How omics and bioinformatics are used in the Precision Medicine Lab
Summary
TLDRDr. Judy Crabtree, an associate professor of genetics at LSU HSC, discusses her journey from sequencing the human genome to leading the precision medicine program. She highlights the impact of genomics on personalized medicine, focusing on its application in oncology and drug development. Crabtree also emphasizes the importance of the 'All of Us' research program in diversifying genomic data to address health disparities. Her presentation showcases the evolution of genomics from basic research to clinical practice, aiming to deliver the right treatment to the right patient at the right time.
Takeaways
- π Dr. Judy Crabtree's academic background includes a PhD in Biochemistry and Genetics from the University of Oklahoma and postdoctoral work at the National Human Genome Research Institute under Dr. Francis Collins.
- 𧬠Dr. Crabtree contributed to the Human Genome Project, which sequenced regions of human chromosome 22 and provided foundational data for understanding human genetic diversity.
- π₯ Her career transitioned from academia to the pharmaceutical industry, where she worked at Wyeth Pharmaceuticals, and then to LSU Health Sciences Center as a professor of genetics.
- π Dr. Crabtree played a pivotal role in implementing COVID-19 testing and viral sequencing efforts at LSU to track variants, showcasing her adaptability in public health crises.
- 𧬠The Human Genome Project, which Dr. Crabtree was part of, revealed approximately 10 million single nucleotide variants in the human genome, emphasizing the genetic diversity among individuals.
- π§ͺ Precision medicine, as described by Dr. Crabtree, aims to tailor healthcare by considering individual differences in genetics, environment, and lifestyle, moving towards personalized treatment plans.
- 𧬠The 'All of Us' research program, supported by the NIH, aims to enroll one million or more participants to better understand genetic variants and their impact on health, with a focus on diversity.
- π₯ Dr. Crabtree's work at LSU's precision medicine program involves using next-generation sequencing to identify genetic variants that can inform treatment strategies for cancer patients.
- π The field of oncology is leading the way in precision medicine, with targeted therapies designed to hit specific molecular targets identified by genomic variants, aiming for fewer side effects.
- 𧬠Genomic testing in clinical settings is becoming more accessible and cost-effective, with the potential to revolutionize patient care by providing evidence-based, personalized medicine.
Q & A
What was Dr. Judy Crabtree's role in the Human Genome Project?
-Dr. Judy Crabtree received her PhD training in biochemistry and genetics from the University of Oklahoma, where she was part of one of the original labs funded to sequence the human genome.
Where did Dr. Crabtree complete her postdoctoral work?
-Dr. Crabtree completed her postdoctoral work at the National Human Genome Research Institute at the National Institute of Health in Bethesda, Maryland, under the direction of Dr. Francis Collins.
What disease did Dr. Crabtree study during her postdoctoral work?
-During her postdoctoral work, Dr. Crabtree studied the biology of an endocrine tumor disease called Multiple Endocrine Neoplasia Type One.
How long did Dr. Crabtree work in the pharmaceutical industry before joining LSU Health Sciences Center?
-The script does not specify the exact duration of Dr. Crabtree's work in the pharmaceutical industry before joining LSU Health Sciences Center in 2009.
What is Dr. Crabtree's current position at LSU Health Sciences Center?
-Dr. Crabtree is currently an Associate Professor of Genetics and the Scientific and Education Director of the Precision Medicine Program at LSU Health Sciences Center.
What significant initiative did Dr. Crabtree implement during the COVID-19 pandemic?
-During the COVID-19 pandemic, Dr. Crabtree implemented the COVID testing program for the LSU-HSC campus and launched viral sequencing efforts to track COVID-19 variants of concern in Southern Louisiana.
What was the cost and duration of the Human Genome Project?
-The Human Genome Project took 13 years to complete at a cost of about 2.7 billion dollars.
What is the All of Us Research Program and how does it relate to precision medicine?
-The All of Us Research Program is a cornerstone of the Precision Medicine Initiative that aims to enroll one million or more participants to understand genetic variants better. It includes collecting surveys, biological specimens for whole genome sequencing, and medical records for population-based studies.
How does the LSU Health Sciences Center contribute to the All of Us Research Program?
-LSU Health Sciences Center is a flagship institution in the Southern region of the All of Us program, collaborating with other major institutions across the Gulf South to enroll participants and contribute to the understanding of the human genome.
What is the significance of the genomic data generated from the All of Us Research Program?
-The genomic data from the All of Us Research Program is significant because it includes a diverse pool of participants, with more than half of the new genomic information coming from people who self-identify with racial or ethnic minority groups, which helps to address the lack of diversity in previous genomic studies.
What is the TSO 500 panel and how does it relate to precision medicine at LSU Health Sciences Center?
-The TSO 500 panel is a next-generation sequencing-based approach that contains 523 oncology-related genes. It is used to support solid tumors and will be expanded into hematological malignancies. It also provides an assessment of microsatellite instability and defects in mismatch repair, which support the use of checkpoint inhibitor therapies and overall tumor mutational burden.
Outlines
π Introduction to Dr. Judy Crabtree's Academic and Professional Journey
Dr. Judy Crabtree is introduced as a distinguished biochemist and geneticist with a Ph.D. from the University of Oklahoma, where she was part of the team sequencing the human genome. Her postdoctoral research at the National Human Genome Research Institute focused on Multiple Endocrine Neoplasia Type One. She then transitioned into pharmaceutical drug development at Wyeth Pharmaceuticals before joining LSU Health Sciences Center (LSU HSC) as a genetics professor. At LSU HSC, she has advanced to Associate Professor of Genetics and serves as the Scientific and Education Director of the Precision Medicine Program. Dr. Crabtree also played a pivotal role in implementing COVID-19 testing and viral sequencing efforts during the pandemic.
𧬠The Genesis and Evolution of Precision Medicine
The discussion delves into the history of the Human Genome Project, which began in 1990 and concluded in 2003, costing $2.7 billion. The human genome reference sequence, a compilation from 20 anonymous individuals, was created to prevent any single person's genome from being exclusively represented and to protect donor privacy. This foundational work has led to numerous questions about genetic diversity and its implications for disease, drug metabolism, and individual health variations. The precision medicine initiative by the NIH, announced in 2015, aims to address these questions by understanding how genetic variations impact health. A key component of this initiative is the 'All of Us' research program, which plans to enroll over a million participants from diverse backgrounds to enhance the understanding of genetic variants and their effects on health.
π¨βπ©βπ§βπ¦ Precision Medicine in Action: The West Family Study
This segment highlights a pioneering study in pharmacogenetics that utilized whole genome sequencing on the West family to predict health outcomes. The study identified genetic variants associated with blood clotting, which helped in predicting the correct anticoagulant medication and dosage for John West, aligning with his actual treatment. The study also forecasted the potential medication needs for John's daughter, Anne, based on her genetic profile, emphasizing the preventive capabilities of precision medicine. This case exemplifies how genomic information can be used to guide personalized treatment plans and risk assessments.
π Targeted Therapies and the Future of Oncology in Precision Medicine
The focus shifts to oncology, where precision medicine is leading the way with targeted therapies based on genomic variants. Traditional chemotherapy's cytotoxic effects are contrasted with newer, targeted therapies that disrupt cancer cell proliferation with fewer side effects. The identification of driver mutations in non-small cell lung cancer and melanoma exemplifies the complexity and potential for personalized treatments. The presentation also discusses the role of immunotherapies that leverage the patient's immune system to combat cancer. The challenge lies in identifying all disease-impacting variants and developing targeted therapies for each, which initiatives like the 'All of Us' research program aim to support.
π§ͺ Genomic Testing and Clinical Decision Making at LSU HSC
Dr. Crabtree outlines the various genomic testing methods used at LSU HSC's clinical precision medicine laboratory, including single gene sequencing, gene panels, and next-generation sequencing approaches like TSO 500, whole exome, and whole genome sequencing. The laboratory's process involves sample review, library generation, sequencing, and data analysis to identify and annotate genetic variants. The data is then integrated into the electronic medical record for clinical decision-making. The presentation concludes with a vision of precision medicine's goal to deliver the right drug to the right patient at the right time, improving treatment outcomes and reducing side effects.
π Concluding Remarks and Q&A Session
The presentation concludes with a Q&A session where Dr. Crabtree addresses the volume of genomic data generated by LSU HSC's lab, the scope of their sequencing efforts, and her personal inspiration for pursuing genomics. She shares a memorable high school biology lesson that sparked her interest in DNA and genomics, highlighting the transformative impact of early scientific education on her career.
Mindmap
Keywords
π‘Genomics
π‘Human Genome Project
π‘Precision Medicine
π‘Pharmaceutical Drug Development
π‘Single Nucleotide Variants (SNVs)
π‘All of Us Research Program
π‘Next-Generation Sequencing (NGS)
π‘Cancer Genomics
π‘Electronic Medical Record (EMR)
π‘Immunotherapy
Highlights
Dr. Judy Crabtree's introduction includes her extensive background in biochemistry, genetics, and her involvement in the Human Genome Project.
Dr. Crabtree's postdoctoral work focused on the biology of multiple endocrine neoplasia type one under Dr. Frances Collins.
Her transition from academia to pharmaceutical drug development at Wyeth Pharmaceuticals.
In 2009, Dr. Crabtree joined LSU HSC as an assistant professor of genetics, later becoming an associate professor.
Dr. Crabtree's role in implementing the COVID testing program for LSU-HSC campus during the pandemic.
Initiation of viral sequencing efforts to track COVID-19 variants in Southern Louisiana.
The anniversary of Dr. Crabtree's postdoc start coincides with her presentation, marking 25 years in genomics.
The history of the Human Genome Project and its impact on understanding human health and disease.
The astonishing fact that there is approximately one single nucleotide variant per 300 nucleotides in the human genome.
The launch of the NIH Precision Medicine Initiative in 2015 by President Obama.
The All of Us Research Program aims to enroll one million or more participants for whole genome sequencing.
The importance of diversity in genomic studies, with over 50% of new genomic information from racial or ethnic minority groups.
LSU HSC's role as a flagship institution in the Southern region of the All of Us Program.
A study in 2011 demonstrated the predictive ability of precision medicine through whole genome sequencing of a family.
The identification of genetic variants related to blood clotting in the West family study and its implications for treatment.
The potential of genomics to predict disease risk and personalize treatment plans.
The leading role of oncology in precision medicine and targeted therapies based on genetic variants.
The challenge of identifying all disease-impacting variants and developing targeted therapies.
Clinical methods for identifying DNA variants, including single gene sequencing, gene panels, and next-generation sequencing.
The LSU HSC Clinical Precision Medicine Laboratory's focus on next-generation sequencing for oncology.
The process of integrating genomic sequencing data into clinical decision-making for patient care.
Dr. Crabtree's inspiration to become involved in genomics, stemming from a high school biology class.
Transcripts
let me introduce
dr judy crabtree
okay
so
please welcome dr judy crabtree dr
crabtree received her phd training in
biochemistry and genetics from the
university of oklahoma in one of the
original labs that was funded to
sequence the human genome
she did her postdoctoral work at the
national human genome research institute
at the national institute of health in
bethesda maryland under the direction of
dr frances collins studying the biology
of an endocrine tumor disease called
multiple endocrine neoplasia type one
from there she entered the world of
pharmaceutical drug development at wyeth
pharmaceuticals
in 2009 she left the pharmaceutical
industry and joined lsu hsc as an
assistant professor of genetics
she is currently an associate professor
of genetics and the scientific and
education director of the precision
medicine program at lsu hsc
more recently in the pandemic she
implemented the covid testing program
for the
lsu-hsc campus and has launched the
viral sequencing efforts to track
coveted variants of concern in southern
louisiana
so please join me in welcoming dr judy
crabtree
thank you laura
so i'm going to share my screen now
get me set up
oh come
on okay
so thank you for this opportunity i mean
this has just been a great meeting the
past two days we've seen so many great
talks and posters i'm very excited
and so um what's interesting though is
as i was preparing this talk
i realized that today is 25 years to the
day since i started my postdoc and so i
had just finished my phd work under the
direct direction of dr bruce rowe at the
university of oklahoma where we were
sequencing regions of human chromosome
22 as part of the human genome project
and on april 1
1997 i began my postdoctoral study at
the nih under the direction of dr
francis collins now i can tell you if
you've never started a new job on april
fool's day it is quite the experience
and so as the new green postdoc i was
immediately the april fool and the easy
target of many practical jokes in my new
lab
but what i didn't realize at that point
was that this was the beginning of a
translational career built on genomics
and its application to human health and
so i was fortunate to not only
contribute sequencing data to the human
genome project but to also be in the
epicenter of human genomic research in
the u.s upon completion of the human
genome reference sequence in 2003
so at that time i was infused with
optimism about what we could do to
understand human health and disease how
we can further understand what makes
each of us alike but also what makes
each of us different so how are we
different in our responses to
environmental stimuli to pharmaceutical
pharmaceutical drugs to chemotherapy
and since this day in 1997 i've studied
cancer and performed large scale
transcriptomic analyses
um of several tumor and cancer syndromes
i've worked in the drug development and
pharmaceutical industry and then now
here we are 25 years later i'm
translating what i've learned in each of
these varied research environments to
supporting patient management in our cap
accredited clinical precision medicine
laboratory
now in order to understand the current
state of affairs with respect to
precision medicine we kind of need to
start at the beginning so i hope this
isn't repetitive to some people
but it's always fun to look at history
so in the late 1980s a group of
scientific thought leaders that included
francis collins of the nih erie petrinos
from the u.s department of energy eric
lander from the broad institute at mit
and several others they sat down over a
pint of lager and outlined on the back
of cocktail napkins a plan for mapping
and sequencing the complete human genome
so this project launched in 1990 and
ultimately took 13 years to complete at
a cost of about 2.7 billion dollars and
so here you can see the publications the
cover the public effort in nature and
the competing private effort in science
now the key thing that i want you to
remember is that the human genome
reference sequence is not the genome of
one individual it's a compilation from
the 20 anonymous individuals mostly
anonymous
further the 20 individuals were selected
from a pool of over a thousand donors
whose information was ultimately
de-identified so that even those who
contributed do not know if their dna was
used or not and so this was done
intentionally by the architects of the
human genome project to ensure that no
single person's genome was exclusively
represented and also so that no
individual could be identified by their
contribution to the reference genome
now once the reference genome was
complete this opened up a huge number of
questions about the genetic diversity of
humans and so one of the astonishing
facts from the human genome project was
that single nucleotide variants occur
approximately one every 300 nucleotides
so if you do the math that means there
are roughly 10 million single nucleotide
variants in the human genome and these
variations are one contributing factor
to the genetic diversity in humans
and so this opened up a whole new set of
questions so what is the intersection
between disease and genetic variants
what's the relationship between drug
metabolism and genetic variation is
there a cancer genome and does that
cancer genome change over time in in
between the the primary tumor and a
metastasis or a recurrence um how does
the genome impact mental health
behavioral health
it had already been observed that some
diseases were more prevalent in certain
populations and so then questions about
what's the role of genetic variation and
ethnicity
and so over the years that followed the
completion of the human genome reference
sequence it became more and more clear
that we knew too little
the genomic community as a whole began a
sort of haphazard way
collecting information we needed to
answer some of the questions about
genetic variability but as time went on
the cost of full and
and as time went on the cost of whole
genome sequencing um decreased so now
it's approaching a thousand dollars with
a turnaround time of seven to ten days
and so so now the big picture idea was
that if we can perform genomic testing
at an acceptable cost get private
insurance and medicaid medicare buy-in
to perform genomic testing in the
clinical setting we can use this as
evidence-based medicine to identify the
best therapeutic and preventative
interventions to best benefit our
patients
and so to set this up in a more
organized fashion um
we realized that there was a need for a
more concerted effort to understand
genomic variation so the nih announced
its support of precision medicine in
2015 when then president obama in his
state of the union address described
precision medicine as an emerging
approach to disease prevention and
treatment that takes into account
people's individual variations in genes
environment and lifestyle
so this was accompanied by a publication
in the new england journal of medicine
written by then director of the nih
francis collins and past director of the
national cancer institute harold barmus
this perspective further supported the
convictions of president obama that
science offers great potential for
improving human health and this
officially launched the nih precision
medicine initiative in 2015.
now a key part of the precision medicine
initiative is the all of us research
program
this was launched officially about four
years ago and this is a cornerstone of
the precision medicine initiative that
sinks to enroll one million or more
participants that represent the broad
diversity of the united states so that
we can understand variants much better
than we do
so patients will complete surveys
provide biological specimens for whole
genome sequencing and then grant access
if they choose to their medical records
for de-identified population-based
studies that correlate genetics and
genetic variants with disease and
environmental factors such as where you
live
now the all of us network is composed of
national partners in regional medical
centers across the u.s to enroll
participants from all walks of life in
all states of health within the united
states so just this month the all of us
research program hit a key milestone and
released the first set of nearly a
hundred thousand whole genome sequences
more than half of this new genomic
information comes from people who
self-identify with racial or ethnic
minority groups and that's extremely
important because until now more than 90
of participants in the large genomic
studies were all of european descent and
so this lack of diversity has had huge
impacts it deepens the health
disparities and hinders scientific
discovery from fully benefiting everyone
so i do want to point out that lsu hsc
is a flagship institution in the
southern region of the all of us program
we affectionately call this program the
y'all of us network for those of you who
know about the southern dialect
and this is in collaboration with tulane
university the university of mississippi
medical center university of alabama
birmingham and other major institutions
across the gulf south
so this is the website where you can
learn more information about the all of
us program and there's still time to
join either through the website down
here or the app which looks like this
blue banner up in the upper left corner
once you've registered you can then make
an appointment to donate your sample for
sequencing
at one of our participating clinics
so all of this is going to contribute to
our understanding of the human genome
and how genetic variants can impact our
health
and so what i'd like to do now is share
a study with you that was one of the
first studies to come out in
phosgenetics in 2011 to show you the
predictive ability of precision medicine
and so this study used next generation
sequencing to evaluate human health in a
predictive way and in this study the
authors performed whole genome
sequencing of four members of a family
mom dad daughter and son
and as an aside
the family used in this study is the
west family and if you look at the
author list carefully you can see john
west and and west are both authors on
this study so john west was the ceo of
celexa at the time so this is the
company that developed the current next
generation sequencing technology that
was then sold to illumina and is now the
foundation for their current almost
market cornering technology for next
generation sequencing
and so this is the pedigree for the west
family if you aren't used to reading
pedigrees um the squares are males the
circles are females um horizontal lines
indicate either a marriage or siblings
and diagonal lines across the symbol
indicate that the individual is deceased
now the arrows indicate the four
immediate family members of the west
family so we have john his wife
the daughter anne and her brother and
note the multi-generational history of
cardiovascular
and blood clotting problems within this
family so there are several incidents of
myocardial infarction congestive heart
failure deep vein thrombosis and
hypertension
john was
hospitalized twice with venous
thromboembolism in two separate
incidents um during the period of time
when he and his doctor were working out
the appropriate anticoagulant for him to
be taking for his condition
so the whole genome sequencing of this
family identified among other things
multiple variants and genes related to
blood clotting so this process utilized
two carefully curated databases verimed
which correlates genetic variants
associated with disease and farm gkb
which catalogs genetic variants
associated with drug responses now there
are many such databases available now
these were just the first two that were
established at the time of the study
back in 2011.
now a blinded um in a blinded
bioinformatics analysis of these data um
the investigators were able to correctly
predict the type and the dose of the
anticoagulant that john was already
taking so he and his doctor had settled
on clopidogrel after an extensive period
of trial and error to get the dose and
drug um correct for one that worked for
him
now imagine if john had been screened
for known variants before he even took
any medication
well that's essentially what happened
for his daughter
so the study predicted what medication
she may need in the future based on her
genetic profile and interestingly the
medication is different from that her
dad is taking mostly because remember
everybody inherits two alleles and
inherited one risk allele from her
father and a different risk allele from
her mother
so ann was 17 at the time of the study
and now she's 29 years old and has no
health problems as of yet because she
was able to implement some simple
lifestyle changes
and increase her surveillance to help
mitigate her risk for cardiovascular
complications
so this is just one example of how
genomics can impact human health and
disease risk assessment
a second example is within oncology so
the field of oncology is leading the way
in precision medicine and targeted
therapies
because the identification of variants
as biomarkers or targets of disease has
led to new targeted therapies for
patients with cancer
now past treatments
have all been focused on tissue specific
mechanisms or systemic therapies so for
example the traditional chemotherapy
such as microtubule inhibitors platinum
therapies and cyclophosphamides
these are all cytotoxic drugs that kill
all rapidly dividing cells and so there
are also other cancers such as
hormone-responsive breast cancer or
prostate cancers
that have obvious hormone dependence so
the first line of therapy in these
tumors is a systemic hormone deprivation
and the problem with all of these
systemic based chemotherapies is that
they often have some really miserable
side effects for the patient
and so more recent focus has been on
variance and the targeted therapies
and as time has gone by and we've
learned more and more about the
molecular basis of cancers and so shown
here is non-small cell lung cancer and
melanoma and we know that each of these
com each of these common cancers is
actually a collection of more rare
cancers so for example many cancers or
many variants have been detected in
non-small cell lung cancer including
driver mutations and the genes for uh
things like egfr b raf mec1 akt and p10
um and then within within each of these
um driver mutations
there's individual variants that add
further complexity so for example within
the egfr mutations in non-small cell
lung cancer there are at least seven
known individual variants and in
melanoma it's similar the common driver
mutations are in the b raft gene
and these include six individual
variants
so imagine if we had drugs that were
specific for each of these individual
variants and how cool would that be
right
well and that's where we are albeit in
the very very early stages
right now the majority of the drugs that
are seeking and receiving fda approval
in oncology are targeted therapies that
are designed to hit specific molecular
targets that are divine defined by a
genomic variant
so these new drugs interrupt cancer cell
proliferation but in theory they leave
other non-cancer cells more intact
with the goal of less intense side
effects for the patient
there are also new immunotherapies that
capitalize on the patient's immune
system to fight types of cancer with
specific genetic signatures and so now
the challenge is can we identify all the
variants that impact disease and develop
therapies that work best for each of
those different disease-causing variants
so the all of us research program will
help with that in the u.s and similar
programs are in place in other countries
and we also have to start to convince
big pharma to change their strategy and
begin to develop targeted therapies for
newly identified variants instead of
seeking that next billion dollar
blockbuster drug
now in the clinical setting we identify
dna variants in a variety of ways
we can look we can use a single gene
sequencing analysis to look for germline
mutations in particular genes such as
bracha one or two
we can do screenings for variants in the
genes that are
metabolic enzymes such as the cytochrome
p450 enzymes that are responsible for
drug metabolism in the liver and we can
perform gene panels such as oncotype dx
or mammoprint with that contain smaller
number of genes to identify variants and
predict tumor recurrence um in some
particular tumor types
or we can do what we're doing at the lsu
hsc clinical precision medicine
laboratory which is focus on the next
generation sequencing based approaches
so this includes tso 500 whole exome
sequencing and whole genome sequencing
so our initial approach for tso500 will
will support solid tumors and then we'll
expand into hematological malignancies
and then we'll implement hereditary
cancer screening risk identification and
some non-invasive prenatal testing or
nipt
all of which runs on the same next
generation sequencing platform and so
this testing is one of the pillars of
support for our future bid for nci
cancer center designation in the region
and so this is the instrument we have
from illumina called the next c550dx
this instrument is currently in use for
genomic sequencing of sars cov2 for code
19
but we will be pivoting soon to run tso
500 which is a panel that contains 523
oncology related genes
and you can see some of those listed
here along with the different types of
cancer with which they are affiliated
this panel also provides an assessment
of microsatellite instability and
defects in mismatch repair
these support the use of checkpoint
inhibitor therapies
as well as overall tumor mutational
burden which is an indicator of
immunotherapy treatment success
so the way it works in our laboratory is
we have tests that are ordered by a
physician
our pathology partners uh review the
sample and submit the tumor in normal
samples for sequencing in the lab we
process those samples perform library
generation and put them on the sequencer
and then the large amounts of raw data
that result from the next seek i run
through quality assurance quality
control and base calling algorithms to
convert those raw image data files into
a text file format you guys have already
heard about fastq
um and there are also the associated
fred quality scores that are associated
with each base and then following this
base calling the sequencing reads are
aligned with the reference genome and
resulting in a bam file
map sequences are then used
to identify variants and result in a
variant call format or vcf
so we partner with puri and dx for this
service and their algorithms identify
and prioritize single nucleotide
variants based on multiple criteria
these include variant allele frequency
strand bias sequencing depth in the gene
region quality scores etc as well as it
draws from their extensive database of
patient outcomes from other nci
designated cancer centers nationwide to
recommend treatment strategies so the
identified variants are annotated
as to the gene and location that's the
avcf file and then they're often
manually curated to ensure accuracy
quality and adherence to the current
current nomenclature and naming
conventions
so all of this data is distilled into a
report that's integrated into the emr
the electronic medical record and it's
made available for tumor board review
and for clinical decision making
so those sample reports look like this
so it has patient information at the top
and then it has a listing of the
variants that are identified in the
analyze sample
so there's also information about the
responsiveness of this tumor with or a
tumor with this profile to certain drugs
and you can see that here in the middle
um as well as the opportunities for
clinical trials that are associated with
this type of variant and so we can set
the distance parameters to limit
available clinical trials to within so
many miles of the patient
mostly for convenience sake
and then down here at the bottom you can
see the results for tumor mutational
burden which is really the emerging um
marker associated with greater
sensitivity of a tumor to
immunotherapies and also microsatellite
instability status which when high this
this example is low but when it's high
it predicts sensitivity to immune
checkpoint inhibitors
so all of this leads us to the precision
medicine ideal of delivering the right
drug to the right patient at the right
time and so right now we're sort of in
this top level here where we have
patients receiving a drug um and then
there's a small proportion of those
patients who actually respond
what we'd like to do is get to this
stage at the bottom where we have a
different drug for different um genetic
variants that are available within the
oncology and another space this doesn't
necessarily have to be only oncology
driven um even though oncology is
leading the way
but this is where we want to go where we
get the right drug and the right patient
at the right time
and so with that all i'd like to thank
you for your attention and this
opportunity and i'd be happy to answer
any questions
you so much dr crabtree that was an
amazing presentation thank you okay
we have a few questions for you
uh the first one is how much data is
being generated by your lab at um lsu
hsc so is it just genomic data or is in
smp data or do they also generate other
types of data so right now the only data
being generated in our laboratory is um
viral sequences for sars code v2
we are not currently running uh the
ts0500 we are not currently doing whole
genome or whole exome sequencing that is
our next
the next endeavor um mostly just because
we kind of got derailed to do sequencing
for sars kobe too and we have yet to
pivot
that makes sense okay our next question
is how many people are you planning to
get sequence data from in the state of
louisiana and also just in the south in
general
sequence data for
um
whole genome whole exome
or is this the question of how many
samples are we going to run
how many samples are you going okay so
once tso is up and running so this the
instrument that we have is a moderate
throughput um instrument there's one
bigger
that we do not yet have but we can
always buy if we end up
having more samples to process
our laboratory is not going to only
support lsu it's going to support the
entire region and so at the moment we
have the capacity in our current
instrument to run um eight tumors normal
pairs per week
um
but then you know as as need and
demand increases we can always scale
that up
got it uh and then one final question
what originally inspired you to become
involved in genomics
so this is kind of a cool study so
or a cool story so i uh
i had a science teacher named jim martin
and he would die if he knew i was
telling the story
back when i was in high school we were
in basic biology
and
he gave each of us a laminated piece of
paper that had either a circle on the
end or a triangle on the end
and some of us had the points and some
of us had the correlating v right and so
essentially what he handed out to the
whole class was nucleotides
and he lined us up in the hallway and
some of us were the parental strand and
then others of us came in and formed the
replicating strand
and so that was really my first
introduction to
to dna and
anything having to do with dna
sequencing
and so he taught us dna replication in
the hallway the high school and and so
that was really you know that was many
many years ago but um that was really my
first introduction to to dna and it's
kind of stuck ever since then gene
therapy you know i'm i've got a huge
interest in not only dna sequencing and
genomics but but into you know gene
therapy and that translation of what we
can learn from genomics to patient care
great that is a fun story thank you for
sharing
he would die
definitely okay thank you very much of
course well that was again a great talk
by dr trouble
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