THAT'S A PUNT PROVIDE ACE ROADMAP FOR MODELING, I THINK IS IMPORTANT BECAUSE NOBODY'S ASKED THIS QUESTION AND IN MY MIND, IT'S CRITICAL IF WE'RE ACTUALLY GOING TO REALLY TRY TO USE THIS AS A MODEL DISEASE. THE LAST 10 SECONDS IS I JUST WANT TO TELL YOU THAT WE MADE WEB TOOLS WHERE YOU CAN GO AND YOU CAN SEARCH THREES MODULES. SO FROM OUR PAPER IN CELL WITH GEOVANY COPEOLA, WE MADE A WEB TOOL WHERE YOU FIND TED MODULES AND LOOK AT THEM AND NAVIGATE YOUR GENES. SO CAN YOU GO, IT'S INTERACTIVE AND SO YOU CAN CLICK ON THIS PEDE ORDER OF MICRONSETTER TO--SPEED ORDER OF MICRONSETTER TO--SPEED O--METABOLIZEDETTER, AND WE CAN SHOW 500 CONNECTIONS, THAT'S WHAT 500 LOOKS LIKE. WE CAN THEN 0 IN ON AN INDIVIDUAL GENES FIND THE CONNECTIONS, LINK OUT TO VARIOUS FORMS OF INFORMATION. BRAIN CARDS BRAIN SPAN, PUB MED, WHATEVER. WE COO FIND THE LINK BETWEEN THE GENES IN PUBLISHED DATA. ALL OF THE DATA, ALL OF THE NETWORK AND EXPRESSION DATA THAT UNDERLIES ALL OF OUR TABLES AND FIGURES, YOU CAN GET BY CLICKING ON THE GENE FELT SO THIS TELLS XANTHLY WHAT THE RPKM IS AND BRAIN SPAN, ET CETERA. AND IT ALLOWS YOU TO VISUALIZE AND GRAPH THE DATA FOR A PARTICULAR GENE THIS, IS SHOWING POGZ, WHAT IT'S EXPRESSED AUTISM SUSCEPTIBILITY GENE IN CHROMATIN. IT'S NETWORK CONNECTIVITY WHICH MODULE, WHICH LAMINA, THIS IS CLEARLY SHOWING IT'S NOT IN LAYER 5 NEURONS, IT'S IN LAYER 2 AND 4 NEURONS, ET CETERA. SO THIS IS THE KIND OF THING THAT YOU CAN KIND OF GO THROUGH AND LOOK AT FOR YOUR INDIVIDUAL GENES OF INTEREST. SO THESE ARE ALL MY PEOPLE IN THE LAB, I MENTIONED NEAL AS WE WENT ALONG, GRANT, VIVEK, LUISAND JASON, IRINA GINA, CONTRIBUTE TOTED--CONTRIBUTED TO EARLY PORTIONS OF THIS WORK AND KEY STATIST CAKE COLLABORATOR, WE GOT TISSUE FOR AUTISM GENE EXPRESSION FROM JONATHAN MILL AT THE IOP, WE CONTINUE TO COLLABORATE WITH HIM ON EPIGENETICS. RITA CANTOR IS A STATISTICAL GENETICIST AT UCLA BEEN CENTRAL TO OW ACCURACYATISM GENETIC STUDIES, ED LIEN AND AMILLIOY BERNARD, THE PRIME ATLAS WAS A STUDY THAT AMY DID, AND 3 LABS THAT GOT US THEIR UNPUBLISHED, GENE EXPRESSION WORK, GENE EXPRESSION FROM THE PROGENITORS, THESE ARE THE 3 LABS, KEN KOSIK, ALLISON AND RUSTY AND RICARDO, AND OUR FUND SUGGEST NIMH, SIMONS FOUNDATION AND AUTISM SPEAKS. THANKS FOR YOUR ATTENTION. [ APPLAUSE ] I APOLOGIZE ON GOING OVER. THAT'S PLAY JETLAG, I'M LAGY, DO I HAVE TIME FOR A COUPLE QUESTIONS. YEAH? A QUICKIE? IT WAS THAT CLEAR. GOOD. BYE. [ APPLAUSE ]