Yale Biorepository Information Session - August 22, 2023

August 22, 2023

Information

An information session on the Yale Biorepository with Chen Liu, MD, PhD, and Wade Schultz, MD, PhD.

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00:07Yeah, we'll give people one
00:08more minute before we start.
00:48I think we just go ahead to get started.
00:51And first of all,
00:53welcome you all for this YSM,
00:56YSM file repository open session.
01:00If the separation will be coordinated by me,
01:05my name is Chen Liu,
01:06so I'm the director for the power
01:09repository and the doctor with the
01:12source and who is the associate
01:14director for the power repository.
01:16I think that the the session is is recorded.
01:19I think we will post it on the website.
01:22You know, for people who miss it,
01:24you still can, you know, look at it,
01:26look at the presentation.
01:28So we just do a kind of kind of a
01:31quick presentation and mainly to
01:33really to answer questions from you
01:36and just tell you what's the the
01:38update from the power repository
01:40and hopefully this you know,
01:42you will know the the existence existence
01:46of this power repository and how to
01:49approach this repository and then
01:51to really support your research program.
01:54So now I'm going to share my screen.
02:03OK,
02:07yeah OK, you wait to use you see
02:09the the screen OK good. So this.
02:11So this is a really the the the lead
02:15the first slide first of all the scope
02:19of the work in the YSM bio repository.
02:21Now can we can summarize into like A5 parts.
02:25The one is supporting general biospecimen
02:29the intake acquisition, processing,
02:31storage and distribution and we also
02:35supported the investigator initiated
02:37or program initiated tissue banking.
02:40So this is actually it constitute a
02:43large part of what our service and
02:46we support a clinical IC validation.
02:49We we support the biospecimen components
02:53of clinical trial and we also support
02:58existing bio banks in on campus.
03:01And we know there are number of existing
03:04tissue banks and we actually wanted to
03:07work with you to see how we can provide
03:10support in terms of standard standard
03:12procedure and also some regulatory issue.
03:16And then eventually this bank would
03:19want will will be you know a CAP of
03:24college American pathologies accredited.
03:26So this is basically our goal to have this
03:30bank to become a credit the tissue bank.
03:32So what in the bank,
03:34you know we call it the power of positive
03:37products and we will have the capacity
03:40and technology to any annotate and
03:44process archive and the fresh samples.
03:47And one other aspect,
03:48you know from this bank protect we would
03:51be able to provide the paired samples
03:54that means liquid or blood and the
03:57solid tissue paired tissue specimen.
03:59And we also provide a live tissue for
04:02organized cultures. And the PDX mice.
04:05You know for whatever the usage you
04:07would like to have for live tissue
04:09and the potential to help people
04:11to develop cell lines and DNA,
04:14RNA protein extractions and the mono
04:17nuclear cell isolations from blast samples.
04:19Those are the examples of this power
04:22repository will be able to provide.
04:24And of course if you have some special need,
04:27special request we are more than happy
04:30to work with you to find to understand
04:33what your need and try to support it.
04:38So this,
04:40this is sort of a timeline,
04:41the preliminary operation because the
04:44debate really back to 2020 is under
04:47weight with the source directorship.
04:50And then the this current bank is actually
04:53officially starting November 2022.
04:55And so so far the bank has been
04:58supported more than 20 clinical
05:00laboratory projects and research studies.
05:03And right now this is the current
05:05structure of the YSM Bauer repository
05:07is I directed the bank and Wade is
05:11the social director and we the two
05:13managers one from you know is work
05:16closely under Wade with his name is
05:19David Ferguson and then other is the
05:22King fan who is closely work with me.
05:27So the bank also kind of tries to
05:29support you for your grant application.
05:32For example,
05:33the bank will provide the letters
05:35of support and help you to do the
05:38budget justification in terms of
05:40cost for biospecimen acquisition,
05:43storage and utilization.
05:46And it really provided this boiler place
05:48for you to for you know for any granted
05:51application you're going to have a
05:53resources facilitating the equipment page
05:55and this is just to give you an example,
05:58while the bank can actually provide it to
06:01your to you know to your grant applications.
06:06So right now this is a temporary space
06:09and well one is located at LMP 2017, 2077.
06:16So this is smaller live module,
06:18this is the diagram.
06:19And then the other live space is and it's
06:23it's in the space of live term medicine
06:25you can see where just so the one at
06:27LMP 2077 is really the primarily it's
06:32tissue samples and the one the space
06:36in the underlying medicine is mainly
06:39blood or other liquid about specimen.
06:47So how this bank is financially supported.
06:49So the bank is right now is the institutional
06:54support mainly and it's from Dean's office,
06:56it runs as a university service
07:00provider basically called USP cards.
07:02You are familiar with the and then then
07:05the others is really the true charge back.
07:07So the charge back of specimen,
07:09the usage will be determined on an
07:12annually basis just like any other US
07:15you know USP car within the university.
07:18And certainly this is also our future goal
07:20is to see if the bank would collaborate
07:24with investigators or even industry
07:26partners and to see if we can get some
07:28of support you know through either
07:31grants or some other service agreement.
07:34And of course there's one other
07:36area you know venue to support the
07:38bank will be fair philanthropy.
07:40But right now I just you know the
07:42bank is predominantly subsidized by
07:44the Dean's office and then we have
07:47the charge back fees which you know
07:51which are posted online, right.
07:52You can see the fees and online and
07:55certainly when we meet you and we'll
07:56discuss this with you and it will
07:58find out what's your need and then you
08:01you are get much clear information.
08:03So this is the current available specimen.
08:06We have blast samples and the like.
08:07Medicine is we have 275,000 eloquent,
08:11we have archived tissues within
08:14pathology and then because of the
08:16COVID and over the past two,
08:19two or three years we have accumulate
08:21accumulate the significant number of the
08:23COVID specimen and 80 from autopsies,
08:26MP swaps,
08:27Saliva's and also some blast samples.
08:31So this is also a summary.
08:32So right now for example this is the
08:36tissue inventories we have you know
08:38with basically we want to we will build
08:40a collection of normal tissues from
08:42all different parts of our organs and
08:45then you will be able to see it as
08:47through online access and that this is
08:50just to give you a snapshot on what
08:52are the you know information looks like.
08:55And then eventually we want to make sure
08:58the bank website will be more user friendly,
09:01more interactive,
09:02you will be getting more information from
09:05the you know from the from the bank.
09:08Right now we are building this portal
09:10and the step by step you will have
09:13more information you know you can
09:16get from the website. All right.
09:18So any questions so far?
09:22Because I can now see you probably
09:24just on mute and speak out,
09:26speak out, please. All right.
09:29That way I'll turn to Wade and
09:31who is going to give you more
09:33for the introduction about the
09:36current blood sample collection
09:38and about specimen support.
09:40And wait, yeah,
09:42sounds great. So yeah,
09:43but as Doctor New mentioned,
09:45we had initially started operations for a
09:48liquid specific biorepository back in 2020,
09:51primarily focused on the collection
09:54and distribution of COVID-19
09:56specimens both for clinical use,
09:58population health and
09:59epidemiologic surveillance as
10:01well as a few research contracts.
10:04And now I have merged that into the
10:07YSM biorepository so that we actually
10:09have a a single biorepository.
10:11It is not managed by a anatomic
10:14path or lab medicine.
10:16Many of the people are
10:17from those departments,
10:17but it is actually the YSM biorepository.
10:21Next slide.
10:23And really what we wanted to, you know,
10:25highlight as part of this effort
10:27is that we aren't just a biobank.
10:29So the goal for us is not just to take
10:32specimens and put them in a freezer,
10:34but rather provide biospecimen management.
10:36So we have a number of projects where we
10:39actually acquire biospecimens and we'll
10:41ship them directly to study sponsors.
10:43We'll move them immediately to one of the
10:46research labs or clinical trial groups.
10:48In cases where we do need to store them,
10:50we can put them in a freezer and
10:52bank them for future use as well.
10:54But really wanted to move beyond just
10:56banking and really have this more
10:58service organization that can provide
11:00a number of different functions for
11:02investigators who need to access
11:04tissue or liquid biospecimens.
11:06Another aspect of that is that we
11:09can actually capture biospecimens
11:10in real time or near real time.
11:13We can do that both for consented
11:16patients where specimens come in
11:18specifically for a research study we can
11:20do consented but excess specimen collection.
11:23So somebody consented,
11:24but we're taking excess from a clinical
11:26collection or with appropriate IRB
11:28approval and de identification can
11:30actually use de identified excess
11:32specimens based off of clinical criteria.
11:35And we've done that for a number of
11:37different disease states or conditions,
11:39lupus, COVID,
11:40some hematologic malignancy as
11:42well as within the clinical lab.
11:45We've done this for a number of
11:47different assay validations as well.
11:48So something that's quite powerful
11:50especially for labile analytes where
11:52we don't have to worry about how
11:54long is the spend in the freezer,
11:55but we can get it soon after the time
11:57that the specimen was collected or
12:00completed for a clinical testing.
12:01Next slide.
12:07And so I've already talked
12:08through both of these.
12:09So those two pathways again are
12:11either the excess clinical samples
12:13which can either be consented
12:14or deidentified specimens as
12:16well as new sample collection.
12:17We've done collections for Sera plasma,
12:21whole blood, we've done PBMC
12:23isolation saliva and P swab.
12:25So really a quite broad set of
12:27specimens that we can collect.
12:30We've also done a couple of specimen
12:32types for CSF as well as urine.
12:34So as long as we have a standardized
12:37collection containers for those biospecimens,
12:39it's something that we can
12:41pretty rapidly get.
12:42And if there are nonstandard collection,
12:44we can set that up on a more
12:46site per site basis.
12:48We also have done collections at other
12:51DN's as well as other care sites.
12:52So we've done a number of biospecimen
12:54collections from like the North Haven
12:56Smylo Center as well as others across
12:59the Yale New Haven Health Network.
13:00Next slide,
13:05some of the different services that
13:06we offer and like Doctor Lu mentioned,
13:08the full list of these as well as the
13:10prices are all on our biorepository website,
13:12which will pull up here at the
13:14end for more complex studies.
13:16There is a study setup charge and then we
13:19have services as basic as just receiving
13:21and DE identifying A specimen and then
13:23handing that to the investigator.
13:25We can also do basic
13:27processing and aliquoting.
13:28We can do aliquoting into our
13:30bio banking tubes which already
13:31have barcodes printed on them,
13:33both a 1D bar code on the side
13:35and a 2D bar code on the bottom.
13:37Or if there are custom tubes that
13:39somebody needs, we can do that as well.
13:41We do have storage capacity
13:43for four degrees -20,
13:45negative 80 and liquid nitrogen is an option,
13:49but we have not had anybody
13:50have that stored with us yet.
13:52There is a retrieval charge,
13:53so specimens are being
13:55stored with us long term.
13:56There is a cost to pull those.
13:58If it is something where
13:59it's for a specific study,
14:00we're collecting it for a couple of
14:02months and then just pulling that plate,
14:03then that's just part of the study.
14:05Cost rather than retrieval
14:07specifically DNA&amp;RNA preparation
14:09are things that we can do.
14:10PBMC preparation,
14:11as I mentioned,
14:12we've done a number of projects on and
14:14then we also have some study support
14:17options for doing informatics support,
14:19shipping manifest development to support
14:22really primarily the sponsored trials
14:25where we might be packaging it up,
14:27filling out custom manifests
14:28and then set it sending that
14:30to a study sponsor directly.
14:32In a couple of unique cases,
14:33we can also do research,
14:34testing within the clinical labs.
14:36So we've done a couple of projects
14:38where people needed COVID antibody
14:39results and we were able to work
14:41with the clinical labs to do
14:43that testing directly and supply
14:44those as research results as well
14:46as a few other assays as well.
14:49Next slide
14:52for the informatics driven
14:53biorepository aspect of this,
14:55one thing I had mentioned was that
14:57we can capture these specimens
14:58in real time or near real time.
15:00And the way we do that is with some
15:01of the infrastructure that we've
15:03developed within the School of Medicine
15:04as well as the health system that
15:06allows us to monitor patient data in
15:08both an identified and deidentified
15:10fashion in in near real time.
15:13So within seconds to minutes or
15:15hours of a test being completed,
15:17we can see those results and
15:20actually then flag biospecimens for
15:22collection and the identification
15:24and then downstream use or use cases.
15:27We've done this for some studies looking
15:29at babesio where we flagged on as
15:30soon as we had a babesio quantification,
15:32if it was over 10%,
15:34those cases were flagged and we
15:36would go get the tube of blood,
15:37prepare another spear and then set
15:39that aside for the researcher.
15:41We've done it for some clinical lab
15:43validations looking at some play bile
15:45analytes in urine as well as blood.
15:47We've also done this for a number of
15:50COVID studies where after patients had
15:52a COVID infection pulling subsequent
15:54sera specimens from the same individuals.
15:57So something that's very powerful
15:58and that we can develop.
16:00The amount of time to develop
16:02those those signatures or alerts
16:03varies depending on how complex
16:05the the phenotype or signature is.
16:07So looking for adults with diabetes
16:10is easier than looking for an adult
16:13admitted to the ICU and put on the
16:14ventilator in the last four hours.
16:16So depending on that complexity,
16:18all things we can potentially work with,
16:19but have a different cost depending on
16:21how long it takes to actually develop.
16:23Next slide,
16:27the current infrastructure,
16:28these are again shared
16:29within the biorepository,
16:31but these this is equipment that
16:33we have over in 55 Park St.
16:34the lab building.
16:35We do have some automation
16:37to help with aliquotting and
16:39processing of our biospecimens.
16:41So the Hamilton star over on
16:43the right hand side that's
16:44hooked up to an automated capper
16:46decapper that goes into our low
16:48format biorepository plates.
16:49So for individuals that can
16:51work with our freezer tubes,
16:53either the half mill or the one mill tubes,
16:55something that we can do in a pretty
16:57automated fashion for both the
16:59aliquotting as well as manifest generation,
17:01we have an additional three
17:02negative 80 degree freezers,
17:03a -20 degree freezer refrigerator.
17:06We have refrigerated and room
17:09temperature centrifuges,
17:10the plate scanners.
17:11We also have a cell counter
17:13to assist with a pre and post
17:15processing cell counts for PDMC's.
17:16And so all of that's already in place
17:18which means that for new projects
17:20that use our existing services,
17:22something that we can usually get
17:23set up and start pretty quickly.
17:25Next slide
17:28that integration then we are pretty
17:30well integrated with the J dot team.
17:31So once we do get biospecimens,
17:33we are able to return through
17:36the biorepository some limited
17:37information demographics,
17:39certain laboratory test results,
17:40things that are directly related
17:42to your patient population
17:44or your phenotype definition.
17:45If we are pulling those specimens
17:47in real time for larger or
17:49more complex data requests,
17:50we can help work with Jada to
17:52supply them the deidentified
17:54list of biospecimens which we can
17:56then link back to the rest of
17:58the clinical data within EPIC and
18:00the electronic health records.
18:01So allows us to do this when you do
18:04have say an exemption from the IRB
18:06to get this clinical excess specimens
18:08where we can do that deidentified
18:10with a a waiver of consent,
18:12but still supply clinical data on the
18:14back end of that without needing to
18:16do additional IRB approvals or work there.
18:19So something that we've done again
18:21for a number projects and is a pretty
18:24fluent process depending primarily on
18:25the complexity of the data request
18:27and how busy JDOT is at any given time,
18:30but something that we can augment
18:32internally at least for key
18:34variables that investigators may
18:35need for their research or studies.
18:37Next slide,
18:40specimens process today to get these
18:42were primarily COVID initially.
18:44We've now done somewhere around 50,000,
18:46maybe 75,000 non COVID aliquots as well.
18:50From those we processed 400,000 have about
18:54275,000 in storage and one of the exciting
18:56things for me is that we've actually
18:59touched about 80% of those specimens.
19:01So not necessarily every Aliquot,
19:03but we have had follow up or use
19:05of about 80% of those specimens
19:07in actual research projects,
19:09many of which have already
19:10had publications go out.
19:11So something where these aren't
19:13just specimens going to live in
19:14the freezer for the next decade,
19:16but something that is really integrated
19:18into those research pipelines and
19:20generating research activities on the
19:22other end and in a pretty rapid timeline.
19:25Next slide,
19:27some of the examples of that for some
19:29of our clinical assay validations.
19:30One of those actually included a
19:32manuscript as well for validating
19:34our COVID antibody assays earlier
19:36on in the pandemic.
19:37Some of the others that we've done with
19:39the chemistry lab included identification
19:41of urine interferences for urine PCP
19:43testing as well as looking at that
19:45amlodipine stability and plasma,
19:47which is one of those where we
19:48really had to be able to get those
19:50specimens quickly because of the
19:52possible ability of that analyte.
19:53And then the last one was using many
19:55of our COVID NP swabs to validate
19:58in house COVID-19 sequencing,
20:00primarily within lab medicine,
20:01but also supplying specimens for
20:03Nate Kruba in epidemiology as
20:05well as anatomic pathology for
20:07some of those state contracts.
20:09Next slide.
20:11More,
20:11this is a little bit more on
20:13that EIP program for Nate Kruba.
20:15So this is where we've been ongoing
20:17providing specimens for SARS Co V2
20:20sequencing that continues today.
20:22In addition to that epidemiologic
20:24surveillance that's now I think up
20:26to seven manuscripts published in
20:27another three or four in preprints
20:29or something that's had a a lot
20:31of academic productivity from
20:32being able to get those specimens,
20:34supply the associated clinical data
20:37then with a really a lot of great work
20:38by Nate's lab to do the the basic
20:40science and public Health Science
20:42on on top of those biospecimens.
20:43Afterwards,
20:45next slide in terms of requesting access,
20:48so there is a Red Cap site where
20:50you can submit a project request.
20:53That link to Red Cap is also
20:55on our biorepository website.
20:57The link for that's down on the bottom.
20:59So the bottom link has the link to
21:01the request form all of our services,
21:03our pricing and contact information.
21:05The general flow of this starts
21:07in the top left.
21:08So you submit the request on
21:10Red Cap within a week at most.
21:12David or Keen will then reach
21:14out to you to see if there's
21:16additional information that we need,
21:17if there's an IRB in place,
21:19at which point we will then work
21:21through what does the specimen
21:23acquisition SOP look like.
21:24So as we get specimens either from
21:27excess specimens or consented patients,
21:29what do we need to do in
21:31the biorepository for
21:32processing stability storage.
21:34Once we know that we can generate an
21:36estimate given our current pricing and
21:37then agree to a project initiation time.
21:39And we've done this successfully
21:41now for over probably over 25
21:44projects at this point over the last
21:46since just November of last year.
21:48So something that we can get
21:49started usually pretty quickly
21:51and scale up as needed. Next line
21:55and that is it.
21:57So yeah, happy to take any questions
21:59or Dr. Lu, if you had any other
22:02comments to start with. OK,
22:03thanks Wait. So now both of me
22:05and Wade are here And really
22:07to answer a question from you,
22:12if you have just unmute and ask the question,
22:19are you gonna make the slides available?
22:21Yes, it will be posted on, on our website.
22:26Yep, the slides as well as a
22:28recording of the presentation. Great.
22:31Thank you both for the information.
22:32This is really helpful.
22:33I have a question for you
22:35about collecting specimens,
22:36specimens from patients in clinic
22:40like at different clinic sites rather
22:42than say the OR from pathology,
22:45archival tissue.
22:45Is there experience with that
22:47or how does that normally go?
22:49Yeah, absolutely.
22:49And so it depends on where the clinic
22:52is at primarily depending on how
22:53quickly you need them processed.
22:55We do, we are,
22:56we are able to use our existing
22:58Courier services across the New Haven.
23:00So if a clinic is has a Courier that
23:03is bringing samples to the main lab,
23:05we can piggyback off of that.
23:07And as long as there isn't a stability issue,
23:09there's no extra cost.
23:11As long as those go routine
23:12for other clinic sites,
23:14we can set up dedicated careers if necessary.
23:16That actually ended up being far cheaper
23:18than I thought it was going to be.
23:19So the price varies depending
23:22on how far they're going and on
23:25whether it's a scheduled or a stat,
23:28but something that we can set
23:30up for dedicated careers and we
23:33have done that as well for even a
23:35couple of sites over by Greenwich
23:38in terms of the collection for
23:40that there is we actually have a
23:42dedicated research order within EPIC.
23:44And so if that's something
23:46that you're interested in,
23:48just fill out the project request and
23:51David or Keen can work with you to go
23:53through the details of what's the IRB.
23:56How can this get ordered when those
23:58research labels get applied to the
23:59tube and brought to the main lab,
24:01those moved directly to the
24:04biorepository from accessioning and
24:05you have to type in your HIC number.
24:07So that's how we then say this
24:09specimen belongs to your study
24:11versus somebody else and then
24:12we follow the appropriate SFP
24:14based off of that designation.
24:17Yeah. Thanks Diane for Diane has
24:20you know put a you know chat
24:23a message on the chat.
24:24Yes, the how to access the site,
24:26you know so we just did that and actually
24:30if you just search under Google,
24:32is that why I sent by repository,
24:34it will show up.
24:35It would link you to the site.
24:37It is under school, year, school.
24:38I wasn't asking about the site.
24:40I was asking about the recording.
24:42Yeah. So the we'll we'll put a link
24:43to the recording and the presentation
24:45on on that website for you.
24:47Thank you. And by repository
24:49website. Thank you
24:50exactly. Yeah. It'll be a new link
24:53that they'll add on hopefully by
24:55my guess would be by Thursday.
24:57They're usually pretty quick.
24:58Understood. Thanks. Yep,
25:03other question, sorry. I have
25:05one more more question for you
25:08regarding archival tissue
25:10that's already been collected.
25:12Is there a mechanism by which we
25:14can request specific like a specific
25:17patient or a specific sort of
25:20specific pathology that we kind of
25:23point out from from clinical sort of
25:26record review or is this more like
25:28of a broad kind of a broad platform
25:30like saying oh you know we want a
25:32liver tumor or something like this.
25:35Yes, I mean I can take this question.
25:38I think wait will tell you,
25:39you know if you want,
25:41yes in the way there is a way to do
25:45that because we just want to need
25:47to know what exactly what's your
25:50you know what is your need right.
25:52Because we want to know is you are certain,
25:55you know you as you mentioned the
25:56minus then is like you want to search
25:59a certain specific patients material
26:00and then we can just work with you and
26:02then identify those tissue and the
26:04specimen assume and you know you have
26:07the IRB cover that because otherwise
26:09you know we won't be able to go to
26:12specific patient without adequate IRP.
26:15We can give you a generous stuff we cannot
26:17right to give you a specific patient.
26:19But If however if you have your IRP,
26:22so that's why you know when
26:23we to show the flow chart,
26:24we know we have an IRP and then we
26:26can help you to identify those tissue
26:28specimen and then certainly we'll see
26:30what's available and then you can get access.
26:32So I advice the way to do it,
26:34it costs you nothing is you just go
26:36to the website, there is a request.
26:38The Red Cap site is very,
26:40you know, very straightforward.
26:42You click that give you,
26:44you know give us your contact
26:46information and one of you know
26:48either King or David will talk,
26:49will will actually contact you
26:51and then you can explain to them
26:54the details what you want.
26:56So wait, did you have anything to add?
26:59Yeah. So yeah, I agree with all of that.
27:01And so whether you have an existing list
27:04of patients or a clinic or a disease type,
27:06all of those are potentially
27:08options by which we can look at
27:11archive tissue and find matches.
27:12If it is something that is more
27:14prospective of you need fresh tissue
27:16moving forward based off of a disease
27:18or a clinic or specific patients,
27:20then we just have to work
27:22through those workflow pieces of
27:24IRB who's doing consenting.
27:25We can sometimes support some of
27:28the consent aspect depending on
27:30the the scope and the timelines.
27:32But in general,
27:33all of them are options and for the
27:35specific use case like Doctor Lu mentioned,
27:37fill out the request form and
27:38we can get a better idea of your
27:41project specifically and what the
27:43best approach would ultimately be.
27:45All right, Thank you.
27:47I appreciate it.
27:48And then somebody else had a question
27:50about PBMC's from healthy donors.
27:52So we do not currently bank routinely
27:54like a healthy donor pool of blood or PBMC's.
27:59It's something that we are looking at doing,
28:01the challenge being that healthy donor.
28:03The definition varies a little
28:04bit sometimes based on the study.
28:06But if that is a need to get PBMC's from
28:09your definition of healthy individuals,
28:12that is something that we can also
28:14work through and figure out what would
28:15a process look like and how could we
28:17acquire those specimens for a specific study.
28:25I'm Sandri, I have a question,
28:27I'm from data at research department.
28:30So a lot of times we get question
28:34on like you know who can we get a
28:38list of people who have provided
28:40who are from the biobank and then
28:42like you know data related to them.
28:44So is there like you know do you
28:48provide access to JDAD so we can
28:51know like you know who are because
28:54often what happens is like you
28:56know we have a requester who is
28:58looking for their patients with some
29:00condition and then not everybody has
29:03some you know in the biobank has a
29:07specimen or anything in the biobank.
29:08So they are looking for specifically
29:11for patients who have some specimens
29:13in the biobank and there is
29:15more data associated with that.
29:17So does JDAT,
29:18can JDAT have access to any table
29:21at least like you know where we can
29:25directly refer and know that you know,
29:27OK these are the patients who have
29:30some specimens and you know whatever
29:33specimen it is like some top level
29:36table like you know I'm not going
29:38into very detailed you know data, but
29:42yeah, so so it's it, it, it's complicated.
29:45So technically yes and Rich and a few
29:48others already actually have access.
29:50All of this is done in our
29:52computational health platform that
29:54I comanage with Charlie Tory over
29:56on the young New Haven health side.
29:58So the the information is
30:00is there and available.
30:02The thing that we are currently
30:04doing is that we have the overall
30:06biorepository within that some specimens
30:09are specifically for individual
30:10investigator studies where they pay us
30:13to acquire and store those samples.
30:15And in those cases,
30:16it's up to the investigator whether
30:19others can access those specimens or not.
30:21And so the way that we've interacted
30:24with your team in the past for
30:26those is that usually we already
30:27know the list and so we'll supply
30:29the list and say here are the other
30:32clinical data metadata that are
30:33needed for this list of specimens or
30:36individuals either through the data
30:38architect group or through Jada.
30:40As we continue to add on more
30:43publicly banked specimens,
30:44the goal is that you will be able to
30:46do what you're describing just that
30:48our number of publicly accessible
30:50already in inventory specimens is
30:53somewhat low with the exception
30:55of the archive ethology tissues
30:57and those do not typically have
31:00structured data around them.
31:02So those have to be searched
31:04through via the path,
31:05the pathology portal.
31:07But longer term,
31:07that is the plan that we will be
31:09having more publicly available
31:11specimens and by public,
31:12I mean Yale accessible specimens and
31:15more direct access for you guys to
31:17be able to query and see what those are.
31:19Okay. Thank you.
31:22There's a chatted question from Denise
31:26whether some already banked or can we do
31:29the prospective collection of samples.
31:32I think both question, yes,
31:34but it's really, we don't know how
31:36to bank every tissue, but I think
31:38there's limited collection we have.
31:40So that's why I showed you on the slides.
31:42You will have some amateur on
31:44the tissue side.
31:45I think for weight,
31:46you know he has a large collection of
31:49the existing plasma serum out there
31:51and really all you need you know
31:55let us know if you make a request
31:57from the website and then tell us
31:59exactly what you are looking for.
32:01We can certainly search the
32:03existing collection to see if
32:05they can be available for you.
32:07And now for the perspectives collection,
32:10actually we will sit down to work
32:12with you and to build a project in
32:14the forward perspective collection.
32:17Thank you Doctor Lu, I'm a nephrologist.
32:19I'm mostly interested in urine.
32:21I'm guessing that's not bang.
32:23So we'll probably have to work with
32:24you guys because that you know that
32:26that's sort of the we would like to
32:28collect your and at the time a specific
32:30time point in a hospitalization.
32:32But I guess that'll require a
32:34prospective collection, I guess,
32:35right, absolutely.
32:37So we we, we do have you know somewhere
32:39around 100 urines but they aren't,
32:40they were specifically collected for like the
32:43amlodipine studies and a couple of others.
32:45There is excess.
32:45So if they fit your
32:46criteria you can use them,
32:47but it would be a small number.
32:49But yeah,
32:50for what you're describing something
32:51that we could set up due to perspective
32:53we could still do depending on
32:55how tight your time window is,
32:58you know if it's within 6 to 24
33:00hours or something like that versus
33:02at 8 hours post hospitalization.
33:04That's something where we still might
33:05be able to work off of de identified
33:08clinical excess specimens with an
33:09IRB exemption versus needing to go
33:12get a dedicated research specimen
33:14with consent at a specific time.
33:16So you know again I think there if
33:19you submit a request we can talk
33:21through what might make the most sense
33:23and whether that's something that
33:25we could support as excess versus
33:27needing a dedicated collection.
33:29Thank you.
33:30Thank you. You know if you just kind
33:33of talk to us and then contact us
33:35and we'll find more detail from you
33:41and then fed for your comment,
33:43you know the the clinical data.
33:46So we from the biorepository will typically
33:49only supply some of the basic demographics.
33:52You know what time was the specimen,
33:54how old was the patient sex,
33:57race, ethnicity.
33:59And then if we triggered that on
34:01specific criteria like you said,
34:03we want you to find patients with
34:06a B&amp;C and get the specimen.
34:08We would tell you,
34:09you know if that was triggering
34:11on a creatinine over the one,
34:13then we would give you be able
34:14to give you the creatinine back
34:15more expansive data requests.
34:16Those are what we would refer to
34:19jade abs and then we would supply
34:20them with the list and that's only
34:22limited by you know what data are
34:25available in epic and figuring out,
34:27you know how do you summarize those data.
34:29So if you want their creatinine
34:31from the hospitalization,
34:32do you want their first or the
34:34average of their creatinines
34:35in the first six hours or every
34:37creatinine from the hospitalization.
34:39But something where we would have
34:40you submit a then a J dot request
34:42and we would work with them to
34:44pair the clinical data to the
34:46biospecimens but get that more
34:47detailed information from their team.
34:49Got it. And do people normally do
34:51that via like submitting a red,
34:52like a red cap or like some like, you know,
34:55a list of variables, something like this.
34:57Yeah. Yep.
34:58It's a Helix submission or some area.
35:00I'm not sure if you've got the,
35:01it might have changed names,
35:02but there's a if you submit it to us, we've.
35:05Yeah, Helix's request.
35:06So if you submit it to us and
35:08tell us you need that data,
35:09we can help you with getting
35:11that other request subsequently
35:12submitted to the JDAT group.
35:14Got it, got it.
35:15Thank you.
35:17Another chatted question from Dr.
35:19Kai, I I think we have some lung
35:25normal healthy lung tissue can.
35:27OK can can you answer the question or.
35:31OK, so now I got the answer you
35:33know King's text me we have a more
35:36than 30 normal lung tissue and more
35:38than 60 Co with a lung tissue.
35:41So Dr. Kai, did I answer a question?
35:45Thank you.
35:46OK. So
35:56any other questions, comments.
36:07Well thank you all very much.
36:08We can Doctor Lu and I can stick
36:10around for a few more minutes
36:11if anybody thinks of anything.
36:12I do want to since Andreas is on,
36:14do you want to highlight some of his
36:16work early on in this project for
36:18helping with some of the initial setup
36:20of the biorepository data feeds and
36:23tracking especially during the COVID
36:25times as well as Keen for all of her
36:27help on the on the projects as well.
36:29The red cap form is probably the
36:31best way to contact us just to make
36:33sure that no requests get dropped.
36:35Dave and Keen usually check the
36:37new requests a couple of times per
36:40week and so at most it would be,
36:42you know days to a week maximum before
36:44you should be hearing back from us.
36:46And if there's anything you we can
36:48help out with, just let us know.
36:50Yeah, I'm sorry. I could just that
36:53you know David just you know wait
36:56that I could just what the wait just
36:59said we are here to help you and
37:01even the things we haven't mentioned
37:03doesn't mean we cannot support you.
37:06Basically you just come contact us
37:09and our goal is really to provide us
37:12support for for your human tissue,
37:16human samples, you know like both
37:19liquid or solid tissue related research.
37:22OK we're here to help you.
37:24I think you can really just type of
37:28e-mail you know through the website
37:30and then we'll can we can have the
37:32conversation and see how we can support
37:34you Anything potentially is possible, right.
37:39All right.
37:39Just we said we'll be here for a
37:42few minutes if you know I hope
37:44you know thanks for your coming.
37:46So we looking forward to working with you.
37:48Sorry,
37:50I guess if you have a few minutes,
37:50I have one more question
37:54for you know, prospective sample
37:56collections. Are you able
37:57to aliquot and freeze them,
37:59you know, in case the team
38:00can't show up within seconds?
38:01Like can you hold them in your
38:03freezer for like 1214 hours?
38:04Yeah, Yep. And and we don't charge
38:06the extra pull fee for those.
38:08And we've also done somewhere,
38:09you know, over 2 weeks,
38:11we collected a series of patients and
38:12we just stick them in a rack in the
38:14freezer and then you just come pick them up.
38:16And the that fee to pull
38:18specimens out is really of okay.
38:20We've been storing these over six months
38:22and you're not taking all of them.
38:23You're taking one from that plate and two
38:25from that plate and three from this plate.
38:27That's when we charge that extra fee.
38:29Otherwise,
38:29if it's a temporary storage of a,
38:31you know, couple of days to even a month,
38:36especially if it's just pulling the bulk,
38:38here is the whole plate of
38:39specimens that belong to you.
38:41We've absolutely got that capacity and
38:42something that we do very frequently
38:45and and to set that
38:46up is sort of through the red cap form.
38:48If you wanted to set up a collection like
38:49that with aliquotting and freezing and
38:51stuff like that obviously would pay for it.
38:53But Yep. And all the service charges for
38:55that are on the site and we can give you
38:58depending on the SOPA more specific quote.
39:00So like the the current Aliquot
39:02charges to get a parent tube and
39:04put it in three Aliquot tubes.
39:07If you say, hey,
39:08I just want that in a single aliquot tube,
39:11then it's 1/3 of a unit.
39:12So we wouldn't charge you the whole price
39:14if it goes into six tubes or two into five,
39:17but those kind of shift or adjust based off
39:19of those units that we charge it off of,
39:21same with the storage fee.
39:23So for long term storage that's based
39:25off of one of our units over five years.
39:28If you're doing it for you know
39:31over that month they're doing the
39:33individuals kind of spread out and
39:34you only want to do it for a year,
39:35it's going to be part of that
39:36fee rather than that whole cost.
39:38So that those are all based off of
39:39the unit and we can get you more
39:41details on that based off of the
39:42SOP we would ultimately write up.
39:45Thank you.
39:46Yeah,
39:57great. Doctor Lu, once you hear back on
40:00the link for the recording, just let.
40:03Me and I guess probably keen know
40:04and then we can work with the the
40:06web people to get it uploaded.
40:08We've also got the updated combined price
40:10list to update on the site too now.
40:12So we'll get that done at the same time.
40:14Good. Thank you.
40:15And Renee is here actually retake
40:16the taking care of all this
40:18recording and upload everything.
40:20All right. That's great.
40:22Yeah. All right. Thanks Wade.
40:24And you know, thanks everyone
40:26for coming and you know,
40:28I think we can handle the session.
40:33Alright. Thank you. Thank you. Bye, bye.