Boot Camp: Genetics

SO OUR OBJECTIVES ARE TO GET A FEELING FOR WHY WE USE GENETIC TESTING. I WANT TO DO A LITTLE BIT OF, AS I SAID, KIND OF BACKGROUND ON GENETICS SO WE'RE ALL SORT OF ON THE SAME LEVEL. AND I DON'T KNOW ABOUT YOU BUT I HAVEN'T HAD A GENETICS CLASS IN OVER 25 YEARS AND A LOT HAS CHANGED. I ALSO WANT TO GO OVER SOME OF THE ADVANTAGES AND DISADVANTAGES OF THE DIFFERENT GENETIC TESTING MODALITIES AND THEN WE'LL ALSO TALK ABOUT SORT OF SPECIFICALLY AUTOINFLAMMATORY GENETICS. AND I'M TAG TEAMING THIS TAL

K WITH IVONA SO I'LL BE STARTING WITH A LITTLE BIT OF BASICS OF GENETICS AND A LITTLE ABOUT THE GENETICS TECHNIQUES AND SOME OF THE PITFALLS OF GENETIC TESTING AND THEN SHE'LL GET INTO SOMG OF THE OTHER SPECIFICS OF AUTOINFLAMMATORY DISEASE. SO WHY DO WE ORIGINATE TESTS? I THINK IT'S OBVIOUS. WE WANT OUR PATIENTS TO HAVE A DIAGNOSIS. IDEALLY, WE WOULD BE ABLE TO USE THAT GENETIC TEST TO GIVE US SOME IDEA OF WHAT TO EXPECT FOR THE PATIENT. GENETICS ARE OBVIOUSLY HELPFUL FOR GENETIC COUNSELING IN

TERMS OF FAMILY PLANNING AND WHAT TO EXPECT FOR FUTURE GENERATIONS. AND THEN I THINK ONE OF THE PIE IN THE SKY ISSUES IS THAT WE COULD POTENTIALLY -- AND THIS IS INCREASINGLY HAPPENING, WE COULD POTENTIALLY USE GENETICS AND THEN TAKE THAT MUTATION AND THEN DECIDE HOW WE WANT TO TREAT THEM. HOWEVER, THERE'S A LOT OF PITFALLS WITH THIS. FIRST OF ALL, A LOT OF TIMES GENETICS IS SUPER NICE BUT MAY NOT REALLY BE THAT NECESSARY. A LOT OF TIMES WE CAN STILL MAKE THE DIAGNOSIS CLINICALLY. IN ADDITION, A

LOT OF TIMES WE GET ALL THIS INFORMATION BACK AND IT'S REALLY INCONCLUSIVE, SO OFTENTIMES YOU'RE MORE CONFUSED AFTER YOU GET THE TEST THAN YOU WERE BEFORE LAND. FOR PROT KNOW CYST, PROGNOSIS, THERE'S SO ME SITUATIONS WHERE THERE'S GOOD GENOTYPE PHENOTYPE AND YOU CAN MAKE PREDICTIONS BUT IN A LOT OF CASES WE REALLY DON'T KNOW, THAT MUTATION DOESN'T REALLY TELL US WHAT'S GOING TO HAPPEN BECAUS THERE'S SO MANY OTHER THINGS GOING ON BESIDES AT THE DNA LEVEL. A LOT OF PATIENTS ARE KIND OF TOO SCARED

TO KNOW ABOUT GENETICS AND THEN THE OTHER QUESTION IS WHAT DO YOU DO ABOUT INCIDENTAL FINDINGS AND OTHER THINGS. AND IT MAY NOT BE THAT IMPORTANT FOR THE FAMILY. THEY MAY NOT HAVE ANY FUTURE CHILDREN PLANNED. AND FINALLY I THINK FOR PHARMACOGENETICS, WE WANT TO BE THERE AND I THINK WE ARE GETTING THERE, PARTICULARLY IN SOME OF THE ONCOLOGY FIELD, BUT WE'RE REALLY NOT THERE YET, FOR BEING ABLE TO DO THAT MUCH SORT OF PRECISION MEDICINE. SO WE'LL START WITH A COUPLE OF QUICK CASES AND IVONA WILL

RETURN TO THEM AT THE END IF THERE'S TIME. TIS IS A KID A LOT OF US SEE IN ROUTINE PRACTICE. HIS FEVER IS PRETTY MUCH THE MOST COMMON PRESENTATION FOR PEDIATRICIANS. AND ACTUALLY PRETTY COMMON FOR INTERNAL MEDICINE DOCS AS WELL, BUT THIS KID COMES WITH A FAIRLY CLASSIC STORY, RECURRENT EPISODES OF FEVER THAT HAPPEN REGULARLY, EVERY MONTH AND LAST ABOUT FOUR DAYS. PRETTY MUCH EACH EPISODE IS THE SAME, STARTING WITH A SORE THROAT, SWOLLEN GLANDS AND FEELING BAD. DOESN'T HAVE ANY SIGNS OF INFECTION

SO WE DON'T SEE ANY OBVIOUS UPPER RESPIRATORY INFECTION SYMPTOMS OR ANY GASTROINTESTINAL SIGNS AND GETS TREATED WITH TYLENOL AND MOTRIN THAT HELPS A LITTLE BIT BUT WITHIN 4 TO 6 HOURS OF THE MEDICINE GOING AWAY, YOU'VE GOT TO GIVE IT BACK AGAIN. THIS IS A KID WHO HASN'T BEEN EXPOSED TO SICKNESS AND OTHER KIDS IN THE FAMILY ARE NOT GETTING SICK FROM THIS KID. SO CLASSIC RECURRENT FEVER KID, DOES THIS KIDNEYS SEQUENCING? KID NEED SEQUENCING? WE'LL SEE AND COME BACK AT THE AGAIN. SECOND IS AN ADUL

T WITH COLD URTICARIA, HAS BEEN SEEN BY SEVERAL DOCTORS, GIVEN ANTIHISTAMINES FOR HIVES AND THEY'RE NOT WORKING BUT ALSO HAS A LOT OF SYSTEMIC FEATURES LIKE FEVER, JOINT PAIN AND CONJUNCTIVITIS. NO FAMILY HISTORY AND ALL SO WHAT'S GOING ON HERE, WHAT DO WE DO AND IS THIS A PATIENT WHERE GENETIC TESTING WOULD BE HELPFUL AND IF IT IS DONE, WILL IT END UP BEING HELP FILL FUL? WE'LL START WITH MOLECULAR BIOLOGY 101. THIS IS A LIST OF TERMS. AND I'M NOT GOING TO GO THROUGH EACH OF THESE TERMS BUT I W

ANT YOU TO KIND OF PUT IN YOUR MIND A LITTLE BIT, LOOK AT ALL THESE DIFFERENT TERMS AND MAKE SURE YOU HAVE A GENERAL IDEA OF WHAT'S GOING ON. IESM GOING TO I'M GOING TO GO THROUGH ALL THESE DIFFERENT THINGS OVER THE NEXT FIVE TO 10 MINUTES AND IF THERE'S QUESTIONS, I'M CERTAINLY HAPPY TO ANSWER THEM EITHER DURING OR AFTER. BUT THE IDEA IS WE'RE GOING TO START FROM DNA AND GO ALL THE WAY TO PROTEIN. THESE ARE ALL SORT OF THE BASIC TERMS THAT ARE HELPFUL WHEN WE'RE LOOKING AT GENETIC TESTING. ALL

RIGHT. SO WE START WITH DNA. WE ALL KNOW DNA IS MADE UP OF FOUR BASE PAIRS, A, T, G, C, WE KNOW THERE'S TWO COMPLEMENTARY STRANDS, WE KNOW DNA GETS ASSOCIATED WITH HISTONES AND GETS WRAPPED AROUND AND THAT'S WHAT FORMS ACTUALLY THE FORM OF THE CHROMOSOMES. WE ALSO KNOW THESE CHROMOSOMES IN GENERAL EXIST IN PAIRS AND THERE ARE SHORT AND LONG ARMS. THAT'S SORT OF BASIC DNA AND CHROMOSOMES, THAT'S WHERE WE ARE WITH THAT. WHEN IT COMES TO WHAT'S ON THE DNA, THAT'S THE ACTUAL CODE, IT FORMS THESE GEN

ES AND THEY ARE MADE UP OF EXONS AND THERE ARE ALSO A LOT OF UNTRANSLATED REGIONS WHICH ARE IN THE BEGINNING AND THE END. ALSO THERE'S ALSO INTRONS IN THE MIDDLE WHICH ARE ALSO UNTRANSLATED, AND THEN EACH GENE HAS A TRANSCRIPTIONAL START SITE AND A STOP SITE, WHICH IS WHERE YOU SORT OF DECIDE WHERE THE MRNA IS MADE. WHEN IT COMES TO TRANSCRIPTION, THAT'S WHEN DNA GETS TRANSCRIBED INTO RNA, AND IN THAT PROCESS, THERE ARE A LOT OF THINGS THAT REGULATE THAT, INCLUDING SEQUENCES IN THE PROMOTER REGI

ON WHICH IS OFTENTIMES UPSTREAM OF THE GENE BUT ALSO CAN BE IN THESE INTRONIC REGIONS AND THERE'S ALSO A LOT OF OTHER THINGS THAT ARE ASSOCIATED WITH THE DNA THAT CONTROL HOW THAT THING IS TRAN TRANSCRIBED AND THAT'S CONTROLLED BY THESE THINGS CALLED HISTONES AND WHETHER OR NOT THINGS ARE METHYLATED OR NOT. AND THAT REGULATES THE LEVEL AND SOMETIMES POTENTIALLY SPICE FORMS AND THINGS LIKE THAT ARE HAPPENING. BUT THERE'S ALSO A LOT MORE TO IT AS WELL AT THE GENE LEVEL, THERE'S THESE THINGS CALLED

MICRO RNAs AND ALSO NON-CODING RNAs WHICH ALSO CAN HAVE AFFECT ON OTHER GENES AND A LOT OF DIFFERENT PROCESSES GOING ON IN OUR BODY. SO IT'S NOT JUST SIMPLE, YOU KNOW, DNA IS THE GENE AND THEN GENE TELLS YOU WHAT'S GOING ON. THERE'S A LOT GOING ON IN EACH DIFFERENT PHASE. ALL RIGHT. RNA ALSO GETS SPLICED AND THE IDEA IS YOU HAVE THESE INTRONS WHICH ARE NOT TRANSLATED THAT ARE SPLICED OUT, AND THEN WHAT CAN HAPPEN THOUGH IS YOU CAN ACTUALLY SUPPLIES ALTERNATIVELY SO YOU CAN ACTUALLY HAVE CERTAIN

PARTS OF THE GENE ACTUALLY COMPLETELY REMOVED SO THEN YOU END UP WITH DIFFERENT SUPPLIES FORMS OF THE GENE, AND THOSE THINGS CAN HAVE COMPLETELY DIFFERENT FUNCTION OR BE COMPLETELY NON-FUNCTIONAL. SO NOW WE'VE GONE FROM WHAT WE THINK IS A GENE IN DNA TO NOW WE HAVE COMPLETELY DIFFERENT FORMS SO YOU MAY HAVE A MUTATION IN A PARTICULAR REGION BUT IT MAY NOT MATTER BECAUSE IT MAY MOSTLY GET SPLICED OUT DEPENDING ON THE SITUATION. AFTER RNA WE GO TO PROTEIN, AND RNA TRANSLATED INTO AMINO ACIDS THAT

'S WHAT MAKES UP THE PROTEIN, WE ALWAYS HAVE A TRANSLATIONAL START SITE WHICH IS METHIONINE, WE HAVE A STOP CODON AND PROTEINS CAN BE MODIFIED IN A NUMBER OF DIFFERENT WAYS WHICH CAN ACTIVATE, DEACTIVATE OR CHANGE ITS STABILITY. AND SO EVEN THOUGH YOU HAVE THE GENE, YOU HAVE THE RNA, AND YOU MAY HAVE YOUR PROTEIN MADE BUT IT CAN COMPLETELY CHANGE DEPENDING ON ALL THESE DIFFERENT PROCESSES THAT ARE HAPPENING THAT ARE REALLY NOT DECIDED AT THE DNA LEVEL. SO THE BOTTOM LINE OF THIS SORT OF -- FROM

DNA TO PROTEIN IS DNA ISN'T THE ONLY DETERMINANT. SO AT THIS POINT, A LOT OF WHAT WE HAVE WITH THIS DNA TESTING OR GENETIC TESTING IS JUST WHAT THE SEQUENCE IS, BUT RNA IS EXPRESSED -- EXPRESSION IS REGULATED IN A LOT OF DIFFERENT WAYS, BECAUSE OF ALL THESE DIFFERENT EP YES EPIGENETICS AND PROMOTERS AND STABILITY, YOU ALSO CAN BE VERY DETERMINED BY WHICH CELLS AND TISSUE AND AGAIN AS I MENTIONED THE ALTERNATIVE SPLICING. AND THEN ONCE YOU GET TO THE PROTEIN LEVEL, YOU ALSO HAVE A LOT OF THINGS T

HAT ARE GOING ON THAT AREN'T AT THE DNA LEVEL. THE PROTEIN CAN BE EXPRESSED DIFFERENTLY BASED ON ITS STABILITY, HOW LONG IT STICKS AROUND OR WHETHER OR NOT IT'S DEGRADED, AND THEN THERE ARE A NUMBER OF DIFFERENT MODIFICATIONS THAT YOU'LL LEARN ABOUT THROUGH MORE OF THIS MEETING THAT ACTUALLY GOES ON AT THE PROTEIN LEVEL THAT ISN'T NECESSARILY GENETICALLY REGULATED. ALL RIGHT. HUMAN GENETICS 101. WE ALSO REMEMBER BACK TO OUR DIFFERENT INHERITANCE PATTERN, WE'RE GOING TO GO THROUGH AUTOSOMAL AND S

EX LINKED AND RECESSIVE AND DOMINANT A LITTLE BIT AND HOW WE DETERMINE OR DEFINE DNA VARIANTS, THAT BEING MUTATION VERSUS A SNP, MUTATION TYPES AND LOCATION AND OTHER GENETIC CHANGES WHICH ARE NOT QUITE AS SIMPLE. ALL RIGHT. THE ISSUES, IT'S NOT ALWAYS CLEAR. WE SORT OF HAVE THIS IDEA OF AUTOSOMAL OR SEX LINKED, BUT IT'S NOT ALWAYS CLEAR IF IT'S RECESSIVE OR DOMINANT AND ACTUALLY WE'VE BEEN LIVING FOR YEARS THINKING FMF IS A RECESSIVE DISEASE, WE'RE RE-THINKING THAT NOW, SO THINGS REALLY CHANGE

AROUND. AND YOU CAN SOMETIMES IN ONE DISEASE AND IN ONE GENE HAVE MULTIPLE DIFFERENT TYPES OF PRESENTATIONS BASED ON WHETHER OR NOT IT'S RECESSIVE OR DOMINANT. SO IT'S COMPLICATED AND THAT'S KIND OF THE MAIN POINT I WANT TO GET TO. IN TERMS OF DNA VARIANTS, IT'S NOT ALWAYS CLEAR WHAT'S A MUTATION AND WHAT'S A SNP. WE ALSO HAVE THESE INCOMPLETE PENETRANT VARIANTS WHICH WE'LL TALK ABOUT A LITTLE BIT LATER, AND THEN THERE'S ALSO THIS CONCEPT OF SOMATIC MOSAICISM IN WHICH WE HAVE MUTATIONS THAT OCCU

R LATER ON IN DEVELOPMENT OR EVEN IN ADULTHOOD THAT CAN TOTALLY LINK TO DISEASE THAT AREN'T THERE PRESENT, SO IF YOU'RE NOT LOOKING AT THE RIGHT TISSUE OR CELLS, YOU MAY ACTUALLY MISS MUTATIONS IN THE PATIENT. ALL RIGHT. A COUPLE THINGS ABOUT INHERITANCE PATTERNS. FOR AUTOSOMAL VERSUS SEX LINKED, IF YOU HAVE MALES AFFECTED ONLY IT'S A PRETTY GOOD IDEA YOU HAVE SOMETHING SEX LINKED. IF YOU HAVE MALE TO MALE TRANSMISSION, THEN YOU'RE LOOKING MOST LIKELY AT AUTOSOMAL DOMINANT DISEASE. IF YOU'RE LOO

KING AT RECESSIVE DISEASE, YOU'RE LIKELY TO HAVE SKIPPING OF GENERATIONS. YOU ALSO COMMONLY SEE IN CERTAI POPULATIONS WHERE THERE'S A LOT OF CON SANK NEWT. THERE'S ALSO THIS GAIN OR LOSS OF FUNCTION. THAT OFTENTIMES CAN BE A DEBATE BECAUSE YOU CAN SORT OF HAVE A LOSS OF A INHIBITORY FUNCTION WHICH CAN LOOK LIKE A GAIN OF FUNCTION, AND THERE'S A WHOLE CONCEPT OF DOMINANT NEGATIVE, GAIN OF FUNCTION IS LEADING TO A NEGATIVE EFFECT. THESE THINGS GET TOSSED AROUND A LOT WITH GAIN OR DOMINANT NEGATIVE

. AUTOSOMAL AND SEX LINKED ARE NOT ALWAYS CLEAR, SAME THING WITH RECESSIVE AND DOMINANT AND AGAIN YOU CAN HAVE THIS INCOMPLETE PENETRANCE WHICH CAN MESS UP THE WHOLE SORT OF CONCEPT AND AGAIN, ALL THESE DIFFERENT IDEAS ABOUT GAIN OR LOSS OF FUNCTION ARE NOT COMPLETELY CLEAR. ALL RIGHT. HERE'S OUR BASIC PEDIGREES. YOU REMEMBER THE AUTOSOMAL DOMINANT, THAT'S UP IN THE UPPER LEFT CORNER AND THERE YOU'RE GOING TO SEE NO SKIPPING OF GENERATIONS, YOU'RE GOING TO SEE MALE TO MALE TRANSMISSION. FOR AUTO

SOMAL RECESSIVE, YOU'RE GOING TO HAVE PARENTS WHO ARE POTENTIALLY UNAFFECTED SO THOSE ARE YOUR CARRIERS AND THEN THEY HAVE EITHER AFFECTED KIDS, CARRIERS OR UNAFFECTED KIDS. FOR THE X-LINKED YOU'RE GOING TO SEE MOSTLY FEMALES AS THE TRANSMITTERS AND MALES AS THE PATIENTS THAT ARE AFFECTED, AND THEN IN VERY RARE SITUATIONS YOU HAVE THE X-LINKED DOMINANT. I'M NOT EVEN GOING TO GO INTO THAT BECAUSE IT'S SO RARE. BUT HERE'S SORT OF A GENERAL IDEA OF HOW THINGS SORT OF HAPPEN WHEN YOU HAVE A DOMINANT

DISEASE, YOU HAVE A 50% CHANCE OF PASSING IT ON, AUTOSOMAL RECESSIVE DISEASE IN TWO CARRIERS, 25% OF IT GOING ON. IT'S ALL BECAUSE WE HAVE TWO DIFFERENT CHROMOSOMES THAT THEN SORT OF GIVE YOU THE OPTIONS EITHER WAY. WITH THE X-LINKED YOU HAVE THE CARRIER MOTHER AND X-LINKED AN AFFECTED FATHER WHO THEN CAN PASS IT ON TO DAUGHTERS WHICH IS EXTREMELY UNUSUAL. ALL RIGHT. WHAT WE TALKED ABOUT MOSTLY ON THESE INHERITED THINGS ARE SITUATIONS WHERE MOM OR DAD PASSES IT ON. THE OTHER POSSIBILITY IS DE N

OVO MUTATIONS. WE SEE THAT A LOT IN AUTOSOMAL DOMINANT DISEASES. BUT THE OTHER THING WE SEE PRIMARILY IN THESE AUTOSOMAL DOMINANT DISEASES IS THIS CONCEPT OF SOMATIC MOSAICISM. WHAT HAPPENS IS THERE CAN BE A SOMATIC MUTATION THAT OCCURS AT DIFFERENT POINTS OF DEVELOPMENT. IT COULD OCCUR VERY EARLY IN DEVELOPMENT, IN WHICH CASE YOU WOULD HAVE A LARGE NUMBER OR PERCENTAGE OF YOUR CELLS WITH THAT MUTATION, BUT CAN ALSO HAPPEN LATER ON IN LIFE AND EVEN JUST PARTICULARLY IN ONE PARTICULAR CELL LINE,

SO IT COULD BE JUST IN MYELOID CELLS LIKE WE SEE IN SOME OF OUR PATIENTS WITH AUTOINFLAMMATORY DISEASES. AND IN SOME SITUATIONS, YOU MAY HAVE AS SMALL AS 5 OR 10% OF A PARTICULAR CELL TYPE LIKE A MYELOID CELL POPULATION THAT'S AFFECTED WITH MUTATION, AND THAT CAN ACTUALLY GIVE YOU A PHENOTYPE. IT MAY BE A LATER ONSET PHENOTYPE, IT MAY BE A SLIGHTLY DIFFERENT PHENOTYPE BUT IT CAN ALSO BE A FULL PHENOTYPE. THIS CAUSES ALL KINDS OF PROBLEMS WHEN YOU'RE THINKING ABOUT GENETIC TESTING BECAUSE, ONE, Y

OU MAY BE GETTING A BLOOD TEST OR A SALIVA TEST TO GET YOUR GENETIC TEST, BUT YOU MAY NOT BE LOOKING AT THE RIGHT CELLS OR THE NUMBER OF CELLS THAT ARE ACTUALLY AFFECTED MAY BE SO LOW THAT YOUR GENETIC TECHNIQUE MAY ACTUALLY NOT BE ABLE TO DETECT AT A LEVEL OF SENSITIVITY THAT CAN ACTUALLY PICK UP THE MUTATION. IT ALSO COMPLETELY MESSES UP OUR ABILITY TO DO GENETIC COUNSELING, BECAUSE IN A LOT OF WAYS, WE WOULD OFTEN SAY OKAY, WE THINK YOUR CHILD HAS AN AUTOSOMAL DOMINANT DISEASE THAT OBVIOUSLY

IS A DE NOVO MUTATION BUT WE MAY BE WRONG BECAUSE IT COULD BE THAT THE PARENT MAY ACTUALLY HAVE A GONAD ALAMO SAKE AND COULD HAVE ANOTHER CHILD WITH THE DISEASE. SO TONS OF SITUATIONS WHERE IT SORT OF MESSES UP OUR WHOLE IDEA. NOW TO MUTATIONS. USUALLY IN MY TALKS I SHOW SURFING PICTURES. THIS TIME I'M ONLY GOING TO SHOW YOU SURFING AS A WORD. ANYWAY, BUT WHAT HAPPENS IN DIFFERENT TYPES OF MUTATIONS IS WE HAVE SUBSTITUTIONS WHERE YOU HAVE A SINGLE CHANGE IN A BASE PAIR, YOU WOULD CHANGE THEN YOU

R SPELLING OF SURFING. YOU CAN ALSO HAVE INSERTIONS IN WHICH YOU HAVE AN ADDITION OF A BASE PAIR OR COULD ALSO BE THREE DIFFERENT BASE PAIRS WHICH WOULD THEN LEAD TO A PROBLEM WITH TRANSLATION. YOU CAN HAVE A DELETION AND THAT COULD BE A SITUATION WHERE YOU JUST LOSE ONE OR SOMETHING IN DIVISIBLES OF THREE IN WHICH YOU JUST LOSE -- DON'T MESS UP THE FRAME OF THE TRANSLATION, OR YOU CAN HAVE A COMPLETE TRUNCATION WHERE YOU HAVE AN EARLY STOP. AND THOSE ARE SORT OF THE DIFFERENT TYPES OF MUTATIONS

THAT WE GET. PROBLEMS, WELL, YOU CAN HAVE A VIOLENT MUTATION THAT DOES ABSOLUTELY NOTHING, IT COULD CHANGE THE AMINO ACID BUT STILL NOT HAVE ANY MAJOR EFFECT OR YOU COULD HAVE A CHANGE IN THE FRAME BUT SOMETIMES THAT CAN BE CORRECTED AS WELL. WHERE ARE MOST MUTATIONS? MOST ARE IN THE EXONS. THERE ARE SOME THAT ARE IN THE SUPPLIES SITES AND THEY MAY NOT AFFECT THE SPECIFIC TRANSLATION BUT COULD ACTUALLY AFFECT WHICH -- HOW MANY EXONS ARE ACTUALLY PUT INTO THIS ALTERNATIVE SUPPLIES FORM, AND THEN

AGAIN, THERE ARE ALSO MUTATIONS THAT CAN OCCUR IN PROMOTERS OR INTRONIC REGULATORY SEQUENCE. AND THAT MAKES A DIFFERENCE DEPENDING ON THE TYPE OF GENETIC SEQUENCING TECHNOLOGY YOU'RE GOING TO USE. ALL RIGHT. SO WHAT ARE SOME OTHER GENETIC CHANGES? YOU CAN HAVE DELETIONS, CAN YOU WE FOUND THAT IN SOME OF THE DISEASES WE'LL HEAR ABOUT LATER. YOU CAN ALSO HAVE COPY NUMBER VARIANTS IN WHICH CAN YOU HAVE ENTIRE GENES DUPLICATED OR ENTIRE GENES DELETED OR YOU CAN HAVE LARGE DELETIONS OR DUPLICATIONS

IN OR ENTIRE CHROMOSOME NUMBER CHANGES AS WELL. DIFFERENT TECHNIQUES OR TECHNOLOGIES ARE BETTER OR WORSE AT PICKING UP THESE DIFFERENT TYPES OF GENETICS CHANGES. SO HOW DO WE DO GENETIC TESTING? OLD SCHOOL, WE USED TO DO VERY MUTATION-SPECIFIC EITHER DONE BY HYBRIDIZATION OR ALLELE-SPECIFIC PCR. THAT'S NOT USED VERY MUCH ANYMORE. THE OLD SCHOOL WAY OF SEQUENCING, WHICH STILL IS CONSIDERED SORT OF THE GOLD STANDARD, OFTENTIMES IS USED TO SORT OF CONFIRM SOMETHING, IS SANGER SEQUENCING, THAT'S USE

LN AN EXON BY EXON TYPE APPROACH, BUT WHAT'S HAPPENING NOW, AND PRETTY MUCH ALL OF THE -- MANY OF THE RESEARCH AND NOW COMMERCIAL TESTING ARE THESE NEXT GENERATION SEQUENCING PLATFORMS AND THIS IS REALLY THE WAY WE DO THINGS, AND THAT CAN EITHER BE USED IN TERMS OF GENE PANELS WHICH WE'LL TALK ABOUT, EXOME SEQUENCING WHICH WE'LL TALK ABOUT, GENOME SEQUENCING OR EVEN TRANSCRIPTOME WHERE WE'RE JUST LOOKING AT THE RNA AS WELL. AND SO IF YOU LOOK AT SORT OF ALL THE DIFFERENT CLINICAL TESTING SITES,

THERE'S A NUMBER OUT THERE, MOST ARE NOW USING NEXT GEN SEQUENCING BUT THERE ARE ISSUES WITH THESE -- DOING THESE IN TERMS OF GETTING INSURANCE TO COVER IT, THAT'S A BIG ISSUE WE'RE HOPING TO SOLVE IN THE NEXT COUPLE DAYS IN OUR WORKING GROUPS, AND THEN ALSO WHEN YOU DO GENETIC TESTING, ARE YOU PREPARED TO DEAL WITH THAT IN TERMS OF GENETIC COUNSELING BECAUSE YOU MAY END UP LEARNING A LOT OF THINGS THAT YOU WEREN'T NECESSARILY EXPECT OR NOT KNOW WHAT TO DO WITH. P CR IS SORT OF THE BASIS OF A L

OT OF THIS STUFF AND IS SORT OF THE BASIS OF BEING ABLE TO REPLOA DUES DNA. IT'S USED BY CREATING THESE PRIMERS THAT SURROUND THE AREA YOU WANT TO AMPLIFY AND THEN YOU CAN THEN EITHER SEE THAT AMOUNT OF DNA OR YOU CAN ACTUALLY SEQUENCE IT AND THAT MAKES A BIG DIFFERENCE. AGAIN SANGER SEQUENCING IS BASED ON SORT OF PCR. IT'S AN IDEA WHERE DYES ARE PUT AT THE END OF EACH DIFFERENTOLOGY MER AS IT'S CREATED, THAT'S HOW WE GET PEACE PEAKS OF DIFFERENT COLORS,. WITH NEXT GEN IT'S MORE SHOTGUN APROA. Y

OU ACTUALLY DO A NUMBER OF DIFFERENT AMPLIFICATIONS AND THEN YOU JUST TILE THEM ALL TOGETHER AND HOPE TO GET ENOUGH COVERAGE SO YOU CAN ACTUALLY TRUST YOUR SEQUENCE. THERE'S A NUMBER OF DIFFERENT WAYS TO DO THAT. 4-5-4, DEEP SEQUENCING, THINGS LIKE THAT, BUT ALL BASED ON GETTING GENOME DNA, CAPTURING IT IN SOME WAY AND USING PCR IN ORDER TO GIVE US A LOT OF DIFFERENT THINGS. BUT THERE'S ACTUALLY A NEWER TECHNOLOGY, THESE LONG ROOT TECHNOLOGIES READ TECHNOLOGIES WHERE YOU CAN GET LONG PIECES OF D

NA AND THAT CAN REDUCE THE ERROR RATE, ALLOW FOR EASIER ASSEMBLY AND BETTER ACCURACY, AND ALSO HELP YOU WITH COPY NUMBER, A PROBLEM WE SOMETIMES SEE, AND CAN ALSO ALLOW FOR TRANSCRIPTOME SEQUENCING. THAT MAY BE SOMETHING WE SEE MORE WHICH THEN ALLOWS YOU TO FIGURE OUT THESE SUPPLIES VARIANTS AND THINGS SPLICE VARIANTS. IT'S LETS YOU CAPTURE HAPLOTYPES, LARGE STRETCHES OF DNA THAT ACTUALLY SEEM TO RUN TOGETHER IN DIFFERENT POPULATIONS. ALL RIGHT. THE PROBLEM WITH ALL THIS EXCITING NEW TECHNOLOGY

IS THAT WE ARE GETTING TONS OF INFORMATION, BUT WE DON'T KNOW HOW TO DEAL WITH IT. AND THE REAL PROBLEM HAS BEEN THAT THE COST HAS COME DOWN SO QUICKLY, FASTER THAN WE'RE ACTUALLY ABLE TO COMPUTE IT AND SORT OF DEAL WITH IT IN THAT WAY AND FASTER FOR OUR MINDS TO BE ABLE TO SORT OF DEAL WITH IT. SO THIS PROCESS OF GENERATING DATA CAN HAPPEN REALLY QUICKLY. AT OUR INSTITUTION, THEY CAN GENERATE A SEQUENCE WITHIN A DAY AND HOPE TO HAVE IT ANALYZED WITHIN A COUPLE DAYS. BUT THE REAL PROBLEM IS THAT

SORT OF HUMAN PART AT THE END, WHERE IT REQUIRES SORT OF HUMANS TO SORT OF DO IT. WHAT'S HAPPENING MORE AND MORE IS AI AND PEOPLE WHO ACTUALLY GET IN THE COMPUTERS TO DO MORE AND MORE OF THESE LAST STEPS OF THE PROCESS, BUT STILL YOU NEED SOMEONE TO THINK ABOUT IT. AND THAT MAY AGAIN COME DOWN TO COMPUTERS IN THE FUTURE, BUT THAT'S WHERE WE'RE AT. SO THE MAIN BOTTLENECK IS REALLY THIS DATA ANALYSIS, SO WE'RE STILL TRYING TO SORT OF FIGURE OUT HOW TO DEAL WITH WHAT TO DEAL WITH ALL THIS INFORMAT

ION, IF IT'S POSITIVE OR NEGATIVE AND WE REALLY ARE DROWNED A LOT OF TIMES IN THIS NEXT GENERATION. IN THE LAST FEW MINUTES, I'LL GO THROUGH JUST SORT OF WHAT WE THINK ABOUT WHOLE GENOME VERSUS EXOME VERSUS JEAN PANELS. SO ON THE TOP OF THE SLIDE, IT SORT OF GIVES YOU -- THOSE OF WHO YOU ARE READERS AND THINK ABOUT -- I WANT TO GIVE YOU AN IDEA OF THE MAGNITUDE OF THIS STUFF. FOR THOSE OF YOU WHO HAVE READ "WAR AND PEACE," I HAVEN'T, ACTUALLY, IT'S 3 MILLION LETTERS. BUT IF YOU'RE GOING TO DO AN

ENTIRE GENOME, A WHOLE GENOME SEQUENCE, YOU'RE LOOKING AT 3 BILLION BASES, SO THAT'S A THOUSAND COPIES OF "WAR AND PEACE." SO TO BRING YOUR DNA SEQUENCE, YOUR WHOLE GENOME SEQUENCE TO YOUR DOCTOR, THAT WOULD NEED A TRUCK TO BRING IT IN. GENOME SEQUENCE IS MORE MANAGEABLE BUT STILL TALKING ABOUT 10 BOOKS OF "WAR AND PEACE" TO GET THROUGH THE WHOLE THING. GENE PANELS MAY BE JUST A FEW CHAPTERS BUT STILL A LOT OF DNA AND A LOT TO GO THROUGH. IF YOU'RE NOT A READER BUT A SPORTS PERSON, THIS IS HOW

IT KIND OF WORKS THIS WAY. FOR A GENOME, YOU BASICALLY WATCH THE ENTIRE FOOTBALL GAME FROM THE BEGINNING TO THE END. YOU GET EVERY LITTLE DETAIL, EVERY LITTLE PLAY THAT'S HAPPENED, ALL THAT KIND OF STUFF. AN EXOME IS LIKE READING ABOUT IT THE NEXT DAY. YOU SORT OF HEAR ABOUT ALL THE IT GOES THROUGH WHAT HAPPENED IN THE FIRST QUARTER AND THE SECOND QUARTER. BUT IF YOU'RE DOING THESE PANELS, ALL YOU'RE REALLY DOING IS FOCUSING ON ONE OR TWO PLAYERS AND SORT OF SEEING WHAT THEY DO. SO YOU GET A SEN

SE FOR MAGNITUDE OF SORT OF WHAT YOU GET WITH THESE DIFFERENT TECHNIQUES. ALL RIGHT. I WON'T GO THROUGH THIS BECAUSE IT'S A LOT TO SORT OF GO THROUGH, BUT THE CONCEPT IS, IS THAT WITH SANGER SEQUENCING YOU'RE LIMITED TO RILEY REALLY A FEW GENES, YOU'RE LIMITED IN YOUR SIZE, AND THE COST IS RELATIVELY CHEAP PER EACH SEQUENCE BUT AGAIN YOU'RE NOT GETTING THE KIND OF INFORMATION YOU GET WITH THESE PANELS, YOU CAN GET SOMETIMES UP TO 300 GENES IN A PANEL, AND YOU'RE ABLE TO GET A& FAIR AMOUNT OF DEP

TH FOR THESE THINGS AS WELL. FOR WHOLE EXOME, YOU'RE LOOKING AT A TOTAL OF 20,000 GENES. MOST OF THE CODING REGIONS ARE COVERED PRETTY WELL BUT NOT ALWAYS, THERE'S ALWAYS SOME AREAS THAT AREN'T REALLY COVERED THAT WELL. YOU CAN GET FAIR DEPTH BUT SOMETIMES YOU'RE NOT THAT GREAT, AND WHEN YOU GET TO WHOLE GENOME SEQUENCING, YOU ARE DEALING WITH NOT JUST THE 20,000 GENES BUT ALL THE OTHER STUFF AS WELL. AND AGAIN YOU DON'T GET QUITE AS GOOD COVERAGE A LOT OF TIMES AND COSTS ARE COMING DOWN TO THE

POINT WHERE WHOLE GENOME IS ACTUALLY LESS THAN WHOLE EXOME IN A LOT OF SITUATIONS. ALL RIGHT. SO THIS IS WHERE I PASS ON THE BATON TO IVONA AND SHE'LL TALK A LITTLE ABOUT HOW WE TAKE ALL THIS INFORMATION AND DEAL WITH IT IN AUTOINFLAMMATORY DISEASES. THANKS SO MUCH. [APPLAUSE]