Secondary or Incidental Findings from Exome Sequence Data - Jennifer Johnston


Uploaded by GenomeTV on 14.10.2011

Transcript:
>> SO I AM JENNIFER JOHNSON WORKING IN THE LAB AND I'M A
STAFF SCIENTIST. AND I'M GOING TO TALK TO YOU
ABOUT SECONDARY VARIANTS. SO IT'S NOT THE EXCITING PART OF
THE PRESENTATION BUT IN SOME WAYS IT COULD BE EXCITING.
AND I HAVE TWO POINTS THAT YOU'LL TAKE HOME TODAY FOR MY
TALK. IF YOU'RE DOING EXOME OR GEE NO
ONE SEQUENCING, THEY FOR YOUR DATA AND I HOPE TO CONVINCE YOU
OF THE SECOND POINT, YOU REALLY NEED TO LOOK AT THEM AND THINK
ABOUT RETURNING SOME OF THEM TO YOUR PATIENTS.
SO I'M GOING TO START MY TALK BY GOING THROUGH RETURNING VARIANTS
BUT A LOT OF MY TALK WILL BE VERY DETAILED LIKE HOW DO YOU GO
ABOUT ANALYZING THEM AND I THINK IT WILL BE MORE IN-DEPTH THAN
SOME OF THE OTHER TALKS SO HOPEFULLY PEOPLE HERE ARE DOING
EXOME SEQUENCING WILL APPRECIATE THIS AND HOPEFULLY I WON'T LOSE
OTHERS OF YOU. WITH THAT, I CAN JUST --
SO, QUAWE HAVE BEEN TALKING ABOUT IS PRIMARY VARIANTS.
AND PRIMARY VARIANTS ARE THE REASON FOR MOST OF YOU DOING
THIS RESEARCH. IT IS A ONE OR TWO VARIANTS SO
RESPONSIBLE FOR DISEASE. WE ARE TAKING PRO BANS THAT HAVE
INTERESTING DISEASES. WE ARE DOING WHOLE EXOME AND
WHOLE GENOME. AS YOU HEARD, WE END UP WITH
TENS OR HUNDREDS OF THOUSANDS OF VARIANTS.
WE USUALLY GET UP TO 100 AND MAYBE GENE DISCOVERY AND
FUNCTIONAL STUDIES. WHAT DO WE DO IS --
MANY IGNORE THEM. WE ARE DOING FUNCTIONAL STUDIES
AND WRITING PAPERS AND THESE VARIANTS ARE LIVING IN OUR
COMPUTER IN A FILE SOMEWHERE. I HOPE TO CONVINCE YOU THAT YOU
NEED TO TAKE THEM OFF THE SHELF, ANALYZE THEM, AT LEAST LOOK AT
THEM AND MAKE SURE THERE IS NOTHING THERE YOU NEED TO BE
RETURNING TO YOUR PATIENTS. IN OUR LAB IT'S THE SECONDARY
LINE OF RESEARCH. WE WANT TO UNDERSTAND WHICH OF
THESE VARIANTS ARE HELPFUL TO OUR PATIENTS AND WHICH ONES DO
THEY WANT TO GET BACK AND WHICH ONES WILL RETURN TO OUR PATIENTS
AND THE THEY USE FOR THEIR HEALTH CARE.
I THINK YOU HAVE AN ETHICAL OBLIGATION TO RETURN THEM TO
YOUR PARTICIPANTS AND HOPEFULLY I'LL CONVINCE YOU BY THE TIME WE
GET DONE. I DON'T THINK I'M THE ONLY ONE
THAT FEELS THIS WAY. THE NHLBI CONVENED A PANEL IF
2010 AND SET FORTH GUIDELINES FOR RESEARCH RESULTS THAT SHOULD
BE RETURNED TO PARTICIPANTS. THEY SPLIT THEM INTO THOSE THAT
SHIP RETURNED AND, COULD BE RETURNED AND THEN THOSE THAT
DON'T NEED TO BE RETURNED. BUT THE CRITERIA THEY PUT
FORWARD FOR RESULTS THAT SHOULD BE RETURNED INCLUDED IMPORTANT
HEALTH IMPLICATIONS FOR YOUR PARTICIPANTS.
THAT WOULD MEAN THERE IS AN ESTABLISHED AND SUBSTANTIAL RISK
OF THAT INDIVIDUAL'S HEALTH. THE FINDINGS SHOULD BE
ACTIONABLE. THERE SHOULD BE THERAPY OR
PREVENTION THAT YOU COULD CHANGE THE COURSE OF THE DISEASE AND I
THINK NEWBORN SCREENING HERE, BUT IT'S THE SAME KIND OF THING.
IF YOU'RE GOING TO GIVE RESULTS BACK TO PATIENTS WHEN YOU'RE NOT
EXPECTING THEM, THERE IS SOMETHING YOU CAN DO ABOUT THESE
VARIANTS. THE TESTS OBVIOUSLY HAVE TO BE
ANALYTICALLY VALID. YOU HAVE TO KNOW THE RESULTS ARE
TRUE. DISCLOSURES SHOULD COMPLY WITH
LAWS AND THE PARTICIPANT HAS TO OPT IN TO RECEIVE THE RESULTS.
AT SOME POINT THERE HAS TO BE A DISCUSSION WITH THE PARTICIPANT
ABOUT RETURN OF SECONDARY FINDINGS AND WHAT THEY WOULD
WANT TO HEAR OR WHAT THEY WILL HEAR IN THE FUTURE.
NHLBI PANEL ALSO PUT OUT THIS RETURN RESULT AND THE MAIN THING
HERE IS THAT THE BENEFIT TO OUT WEIGH THE RISK AND THEY SAID IN
THE PARTICIPANT'S PERSPECTIVE. NOW THIS IS REALLY INTERESTING
BECAUSE UNLESS YOU HAD THAT CONVERSATION WITH YOUR PRO BAN,
YOU WILL NEVER KNOW WHAT THEIR PERSPECTIVE IS SO THIS IS GOING
TO BE SOMETHING THAT I THINK IS GOING TO BE HARD FOR SCIENTISTS
TO NECESSARILY DO BUT THIS IS WHAT NHLBI SUGGESTED WE SHOULD
THINK ABOUT PERSPECTIVES OF OUR PARTICIPANTS WHEN THINKING ABOUT
WHAT RESULTS WE WILL RETURN THAT DON'T FALL INTO THAT "SHOULD
RETURN" CACATEGORY. SO COMPLAIN WITH LAWS.
I THINK THE MAIN THEN WHY S. WE HAVE TO THINK ABOUT IS THE
CLINICAL LABORATORY IMPROVEMENT AMENDMENT ACT OF 1988.
BASICALLY THIS SAYS THAT WE AS SCIENTISTS AND RESEARCH LABS
CANNOT RETURN THESE RESULTS TO INDIVIDUALS UNLESS THEY HAVE
BEEN VALIDATED IN A CLINICAL OR A CERTIFIED LABORATORY.
YOU CAN CERTIFY YOUR OWN LABORATORY OR OUTSOURCE THIS.
IF YOU ARE GOING TO RETURN THESE RESULTS, BEEN THE FACT THAT
THERE ARE LAWS THAT SAY THEY REALLY SHOULD BE VALIDATED.
I'M JUST GOING TO MENTION THE FACT THAT IN 1995, WELL BEFORE
THE AGE OF EXOMES AND WHOLE GENOMES, THE AMERICAN SOCIETY OF
HOW MANY GENETICS SUGGESTED WE SHOULDN'T BE TESTING MINORS FOR
DISEASES, DISEASE MUTATIONS, FOR THAT KNOWLEDGE WASN'T GOING TO
HELP THEM UNTIL THEY WERE AN ADULT.
OF COURSE IF YOU'RE RUNNING EXOMES AND GENOMES, EVEN IF
YOU'RE NOT TRYING TO TEST FOR BRCA1 MUTATIONS, YOU ARE, BY THE
NATURE OF WHAT YOU'RE DOING TESTING FOR THE 1 OR 2
MUTATIONS. YOU NEED TO THINK ABOUT THIS
BEFORE YOU DO THE TESTS. WHAT ARE YOU GOING TO RETURN TO
THESE MINOR PATIENTS? HOW ARE YOU GOING TO DO THAT?
HOLD THE RESULTS? GIVE THEM BACK NOW?
NOT GOING TO TELL YOU THE RIGHT THING TO DO BUT IT'S SOMETHING
YOU NEED TO THINK ABOUT. SO AT THIS POINT, YOU HAVE
DECIDED YOU ARE GOING TO RETURN YOUR SECONDARY VARIANTS.
I'M JUST GOING TO GO O IF YOU WANT TO AGREE THAT'S FINE.
WHAT DO YOU RETURN? I THINK ABOUT THIS IN THREE
DIFFERENT LEVELS. I THINK ABOUT DISEASES THAT ARE
IMPORTANT TO MY PATIENTS. I THINK THE GENES THAT I KNOW
FOR SURE CAUSE THOSE DISEASES AND THEN I THINK VARIANTS THAT I
FEEL HAVE ENOUGH EVIDENCE OF CAUSATION THAT I'M GOING TO
RETURN THEM. WE ALREADY TALKED ABOUT THE FACT
THAT THE DISEASES SHOULD HAVE AN OBVIOUS AND SEVERE THREAT.
IT SHOULD BE ACTIONABLE AND TREATABLE.
YOU CAN THINK ABOUT THE FACT THAT IF YOUR PATIENT IS GOING TO
BE DIAGNOSED WITH THIS DISORDER IN ANOTHER WAY, IF HE IS GOING
TO WALK INTO HIS DOCTOR'S OFFICE AND HIS DOCTOR WILL SAY, YOU
HAVEAL BINISM, FOR EXAMPLE, THEN YOU DON'T NEED TO RETURN A
VARIANT TO HIM TELLING HIM HE HAS SOMETHING THAT IS OBVIOUS
BUT IF IT'S SOMETHING THAT IS NOT OBVIOUS, MAYBE
SUSCEPTIBILITY VARIANT, THAT'S SOMETHING YOU SHOULD CONSIDER
RETURNING TO HIM. PRO BAN VERSUS DESCENDANT RISK.
I LOOK AT, IF IT AFFECTS THE PRO BAN, THAT'S MORE IN THE SHOULD
RETURN CATEGORY. IF IT'S AFFECTING DESCENDANTS,
MAYBE THAT'S IN THE KICKED RETURN CATEGORY.
THESE ARE SOME OF THE DISEASEY WE CONSIDER WITH OUR CLIN SEEK
COHORT. IT'S A CLINICAL SEQUENCING STUDY
WE ARE INVOLVED INO OUR LAB. WE ARE ANALLING FOR OVER 1000
EXOMES. THE DATA SOURCES LI SHOW YOU IS
572 EXOMES. WE ARE TAKING ANITTATIVE
APPROACH TO SECONDARY VARIANTS. WE HAVE ALREADY ANNOTATED CANCER
PREDISPOSITION SYNDROMES IN THIS STATUS SET.
WE LOOKED AT HYPERTROPEIC CARDIOMYOPATHY, MALIGNANT
HYPOTHERM YACHT THE LIST GOES ON.
WE HAVE ALREADY DONE THESE ANNOTATIONS IN OUR DATASET AND
THEY ARE ONGOING. WE ARE CAN --
WE ARE WORKING ON THEM. OTHER THINGS TO THINK ABOUT IS
THROMPHILIA, HEMACHROMATOSIS, PHARMACOGENETICS, SOMETHING WE
HAVEN'T TOUCHED, ADULT ONSET DISORDERS AND CARRIER VARIANTS
WHICH WE HAVE DONE SOME ANNOTATION NO, SIR THIS PATIENT
SET. SO I MENTIONED THE THREE LEVELS.
THE GENE LEVEL, YOU CAN GET INFORMATION ON DISEASES EITHER
IN HUMAN GENE MUTATION DATABASE, ONLINE MANDELIAN OR GENE TESTS.
A LOT OF OTHER PLACES. YOU WANT TO MAKE SURE THIS ISN'T
RESEARCH. YOU WANT TO MAKE SURE YOU'RE
LOOKING AT GENES THAT YOU THINK REALLY ARE HAVE A LINK TO THE
DISEASE YOU'RE INTERESTED IN. AS FAR AS VARIANTS, YOU WANT TO
RETURN VARIANTS THAT ARE KNOWN TO BE CAUSATIVE.
YOU CAN RETURN NOVEL VARIANTS. THEY WILL BE VARIANTS THAT LOOK
MUCH LIKE THINGS YOU KNOW ARE CAUSATIVE THAT WILL BE HIGHLY
LIKELY TO BE CAUSATIVE IN A GENE YOU KNOW THAT CAUSES DISEASE.
YOU MIGHT UPON WANT TO RETURN THEM AND YOU SHOULD CONSIDER THE
AFFECT OF TELLING VERSUS NOT TELLING.
IF YOU HAVE VARIANTS WHERE YOU'RE NOT 100% CERTAIN THAT
THEY CAUSE DISEASE, IF IT'S A CARRIER VARIANT, THAT'S ONE SET
OF THINGS YOU WILL HAVE TO THINK ABOUT.
IF IT'S CDH1 THAT CAUSES STOMACH CANCER AND THE ONLY THING THEY
CAN DO IS HAVE THEIR STOMACH REMOVED TO PROTECT THEM, YOU
BETTER BE 100% SURE THAT VARIANT IS CAUSATIVE BEFORE YOU RETURN
THAT TO YOUR PRO BAN. NOW WE HAVE TO START FILTERING
VARIANTS. THIS IS WHERE IT GETS KIND OF
HEAVY. SO FOR THOSE WHO AREN'T DOING
WHOLE EXOME AND WHOLE GENOME SEQUENCE, I APOLOGIZE AHEAD OF
TIME. I'M GOING TO TALK ABOUT THE
TOOLS THAT WE USE IN OUR LAB, MANY OF YOU USING DIFFERENT
TOOLS. I'M GOING TO TALK ABOUT THIS
KIND OF IN A SET SEQUENCE. YOU CAN DO THIS IN MANY
DIFFERENT WAYS. IT ISITTATIVE.
BUT THIS IS WHAT WE DO -- ITERATIVE.
WE USE BAR SISTER AS OUR ANNOTATION SOURCE.
ONCE WE DO OUR INITIAL FILTERING, WE GO OUT TO
DATABASES. SO IN OUR LAB, WE USE THE HUMAN
GENE MUTATION DATABASE AND LOOK AT SPECIFIC DATABASES TO
GATHERER INFORMATION ABOUT OUR VARIANTS.
WE ANALYZE THE SUPPORT FOR CAUSATION WHICH MEANS THOSE
GOING TO THE DATABASES AS WELL AS TO THE PRIMARY LITERATURE AND
THEN WE DECIDE WHETHER TO RETURN THESE VARIANTS.
SO WHAT DOES THIS LOOK LIKE? LUCKILY FOR MOST OF YOU YOU, I
THINK YOU WILL BE WORKING ON TRIOS.
THAT'S A SMALLER NUMBER. WE ARE WORKING ON CLIN SEEK
RIGHT NOW AND I THOUGHT I'D WALK YOU THROUGH THIS DATASET.
SO RIGHT NOW WE HAVE 572 PRO BANDS THAT WE ARE LOOKING AT.
THERE ARE TWO MILLION UNIQUE VARIANTS.
HOWEVER, IN ORDER TO USE OUR COMPUTERS AND HAVE IT WORK AT A
SPEED THAT IS REASONABLE, WE USE FILTER DATASET TO NON71 MUS,
STOP AND SLICED VARIANTS AND GOT 10 DOWN TO 182,000.
THESE ARE OUR SECONDARY VARIANTS TO LOOK AT AND ASK OURSELVES DO
WE RETURN THEM OR NOT RETURN THEM?
I ALREADY TOLD YOU THAT THE FIRST THING WE DO IS ITERATIVE
PROCESS. WE LOOK AT CERTAIN DISEASES AND
THE FIRST THING WE DID WAS WE LOOKED AT GENES KNOWN TO CAUSE
HIGH SUSCEPTIBILITY CANCER SYNDROMES.
THIS IS JUST A LIST OF 37 GENES TAKEN FROM LYNN.
THESE ARE ALL KNOWN TO CAUSE CANCER SYNDROMES IN ADULTS.
OUR COHORTS WHICH YOU HAVE TO THINK ABOUT THAT, OUR COHORT IS
45-65 YEARS OF AGE. THEY ARE UNLIKELY TO BE GETTING
CHILDHOOD CANCERS THEY DON'T KNOW ABOUT AT THIS POINT.
SO WE FOCUSED REALLY ON ADULT ONSET CANCERS.
AS JAME HE SAID, AND OTHER PEOPLE SAID, YOU CAN USE A LIST
OF GENES FIT INTO VAR SISTER FILTER BASED ON THAT AND THAT
GETS US DOWN TO 455 VARIANTS. IT'S STILL A BEING NUMBER IF YOU
WILL LOOK AT EVERY VARIANT BUT IT'S MUCH MORE MANAGEABLE THAN
182,000. YOU NOW HAVE TO START FILTERING.
WE TALKED ABOUT FILTERING BASEDDA QUALITY.
WE ALREADY FILTER ON THE MOST PROBABLE GENOTYPE SCORE.
IF THE SCORE IS IN 10 OR GREATER, IT'S NOT INCLUDED IN
BAR SISTER. THE NEXT THING WE DO IS WE LOOK
AT MPG THE MOST PROBABLE GENOTYPE SCORE COMPARED TO THE
COVERAGE. EMPIRICALLY, A NUMBER OF 5 HAS
BEEN DETERMINED TO BE WHAT YOU NEED FOR A QUALITY SCORE.
YOU CAN SEE HERE IN THE LOWER LEFT OF THE PANEL YOU CAN BREAK
OUT INDIVIDUALS BY GENOTYPE AND IT'S VERY EASY.
SO HERE IS THE GENOTYPE FOR THE DIFFERENT INDIVIDUALS.
WE HAVE GENOTYPE SCORE SHOWN HERE AND THE COVERAGE AND THE
HIGHLIGHTING HERE IS FOR AN INDIVIDUAL THAT DID NOT PASS THE
MPG COVERAGE QUALITY -- QUALITY FILTER.
IT IS THE ONLY INDIVIDUAL IN THE DATASET WITH THIS VARIANT AND SO
THIS CAN BE THROWN OUT AND DOESN'T HAVE TO BE CONSIDERED
FURTHER. THE NEXT THING WE DO IS WE THINK
ABOUT FILTERING BASED ON FREQUENCY.
THIS IS WHEN YOU REALLY HAVE TO THINK ABOUT WHAT IS THE DISEASE
THAT I'M LOOKING AT? LOOKING AT A RARE ADULT ONSET
CANCER SYNDROME? LOOKING AT RECEPTIVE VARIANTS
THAT MIGHT BE AT ONE-30 IN YOUR POPULATION AS A CARRIER
FREQUENCY? YOU CAN USE CLIN SEEK IF YOU'RE
USING BAR SISTER, YOU CAN USE IT WITHIN TO FILTER YOUR VARIANTS.
YOU CAN USE CD SNP INCLUDING PATHOGENIC VARIANTS.
SO YOU NEED TO CONSIDER THAT. HOPEFULLY YOU CAN USE 1000
GENOMES. IT'S NOT IN BAR SISTER, BUT
HOPEFULLY IT WILL BE INCORPORATED SOME DAY SOON.
THAT WILL BE HELPFUL AS WELL. THIS IS TO SHOW YOU THE CLIN
SEEK INFORMATION CAN BE INCLUDED IN BAR SISTER.
-- SUFFICIENTER.
YOU HAVE TO FIND OTHER WAYS TO INCORPORATE THIS.
SO FOR OUR CANCER SET OF GENES, WE HAVE 1% FOR CLIN SEEK AND .
SWROAP 15 OF THE MINOR ALLELE FREQUENCY FOR DP SNP BECAUSE OUR
GENE LIST INCLUDED THE MOST COMMON DISEASE THAT WE WERE
LOOKING AT WAS HEREDITARY BREAST AND OVARIAN CANCER FOUND IN A
FREQUENCY OF ONE-500 AND 1% IS 1-100.
WE THOUGHT IT WAS A SAFE CUT OFF.
I SHOULD TELL THAT YOU IF YOU'RE USING CLIN SEEK TO FILTER YOUR
VARIANTS, THERE ARE IS A HIGH POPULATION OF JEWISH INDIVIDUALS
IN OUR CLIN SEEK COHORT AT 17%. FOR THINGS THAT HAVE FOUNDER
MUTATION NO, SIR THAT POPULATION, THIS CAN TRIP YOU
UP. SO IF YOU KNOW THAT YOU'RE
FILTERING FOR HEREDITARY BREAST AND OVARIAN CANCER IN A JEWISH
INDIVIDUAL WHERE THEY HAVE FOUNDER MUTATIONS, MAYBE YOU
WANT TO DO A POSITIVE FOR SCREEN SO YOU DON'T MISS THEM IN YOUR
INDIVIDUALS. SO WE HAVE TAKEN OUT A THIRD 6
OUR VARIANTS BY DOING THE FILTER.
WE HAVE GONE FROM -- I HAD 455 ON THE LAST SLIDE.
THERE ARE A COUPLE THAT DID NOT CHANGE PROTEIN SEQUENCE SO WE
TOOK THEM OUT INNICY. THAT'S HOW WE GOT TO 451 AND NOW
DOWN TO 334. SO HOW DO WE EVALUATE THESE
CANDIDATES? FOR THIS 334, YOU ACTUALLY HAVE
TO GO OUT FOR THE DATABASES. SO FOR EACH ONE YOU HAVE TO GO
OUT AND LOOK AT THE DATABASE USING THE HUMAN GENE MUTATION
DATABASE OR LOCUS SYSTEM, YOU NEED TO ASK THE QUESTION, WAS
THIS FOUND IN CONTROLS? MULTIPLE REPORTS OF THIS VARIANT
OR ONLY SEEN IN ONE PAPER? IS THERE FUNCTIONAL DATA OUT
THERE? DO I BELIEVE THE FUNCTION
FUNCTIONAL DATA? IS IT PRESS WENT OTHER CAUSATIVE
MUTATIONS? ALL OF THESE THINGS AS EVIDENCE
FOR OR AGAINST THE VARIANT BEING CAUSATIVE.
THE LAST THING IS SEGREGATION. A LOT OF PEOPLE USE SEGREGATION
AS A GOLD STANDARD. YOU NEED TO BE AWARE, ESPECIALLY
WHEN YOU'RE WORKING OR LOOKING AT SECONDARY VARIANTS WHERE YOUR
INDIVIDUALS DON'T HAVE DISEASE, IT'S DIFFERENT FROM THE ONES WE
HAVE DONE BEFORE WHERE YOU HAVE A FAMILY.
THEY HAVE A DISEASE. YOU KNOW IT'S A CANCER SYNDROME
AND NOW YOU HAVE A GENE THAT LOOKS LIKE IT IS A
CANCER-CAUSING SYNDROME. HERE YOU HAVE A HEALTHY
INDIVIDUAL STANDING IN IN FRONT EVER YOU AND THEY HAVE A
VARIANT. YOU NEED TO BE SURE IF THERE IS
SEGREGATION DATA IN A PAPER OUT THERE.
YOU HAVE TO THINK ABOUT THE FACT THAT THERE COULD BE LINKAGE TO
EQUILIBRIUM WITH ANOTHER CAUSATIVE MUTATION THAT THEY
JUST DIDN'T DISCOVER. SO WHEN YOU'RE LOOKING AT YOUR
INDIVIDUAL THAT HAS A SNP, AND YOU THINK, IT DOESN'T CHANGE THE
CHARACTERISTICS OF THAT AMINO ACID, ALWAYS CONSIDER THE FACT
THAT SEGREGATION ANALYSIS ISN'T 100%.
IF YOU'RE USING HCMD, USE SHORTCUTS.
IT'S GOING TO TELL YOU IT IS INCLUDED IN BAR SIFTER.
IT INCLUDES BOTH THE GENES AND THE DISEASE THOUGHT TO BE CAUSED
BY THE VARIANT. THERE IS A QUESTION MARK
INCLUDED AT THE END OF THE DISEASE NAME.
IF THE CURATOR FEELS THAT THE EVIDENCE ISN'T 100%.
SO YOU CAN USE THAT AS A FILTER. THE HGMD TAG SHOWN HERE IS
INCLUDED IN BAR SIFTER. CM MEANS DEC COPY.
IT MEANS THAT THE CURATORS ASSUMPTION IS THAT THE PRIMARY
LITERATURE -- THEIR INTERPRETATION OF THE
PRIMARY LIT TERIS THAT INDIVIDUAL --
THAT AUTHOR SAYS IT WAS DISEASE-CAUSING.
IT'S NOT ALWAYS THE CASE WHICH I'LL SHOW YOU IN A MINUTE.
I WANT TO MAKE SURE YOU THAN THERE IS A DIFFERENCE BETWEEN
HGMD THAT YOU CAN GET OUT THERE ON THE WEB FOR FREE AND HGMD
PROFESSIONAL. IF YOU'RE DOING THIS USE HGMD
PROFESSIONAL AVAILABLE THROUGH THE LIBRARY.
GET A LOG ON THROUGH THE LIBRARY.
I INCLUDED THE LINKS FOR THE LIBRARY.
THE FREE HGMD DOESN'T HAVE HAVE ALL THE USEABLE FEATURES THAT
THE PRO EVENTUAL VERSION DOES. IF YOU GO INTO HGMD PROFESSIONAL
SEARCH ON GENE. IF YOU'RE USING BAR SIFTER IT
INCLUDESES THIS INFORMATION AND YOU CAN SEARCH ON MUTATION.
SO HERE I'M SEARCHING FOR APC BUT IF I WAS USING BAR SIFTER, I
WOULD PLUG MY MUTATION INTO THIS.
YOU CAN DRILL DOWN ON MUTATION AND THIS IS ANOTHER THING I WANT
TO POINT OUT, ESPECIALLY IF YOU'RE NOT USING BAR ASSISTY.
SO HGMD IN ANY DATABASE, SO IT WILL BE BASED ON A SPECIFIC
REFERENCE TRANSCRIPT. AND THERE ARE MANY TRANSCRIPTS
FOR A LOT OF GENES AND SO THE AMINO ACID NOMENCLATURE
SEARCHING BASED ON THAT WILL VARY BASED ON YOUR TRACK.
SO HERE WHERE IS THE TRANSCRIPT. RIGHT HERE.
HERE IS THE TRANSCRIPT INFORMATION.
YOU NEED TO MAKE SURE THAT TRANSCRIPT IS THE SAME
TRANSCRIPT THAT YOU'RE USING TO GET YOUR AMINO ACID NOMENCLATURE
YOU'RE COMPARING BACK. SO HERE IS PRIMARY LITERATURE.
HGMD LINKS YOU OUT TO THIS DIRECTLY.
I WANTED TO SHOW YOU THIS IS A BRCA2 MUTATION.
WE HAVE 82GDA IN OUR COHORT. IT'S LISTED AS DISEASE-CAUSING
AND HGMD THERE IS NO QUESTION MARK AFTER BREAST AND OVARIAN
CANCER. BUT IT HAS ALL THREE
HETEROZYGOAT VARIANTS OBSERVED IN TWO HEALTHY WOMEN WITH A
HISTORY OF BREAST CANCER. THE RISK IS UNCERTAIN.
AND THIS IS THE PEDIGREE. THERE IS ONE INDIVIDUAL WITHIN
THIS MUTATION, SHE DOESN'T HAVE BREAST CANCER ALTHOUGH A A
HISTORY OF BREAST CANCER. MOST WOULD LOOK AND SAY, YES,
SHE HAS A FAMILY HISTORY OF BREAST CANCER BUT THERE IS NO
SEGREGATION DATA. SHE IS NOT AFFECTED.
THIS IS NOT DISEASE-CAUSING. SO HGMD TED SAID IT WAS, BUT
BEFORE YOU RETURN SOMETHING YOU HAVE TO GO TO THE PRIMARY
LITERATURE. IN ADDITION TO HGMD, THERE ARE
TWO WEBSITES THAT I USE THAT ARE LISTED AT THE BOTTOM OF THE
SCREEN AND ON THE SLIDE FOR A LIST EVER ALL THE DIFFERENT
LOCUS SPECIFIC DATABASES, THE NICE THING ABOUT THESE IS THEY
ARE CURATED BY EXPERTS FOR THE MOST PART AND SO, IN OUR LAB, WE
TRUST THE DATA AND THEY MAY BE MORE THAN WE TRUST WHAT HGMD
SAYS. YOU CAN GO TO WHATEVER GENE YOU
WANT. THERE ARE OFTEN MANY DATABASES
FOR A GENE. THESE ARE ALL FOR APC.
WE TYPICALLY ONLY GO OUT TO ONE DATABASE.
WE DON'T GO AFTER ALL THE DATABASES AND WE LOOK FOR OUR
MUTATIONS. IF WE FIND THE MUTATION IN OUR
DATABASE AND HAS SUFFICIENT INFORMATION, BECAUSE OF THE
NUMBER OF VARIANTS WE ARE DEALING WITH, WE DON'T GO OUT TO
EVERY POSSIBLE DATA BASE. AGAIN WHEN YOU DRILL DOWN, THEY
ARE USING A SPECIFIC TRANSCRIPT. THIS IS THE MAIN THING TO
REALIZE. YOU HAVE TO ASSESS EVEN IN HGMD
INFORMATION INCLUDED IN BAR SIFTER.
YOU HAVE TO MAKE SURE YOU'RE USING THE PINK TRANSCRIPT OR YOU
WILL MISS THINGS THAT ARE THERE BUT THE AMINO ACID NOMENCLATURE
DOESN'T MATCH UP BECAUSE YOU'RE NOT USING THE SAME TRANSCRIPT
NUMBER. THIS IS A LIST OF THE VARIANTS.
CUT OFF THE LEFT HAND SIGHT OF THE SCREEN OVER HERE.
IF YOU GO TO THE DATABASES, THIS IS THE PATHOGENICITY SCORES.
THERE ARE SCORES IN THE NUMERATOR FOR WHAT THE PAPER
SAYS WHETHER THEY BELIEVE THE VARIANT IS PATHOGENIC OR NOT AND
THE DENOMINATOR IS WHAT THE CURATOR BELIEVES.
ANOTHER WORD OF WARNING HERE FOR THIS DATABASE, THIS CURATOR HAS
BEEN A QUESTION MARK FOR ALL OF THE VARIANTS.
SO, JUST BECAUSE THIS CURATOR SAYS THERE ARE VARIANTS OF
UNCERTAIN SIGNIFICANTS, IT DOESN'T MEAN IT IS LOOKED AND
DETERMINED THAT. IT IS BASICALLY NO INFORMATION.
YOU HAVE TO BE AWARE THAT THE CURATOR MAY OR MAY NOT HAVE
ACTUALLY LOOKED OR INTERPRETED EACH AND EVERY VARIANT.
THE NUMERATOR FROM THE PAPER, THE DENOMINATOR IS WHAT HE
THINKS. MANY OF THEM ARE JUST QUESTION
MARKS. THE IMPORTANT THING SHEAR YOU
HAVE AMINO ACID INFORMATION THAT ALLOWS YOU TO COMPARE YOUR
VARIANTS. HAVE YOU DNA INFORMATION BUT IF
YOU SCROLLED OVER TO THE RIGHT, WHICH I'M NOT GOING TO DO, THERE
IS A LOT OF INFORMATION. IT VARIES BY DATABASE AND HAS
MUTATION FOUND IN CONTROLS. IS IT FOUND INEFFECTIVE OR FOUND
MULTIPLE TIMES? WE LOOK AT DIFFERENT REPORTS OF
A VARIANT AS EVIDENCE OF CAUSATION.
I JUST WANT TO SHOW YOU HERE SO THIS VARIANT IS THE SAME VARIANT
REPORTED THREE TIMES BUT IF YOU LOOK TO THE RIGHT IT'S ALL IN
THE SAME PAPER. IF YOU GO OUT TO THE PAPER, IT'S
ONE FAMILY. SO REALLY IT'S ONLY ONE
INDEPENDENT REPORTER OF THAT VARIANT.
NOT THREE INDEPENDENT REPORTS. IT'S JUST ANOTHER THING YOU HAVE
TO THINK ABOUT WHEN YOU'RE LOOKING AT THIS DATA.
REALLY QUICKLY, IF YOU'RE TRYING TO COMPARE AMINO ACID
NOMENCLATURE, THE EASIEST WAY TO TAKE WHAT YOU HAVE AND CONVERT
IT TO WHAT IS IN YOUR DATABASES IS BY TAKING GENOMIC POSITIONS
YOU'RE GIVEN IN WHATEVER YOUR ANNOTATION SOURCE IS.
YOU CAN GO TO THIS WEBSITE UTILIZER, PUT IN THE GENOMIC
POSITION, IT WILL GIVE YOU A LIST OF VARIANTS WHICH COVER
THAT POSITION, PICK THE CORRECT VARIANTS FOR WHATEVER DATABASE
YOU'RE TRYING TO COMPARE TO AND THEN IT WILL EVENTUALLY GIVE YOU
THE CORRECT -- AMINO ACID DESIGNATION.
YOU CAN DO THIS AS A BATCH FILE. TYPICALLY I TAKE MY BAR SIFTER
FILES AND DO THE WHOLE ENTIRE LIST OF GENOMICS COORDINANTS AND
UTILIZE IT AS A BATCH FILE. SEEK OUT THE CORRECT TRANSCRIPTS
FOR OTHER DISEASES AND CONVERT THEM TO THE CORRECT AMEANO ACID.
IT SAVES A LOT OF TIME. SO WHAT DID WE FIND IS THE IN
ACCIDENT QUESTION IN OUR 334 VARIANTS?
JUST REALLY QUICKLY, IT'S HARD TO KEEP TRACK OF 334 VARIANTS.
YOU NEED TO BREAK THEM OUT SOME WAY SO WE ADAPTED A
PATHOGENICITY SCALE THAT WAS INITIALLY PUT FORTH BY THE
INTERNATIONAL AGENCY FOR RESEARCH ON CANCER AND THEY WERE
USING THIS TO GRADE PATHOGENICITY OF VARIANTS IN
CANCER SYNDROMES AND THAT'S WHAT WE STARTED WITH BUT WE STILL
NEWS SCALE FOR ALL OF OUR VARIANTS NOW.
AND BASICALLY, IT ALLOWS YOU TO BRING THINGS OUT FROM DEFINITELY
PATHOGENIC TO BENIGN WITH THE PROBABILITY OF 1% AT THE TOP AND
BOTTOM AND THEN THE 5% AT THE TOP AND BOTTOM BELOW THAT IS
LIKELY PATHOGENIC OR LIKELY BENIGN AND THEN A HUGE THING
FROM 5-95% WHICH IS UNCERTAIN WHICH IS WHERE MANY OF THE
VARIANTS WILL FALL. WE HAVE ADDED A QUALITY SCORE OF
ZERO JUST BECAUSE IT WAS HELPFUL FOR US FOR OUR VARIANTS.
I THINK THESE FILES ARE OR SLIDES ARE AVAILABLE ONLINE.
THIS IS JUST A SUBSET OF OUR ANALYSIS AND BASICALLY IT'S JUST
A SUBSET OF OUR CANCER GENES WITH THEIR GENOMIC COORDINANTS.
OVER HERE ARE THE REASONS THAT WE SCORED THESE THINGS
PATHOGENIC OR NOT PATHOGENIC. WE HAD A BRCA2 VARIANT THAT
COSEGREGATES AND IT'S A FRIENDSHIP IN THE PRIMARY LIT
TERAND IT'S A FRAME SHIP. WE HAVE THINGS THAT HAVE BEEN
FOUND IN UNAFFECTED RELATIVES, FOUND THE CAUSE OF MUTATION IN
CONTROLS, SO WE MOVED THEM DOWN TO A 2.
AND WE DID THIS FOR 334 VARIANTS.
SO BOTTOM LINE IS YOU HAVE TO READ THE PRIMARY LITERATURE.
YOU CAN START WITH HGMD, BUT THERE IS CONFLICTING INFORMATION
THINKS IT'S NOT ALL CORRECT. CERTAINLY BEFORE YOU RETURN --
SOMETIMES IF YOU HAVE ENOUGH AREAS TO FILTER BASED ON THESE
ANALYSIS, IF YOU'RE GOING TO RETURN THINGS, HAVE YOU TO GO
AFTER THE PRIMARY LITERATURE. THIS IS HOW OUR 334 VARIANTS
BROKE OUT. WHAT CAN YOU SEE IS THE
INTERESTING THING WE HAD 7, 5 TO 7 VARIANTS OUT OF THE TOTAL.
WE THOUGHT IT WAS PATHOGENIC AND NEEDED TO BE RETURNED.
AND WE THOUGHT WERE LIKELY TO BE PATHOGENIC.
THIS IS ONLY 37 GENES. SO FOR THE SUBSET OF GENES, THIS
IS WHAT WE ENDED UP THINKING WE NEEDED TO VALIDATE.
THIS IS A PIE CHART JUST TO EMPHASIZE THE FACT THAT MOST OF
YOUR VARIANTS WILL BE UNKNOWN SIGNIFICANTS OR BENIGN AND THESE
ARE THE ONES THAT WE FILTERED OUT BASED ON FREQUENCY.
SO IT'S A LARGE PERCENTAGE OF VARIANTS.
SO WHAT DID WE FIND? WE ACTUALLY FOUND --
THERE ARE FIVE VARIANTS IN BRCA1 AND 2 THAT ARE PATHOGENNICS.
THEY ARE IN 7 PARTICIPANTS AND 5 VARIANTS.
WE FOUND TWO VARIANTS THAT WERE FOUND IN A RECESSIVE PHENOTYPE
OF COLON CANCER AND THEN THERE WERE TWO VARIANTS THAT WE
THOUGHT WERE SCORE FORE, ONE IN THE PARAGANGLIOMA.
YOU CAN SEE THE LOCUS SPECIFIC DATABASE, THE PAPER SAID THEY
WEREN'T SURE BUT THE CURATOR THOUGHT IT WAS PATGENIC PROBABLY
BECAUSE IT'S A STOP EARLY ON IN THE PROTEIN.
WE DIDN'T THINK THIS WAS ENOUGH EVIDENCE TO GIVE IT A SCORE OF 5
AND THEN A GENE WAS QUESTIONED BY THE CURATOR AS TO IF IT WAS
TRULY PATHOGENIC BUT THE PAPER THOUGHT IT WAS.
AND THERE WAS NO INDICATION IN OUR PEDIGREE, WHICH IS ANOTHER
TOOL THAT YOU CAN USE TO LOOK AT, NO INDICATION IN THE
PEDIGREE OF THIS DISEASE SO WE LEFT IT AT A 4.
SO 7 IS A BIG NUMBER. WE THINK SO.
IT'S MORE THAN 1-100. YOU MAY BE SITTING HERE I'M JUST
DOING A A TRIO. I'M NOT DOING 572 EXOMES.
1-100 INDIVIDUALS MAY HAVE A BRCA1 OR BRCA2 VARIANT.
ALL OF THESE VARIANTS WERE PREVIOUSLY DESCRIBED.
THEY WERE OBVIOUSLY CAUSATIVE IN OTHER FAMILIES AND ALSO HIGH
FAMILIAL HIGH PENETRANTS CAMPUS SYNDROMES AND THE MOST IMPORTANT
THING IS ONLY 4 OF THESE 7 INDIVIDUALS ACTUALLY HAD
PEDIGREES THAT WE WOULD HAVE LOOKED AT AND THE SAID, THERE IS
A HIGH PENETRANT CANCER VARIANT HIDING IN THIS PEDIGREE.
THE OTHER THREE PEDIGREE DISNOT SUGGEST THAT WE WERE GOING TO
FIND THIS AT ALL. AND SO WE THINK THAT FOR THESE
THREE PEDIGREES AT LEAST, THESE ARE POTENTIALLY LIFE-SAVING
RESULTS THAT WE ARE GETTING BACK TO THEM.
THIS IS JUST ONE OF OUR PEDIGREES.
THIS IS OUR PRO BAND HERE THAT CAME IN AND HAS A BRCA2
FRIENDSHIP. YOU CAN SEE HIS MOTHER DID HAVE
BREAST CANCER IN HER 50s BUT SHE IS THE ONLY ONE IN THE
PEDIGREE THAT HAD OR REPORTED TO HAVE CANCER IN THE PEDIGREE.
YOU CAN ALSO SEE THESE ARE ALL BROTHERS.
HE HAS TWO NIECES BUT THEY ARE STILL IN THEIR 30s.
AND SO, THIS IS SOMETHING WHERE THESE TWO INDIVIDUALS MAY BE AT
RISK FOR BREAST AND OVARIAN CANCER.
THESE INDIVIDUALS MAY BE AT RISK FOR PROSTATE CANCER.
THIS COULD BE INFORMATION THAT WILL SAVE SOMEBODY'S LIFE.
AND I BELIEVE THIS ONE HAS BEEN RETURNED AT THIS POINT.
I JUST WANTED TO SHOW YOU THIS BRIEFLY.
AGAIN, IT'S IN THE HANDOUTS. YOU CAN LOOK AT IT.
WE ARE TRYING TO MAKE THIS MORE SCIENTIFIC SO IT'S NOT LIKE IT
LOOKS LIKE WE HAVE TWO PIECES OF EVIDENCE.
BUT IF YOU'RE GOING TO DO THIS AND BREAK OUT WHETHER THINGS ARE
PATHOGENIC OR NOT, YOU NEED TO TAKE WHAT THE BASIC DATABASE
SAYS SO WHETHER THINGS ARE NOVEL AND FOUND IN THE DATABASES OR
PATHOGENIC ACCORDING TO THE DATABASES, A VERY NORMAL
SIGNIFICANTS OR BENIGN AND WHAT TYPE OF MUTATION IT IS AND THEN
ADD IN WHAT YOU KNOW. SO ADD IN, IS MY PEDIGREE
SHOWING ME THIS VARIANT SHOULD BE THERE?
IS IT FOUND IN CONTROLS? ULA THE DIFFERENT THINGS I
TALKED ABOUT. AND THEN YOU CAN USE THIS TO
GRADE YOUR VARIANTS AND AT LEAST IN OUR LAB WE ARE RUNNING 5S.
NOT 4S, THINGS THAT ARE LIKELY, FOR THE MOST PART.
FOR THESE SYNDROMES WE WEREN'T RETURNING 4S.
THINGS LIKELY TO BE PATHOGENIC, ALTHOUGH, DEPENDING ON THE
DISEASE AND THE GENES, YOU MAY DECIDE TO TURN THINGS THAT ARE
LIKELY PATHOGENIC. CAUTIONARY TALE.
SO CDH1, I MENTIONED EARLIER IN MY TALK.
WE IDENTIFIED A MUTATION IN ONE OF OUR CLIN SEEK INDIVIDUALS AND
THE MUTATION IS THISAL 19298. IF YOU GO OUT TO THE LITERATURE
IT WAS FOUND IN AN INDIVIDUAL WHO WAS 36 YEARS OLD.
HE HAD THE MUTATION. HE HAD TWO FAMILY MEMBER WHOSE
GOT GASTRIC CANCER IN THEIR 30s.
THEY WERE NOT TESTED FOR THE VARIANT.
BUT SAID ALL THREE MUTATIONS CONFERRED LOSS ADHERENT FUNCTION
IN AN IN-VITRO ASSAY. SO IT WAS SAYING THIS ACTUALLY
CHANGES THE FUNCTION OF THE PROTEIN.
THIS LOOKS LIKE IT IS CAUSATIVE. AND THIS REALLY CONCERNED US.
I DON'T THINK WE REALLY EXPECTED TO FIND SOMETHING WITH CDH1 IN A
HEALTH 60-YEAR-OLD INDIVIDUAL. THIS IS THE PEDIGREE.
WE HAVE A HEALTHY 61-YEAR-OLD INDIVIDUAL.
SHE HAS RELATIVES WHO DIDN'T HAVE GASTRIC CANCER.
SHE HAD SIBLINGS, THIS INDIVIDUAL DIED TOO EARLY TO
HAVE DETECTED GASTRIC CANCER GENE.
SIX INDIVIDUALS ARE IN THEIR 40s TO 50s.
HIGHLY UNLIKELY TO HAVE A HIGH PENETRANT GASTRIC CANCER DISEASE
VARIANT SEGREGATING IN THIS FAMILY.
WE SAT ON THIS FOR A WHILE AND THEN HAD A SECOND INDIVIDUAL
THAT HAD THE SAME KIND OF PEDIGREE WITH THE SAME VARIANT
AND AT THIS POINT, WE SAID THIS CAN'T BE A HIGH PENETRANT
GASTRIC CANCER VARIANT AND WE DOWNGRADED IT.
HAD WE TOLD HER, HER ONLY OPTION WOULD HAVE BEEN TO HAVE HER
STOMACH REMOVED TO PREVENT STOMACH CANCER.
IT WAS SOMETHING WE STRUGGLED WITH INITIALLY.
SO, I THINK I'M FINE ON TIME. CARRIER VARIANTS.
I THINK CARRIER VARIANTS FALL UNDER THIS AND COULD RUN AND NOT
SHOULD RETURN CLASSIFICATION AS FAR AS NHLBI.
BUT, YOU HAVE TO THINK ABOUT THE SAME KIND OF THINGS THAT I
TALKED ABOUT BEFORE AND YOU MAY ALSO THINK ABOUT THE THRESHOLD
SET FOR DISEASE INCIDENTS. SO REALLY COMMON CARRIER VARIANT
LIKE CF KEEPING MORE TEMPTED TO RETURN VERSUS SNAG IS ONE IN A
MILLION, MAYBE LESS LIKELY TO RETURN.
YOU HAVE TO THINK ABOUT THE FRAMEWORK AGAIN, WHAT ARE THE
FREQUENCY CUT OFFS THAT YOU'RE GOING TO USE?
WE USE A 15% FREQUENCY CUT OFF FOR CLIN SEEK.
THE REALITY IS FOR OUR COHORT WHEN WE ARE LOOKING AT CARRIER
VARIANTS, WE DIDN'T USE A DB SNP CUT OFF BECAUSE WE FELT THAT 572
EXOMES WAS ENOUGH OF A FILTER. YOU COULD USE THE MINOR ALLELE
FREQUENCY OR 1000 GENOMES. AND THEN, THE LIST OF RECESSIVE
DISORDERS IS HUGE. IT'S CLOSE TO TWO THOUSAND.
IF YOU DO A SEARCH, THAT IS TOO MANY GENES, TOO MANY DISORDERS
FOR US TO LOOK AT RIGHT NOW. IT WOULD RETURN TOO MANY
VARIANTS. SO THE ONE THING YOU DOCK IS
LIMIT YOUR SET AND WE LIMITED IT TO 78 GENES THAT ARE OFFERING A
PRENATAL PANEL BY AMGEN, A COMPANY THAT OFFERS PRENATAL
TESTING. BELL et al. IS LISTED ON
THE SLIDE AND THEY ACTUALLY HAD SUGGESTED 448 SEVERE RECESSIVE
CHILDHOOD DISORDERS THAT THEY LOOKED AT BUT THE BOTTOM LINE
HERE IS, THIS IS ALL ITERATIVE. HOPEFULLY SOME DAY THERE WILL BE
A MAGIC PROGRAM THAT COMES THROUGH ALL OF OUR VARIANTS AND
GET A LIST OUT AT THE OTHER END JUST LIKE 10 VARIANTS.
AND YOU THAN THEY ARE IMPORTANT AND YOU CAN RETURN THEM.
WE DON'T HAVE THAT RIGHT NOW. WE ARE JUST TRYING TO START SOME
PLACE AND GO BACK AND JUST KEEP LOOKING AT THE STATUS SET FOR
OTHER VARIANTS. SO I JUST WANTED TO MENTION THAT
I WAS ONE OF THE FIRST ONES THAT SAID, LET'S NOT RETURN THINGS
FOR LIKE ONE IN A MILLION IN A POPULATION F IT'S ONLY ONE IN A
MILLION. HOW IMPORTANT WILL THIS BE TO
OUR PRO BAND ANY WAY? ASSUMING OUR PRO BAND STILL
HAVING CHILDREN, WHICH OURS PROBABLY AREN'T BUT AT LEAST
SOME OF YOURS MAY BE IF THEY ARE TREATED TO RARE DISEASES.
IF YOU HAVE COMMON DISORDERS, LET'S TAKE CF, I ROUNDED IT UP
TO A ONE-30 CARRIER FREQUENCY IN THE POPULATION.
IF YOUR PRO BAND IS A KNOWN CARRIER FOR CF MUTATION, YOU
HAVE TAKEN THEM OUT OF THE EQUATION AND NOW THE RISK FOR
PREGNANCY OF THAT INDIVIDUAL IS 1-120, 30 TIMES THE POPULATION,
I THINK MOST OF YOU -- I THINK YOU WOULD AGREE 1-120 IS
HIGH WITH HAVING A CHILD WITH CF.
IT'S SOMETHING WE MIGHT WANT TO RETURN.
BUT LET'S LOOK AT SOMETHING ONE IN A MILLION.
WHAT DOES THAT MEAN. IT MEANS 1-500 CARRIER FREQUENCY
AND IF WE HAVE A KNOWN CARRIER, IF ONE OF OUR PRO BANDS IS A
KNOWN CARRIER AND WE TAKE HIM OR HER OUT OF THE EQUATION, WE ARE
JUST NOW DOWN TO A RISK OF 1-2000.
THAT'S 500 TIMES THE POPULATION RISK.
YOU MIGHT ARGUE WITH ME THAT 1-2000 IS SOMETHING YOU'RE
WILLING NOT TO RETURN TO YOUR PATIENTS.
I DON'T KNOW WHERE THE CUTOFF SHOULD BE.
REALIZE IT'S SOMETHING THAT SOUNDS LIKE 1-1 MILLION.
ONE IN 2000 ISN'T QUITE AS HUGE. THINK ABOUT THIS WHEN YOU'RE
THINKING ABOUT CARRIER VARIANTS. WHAT DID WE FIND?
THE BELL PAPER SUGGESTED YOU WILL GET ABOUT THREE VARIANTS
PER INDIVIDUAL FOR RARE RECESSIVE CHILDHOOD DISORDERS.
JUST LOOKING AT 78 INDIVIDUALS, 78 GENES AND 572 INDIVIDUALS, WE
GOT 10 STOPS THAT WERE IN THE HUMAN GENE MUTATION DATABASE 216
NONSYNONYMOUS VARIANTS. WE ALSO GOT NOVEL STOPS.
WE GOT FRIENDSHIPS BECAUSE OF THE WAY BAR SIFTER DOES THIS,
THEY ARE NOT LINKOD TO HGMD. WE GOT FRAME DEALATIONS AND
SPLICE SLIGHTS AND THEN NONSYNONYMOUS CHANGE THAT IS WE
REALLY HAVEN'T FOLLOWED UP ON. HOPEFULLY WE WILL KEEP GOING
BACK TO THE STAT US AND MORE OF THOSE WILL BECOME ANNOTATED BUT
TODAY THEY HAVE NOT BEEN ANNOTATED.
IF YOU LOOK AT THE INDIVIDUAL VARIANTS, YOU WOULD EXPECT TO
FIND THIS IN 7 INDIVIDUALS, WHICH IS MAYBE A LITTLE LOW.
WE FOUND BBS10 MUTATIONS AND I WORK ON THAT.
SO BOTTOM NUMBER IS THE NUMBER OF INDIVIDUALS WHO ARE GIVEN
BACK A POSITIVE GENOTYPE THAT COULD BE INTERPRETED INCLUDED IN
THE BAR SHIFTER FILED SO IT'S NOT AWLS 572.
BECAUSE WE HAVE A HIGH POPULATION OF JEWISH
INDIVIDUALS, WE HAVE THE FOUNDERS FOR RARE DISEASES.
AND YOU CAN SEE THERE ARE OTHER RARE DISEASES UP HERE ON THIS
SCREEN. IF YOU WERE DOING A TRIO WHICH I
THINK IS WHAT MANY WILL BE DOING, IT WILL BE A LITTLE BIT
DIFFERENT IN THAT YOU ARE GOING TO START WITH MAYBE 90,000, I
SAID TENSE TO HUNDREDS OF THOUSANDS OF VARIANCE.
FOR JUST ONE WE STARTED WITH 90,000.
INSTEAD OF INITIALLY -- LET ME TAKE THIS DOWN FOR THE
NEXT SLIDE. INSTEAD OF TAKING IT DOWN TO THE
NONSYNONYMOUS STOP FRIENDSHIPS AND SPLICE, WE FILTERED IT
DIFFERENTLY. WHAT WE SAID IS HOW ABOUT IF WE
LOOK AT EVERY VARIANT THAT IS IN GENES THAT IS KNOWN TO CAUSE
DISEASE IN THE GENE MUTATION DATABASE.
YOU CAN DOE THIS WITHIN BAR SIFTER.
THAT GOT US DOWN TO 9,264 VARIANTS.
IF YOU LOOK AT THE ONES ANNOTATED IN HGMT, YOU CAN GET
DOWN TO 362, AND THEN DISEASE-CAUSING WAS 113.
AND THAT'S THE PRETTY REASONABLE --
THAT'S NOT EVEN FILTERED FOR FREQUENCIES.
BUT 113 IT'S REASONABLE IF YOU FILTER FOR FREQUENCIES, YOU CAN
GET DOWN TO 65 VARIANTS. YOU HAVE TO CONSIDER NOVEL
VARIANTS AND THERE WERE 19 NOVEL IN THIS ONE TRIO.
SO IT LEAVES US WITH ABOUT 80 VARIANTS TO LOOK INTO.
SO TO PAIR IT UP HERE, WE ARE GENERATING A TON OF INFORMATION.
A LOT OF IT IS IN OUR COMPUTERS. THIS INFORMATION CAN BE LIFE
CHANGING FOR OUR PARTICIPANTS. THE ONLY WAY THAT THEY ARE GOING
TO CHANGE THEIR LIVES BASED ON THIS INFORMATION IS IF WE GIVE
IT BACK TO THEM. AND IN ORDER TO DO THAT, AS YOU
HAVE SEEN, IT'S GOING TO TAKE A LOT OF TIME IN EFFORT FOR THE
RESEARCHERS HERE OR MAYBE FOR A HANDFUL OF RESEARCHERS TO DESIGN
A GREAT TOOL FOR US SO WE CAN GET DOWN TO OUR 10 VARIANTS WE
NEED TO RETURN FOR INDIVIDUALS. BUT WE NEED TO THINK ABOUT THIS
AS A FIELD, HOW ARE WE GOING TO ANSWER THIS PROBLEM OF SECONDARY
PARENTS AND WHAT ARE WE GOING TO RETURN TO OUR PARTICIPANTS SO
THEY CAN MAKE HEALTH CARE DECISIONS BASED ON THE
INFORMATION WE GIVE THEM? SO, THIS IS THE SAME THING.
SECONDARY ORIENTATION IS A BURDEN.
IT TAKES A LOT OF TIME. BUT IT IS IMPORTANT.
I HOPE I CONVINCED YOU OF THAT AND WE NEED TO IMPROVE THE TOOLS
SO WE HAVE AVAILABLE, AND THAT'S IT.