Yale School of Medicine Biorepository Open Information Session

Name: Yale School of Medicine Biorepository Open Information Session
Uploaded: 2023-03-16T18:28:44.7433333Z
Duration: 55 min 20 s
Description: Yale School of Medicine Biorepository Open Information Session: March 10, 2023, with Chen Liu, MD, PhD, Interim Director, and Wade Shultz, MD, PhD, Associate Director.

March 16, 2023

Yale School of Medicine Biorepository Open Information Session: March 10, 2023, with Chen Liu, MD, PhD, Interim Director, and Wade Shultz, MD, PhD, Associate Director.

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ID: 9688
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00:00First of all, thank you very
00:03much and for coming to this well.
00:06Yale School of Medicine by
00:09repository open information session.
00:11So the session will be organized by me.
00:15My name is Chen Liu from Department
00:18of Pathology and the Doctor water
00:21source from laboratory medicine.
00:24So this is actually the first time we,
00:27you know, we.
00:29Gave with this session since we officially
00:33launched the YSIV Pastor last November.
00:36So we we about three months from
00:39from the launch we plan to give
00:43to do to do a regular update.
00:46We think about every three months
00:48we'll do a short for zoom or
00:52web-based open information session
00:54and to provide an update on the
00:58activities in the biorepository.
01:00So the information session is designed
01:03to be interactive and so please feel
01:06free to ask questions as we go along.
01:09I will first start to give a brief
01:12overview and about repository and
01:14the way that will take over and it
01:17will give you more detail you know on
01:21the operation and how you actually
01:23interface with the power repository.
01:26So the presentation is about 20 minutes.
01:29I think most of the time we really
01:31wanted to hear from you and to answer
01:34some of the questions you may have.
01:36So they bought repository was you
01:39know was launched you know with the
01:42strong support from the from the
01:44Nancy Brown and the the Dean's office.
01:47So the scope of the work in the
01:50about you know in about repository
01:52is general specimen intake,
01:55acquisition,
01:55processing storage and distribution.
01:58So this is 1 main area will work.
02:02The other part is also very important
02:04for the bowl repository.
02:06To the Biorepository will also
02:09support investigator initiated or
02:12program initiated or program focused
02:14the tissue banking in other words
02:17this is a shorter for we not just
02:19a banging tissue actually the the
02:22Red Bull repository will work with
02:24individual program leaders and to
02:26set up whatever that their repository
02:29you know would be specific design to
02:32support their research program and
02:34that there is you know is a clinical.
02:36State validation or development and the
02:38next one is a clinical trial support.
02:41In other words we're moving forward
02:44when we have clinical trials.
02:45So the repository will be very
02:47happy to talk with the you know
02:50the investigators to see how we
02:51can provide about specimen so far.
02:54And at the same time this repository
02:57will this is a school wide,
03:00our repository is called a
03:03centralized power repository.
03:05However it does not mean.
03:07Will or will will take over
03:09every other existing bank,
03:11not even close to that in other words.
03:13So this central bank is really building
03:16a platform to have a more uniform
03:20you know operating procedure based
03:22practice and all that at the same
03:25time for all the investigator in the
03:28wrong power bank which we know we
03:31have hundreds of them on this campus.
03:33So with that you know the ball
03:36repository is happy to.
03:37Support your need in other words in terms
03:41of personal training or standardization
03:43or protocols or some basic practices.
03:46So this is also the area you know where is
03:49part of the the work for the Bowery Pastor.
03:53So the biorepository eventually you know
03:55we would like to have is to have a College
03:59of American pathologists accreditation
04:00because CAP credit accreditation which
04:02is really is the highest standard
04:05for teacher banking in the country.
04:07Accreditation by CAP will will really
04:10give the bank more leverage in terms
04:13of engaging clinical trial and also
04:16make a banking tissue connection
04:19with the clinical operation,
04:21particularly for clinical
04:23diagnosis more seamless.
04:25So what do we do in this bank?
04:27So right now I mean the bank has a
04:30capacity technology to annotate and
04:32process archived tissue and fresh
04:35samples both in you know you know,
04:37including both blood and solid tissue.
04:40I think one important area for the
04:42Central bank will be able to develop
04:44is a matched blood and solid tissue
04:46as you know more and more the study
04:49right now is how to link you know
04:51human tissue or diseased tissue in
04:53particular cancer or other disease.
04:56Issue with the corresponding blood.
04:58So this is 1 area you know the bank will
05:01be really focusing on is to building
05:04the paired samples and then the bank
05:06also can also provide a live tissue.
05:09We have the feature culture capacity to
05:12provide live tissue for investigators,
05:16you know work on organelles or PDX mice or
05:19whatever reason they want to live tissue.
05:22Remember the bank does not
05:24provide organized essay but the.
05:26Banker will be able to provide the
05:28first pass and get the tissue and
05:30pass it on and to the investigator.
05:32So certainly the bank who has the capacity
05:34to grow cell lines and making you know RNA,
05:37DNA, protein extractions we call
05:39so-called molecular banking,
05:40this is all doable.
05:42Certainly the mononuclear cell isolation,
05:44you know, the,
05:45the,
05:46the PBMC's,
05:47you know collection and also
05:50storage those are also available.
05:54OK. Next, next one. Ohh Sir. OK.
06:00So the current, you know let's see
06:02OK here it is currently for example
06:05this bank you know is really you know
06:08unofficially starting preliminary work
06:10particularly under the leadership of
06:12weight through the light medicine.
06:14So they started 2000 you know
06:16what it really in the during the
06:19pandemic and also you know pathology
06:21has done something as well.
06:23So this was a really those are the
06:26preliminary work and now we're all
06:28getting together now with this.
06:29Some bowel repository as I mentioned
06:32earlier the official launch date
06:35was November 2000, 2020, 2022.
06:37Right now the start of a bank has
06:39been supporting quite a number of
06:41research projects and we will be able
06:44to provide you some of the information.
06:46And so currently the, the bank,
06:48the in terms of the the leadership
06:51or organizational structure is
06:52I serve as a you know,
06:55director of right now the interim.
06:57So we'll be you know just when time is right.
07:00Gossip, you know,
07:01will appoint the permanent
07:02director to run this bank.
07:03And the weight is also is a social director.
07:07And so there are two managers or Co managers,
07:11you know that David Ferguson,
07:12who is on the line, and the King fan,
07:14you know who is out of town.
07:15So both of them real,
07:17you know.
07:18Later on I will show you how
07:19you actually interface with
07:20them through the website.
07:24So the other functionality of the
07:27bank is really provide support
07:29for all your grant applications.
07:32So what that means we'll provide lateral
07:34support as you as you wish and to really
07:38specific to your research project and
07:40then we will be working with you.
07:42We have financial,
07:44you know coordinator and jump Amir
07:47who is this banks financial person.
07:49So he can really work with you if I could.
07:54Work with you to build the budget
07:56for your grant application in terms
07:57of how to use the power repository.
08:00What's what kind of budget you should
08:02build into it for your research you know
08:05application and then you know we have
08:08standardized template documentation.
08:10Do you know this is just give you a
08:12snapshot here so we have the documents
08:14already I think it's kind of with the blank.
08:16And fill in the information you need and
08:19for you know to document the support you
08:21know for you know for your grant application.
08:24I think that one of the ideas,
08:26the more granular you have,
08:27there's more.
08:28Likely you will be able to, you know,
08:30have you know full access of the
08:32power repository and then you will
08:34have the financial resources to you
08:36know to support this type of work.
08:38So far. Any questions, please stop.
08:40You know,
08:41if you know I cannot see everybody,
08:43if you can just raise your hand or you can
08:46turn on your video and ask a question.
08:49Alright, so.
08:51So where we are right now we are,
08:53we have a temporary space which
08:54is on the 2nd floor.
08:56The MP building is close to the cafeteria.
08:59So this is you know it's a small
09:02area but it's enough for us
09:03to do most of the basic work.
09:06We have freezers and also in tissue
09:08culture hood as I said will be
09:11able to provide like a live tissue
09:13support including single cell.
09:16You know if you do single cell work
09:17we'll be able to support you to gather
09:19the first pass of single cell and the pass.
09:22To you so and then the other area for
09:25particular for the liquid samples,
09:27bladders,
09:29processing or plasma serum storage
09:31is all in the live medicine space.
09:34So this is our temporary space.
09:36So we are in the process to find
09:38a permanent home.
09:39It will be much larger and you
09:42know in the near future.
09:44So as I said we'll keep you updated.
09:48So finance how this bank is supported.
09:51So the bank,
09:52you know,
09:52this is the list of all the
09:54things we can't for how the bank
09:57is currently supported mainly is
09:58from the institutional support.
10:00This that means it's Nancy Brown support.
10:04So Nancy Browns provided the startup
10:06package for this bank to start and certainly,
10:10you know, in the future, you know,
10:12we'll have to think about the bank
10:14itself and actually apply for grants.
10:16You know,
10:17there are grants.
10:18God and nature or different Funding Agency,
10:21they wanted to have a banking
10:24initiative so that certainly the
10:26biorepository will directory can you know
10:29apply ground by itself and then the others
10:32will be like a collaboratively with.
10:35You know pro research program like
10:38a centers PO1 and also multi you
10:41know Pi projects you know with
10:43particular need for bowel repository.
10:46So those are that some I mentioned earlier.
10:49So the bank is fully ready
10:51to provide our part.
10:52You know we'll do the all the write
10:54up on the biobank by side and it
10:56will work with you to get those
10:58funding and moving forward that
10:59there is a possibility to work with
11:02industry particularly for clinical
11:03trials you know like a.
11:05Pharmaceutical companies,
11:06they sometimes do conduct clinical trials.
11:10They will have the need for
11:12both specimens support.
11:13So those are the financial part.
11:15Obviously it would be philanthropist
11:17part is very important.
11:19So this is the one area the Dean's
11:21office and you know we as a bank
11:23leadership was also thinking about
11:25how we can secure some gifts and
11:27to support the bank and obviously
11:30there is another component that will
11:32be the chargeback of special uses.
11:35But that means the users you as
11:38an investigator will need to pay
11:42some fees to use the services.
11:44Later later the presentation I will,
11:47I will show you on the website we
11:49have complete the chart by you know
11:51charge back rate depending on what the
11:54levels the service support you need,
11:56there's a specific.
11:58Price for you know for this
12:01all the services we provide.
12:03So I think this is the USP card.
12:05As you know the USP card means it is
12:08universally around the core services
12:10there is no benefit and I mean there
12:13is no profit or margins to be made.
12:16So on a yearly basis all the expenses
12:20from the the bank and will have
12:23to be somehow covered through a
12:25number of different mechanism from
12:27the institutional support grants.
12:29Industry or other gifts at the end
12:31they will design A chargeback rate and
12:34to pay you know to support the back.
12:37So this is basically the the finances
12:39covers every aspect you can see
12:41there are number of certainly if the
12:44chargeback rate is I think for most of
12:46you probably will be more interested
12:48in that is a see how you know how to.
12:52Gathered the best service with the
12:54lowest in you know price, right.
12:57This is all the value we all strive for it.
12:59So that means if we have more
13:02people to use the bank,
13:04the overall price of services,
13:06you know fees will be lower, right.
13:08So This is why I think it's important.
13:11You know,
13:12we wanted to your participation
13:14participation and since this is a new
13:17bank that that means that there are
13:20some areas we still need to develop.
13:23We are very open minded and to be really,
13:26really specifically specifically
13:27to support your need and we want
13:30to hear your ideas,
13:32feedback and you know at the
13:34end of the day
13:35we know this is truly shared resources.
13:38In other words, we collectively own
13:41these shared resources as USP, right.
13:44So this is a very important you know that we
13:47wanted to have more interaction with you.
13:50So right now this is archived
13:52tissue water since we just started,
13:54you know there's some of the archived
13:57tissue stored in department pathology in
13:59the live medicine will have to be gradually
14:02transferred into the the central bank.
14:04So we are developing that.
14:06This may take some time.
14:07You can see the blood
14:08sample inlet medicine side,
14:10there is about 275,000 eliquid,
14:12you know blood samples available
14:14right now in the freezer.
14:16So in pathology we have almost
14:183.5 million patients.
14:20Archive the tissue blogs,
14:22so the tissue all the way to 1960s.
14:24So with all those tissue blocks
14:27available in the storage side
14:29as I said it's all in storage.
14:31So what are we going to do is to
14:33bring all those you know archive
14:35the tissue back to the Central bank.
14:37So that will make building category
14:39catalog to make it available for all
14:41investigators see from our website to
14:43see what kind of tissue you may have.
14:46And currently during this it
14:48really the bank had done.
14:50A lot has done quite significant work
14:52or during the pandemic, the COVID time.
14:55So we do have a lot of samples you know
14:57including the live medicines plus samples
14:59they were actually from the you know,
15:01they covered the patients on the
15:04pathology will help by the 80 autopsies.
15:06All the all organs are collected
15:09from the COVID patients with some
15:12saliva samples and also NP swab,
15:14all the upper respiratory specimens
15:17all available for requests.
15:19Those are the availability.
15:20Available one,
15:21but we do not have a lot to say.
15:24In other words we just started to collect
15:28fresh tissue from normal organs or
15:31you know cancer tissues or different kinds.
15:35Since we just started collecting,
15:37we don't have really inventory yet.
15:40So moving forward,
15:41so we will build an inventory
15:43will be enough to you know for
15:46the investigator to request.
15:48So I stop here and I stopped there
15:52and any question to me and before
15:54I had a transition this to wait
15:56to give you more details or you
15:59can save the question later when
16:01we have this open discussion.
16:05So I do not see any hands up or I do not see.
16:09Anybody has a question, OK.
16:11And the way that maybe you know,
16:13how about you take it over.
16:15Yeah, if you want to turn off your
16:16sharing, I can just kind of pick up on
16:17you. Just tell me otherwise your slides.
16:19OK, sounds good, perfect.
16:20So go ahead and move on to the next one.
16:23So yes, doctor, you mentioned that,
16:25you know, we've been working on
16:27some of the preliminary work
16:28for this for a few years now.
16:30And if we go back to this one, you know,
16:33the one thing I want to highlight
16:35is that beyond just biorepository,
16:38we're really trying to provide.
16:39Biospecimen management
16:40and management services.
16:42So it's not just about getting specimens
16:44and sticking in them in the freezer,
16:46but really making sure that we can
16:48use specimens and leverage them
16:49for research and research projects.
16:51And so whether that is bringing
16:53a specimen in,
16:54processing it and moving it immediately
16:56to the investigator for immediate
16:58use or storage within their labor
17:00biorepository or potentially storing
17:02it within the DSM biorepository,
17:04both of those are options.
17:05And so it's not just a bank
17:08where we put things but.
17:10One,
17:10where we can actually acquire things
17:12in real time and move them rapidly
17:14to those downstream use cases.
17:15Next slide.
17:18And there's really 2 pathways for
17:20getting these specimens.
17:21The 1st that we've done quite
17:23extensively through COVID was
17:24from excess clinical samples.
17:26And so that's where we can actually
17:28leverage some of the work that we've
17:29done on the informatics side to
17:31identify specimens that meet specific
17:33cohort or phenotypic criteria.
17:34So one example is identifying
17:36individuals who had COVID or a
17:38history of COVID and then being able
17:40to capture those clinical excess
17:42specimens once they are done in the
17:44clinical testing pathway and then
17:46de identify them for research use.
17:48We've also worked with the Phase
17:50One Group and others where whereby
17:52patients who have signed things
17:53like the umbrella consent,
17:55we can grab additional specimens.
17:57And then the other pathway outside
17:59of that clinic excess clinical
18:01sample way is by doing specifically
18:04research sample collection.
18:05And for those sample collections there's
18:08a couple of pathways to do that as well.
18:10One is where the researcher may get
18:13those tubes and send them directly from
18:16a research draw to the biorepository.
18:18For processing and or storage and the
18:20other one is by doing an order in Epic
18:24to actually collect those and they
18:26will go through that clinical pipeline.
18:29But as a dedicated research tube the
18:31if people have questions about how to
18:33enter those research orders in Epic,
18:35definitely feel free to reach out.
18:37There's a couple of different
18:38orders that can be used but allow
18:41us to pretty fluently capture
18:43those specimens and get them into
18:45that that research direction.
18:46Next slide.
18:49And we have a number of different
18:50services that we're already performing.
18:52The list here is also if you
18:54go to the Biobank website,
18:56you can see the list and the
18:58actual charges and I can pull
18:59that up in a little while as well.
19:01The most common things that we
19:02end up doing are the centrifuge,
19:04centrifugation,
19:05aliquoting in from the parent tubes
19:08into specific biobank aliquot tubes or
19:11whatever the researcher might
19:12need for the the tube type.
19:14We also do have a number of projects where
19:16we do store and retrieve the specimens.
19:19From our our freezer storage
19:21DNA and RNA prep, we've scoped
19:23out but have not performed yet.
19:25And then PDMC preparation and
19:27processing we have ongoing for several
19:29different stories studies as well as
19:33some ability to provide IT technical
19:37and data support either individually
19:39through the BIOREPOSITORY or in
19:42conjunction with JADAK if and as needed.
19:44We also have some initial studies that have
19:47leveraged the clinical laboratory testing.
19:49To perform research based testing,
19:51so looking at things like COVID antibody
19:54results or COVID antibody titers where
19:56we actually use the clinical assay
19:58and can bill and charge that through
20:01at a slightly more reasonable rate.
20:03That is 1 service that we are
20:05working to better scale and make
20:07more accessible as we move forward,
20:09but have to balance out some of the
20:11clinical needs of the clinical lab
20:13while also making that available
20:14on the research side. Next slide.
20:18And just to you know highlight the
20:20the informatics driven aspect of
20:21some of the sample collection that
20:23we've put in place as part of the
20:25computational health platform that
20:26was deployed at Yale New Haven
20:28over the last couple of years.
20:30We do have the ability then to as
20:32I mentioned on a couple of earlier
20:34slides really identify some of these
20:36specimens in real time which can
20:38be quite beneficial for things that
20:40might be labile analytes where we
20:42need to go and grab them quickly
20:43to be able to move to downstream
20:45testing or for rare events.
20:47So if there is a.
20:48A unique syndrome,
20:50disease disorder or set of phenotypic
20:52criteria that we may only see infrequently.
20:55One example,
20:56there was a study we had worked on
20:58with Henry Rinder and Lab medicine
21:00during COVID as well looking at
21:02patients who went on a ventilator
21:04after being diagnosed with COVID.
21:06And so we needed to identify
21:08a very specific phenotype,
21:10identify those specimens and in some
21:12cases we can also push those into
21:15dedicated consent pathways outside of
21:17the excess clinical pathways as well.
21:20Tied to that well we can do identify,
21:22we can leverage the ability of JADAK
21:24to use those D identified ties back to
21:27the EHR to also pull out covariates,
21:30outcomes and other clinical data from
21:32the Epic data repository while acting
21:34as an honest broker to the investigator.
21:36So we we do have some templated IRB
21:38language that we're also happy to
21:40share if that's something that's of
21:42interest to individual investigators.
21:44Next slide.
21:46Our current infrastructure,
21:47just to extend on some of the
21:49things Doctor Lou mentioned that
21:51are more on the tissue side,
21:52we also have some automation
21:54over on the liquid side for doing
21:57processing and aliquoting some
21:58robotics to help support that.
22:00I think we're actually up to now 4
22:03freezers as well as a backup for -,
22:0580 storage and are starting to scope
22:08out liquid nitrogen storage as well.
22:10We have centrifugation including
22:12refrigerated for doing PBMC and
22:14other types of purifications.
22:16And a plate scanner that allows us
22:18to do these low profile biobanking
22:20tubes to really increase our storage
22:23capacity and efficiency for storing
22:25specimens as well as pulling those
22:27out of storage and transitioning
22:29them off to research studies.
22:31On the lab side,
22:32we've got Dave or on the liquid side,
22:34Dave who helps oversee a research
22:36associate as well as the laboratory
22:38associate in addition to the staff that
22:40we have helping on the tissue side as well.
22:43Next slide.
22:45This is just a little bit more
22:47detail of that informatics driven
22:48approach to sample identification.
22:50So as we're able to pull in data
22:52from Epic both the EHR as well
22:54as the laboratory information
22:56system which is speaker,
22:57those give us yesterday's data
22:59for some of those more labile
23:00analytes or things that we need
23:02to identify in real time.
23:04We do have some real time
23:05connections that are fed
23:06into the environment that's largely
23:08supported by the data science group at Yale,
23:10New Haven through Charlie Tori
23:12and then with the help of.
23:15Several different data architects,
23:17data scientists who help
23:18manage those platforms.
23:20Once this data are in the platform,
23:21we can then put on what we call watches
23:23to help identify those specimens,
23:25generate those specimen
23:26lists as well as integrate,
23:29you know the feedback from
23:30the add-on research,
23:31testing that can be done at
23:33least at limited scale right now
23:35within the clinical laboratory.
23:36Those data we can return to
23:38investigators depending on the terms
23:40of the IRB and the specific study.
23:42We try to do that through Redcap or
23:44through the computational health platform.
23:46Do you have some other options
23:48that exist depending on the exact
23:50computational and storage needs,
23:52as well as the scope and how
23:54sensitive the data that are
23:56being returned to our next slide?
24:00To date again we processed a number
24:02of specimens as Doctor Lee mentioned,
24:04we've got about 275,000 aliquots
24:05that we do have in storage primarily
24:08from COVID or COVID.
24:10We needed patients over the last
24:12couple of years we've processed
24:14somewhere between 405,000 aliquots
24:16just that we many of those get pushed
24:18immediately into research pathways or
24:20are screened for their appropriateness
24:22for specific research studies and
24:24this is a supported a riot wide
24:26range of clinical operations and
24:28research activities from clinical.
24:30Say validation in the in the
24:32laboratory Medicine Department
24:33to public health surveillance,
24:35as well as a number of biomedical
24:37research projects.
24:37Next slide.
24:40Some of the assays that we validated
24:42this was very helpful during COVID as we
24:45were working to validate both antibody
24:48as well as antigen and viral testing
24:50with some of our different platforms.
24:52So we were very easily able to go back and
24:54find the number of specimens we needed
24:57with patients with specimens drawn some
24:59number of days after presentation or
25:01symptoms and use that to actually go back
25:04and validate those diagnostic assays.
25:06Outside of COVID, we've also used
25:08it for a drug of abuse screening.
25:10And load opine stability as well
25:12as more recently validation of our
25:15in-house COVID-19 sequencing platform.
25:17Next slide.
25:19On the public health side that this is
25:21primarily been with Nate Grubaugh and
25:23the excellent research team over there.
25:26This has been ongoing really since
25:27the the start of the COVID pandemic
25:29providing somewhere as when we had
25:31enough samples 200 to 300 positive
25:33samples per week that they were
25:35sequencing for both the state as well
25:37as I believe the CDC since that time.
25:40This is also expanded now to provide
25:42specimens for both lab medicine and
25:44pathology for reporting back to both
25:47state and national databases and has led to.
25:49Several research manuscripts as well.
25:52Next slide.
25:55And then I don't know if we have the
25:57slide with the other research projects,
25:59but for the other research
26:00projects that we've done,
26:01this is also included work with a
26:03number of different investigators.
26:05Again a lot of those started
26:06off in the COVID-19 area,
26:08some others in just respiratory disease,
26:12some that we've done with phase
26:13one as well as hematology.
26:15And so really starting to expand
26:16out now and going from we have a
26:19biorepository that's just starting
26:21those operations and now moving
26:22into really having the full
26:24functioning by our repository.
26:25That we do have staffed or scaling
26:27up and have a formal process to
26:29go through for requesting and
26:31getting projects initiated.
26:32For people who are interested,
26:33you can find the why SM Biobank
26:35just by going to Google.
26:37The link down on the bottom is also
26:39for that primary website on there
26:41the link to Redcap for submitting
26:44a request for biospecimens or
26:46for a biorepository project is
26:48available on that website.
26:49It's also on the top of this slide.
26:51The process that we really
26:53recommend is filling out that form
26:54just so that we can make sure.
26:56We can track everything and that we
26:58can start to track turnaround times
26:59and making sure that nothing gets
27:01lost as we start to see more requests.
27:03I know when we were.
27:05Initially starting we we didn't
27:06always have a great mechanism other
27:08than doing this by e-mail and so
27:10we're hoping with a little bit more
27:12infrastructure down we can make sure
27:13that we don't miss or delay projects
27:15as we give them formally into this process.
27:18Once that request is received in Redcap,
27:20David and Keen will reach out to set
27:22up an initial project scoping meeting,
27:24identify whether IRB's are needed,
27:26what type of specimens will be needed,
27:28what processing requirements,
27:31storage requirements.
27:32Once that's scoping and if
27:34needed the IRB are done.
27:35We'll then collaboratively work to
27:37design out an SOP for how we will
27:40acquire and transition and or ship
27:42specimens and as part of that process
27:44also generate an estimate of what
27:46that will cost per specimen and per
27:48project and then ultimately initiate
27:50that project which has been I think
27:53going generally pretty well to date.
27:55Next slide. And yeah, that's it.
27:58Perfect.
27:58And so,
27:59doctor,
27:59I'm not sure if you're able to
28:02pull up the that red cap link.
28:05Website, actually.
28:06Thank you, wade. Sounds good.
28:08Yeah, I will share.
28:09OK. Let me share it.
28:11Open up, share the website.
28:17So this is a website that you
28:18see my screen, right. Wait,
28:20can you see it? Yes. Yeah. OK yeah.
28:22See that you know this is under the
28:25school medicine and under the resources
28:27we investigator you have ISM Biobank.
28:30So you click it, this will,
28:32you know there are several type and
28:34you are available here that you know
28:37with some brief description and we
28:39mentioned to you is you know is critical.
28:42It's just ask you know when you
28:44have inquiries there's a phone
28:46number here and also they send.
28:47E-mail and the most important
28:51part is let's say.
28:54That the price pricing is all here
28:56who you are for your reference you
28:58know this is like the charge charge
29:00back rate for all the you know liquid
29:03pricing and tissue pricing and all
29:06the different services we provide
29:08and you can go from there and then
29:11the this is a brief description of
29:13the inventory you know David you
29:16know weight already mentioned you
29:17see this white this is what you need
29:20to do if you have any questions you
29:22say you wanted to build a study you.
29:24Wanted to find out what whether or
29:26not the Bank of Pennsylvania will in
29:28what aspect can support your research.
29:31This button request data specimen.
29:33You just click this button,
29:34this will come up.
29:37Yeah, you know how to do this with cars.
29:45Ohh, I'm useless.
29:50OK, begin survey.
29:51It's very simple one.
29:53All you need is the basic information
29:55you fill in and then either Kevin
29:58or David will reach, you know,
30:01reach out to you and to have a.
30:03Conversation with you to see what's your
30:06need and what how the bank can support you.
30:08I I think that this was a the in
30:10my moving forward that we would
30:12like to have you know it's you know
30:14certainly this would be probably
30:15will take some time to build you
30:18see the inventory area what we hope
30:21is someday is with all the you know
30:24start the tissue specimen within the
30:27bank will be categorized and with
30:29all the basic information for every
30:32investigator they will be able to
30:34see what kind of tissue what kind
30:37of specimen you know are there.
30:38In the bank and as before the general,
30:41you know start a bank.
30:42So, but that will take some time for
30:45us to build this entire inventory and
30:48make make it more more user friendly.
30:51So this is just a space holder
30:53right now that's what we have.
30:55OK.
30:56I think that that's about it the
30:58the brief introduction and more
30:59importantly is all you need is
31:02a go to website if you have it,
31:04just submit this request and we'll
31:07guarantee to talk with you and in
31:09in a timely manner and then then
31:12we go from there.
31:13So now we stop sharing and I think
31:15as I said what we really wanted to
31:17answer some of the questions you may have.
31:24Also. David, David Rim.
31:28Yeah, if you had David,
31:31you if you have you know
31:32you can share some of the
31:33inventory that would be good.
31:35So hi, this is Dave Rim.
31:37I'm the director of YP TSTL
31:39pathology tissue services.
31:40And just to give you a history,
31:42since 2007 we've been
31:43collecting tissue from the OR.
31:45So we've never collected blood.
31:47That's always been Wade Schultz
31:49and the laboratory medicine gang,
31:50but we have collected a fair
31:52bit of surgical tissue.
31:54But because of the financial
31:55situation at the time that as
31:57we were entirely cost recovery,
31:58we have Federated banks.
32:00And so here's our Federated banks that
32:02currently are present at the institution.
32:04You can see there's 11 Federated.
32:06Banks with some with dozens of specimens,
32:08some with hundreds of specimens and
32:11the PI's of these Federated banks
32:13are shown and this each of these are
32:16sort of a little bit under their own
32:19tent because we while we collect and
32:22distributed the tissue to them we
32:24did not govern what they did with it.
32:26They just had to sign that
32:28they were willing to share it.
32:29So there is if you look at this list
32:31and this is I can make this more
32:34publicly available but this is from.
32:36Collected by Ali Bhai who who leads
32:39the tissue distribution and analysis
32:41service and this this list allows you
32:44to find historical tissue specimens.
32:47Although some of these,
32:48for example tissues given to CD
32:50Chan and Richard Flavell are usually
32:52convert not stored but rather
32:54converted into PDX mice or similar.
32:57So they some of these banks
32:59have tissue and storage,
33:00some of them much less so.
33:02And they just used the tissue that and Yelp,
33:04Yelp pathology tissue services
33:06continues to provide service for
33:09delivering tissues from the OR
33:11to investigators and including
33:13to what we hope will soon be our
33:14biggest client to yell Biobank.
33:19Thank you, David.
33:25Any questions? Ohh, I have a one
33:27question you know I'll start reading.
33:29So someone asked for the historical samples,
33:32are they are there clinical correlates?
33:35The answer is yes.
33:37You know we all of the the the archived
33:41pathology tissue we have the corresponding.
33:45Solitary part that means some of the basic,
33:49you know, information related
33:51to the demographics and also
33:54pathological diagnosis are available.
33:57And the next question,
33:59is the Biorepository intended
34:01to accept only human samples?
34:04At the moment, yes, only human samples.
34:06We do not have plan on
34:10for animal tissues yet.
34:12But that is interesting question.
34:14We never thought about that but you know in
34:17I I think if we have the infrastructure,
34:20we have the resources,
34:21if there is a need, why not, right.
34:23But I think we we open to that
34:26idea but right now it's everything
34:28is focused on human tissue.
34:29The next question for cancer specimen
34:32is my is any sequencing or genomic
34:35data associated with the samples? Uh.
34:40I think that's a very complex question.
34:43In other words,
34:44a lot of our patients would have
34:46genomic sequence available, right.
34:48I mean it's part of as a part of
34:51their clinical pathological diagnosis,
34:53but right now we don't.
34:56We don't have a mechanism to
34:59link the archive tissue with the
35:02genomic data yet right.
35:03So that certainly is the put that
35:07way certainly they are there.
35:09You know we have probably sequence
35:11close 3000 cancer tissues you know in
35:14Department of Pathology alone right.
35:16So those genomic information are
35:18available but The thing is linking back
35:20so that neither worked one not only.
35:23So we haven't overcome the IRB issue yet.
35:26How can we link that back after we link
35:29those tissue with genomic information back,
35:32so how we can use that
35:34information for research.
35:34So it's very active conversation right now.
35:37I think that's the thing you know,
35:39I hope that the bank will be
35:41able to to to help in this area.
35:43That's for now then they they next
35:47question are there healthy control
35:49samples able able to you know
35:52able to age and gender match with
35:56the study samples we may have?
35:59Yes, this can be done, no.
36:01But The thing is it's certainly not
36:04the regular banking functionality and
36:06for your risk particular research
36:09project you wanted to build age
36:12matched cohort and that's exactly
36:14you need to work with us.
36:15We build a you know project for you
36:18and then we will be able to help you
36:21to get all those samples for you.
36:23Next question.
36:26Is there a plan for how investigator
36:30initiate the samples can be shared to
36:33reduce waste for compatible research goals?
36:36For example,
36:37if one person is collecting biopsy,
36:39is there a way for other investigator
36:42to be aware of actual samples?
36:45You know our request,
36:47this is exactly you see David showed
36:50you all the federal Federated banks
36:53and with different investigators.
36:56Right now there is no common
36:58platform to make those
36:59tissues visible.
37:00Actually we have been talking with all those,
37:03some of the investigators who holding
37:06their programs basically banks.
37:09So that idea moving forward is all those.
37:13Individual organize the banks,
37:15at least they their tissue will be somehow
37:20visible through the Y Ambar repository.
37:23So in other words,
37:24while while some repository serve
37:26as a information bulleting board
37:28or like inventory for example,
37:31you will be able to see all the
37:33Melanoma tissue collected over time
37:34and all the you know the lymphoma
37:37bone marrow collected over time.
37:39However, the BIOREPOSITORY can
37:40serve as a liaison to connect.
37:43In the individual investigators
37:46with the original bank.
37:48Owners in other words, right.
37:50So this is a part of that you can see
37:52the scope of the work for the power
37:54repository is really set up you know
37:57program specific or program focused banking.
38:01So we just wanted to hope this
38:04invest this wise I'm positive.
38:07There are positive to serve
38:08as a common platform.
38:09It's kind of a I may not
38:11be a very good analogy.
38:13It's almost like an Amazon
38:15type of thing you have,
38:16you go through Amazon,
38:18you will be see everything and
38:19actually there are different users
38:21and behind the scene to surreal.
38:26Uh.
38:30I I think that's about it.
38:31So far I have any.
38:34Other question you may have
38:36or comments please just turn
38:38on your speaker and this is
38:40the talk we have several pages
38:43we I cannot see everyone.
38:56There's another question
38:56in the chat now, doctor. OK.
39:00An extra tube of blood for research
39:03is consented for and draw in an
39:06off main campus your clinic.
39:08Is there existing workflow to
39:10transport the tube of the fresh
39:12blood to the biorepository and all?
39:14Does the patient have to come to Disney?
39:17Philip. Any area on the main campus for
39:21research applied to draw, maybe I will,
39:23I will turn this to a weight.
39:26I think that there is a mechanism
39:28to to do the job.
39:29But I think so far at the moment
39:32we don't have a regular Courier,
39:34we don't have a service in the weather.
39:37So we do for some select sites.
39:39So it depends a little bit on the sample
39:42stability as well as which site and what
39:44type of tube or blood is being drawn.
39:46So we have been doing this with.
39:49North Haven barely successfully
39:51and have options for other sites
39:54and so there I would say it it
39:56depends a little bit on frequency.
39:57You know if it's a site that
39:59doesn't do it often even if they
40:01mechanism in place just not having it
40:03routine in the workflow can lead to
40:04mistakes or things getting missed.
40:06But I would say if there is a study that
40:09needs it is something that we have scoped
40:11out and can potentially work through.
40:13Dave not sure if you have any other comments.
40:15So we right now we've basically
40:17piggybacked with the clinical lab to.
40:19To move samples to us,
40:21but we do have a an account with the
40:24Courier that they use separately that
40:26we've not deployed on a wide scale yet.
40:28But a question like that is we
40:30handle it on a one off basis.
40:32We we find out you know where it comes from,
40:34if it,
40:34if the group that's handling it
40:36is like a clinical lab it's easy.
40:38If it's a if it's not it gets a little
40:40more complicated but it's possible.
40:46So that for tracking the storage of
40:48the samples right now the ones that we
40:51have on our side we keep in basically
40:54one of our internal IT systems and our
40:56moving more and more of that into a
40:59platform called Freezer Works and the
41:02freezers themselves are temperature
41:04monitored using the aeroscout system.
41:06So we've got the appropriate monitoring on
41:08on those freezers to track the location,
41:11the inventory and.
41:12The storage conditions for them.
41:16With another question for you is,
41:17is there a supply of human health?
41:22Healthy human blood. Yeah.
41:24So right now, no, often because the
41:26definition of healthy can vary a
41:27little bit depending on the study.
41:29So it is something that we are
41:31interested in of if we can make
41:32a more generic here are just here
41:35is blood from those patients.
41:37But because of the range of specimen
41:39stability and what counts is healthy,
41:41we don't necessarily have an inventory of it.
41:44One thing we can do is if there
41:46is a specific request for that.
41:48So if you said we would like to
41:50get 50 samples in this age range
41:53without this medical history.
41:54Zero or red cells or whole blood
41:57obtained within this time frame.
41:58Those are projects that we can do and
42:00then do those collections potentially
42:02through clinical excess or through
42:04consented pathways depending on the
42:06needs of the study and IRB requirements.
42:11So the next question that we'll each
42:13sample have integrated annotation
42:15diagnostic description from IPEC into
42:18the power pastoralis freezer works
42:20question mark all will there will there
42:23need to be another manually wait yeah
42:27yeah so you know they're again
42:29depends on the scope and need
42:31as well as the RV limitations.
42:33So if you have approval to see
42:35identifiers for the biospecimens
42:37manually annotation is an option
42:39then if it's deidentified.
42:41Which is not currently
42:42for the specimens that Rd.
42:44identified depending on the scope of
42:47the data request that is something
42:49that we do have a charge system to
42:52be able to support or work with
42:53J at the joint data analytics
42:55team to provide those data.
42:56So while it's deidentified
42:58to the investigator,
42:59we can work with Jack to operate as an
43:02honest broker to get clinical annotations.
43:05The complexity and timeline
43:06for that depends on how many
43:09clinical variables are needed and.
43:11How many of those are direct
43:13annotations or structured within
43:15Epic versus less structured?
43:16Or maybe in clinical notes and might
43:18need actual manual abstraction?
43:22And then the next question,
43:23what is the relationship of this
43:26versus the White YTS and which
43:29is now your pathology service,
43:31tissue service is a specimen
43:33collection that had been done by them
43:36now being done by this fall back.
43:38No, I think this is sort
43:40of a separate entity.
43:41You know this still YTS is another
43:45university USP core service and the
43:48BIOREPOSITORY is a different USB service.
43:51So we worked.
43:52That we work together collaboratively
43:55depending on need as therefore YT PS service
43:58you know they provided you know different,
44:01you know to all the investigator
44:04depending on the specific need.
44:06So I think that that function
44:09anality continued to exist.
44:10There is no merge,
44:13you know there is no.
44:16Exclusivity.
44:16In other words,
44:18both entities exist as separate call.
44:27OK.
44:30Any other questions?
44:36I hope after the session we'll receive
44:38more requests through the website, right?
44:41As I said, the more we use it,
44:44the better, because we are.
44:46In the business of trying to say,
44:48promote human tissue usage for your research,
44:52and the other thing is right
44:54now for for your grand support,
44:57there is really no fees
44:59for supporting your grant.
45:01In other words,
45:01if you want to submit a proposal,
45:04you want to build a budget for,
45:05you know, for our repository,
45:08we can work with you to help you
45:10to build the budget and help
45:11you to write it all the pages,
45:13all the documents needed for the power.
45:16Grocery and there's no fee for
45:18that and then you just we can
45:20work with you on that as well.
45:23And one more question,
45:24is there a process by in place so that
45:26if the patient decides they do not
45:28want their samples used for research
45:30or certain aspects of research,
45:31they can be withdrawn? Yes.
45:33So for clinical excess specimens in
45:37particular, if a patient has done
45:39the opt out process through EPIC,
45:42we will not those get screened
45:44out before we even get them.
45:45And if that opt out comes later
45:48for the identified specimens,
45:50we would no longer pull those specimens.
45:52There is not currently an easy way to say.
45:55Withdraw from certain aspects
45:56of research at Yale,
45:58it's mostly a opt in or opt out.
46:01But then there are some of the
46:03additional things like the umbrella
46:05consent that we can screen specifically
46:07for those types of consents for
46:10more extended use of the specimens.
46:12So that the the easy answer is yes,
46:14there is a process.
46:15It can be more nuanced and something
46:18that we are continuing to work
46:20through with the IRB on a per study
46:23basis as well of making sure that.
46:25Those protections and options are in place.
46:33OK. Umm. There are another question here.
46:38This may be a naive question,
46:41but do we need to participate in the?
46:45Replenishment of samples we request.
46:49All will we help facilitate that.
46:55So if I'm understanding the question right,
46:59so let's say that we have a set of
47:01COVID specimens from COVID patients
47:03that you requested and wanted to use.
47:06There is a charge for doing those
47:09specimen polls as well as the, you know,
47:12the storage and everything else.
47:13If we, if those are part of just
47:16our general COVID biorepository,
47:19there's no need for the investigator to go
47:21replenish that or find a new patient to
47:23fill it in or anything along those lines.
47:26And on a per biospecimen,
47:28you know per if it's more of a
47:30Federated biorepository type model,
47:32same thing that would be really up to the
47:34terms with those API's are investigators.
47:36So there wouldn't be like a a a
47:38second charge to go obtain another
47:40specimen to put into inventory,
47:42you would just be charged for the
47:44one that was removed from inventory.
47:48Next question, which samples are
47:50stored in Bower pastoring right now?
47:53As I mentioned,
47:53you know you go to the website,
47:55you'll see there's some blood samples
47:58and also some archived material.
48:01But the question is right now we we,
48:05we are not.
48:06We we haven't been able to categorize
48:09all of that yet and this one stay tuned.
48:13So we'll have the you know inventory.
48:16However at the moment you know you
48:18can always you know make a request
48:20and tell us what you are looking
48:23for and then we can be more targeted
48:25to expedite what's your request
48:27and for us to really inventory
48:29the entire you know like we talk
48:31about millions of different type of
48:33tissues that's will take some time,
48:35right, we can prioritize.
48:37What are your needs?
48:39And the other question is what
48:41about the pediatric samples?
48:43Is there an informed consent to
48:46Bank of pediatric oncology samples?
48:49Right now, we don't.
48:50I will specific pediatric consenting form.
48:53So all we do for the tissue side right
48:55now for the bank to have is really
48:59providing so-called non consented
49:01deidentified specimen for pediatric
49:04oncologists stuff for example.
49:07This has to be a specific project and
49:10we set up a prospective collection
49:13and with adequate patient concerns.
49:16So we
49:17have and I would say not unconsented,
49:19just limited consent.
49:20It's part of the standard consent
49:22for receiving healthcare.
49:23There are some restrictions
49:24on what those samples,
49:26those limited consent samples
49:27can be used for. For example,
49:29the FDA will not accept that level of
49:32consent for use in a clinical trial.
49:34It needs to be a more dedicated consent.
49:36So even the deidentified ones have
49:39a consent just basic with some
49:42downstream limitations on use.
49:45Yeah.
49:48So the next question for the brain
49:51samples in the Bower repository at
49:54these postmortem brain samples,
49:57the question yes you know usually we
50:00we cannot archive very unlikely we will
50:04archive the surgical brain as you know the
50:07brain tissue storage is really limited.
50:10So right now all the brain tissue
50:12we have is really from autopsy.
50:14So I did not talk about more related to.
50:18A program or in pathology we're
50:20doing is the rapid autopsy program.
50:22This is actually going to be one
50:28important way for us to procure
50:31human tissue from rapid autopsy
50:33that means and will perform autopsy
50:36between four to six hour period of
50:40time and after patients disease.
50:43It's all very well documented when
50:45you collect the tissue in that
50:47window period time, in other words,
50:50the photos like 4 to 6 hours,
50:52the tissue quality is really good and
50:55for so even for some culture those are
50:58will be useful for the brain tissue
51:00again you know we do have some of the
51:03tissue collected in the very short.
51:08Period of time, yeah after patients death.
51:10So this is going to be a program
51:14we're going to continue to to to
51:18expand to rapid autopsy program.
51:22So the next question is can I DNA
51:26sequencing be performed in general on
51:29these samples or is specific RB review
51:32requirement for each required requested use.
51:36So this is a, I mean most of the
51:38samples we have collected, yes,
51:40you can do DNA RNA sequencing but right
51:43now when you request tissue from the bank,
51:47right now the bank if you don't
51:49have existing IRP, you don't have
51:51a specific consent to determine.
51:53Will say to link the patients to the,
51:55you know, to the sequencing
51:57that that that means.
52:00We can, you know you don't like,
52:02we cannot give you more information,
52:04you know specific information
52:05you can use that for sequencing,
52:07but you cannot really link
52:10specifically to the, to the,
52:12to the patient for the downstream study
52:14and that's basically RB probably required
52:17in that as you know the genetic study
52:20by itself it's kind of really touching,
52:23it's very.
52:24Yeah, difficult area to evaluate.
52:27So genetic information by itself is
52:30can be considered as an identifier.
52:32I think this is all depend on what
52:35kind of study you do you're doing
52:37and how you're going to present the
52:40data you know and for your research,
52:43I think that on the safer side is
52:45probably more important to have
52:47specific RP if you really conduct
52:49the genomic research,
52:51that's just my recommendation,
52:52it is save you a lot of downstream.
52:55Diesel.
52:57There is a certainly a a a school
53:01of thought that thinking all the
53:04genetic sequencing is a patient
53:06identifier maybe true right.
53:08I think it just depending how
53:10you will see it.
53:11So that's why I think for the
53:13genetic study is better you have
53:14RP coverage rather than do that
53:16totally deidentified fashion.
53:22Uh.
53:26Hey we almost at the hour and
53:294 minutes left and any other
53:31not always say last question or
53:33last comment from the audience.
53:37I think we, I mean on behalf of weight
53:40and myself I really appreciate your
53:42spend Friday afternoon to this session.
53:45I think this is a I mean as I mentioned
53:48I just want to re emphasize this
53:50again this is a shared resources OK.
53:52It's not anybody's private property
53:54or trying to do this and that
53:57this is collectively for all
53:59the Yale investigator tool.
54:01Share this resources so that means
54:04we are just start so that you know
54:07it's really the time for us to you
54:10know collectively to make this.
54:12You know about repository function really
54:15well and really meet your need for human,
54:19you know, human specimen research.
54:21So we want to hear from you.
54:23It's important for you to participate
54:25in the process, and we'll see.
54:27That's the only way to make
54:29this bank to be truly, truly.
54:34Friendly bank and a very efficient
54:36and effective bank for your research.
54:39Alright.
54:40And as I said,
54:41we probably would would come
54:43back again in three months.
54:44So our idea is probably will
54:46do a quarterly update on the
54:49banking activity and some nuances,
54:50some ideas,
54:52you know some new services available
54:54or what we will learn from that.
54:57So this is at least in the near future
55:00we're going to have this regular like a
55:03quarterly information session just like this.
55:06Yeah, no.
55:06OK.
55:06So really wanted to hear from you.
55:09As you know,
55:10wait,
55:10we have a last comment.
55:14Look, that sums it up.
55:15OK, great. Thank you all
55:17and you have a nice weekend.