Department of Pathology William Barriss McAllister, Jr., Memorial Lecture with Cristina Antonescu, MD

June 04, 2024

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The annual William Barriss McAllister Lecture featuring Cristina Antonescu, MD, Attending Pathologist, Memorial Sloan Kettering Cancer Center, presenting on, "From Molecular to Genomic Era: Moving the Needle in Sarcoma Discovery." May 9, 2024

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00:00Good afternoon.
00:03This year's McAllister Award recipient
00:07is Doctor Christina Antonescu. Dr.
00:11Antonescu is a renowned bone and soft
00:15tissue pathologist from Memorial
00:18Sloan Kettering Cancer Center where
00:21she's the director of the Bone and
00:24soft tissue subspeciality and also
00:27Co Director of the Sarcoma Center.
00:31Doctor Antonescu completed her
00:33MD from Bucharest, Romania where
00:37she began a pathology residency,
00:40but she completed it in 1996 at
00:44Lenox Hill Hospital in New York.
00:48After that, she went on to do a
00:52three-year fellowship at Memorial
00:54Zone Kettering Cancer Center,
00:56doing the first two years in general
01:01oncologic surgical pathology and the
01:04third year as a special Research fellow
01:07in born and Soft Tissue Pathology.
01:10And then she stayed on to become an
01:15attending at the same center at the bottom.
01:21Dr.
01:21Antonescu is a consummate surgical
01:25pathologist and she went on to build
01:28her scientific research on an excellent
01:32foundation of morphology to become
01:35a well funded clinician scientist.
01:39She's published more than 450 original
01:44articles, 24 review articles,
01:47written nearly forty book chapters,
01:51and co-authored 4 books.
01:53She's a She's made significant
01:56contribution to The Who Blue Book series,
02:00The Bone and Soft Tissue Tumors
02:02for more than 20 years,
02:04starting starting when when she
02:07was a junior attending.
02:10She's many awards and honors to her credit,
02:15starting from her training days,
02:18but I'll mention only two of those,
02:21the Ramsay Cortrans Young Investigator
02:24Award at given at US CAP in 2012 and
02:29the Maude Abbott Lecture in 2022.
02:35Doctor Antonesca has dedicated her work
02:38to the discovery of unique molecular
02:41signatures to help in defining,
02:43redefining and reclassifying sarcomas,
02:46and a brief list includes reporting
02:51the CHOP gene fusions and liposarcomas
02:54early on in her career.
02:57Expanding on EWSR 1 fusion partners
03:01in various soft tissue tumors,
03:05defining B core family of round cell
03:08tumors and sick fusion sarcomas and
03:12more recently in epithelioid hemangio
03:16endotheliomas defining the CAMPTOR 1
03:19fusion and the YAP 1 TFE 3 gene fusions.
03:24Even more recently,
03:25she's defined the genomic landscape
03:29of post radiation angiosarcomas
03:32and has laid down the criteria for
03:36grading primary breast angiosarcomas.
03:40In short,
03:41Doctor Antonesco's work touches
03:43on almost every sub speciality,
03:47and she is indeed a futuristic model
03:51of a general surgical pathologist.
04:03Thank you, Manju. Oops. Sorry.
04:09Thank you, Manju.
04:09Thank you. The committee.
04:10Are you hearing me well or?
04:12It's a bit? Yeah. OK.
04:17It's a great honor to be here,
04:21to be back in this amphitheater
04:23and to give the McAllister
04:25lecture and awards.
04:30Mind you, you, you know, overdid it.
04:32You, you guys treated me as royalty today.
04:35So I'm I'm very grateful and
04:38thankful so we can we can start
04:42since we have a diverse audience here.
04:46I will start with a very,
04:47very brief introduction of the
04:50sarcoma field where as you've
04:53heard I spend most of my efforts
04:56clinical and research energy.
04:59Sarcomas pose certain challenges
05:02as you as you know they are rare.
05:06They have a wide morphologic spectrums
05:09with more than 100 tumor types.
05:12The research level there is also
05:15limited number of cell models,
05:18both in vitro models and and mouse models.
05:23And what's very important is that
05:25you know at the clinical level that
05:28there is a still a huge gap between
05:31the advances that we've made in the
05:34pathogenesis of sarcomas and the
05:37available drugs and therapies out there
05:40that our colleagues medical oncologist
05:43can provide to the sarcoma patients.
05:47So in order to simplify our understanding and
05:50give a perspective to their pathogenesis,
05:53sarcomas can be defined divided
05:56in two main categories based on
06:00simple versus complex genomics.
06:02The first category are sarcomas that are
06:05driven by a single specific alterations,
06:07either a fusion or a activating
06:11mutation such as kitting GIST and
06:14these tumors have historically being
06:17diagnosed at the molecular level
06:19by a single assay molecular test.
06:23The second category is is represented
06:28by sarcomas with complex genomics,
06:31typically mutations in tumor suppressor
06:34genes or copy number alterations.
06:37And in this category,
06:38we have most of the adults 5 sarcomas
06:41such as UPS, mix of fibrosarcoma,
06:44liomal sarcoma support and these tumors
06:48can be best approached by an NGS tool.
06:55The impact of molecular discoveries to
06:57the sarcoma field have been remarkable,
07:00especially at the diagnosis
07:03and classification area,
07:05and mainly because it allowed us to have
07:09a more objective interpretation as well
07:13as empowering surgical pathologists that
07:16do not have a special sarcoma expertise.
07:20It also allowed us some of our
07:23objective diagnosis when the material
07:26was very scant or suboptimal.
07:30As we became more and more aware of
07:34the genomic complexity of sarcomas,
07:37as well as due to the continuous
07:40decrease in sequence sequencing costs,
07:45we have witnessed for the past decade
07:49a significant platform shift from a
07:52single gene assay to a targeted NGS panel.
07:57Almost obsolete these days are RTPCR
08:02tests for fusion detection or DNAPCR
08:06tests for a single activating mutation.
08:09Even FISH assay that interrogates
08:12only one gene rearrangement at the
08:15time is not as popular as before and
08:17the main reasons being that it has
08:20low resolution and cannot be cannot
08:22pick up certain translocation such
08:25as cryptic or intrachromosomal that
08:27will go over in more detail later.
08:30There also also limited number of
08:33FISH probes available commercially
08:35that can be used.
08:36And even if we have a positive
08:40FISH result due to the significant
08:43gene promiscuity that we we know,
08:46especially in the EWS gene family of tumors,
08:49we may not necessarily know what
08:52the accurate diagnosis is.
08:54And lastly,
08:55even in the assets like array,
08:58CGH or SNIP array,
09:00they are not not necessary anymore
09:03since most of the copy number
09:06alterations results can be obtained
09:09from an Ng targeted NGS panel.
09:13This diagram just gives you a glimpse
09:17of the current complexity of sarcomas
09:20that are driven by EWS or FUS gene
09:25fusions and you can imagine EWS
09:28positive FISH may definitely not tell
09:32the whole story and the diagnosis.
09:36In particular for small blue
09:38round cell tumors,
09:39which is the panel in the
09:41center with the black boxes,
09:42it is not unusual for for a case to
09:48be tested by 4 to 5 FISH probes before
09:51we arrive to the correct diagnosis.
09:54And that's not saving us any
09:57time or any costs.
09:59So the most widely applied targeted RNA
10:04sequencing is Archer and I understand
10:07that's what you're using here as well.
10:10And in our department,
10:12we use a panel of 123 genes that are
10:17commonly involved in in sarcomas as well.
10:19Archer is a anchor Multiplex PCR that
10:23uses a one side nested primers and is
10:28able to detect agnostically a gene
10:31rearrangement by targeting a gene
10:34that is commonly involved in the fusion.
10:37It requires 7 to 10 on stain slides and
10:40the results are out in about a week.
10:46For the targeted DNA based NGS,
10:51most platforms out there
10:53include about 500 cancer genes.
10:56They have high coverage in our
10:59hospital more than 700 range and
11:02the the report of the targeted
11:05NGS will provide information on a
11:08number of things including single
11:11nucleotide variants and intra
11:14genic alterations as well as arm
11:18level copy number changes which are
11:21deletions or amplifications and a
11:23very limited number of gene fusions
11:26such as EWS and and track fusions.
11:29It's required more materials such as
11:3210 to 20 unstained slides depending
11:34on the size of the tissue and the
11:37estimated turn around time is about a month.
11:42So this is what we use at MSK.
11:45Is this in house targeted NGS panel?
11:48We call it MSK impact.
11:51And this particular platform requires
11:55both tumor and germline normal DNA
11:59and therefore a patient consent is
12:02required as part of a protocol and
12:05can be activated only by medical
12:08oncologist and not by pathologist.
12:11Briefly,
12:11the tumor and the normal DNA is
12:15being pulled together with the
12:18Multiplex cup captures of the bio
12:21biotelated probes and then it's being
12:25sequenced and provided 100 base pair
12:30paired and fragments and then these
12:34are runs through an OPPO KB pipeline
12:37and a report is being generated.
12:42In contrast, most of the targeted NGS
12:45panels that are commercially available or
12:49that are running other academic places,
12:53they require only tumor DNA and because
12:57of that those reports may not be able
12:59to tell you the difference between
13:02a germline and a somatic mutation.
13:05So that's the major difference
13:07between the two platforms.
13:11So why am I giving this talk
13:15to you now and the reason,
13:18the main reason being that more than 10
13:21years have passed since we at Memorial
13:24have been using a systematically
13:26NGS in our clinical practice.
13:28So a lot of time has a lot of data
13:31has accumulated and analyzed in
13:34different projects and studies.
13:36As you will see.
13:38It also gives me an opportunity to
13:42discuss the contributions for NGS
13:45in diagnosis and classification
13:47and to highlight the the pros of
13:51of this method in contrast with
13:54FISH or PCR or so forth.
13:57And I would also like to give
13:59you some examples to make the
14:02case that there are additional
14:04applications to NGS besides diagnosis.
14:06So for this talk,
14:09I will try to cover five different topics
14:13including with the impact on diagnosis,
14:16impact on survival,
14:19targeted therapy,
14:20risk stratification and at the end,
14:22if we have time also to give you
14:26an example how NGS can be used in
14:29the genomic sub classification
14:31of molecularly complex sarcomas.
14:33So we can start with the obvious,
14:36the use of NGS in routine diagnosis.
14:39And here I will first discuss the
14:43NGS increased diagnostic accuracy
14:46in undifferentiated tumors,
14:47mainly where the the morphology and
14:51immunostoc chemistry has failed to
14:54provide a more specific characterization.
14:56And then a few examples of the NGS
15:00increased sensitivity of detection
15:02if you we compare it to other
15:05lower resolution methods.
15:08So in order to give some examples of
15:12the NGS increased diagnostic accuracy,
15:14I selected few examples that I
15:17believe there are a little bit
15:20more often pitfalls in our soft
15:24tissue sarcoma practice.
15:26And I will start with an example
15:29of undifferentiated leomorphic
15:31sarcoma of the extremity.
15:33And this is how the morphology of
15:36the resection specimen look like
15:38had had different components.
15:40This was a 34 year old man with the
15:4311 CM tumor of the thigh and you
15:46can see on the lower panel very
15:49leomorphic spindle bizarre cells.
15:52The tumor also has some ossification
15:55and the upper panel if you can
15:57appreciate they were had a completely
16:00different morphology with mononuclear
16:02cells and osteoclastive giant cells.
16:04So our interpretation on this case
16:06is that was most likely a Sarcomatus
16:09transformation in a tenosynovial
16:12giant cell tumor.
16:13However,
16:14the patient developed lung meds
16:16and the local recurrence.
16:17So he behaved in a very aggressive
16:20fashion and as it happens to all
16:23these recurrent metastatic cases that
16:25the tumor are being tested by MSK impact.
16:28And to our surprise,
16:30the results showed a very high level
16:33of amplification of MDM two and CDK 4,
16:36so that raising the possibility of
16:39a day differentiated liposarcoma.
16:40Of course we did the immunos based
16:43on this result which showed strong
16:46nuclear positivity for both markers.
16:48And of course we went back to the
16:51specimen and we tried to find
16:54any areas of well differentiated
16:56liposarcoma and indeed we did in
16:59probably in in retrospect these were
17:03interpreted as as normal fat which
17:06is being infiltrated by the tumor.
17:08The second example is one that refers
17:12and relates to round cell sarcomas.
17:15A few years back we we did this small
17:18study with Doctor Argani from Hopkins.
17:21He had a couple of cases of round
17:24cell sarcomas of the kidney in young
17:27adults that were CD 34 negative,
17:29B core strongly positive.
17:32And the leading diagnosis for
17:34for these tumors was a clear
17:37cell sarcoma of the kidney.
17:39And to our surprise,
17:41when we did the RNA sequencing on
17:44these cases and NAP to STAT 6 fusion
17:46was discovered in keeping with the
17:49malignant solitary fibrous tumor which
17:52triggered of course an immuno stain
17:55which showed 4 plus STAT 6 positivity.
17:59We were truly puzzled of the B
18:01core of our expression of these
18:04malignant SFTS in the kidney.
18:06And we look back at the RNA sig data
18:09which showed indeed I don't know
18:11if you see on that panel very high
18:14expression or B core at MIRMRNA level,
18:17suggesting that what we see
18:20on immunostochemistry,
18:21it's not some kind of background
18:24false positive result.
18:25We then expanded the study with
18:28other non renal SFT and indeed
18:31the majority of malignant SFT
18:33also Co expressed B core that may
18:37represent the pitfall in diagnosis.
18:40And the last example I want to briefly
18:43go over is the NGS contribution to
18:46undifferentiated sarcomatoidiaeoplasm.
18:47So this was a tough case.
18:52This was a 70 year old man
18:54with the arms of tissue mask.
18:56It looked like this blue
18:58vesicular monomorphic.
18:59Our leading diagnosis was
19:01a high grade and PNSD.
19:03However,
19:04the immuno profile was not supportive
19:07S100 Sox the negative and the
19:10H3K27 trimethyl was retained.
19:12He had a very high proliferation rate,
19:15which is kind of unusual for sarcomas,
19:18so close to 90% and the Archer
19:21was negative for fusions.
19:23So then the patient next year
19:26developed a small bowel metastasis,
19:28which once again is quite unusual
19:30for sarcomas to go in the bowel.
19:33We've seen it of course,
19:34but and then we of course ran the
19:37impact and the impact show the high
19:40tumor mutation burden of 20 mutations
19:44And then of course the diagnostic piece,
19:47the B RAF V 600 E mutation as well as
19:51the GA and CT transition mutations that
19:54were consistent with the UV signature.
19:57So the diagnosis of the differentiated
20:01spindle cell Melanoma was rendered.
20:04The patient was treated successfully
20:06with the immune checkpoint inhibitors.
20:09And he's still alive 2023 with the
20:12liver meth and and then we had the
20:15opportunity to run the immunosochemistry
20:17for B RAF which was diffusely positive.
20:20So moving on to the next topic,
20:25the increased sensitivity of detection of
20:29NGS compared to other molecular methods.
20:33And here I think 1 good example are
20:38tumors that are driven by a wide
20:41spectrum of alteration in one gene,
20:44such as the loss of function mutation
20:47in smart B1, which can be deletions,
20:51mutations, arm level deletions,
20:53translocation and so forth.
20:54And you can imagine such a spectrum
20:58of alterations can be picked up
21:00mainly by NGS and not by other
21:03low resolution studies.
21:05So few years ago we we looked specifically
21:09at the spectrum of mutations alterations
21:12in smart P1 deficient sarcoma.
21:15As it is, as you probably know,
21:17it's a growing family of
21:19bonus of tissue tumors.
21:21And our main question was,
21:23can can we tell if the type of genetic
21:28alteration may correlate with Histology,
21:31with the histotype So included 78 such
21:37cases including epithelial sarcoma,
21:40rhabdoid tumors, epithelial and
21:43PNSD pro differentiated cordoma,
21:45all of them being I and I-1 deficient.
21:49And we studied them all with
21:51NGS as well as FISH.
21:54So the short answer to
21:55our question it was no,
21:57there was no correlation between alter
22:00genetic alteration and Histology.
22:02Most Histology showed large homozygous
22:05deletion of SMART B1 and about
22:091/3 showed introgenic alterations.
22:11So I'm trying to,
22:12you know,
22:13hear that obviously would never
22:16be picked up by FISH assays.
22:19We then wanted to look more
22:22into this and and see if the
22:25extent of the deletion at 22 Q,
22:27the locus of I91 may correlate
22:31with histotype.
22:31And although there was no
22:34black and white answer,
22:35it became clear that some
22:38histologies like epithelial
22:39sarcomas have smaller deletions
22:42mostly centered on SMART B1,
22:45while tumors like a poor
22:47differentiated cordoma here in
22:49yellow have larger deletions
22:51showing code deletions of other
22:53gene on both sides of SMART V1.
22:58OK, moving on to a different example
23:02to show the NGS increase sensitivity
23:06detection in a certain translocation
23:10and the there are two examples
23:12here that I would I would like to
23:14share with you the unbalanced or
23:16cryptic translocation as well as
23:19intrachromosomal translocation.
23:20And by far the best example of
23:23cryptic translocation is the EWS
23:25Org fusion which is the second most
23:28common alteration in Ewing sarcoma.
23:31And the reason that this results in
23:34a cryptic alteration is because EWS
23:36and Org show opposite directions
23:38of transcription.
23:40So in order to form a functional fusion,
23:43they needs to invert.
23:45And in order to invert,
23:46they usually lose genetic material that
23:50cannot then be picked up by fish resolution.
23:54So the idea here is that if you
23:56have a case that looks like Ewings,
23:58stained like Ewings and EWS,
24:01fish is negative,
24:02which actually can be negative
24:04in 50% of these cases, right?
24:06The next step would be for you to
24:09do the Archer and GS panel talking
24:14about intracromosomal fusions
24:16that also can be not can.
24:21Fish cannot be reliable for
24:23detection and here one very good
24:26example are the N track 1 fusions.
24:29Most of these fusions are intracromosomal,
24:32either deletion such as INTRAC 1
24:36LMNA which is by far the most common,
24:39as well as inversions,
24:41either TPM three or TPR.
24:44Here on the left side,
24:45the diagram shows one of these
24:48inversions of these two genes
24:50that are truly nearby on one Q.
24:54So once again,
24:56in order to have a functional fusion,
24:58you have to have inversion and
25:01that cannot be picked up by fish.
25:04Just briefly mentioning the anthrax
25:07fusion positive spindle cell
25:09tumor is a relatively new entity
25:12emerging in AWHO classification.
25:14It's composed of these monomorphic
25:17spindle cells or patternless
25:20pattern and very characteristic.
25:22There are these stromal collagen bands
25:26and very vascular rings which are,
25:30you know, highly,
25:32highly suspicious of this entity.
25:35And another clue to the diagnosis is
25:38the Co expression of S100 and CD34.
25:42Pan and track is helpful.
25:45Of course, it's sensitive,
25:46but far from being specific.
25:48So this diagnosis has a very
25:53important impact on therapy.
25:56So in our opinion that when
25:58you have a case like this,
25:59a molecular confirmation is truly required.
26:05OK. And the last example here,
26:08the increased sensitivity in alterations,
26:11in unusual gene alterations.
26:12And here I thought a good example maybe
26:16B core internal tandem duplication.
26:18So what are what is the B core ITD?
26:21Are these Reds small strips of
26:27of DNA illustrated here in red.
26:31They're duplicated at the last at
26:34the portion of elastic B core exon,
26:38which somehow up regulate B core expression.
26:43B core ITD are the driver of about 40%
26:47of round cells sarcomas in infants.
26:50So this is very important to to remember
26:54as well as most tumors of the primitive
26:58mixed with mesenchymal tumor of infancy.
27:01However, the B core ITD have later
27:04on show to you know to be present
27:07in other undifferentiated sarcomas.
27:09It's something that you should be familiar
27:12and aware of regardless of your specialty.
27:15So these are pretty much in 90% of
27:19clear cells sarcoma of the kidney,
27:21the CNS peanuts with B core ITD as well
27:25as and these are not pediatric cases,
27:27some high grade endometrial stromosarcoma
27:30as we have noted some shared histologic
27:35features among all these members.
27:38They are not perfect but clearly some
27:41shared features as well as diffuse
27:43up regulation of B core both at RNA
27:46level as well as protein level,
27:49which can be used again for diagnosis.
27:53However, as we saw,
27:54SFTS can show as high level.
27:57So for this diagnosis,
28:01NGS again is the gold standard.
28:05Moving on to the second big topic to
28:08discuss the impact of NGS on survival.
28:12So here we'll talk about the driver
28:15gene alteration impact as well as
28:17the global landscape beyond the
28:21driver alteration.
28:22So for the driver gene alteration,
28:26I picked two different
28:28example in Rhabdomyo sarcoma,
28:30MYO D1 mutation and Dicer 1 alteration.
28:33And then we'll give some examples
28:36of fusions in round cells.
28:39So let's start with MYO D1.
28:42You may know that MYO D1 mutation
28:44defines a very specific and
28:47aggressive type of Rhabdoma sarcoma,
28:50spindle and sclerosing Rhabdoma sarcoma,
28:53which is included now a standalone
28:57entity from embryoner Rhabdoma
28:59sarcoma and The Who classification.
29:02And why is that?
29:03Because it has distinct morphology
29:06can either be spindle or more common
29:08is composed of these uniform round
29:11to avoid cells that are separated
29:14by this sclerosing stroma.
29:16Also importantly, as I mentioned,
29:20they have a very aggressive outcome even
29:23worse than alveolar abdominal sarcoma.
29:25In our study they showed an 18%
29:28four year survival.
29:29They typically are occurring older
29:32children and young adults and more often
29:35in the head and neck and and and trunk.
29:42This is to be distinguished from
29:44another spindle cell Rhabdoma sarcoma
29:47that occurs at birth or or or infants.
29:50Yeah that have this vesicular
29:54herring bone appearance.
29:56These particular Rhabdoma sarcomas
29:58are characterized by recurrent fusions
30:01either involving site two or NCOA 2.
30:06Importantly,
30:06these tumors have a very favorable
30:09outcome with almost no metastatic
30:12potential and therefore they behave more
30:15in keeping with an infantile fibrosarcoma.
30:20Moving on to to touch base
30:24a little bit on the Dicer 1 alterations.
30:27It's a, you know new expanding fields.
30:32We recently did this study that
30:34we presented at USE CAP this year
30:37comparing a a molecularly a group of
30:42botuloids type for Rhabdomyo sarcoma
30:45with a conventional Rhabdomyo sarcoma.
30:48And the short story is that we observed
30:52Dicer 1 alterations either somatic
30:55or germline only in the boteroid
30:59type Rhabdomyo sarcoma and that was
31:03associated with a very favorable outcome
31:06as you can see here the red line.
31:10OK, moving on to discuss few
31:14fusions that truly have an impact
31:18on survival and therefore a,
31:20you know, detailed NGS or Archer
31:24character characterization is needed.
31:27And of course we will start with
31:31chick docs probably all being aware
31:34of this small borons of sarcoma that
31:38is characterized by a fusion that
31:41results in switching the function
31:44of CHICK from a repressor to an
31:47oncogenic activator of transcription
31:51especially up regulating ATV1ATV4.
31:54And because of this function ETV 4 as
31:58shown here is by immunostochemistry
32:00is one of the most reliable ancillary
32:04immuno marker in the diagnosis
32:07of chick ducks for sarcomas.
32:09These tumors occurs in the deep soft tissues.
32:13They are large heterogeneous as shown here.
32:16They occur in young adults.
32:19They rarely are seen in children or bone.
32:24And morphologically they look
32:26like small blue round.
32:27So tumor at a very quick low power view.
32:31However at the higher power they have
32:33you know more cytoplasm and we look
32:37epithelioidal focus spindling and so forth.
32:39Importantly,
32:40the diagnosis is required because
32:43of the very poor outcome and you
32:46can see here in this couple mark
32:49comparison with the E wing sarcoma
32:51which are you're matched for stage
32:54and you can see that the chick docs
32:57four has a five year survival of 43%
33:00compared to 77% the E wing sarcoma.
33:04And more than that,
33:05why the clinicians need to know about
33:08this is because they do not respond
33:11well to even sarcoma regimens.
33:13And so far that was, you know,
33:16the only type of therapy that
33:18was used as the first line.
33:20However, nowadays knowing that these are,
33:23you know, quite resistant,
33:25they may be approached with more adult
33:29type sarcoma chemotherapy such as AIM.
33:34One caveat here that we've noticed
33:37is that the chick docks for sarcomas
33:41have a high risk of negative results
33:45both by fish as well as by NGS.
33:48And that is due to the very
33:51repetitive sequences of docks for.
33:53So when that happens,
33:54if our suspicion is a chick docks for
33:57and every other Archer is negative
34:00for other fusions is to look manually,
34:03you know to ask the molecular lab to look
34:05manually at the levels of ETV 1/4 and five.
34:08And you can see here there are
34:10very high levels of over expression
34:13compared to other sarcomas,
34:14which confirms the diagnosis
34:16of a chick docs for fusion.
34:19This has been shown by many groups
34:22including our showing that by RNA sequencing,
34:25the chick docs for sarcomas have their
34:28own cluster on the group separate
34:31from all the other round cell tumors.
34:34So this chip docs 4 makes a very good
34:37contrast with the B core CCNB 3 sarcomas.
34:41B core CCNB 3 is a very peculiar
34:45translocation which is an
34:48intrachromosomal X paracentric inversion.
34:52Again cannot be detected by FISH.
34:55It requires Archer for the diagnosis.
34:59Clinically the demographics are
35:03more closer to E wing sarcoma and
35:05very different than CHIC docs.
35:07They occur in bone mostly in in
35:11children and morphologically they
35:13have a hybrid morphology between an E
35:16wing sarcoma and a synovial sarcoma.
35:18They have both round and spindle
35:21cell components and of course the
35:24important stain here is the B core
35:27which shows 4 plus positivity.
35:29Clinically.
35:30Again,
35:31very important since B core does
35:34much better than chick ducks four
35:36and pretty much similar outcome
35:39with synovial sarcoma.
35:43OK, so we looked at the impact of driver
35:47alterations either mutations or fusions.
35:51Now let's look at the impact and
35:53survival on like secondary events,
35:55right global landscape besides the
35:58driver and in translocation associates
36:01sarcoma secondary events are rare,
36:04but when they occur,
36:05they usually are associated very bad
36:07outcome and resistant to chemotherapy.
36:10So if we take the example
36:12of Ewing sarcoma here,
36:14the secondary events are usually
36:16alteration in tumor suppressor genes.
36:19As you can see P53 citican 2A stacks 2,
36:24about 8 to 10% each,
36:26usually mutually exclusive.
36:28But when these occur, as I said,
36:31the the evening sarcoma patients
36:33do very badly as a whole of
36:37translocation associates sarcoma.
36:38The secondary events most common
36:41are the P16P-15 deletion as well
36:44as a turret promoter alteration.
36:47So very recently we,
36:49we performed this study which
36:51where we included sarcomas that
36:54are defined by EWS Kreb fusions,
36:57right, ITF Kreb Kreb one.
37:00And we wanted to, to,
37:02to question to address if the secondary
37:07genetic events may be different
37:09in different histotypes, right?
37:10So here we have angiomatoid fibro,
37:12he's just cytoma clears as sarcoma,
37:15gastrointestinal creases,
37:16sarcoma and so forth.
37:18So although was not again
37:20a black and white picture,
37:22we noted that there are,
37:23you know,
37:24some alterations were called more
37:26common in certain histologies like AFH
37:29had more common CDKN to AB deletion,
37:32while all the tarts promoter mutations
37:35or card in clearances or coma.
37:38So then we wanted to,
37:40to see if these alterations also
37:44have an impact on survival, right?
37:46Because that's that's why we do
37:48NGS on these patients that we
37:50already know the fusion type.
37:52And the answer was truly clear cut.
37:56Here you have the AFHS
37:59angiomotor fibrohistocytoma.
38:00The only two patients that had CDKN 2
38:03AB were the ones that metastasized.
38:06And here you have the clears of
38:08sarcoma and you have the the patients
38:11in green that died of disease
38:13were highly enriched by cases
38:15that had secondary genetic events
38:20moving away from translocation.
38:23This is another textbook example
38:26that I'm sure the pediatric folks
38:29here are very familiar with.
38:31And this is about the impact of P53
38:36mutation in Embraer abdominal sarcoma,
38:40which of course has clinical implication,
38:43risk escalation, more chemo and so forth.
38:47And of course different
38:49survival as you can see here.
38:51And you may, you may say, well,
38:53the presence of anaplasia
38:56on Histology correlates,
38:57correlates with the mutation with a genotype.
39:01And that's true for most parts.
39:03However, we've seen discrepancy
39:04cases that do not have anaplasia
39:07and AP53 mutation and vice versa.
39:10So I mean, at least at our institution,
39:13we do NGS on all Enbrana abdominal sarcomas,
39:17especially since sometimes
39:19our sample is so small,
39:20they may not catch the anaplasia.
39:24OK, moving on to third topic,
39:26the impact of NGS to targeted therapy.
39:29This will be by brief.
39:31I assembled here a list for you of highly
39:34relevant examples for soft tissue field.
39:37And of course, top,
39:39top of the list are the mutations in KIT,
39:42PDGFR alpha and B Raff in GIST.
39:45I don't have to,
39:46you know,
39:47tell you much,
39:48but based on these mutations,
39:50we choose what type of thyroid
39:53tyrosine kinase inhibitor
39:54and based on this alteration,
39:56we may decide if the patient is a
40:00candidate for adjuvant therapy or not.
40:04The second example are sarcomas that are
40:06driven by MDM to CDK 4 amplification.
40:09And here we care about this
40:13because they are for a while
40:16now CDK 4 inhibitors available
40:18with relatively good responses,
40:20at least in the D flypool.
40:23The third example here,
40:25I cannot stress enough how important
40:28it is for us pathologists to recognize
40:32in real life the kinase fusion tumors.
40:35And that is of course because of
40:39the dramatic responses that we have
40:41seen with kinase inhibitors and
40:43depending on what type of kinase or
40:47different tyrosine kinase inhibitors.
40:49So for INTRAC of course is
40:51lateral tracting it,
40:52but now they have a second and third
40:55generation of INTRAC inhibitors.
40:58The next point here are the the
41:00Smart B1 loss of function sarcomas,
41:03again very important to diagnose
41:05them correctly since now we
41:08have a targeted therapy for,
41:10for this disease,
41:11the easy H2 inhibitor called tazemetostat,
41:15which have shown decent responses,
41:18especially in epithelial sarcoma.
41:21The differentiating Melanoma I guess
41:24with the UV signature completely
41:26different therapy than sarcomas with the
41:29immune checkpoint inhibitors with very,
41:31very good responses.
41:34And lastly,
41:35I want to share with you 2 examples
41:40of something completely unexpected to
41:43us in which the secondary alterations
41:47became were were targetable while
41:50the driver mutation was not.
41:53Sounds a bit confusing, but let's see.
41:56So the first example is this patient
42:00with an angiomatoid fibrocystiocytoma
42:02having a fulminant course,
42:04rapid local recurrences,
42:06metastasis to the adrenal gland.
42:10Archer confirmed the classic
42:12AWS Kreb 1 fusion impact showed.
42:16In addition,
42:17CDK into AB which we know it can
42:21happen in this disease as well
42:23as AB RAF V 600 E mutation
42:26which is almost unheard of to see
42:31this mutation in in translocation
42:33associated sarcoma as a secondary event.
42:36And you can see here the tumor was also
42:39positive by this marker immunostochemistry
42:44patient of course was had first line
42:47the sarcoma chemotherapy aim and failed.
42:50And then because of the B RAF
42:52second side mutation was put on a
42:57combo therapy of RAF and make inhibitor.
43:00And this is the the imaging,
43:02the MRI and CAT scan showing on the
43:06upper panel the primary time mask.
43:08The 1st 2 show the dramatic increase in size.
43:12This is before the targeted therapy and
43:16the last one is after a few months of
43:20the ancorafenibinimetinib combination.
43:22And here lower is the adrenal
43:25gland metastasis that you know,
43:28grew extremely fast in one month
43:30and then decreased in size after
43:32a few months on therapy.
43:34So this was a remarkable result,
43:37unexpected and you know, I,
43:41I think even if the the clinician
43:43had the results in hand still is
43:46they will start with first line
43:49chemotherapy as as a sarcoma protocol.
43:52OK, Second example as dramatic
43:54as the first one.
43:56This was a Dicer one associated
44:00anaplastic sarcoma of the kidney
44:04young patient again fulminant
44:07course failed sarcoma chemotherapy
44:10and then IMPACT was done and show
44:152 somatic dicer 1 alterations.
44:18So there was no germline in addition
44:22to a PDGFR alpha hotspot mutation.
44:26You can see here the the panel E shows
44:30the strong PDGFR alpha expression.
44:34So then this patient got was treated
44:38with a PDGFR alpha inhibitor,
44:40which is called Ava pritinib.
44:42And you can see appreciate here
44:44based on CAT scan and PET scan,
44:46the decrease in size and metabolic
44:48activity after this treatment.
44:50So again,
44:52quite remarkable change of clinical
44:55course due to these unexpected
44:58targetable secondary genetic events.
45:03OK topic #4 I hope we are
45:06doing good with time.
45:08I don't know is the impact of
45:13NGS in risk stratification.
45:15And here I, I want to share our very
45:19recent work on GIST where we developed
45:22the next generation genomic nomogram
45:26that truly incorporates both the
45:29traditional clinical pathologic factors
45:32as well the genomic alteration from NGS.
45:35So I don't know how many GI pathologists or
45:38soft tissue pathologists are in the audience,
45:40but you know, risk,
45:43risk prognostication in GIST is not,
45:46not a pickle, right?
45:48It's kind of complex.
45:49You have to have this cheat,
45:51you know, with you all the time.
45:53And here are some of them,
45:55all of these different tier systems schemes,
45:59the two most common you probably know
46:03are the Fletcher and IH and Yetinen.
46:06Even between these two there
46:08are significant differences.
46:09Yetinen has five tier system because
46:12they include a benign category,
46:15while Fletcher has four.
46:17Fletcher and IH does not take into
46:20consideration the anatomic site and
46:23therefore because of that this is
46:26a chit chat for the gastric tumors,
46:28it typically overestimates the gastric
46:31GIST with low mitotic activity.
46:34So as you can see,
46:36there are problems with this,
46:38right,
46:38problems with these especially for
46:41clinicians that use this as a gold
46:45standard to select patients who are at
46:48moderate to high risk for adjuvant therapy.
46:53So we are at Memorial,
46:55we do a lot of sequencing and most
46:57just patients are being sequenced.
46:59We get these fancy reports, right?
47:02They're very comprehensive.
47:04And then what,
47:05what exactly is being used from the report,
47:08right?
47:09We spent a lot of money
47:10and we want to know what,
47:12what can we get out of it.
47:14So the first information we get out of
47:16it is the primary alteration, right?
47:19The primary driver,
47:20the kit PDGFR alpha and we can
47:24tell if it's responsive or not
47:25to E nothing even based on that,
47:27you know the the clinicians make
47:30certain decisions on type of TKI or
47:33decision to to put the patient on adjuvant.
47:36The second information they use
47:39from this report is the secondary
47:42site mutation usually in kit.
47:44And this is just to inform them on
47:47the mechanism of resistance to the
47:49TKI when they are going to switch
47:52the TKI to the second type of drug.
47:55And based on the second site mutation,
47:58they may do those decisions.
47:59So this is pretty much what's being used.
48:04So what is not used?
48:06When we started study, we were,
48:08you know,
48:09kind of perplex that a lot of
48:12stuff it's not used.
48:13We don't use any of this data for
48:16risk certification and we do not use
48:19any information from the non kits,
48:22non driver alterations.
48:24So then we, you know,
48:26set up,
48:28trying working very closely with a
48:31bioinformatic person and use machine
48:34learning methods called Oncocast.
48:36This has been used at Memorial
48:39trying to do genome risk,
48:41risk stratification in lung
48:43cancer in mesothelioma.
48:45So we,
48:46we applied that in GIST and this is
48:49this, these are the results in gastric GIST.
48:52So using this method that as I
48:55said incorporates traditional size
48:57mitosis as well as the most recurrent
49:01alteration that we're seeing on impact.
49:03And you can see here,
49:04we were able to divide the gastric
49:07gist in three genomic tears.
49:09The first one here in red is high risk,
49:12which is which is defined by 1P
49:15deletion or SDHB alterations.
49:18The one in green is intermediate risk
49:20with 14 Q deletion here and what else?
49:24An absence of KIT X111 mutation
49:27which is very important.
49:29Same thing in the small bowel.
49:30You may not be able to see it very well.
49:333 tier system.
49:34The red one is high risk if if the gist
49:37has a mutation in the mic Max axis RB
49:40or CD can to A then it's high risk.
49:43If not, if it does what presence of
49:491P deletions or five Q amplification?
49:51That's it's intermediate risk and the
49:55same alterations could be confirmed
49:57only if we looked at Exoni Lucky
50:00Taxon 11 small bulges.
50:02So we wanted to validate this since it was,
50:05you know,
50:06relatively new method used in GIST.
50:10So we we used a different statistical method,
50:13the multivariate cost proportional
50:15hazard and we confirm pretty much the
50:19same alterations that were statistically
50:22significant with the machine learning
50:25method even in the SDH deficient GIST.
50:28And you may probably know these
50:30are have a different biology,
50:34different clinical behavior and
50:37the current risk certification
50:39does not apply to these at all.
50:42Using the same methods we were
50:45able to distinguish a more high
50:48risk of SDH mutagists that have
50:51P53 mutations or 1Q amplification.
50:55So we we are very optimistic and
50:59positive about these results.
51:01We are hoping to maybe apply
51:04in other sarcomas.
51:06Of course comma sarcomas
51:07you need a lot of numbers.
51:09You cannot do this in chick ducks 4.
51:13So we think that this will be very
51:19useful for the clinicians that may help
51:21them at a different level to choose
51:24the patients for adjuvant therapy.
51:26We also think that it might
51:29bypass of the heterogeneity I just
51:31mentioned in the beginning on the
51:34traditional risks stratification,
51:36especially knowing that all of these
51:39were designed before the imatinib
51:41era and they do not take into
51:44account the kid mutation pattern.
51:48So our work also for the first
51:52time raises the the point of that
51:56kid independent gene alterations
51:58may play a role in survival.
52:00And of course this can be we think
52:03that this can be widely applied
52:06because most of the targeted NGS
52:08panels out there give information
52:11about the single nucleotide variants
52:14make Max RB and so forth that can
52:18easily applied in non impact targets.
52:22OK.
52:22Lastly,
52:23if we have time,
52:25we can go over the additional
52:30applications of NGS and here I
52:34thought to share with you the
52:38importance of NGS in working with
52:41genomically complex sarcomas.
52:43And the first example here is
52:46this relatively new entity mixoid
52:49neomorphic liposarcoma.
52:51You may or may have not heard of this
52:54last WHA classification has been
52:58made a stand stand alone subtype of
53:02liposarcoma as a hybrid morphology.
53:05In areas looks like mixoid liposarcoma,
53:07in areas looks like theomorphic liposarcoma.
53:10It occurs in young patients
53:12in the media Steiner mainly.
53:14But then we've seen a wide
53:17age range and locations.
53:18And if we just look at the NGS
53:21of these three different types,
53:23the green is mixed with pleomorphic,
53:25the red is pleomorphic lipo and
53:27the blue is the mixoid round cell.
53:30The mixoid pleomorphic liposarcoma
53:33is a closer genomic signature
53:36with the pleomorphic lipo and
53:38very different than Mixoide.
53:40And this maybe not so unexpected right?
53:43Mixo liposarcoma have starts mutations and
53:46have the peak peak three CA alterations.
53:50But then when we looked at the allele
53:53specific copy number here on top right,
53:55a completely different picture could be
53:57seen in in Mixoide theomorphic liposarcoma,
54:00very different than theomorphic liposarcoma,
54:03for example,
54:04showing this widespread loss
54:06of hell heterozygosity,
54:08which was pretty much globally more
54:11than 85% of the genome shows this LOH
54:14type signature compared to for example,
54:17a mixer lipo here that is very flat.
54:20In addition, they have very interesting
54:23copy number alterations here on top.
54:27It's a primary tumor or mixopleomorphic
54:29liposarcoma.
54:30You probably don't see it,
54:32but this is a near haploid that here you
54:34have #1 which is total of copy number.
54:37And then in the metastasis, it became 2,
54:40meaning that you have a hyper deployed,
54:45deployed after doubling of the
54:49haploid phenotype.
54:50So very intriguing, very specific,
54:53very different alterations.
54:55And all this information would be
54:59extracted from our Impact NGS panel.
55:03So no,
55:04no whole genome or no whole transcriptome,
55:07everything that you see was extracted
55:10from the targeted DNA panel.
55:13Why is this important?
55:14Well, it's important because once again,
55:16you know the impact on survival.
55:20The mixed with theomorphic do even
55:22worse than the pleomorphic liposarcoma,
55:25although these are young patients and
55:26these are older patients, of course,
55:28much better than the mixed with drone cell.
55:31OK.
55:32And one last example, you know,
55:36is, is to,
55:37to illustrate our recent work that we can
55:40use NGS in the differential diagnosis
55:44of genomically complex sarcomas.
55:46We've seen too many mistakes or errors.
55:50So we, you know,
55:51in various diseases that we thought
55:54let's look at this more carefully.
55:56And here I will give you 2 examples,
56:01embryonorabdomal sarcoma to
56:03distinguish from Triton tumor
56:05and embryonorabdomal sarcoma to
56:08distinguish from theomorphic Raptor.
56:10So this first study that we did recently
56:15was to compare embryonorabdo with Triton
56:17tumor or MPNST with Raptor component.
56:20And you may not know that in fact NF1
56:24alterations is the second most common
56:27genetic event in embryonoraptil.
56:30So having an F1 alterations,
56:32you cannot distinguish between
56:34umbrella and tritone tumor.
56:36So that's one thing.
56:38Second,
56:38that this particular study was
56:41triggered by three cases that were
56:45three cases of tritone tumor that
56:47were misdiagnosis and Bronner
56:49reptile and one of them had
56:51therapeutic repercussions.
56:52The other two the diagnosis was changed
56:55in real time due to the impact results.
56:59So I know it's a complicated figure,
57:02but you have to kind of believe me that
57:07tritone tumor has the same genomics as MPNST.
57:11They have alteration in the PRC two
57:15complex as well as the CDKN 2AB.
57:17While the embryonic of the master coma has
57:21Ras mutations and B core loss of function.
57:23So for most cases,
57:26if you look at uncle prints of the impact,
57:29you can actually favor one over the other.
57:32I'm not saying that this can
57:34be done in 100% of the cases,
57:36but in more than 70% of the cases,
57:38we are able to tell the genomic
57:41difference between a tritone slash
57:43MPNST versus and Bronner Optima circle.
57:49OK, what's important? Well,
57:51the the survival again it's like black and
57:55white and Branarabdo very good prognosis.
57:59The NF one mutant and Branarabdo responds
58:02very well to like any other and the NPNST are
58:06doing the Triton tumor are doing very poorly.
58:10And lastly, we used NGS to try to distinguish
58:15and Branarabdo from theomorphic rhabdo.
58:18And why is that, you may ask?
58:19Because we seen embryonorabdo with
58:22anaplasia in young adults or even,
58:25you know, not so young adults.
58:27So we struggle sometimes, you know,
58:30is it truly an embryon anaplasia?
58:32Is it pleomorphic?
58:33So we try to look into this more
58:36carefully to see if, you know,
58:38since we have all this data available anyway,
58:40right?
58:41These are sequenced as I mentioned.
58:43So why not just to try to see if in,
58:46you know, a challenging case.
58:47Could this be helpful?
58:49And again embryonorabdomal sarcoma
58:51has NF1 mutation and Ras mutation,
58:54V core alteration very different.
58:56While pleomorphic rhabdoma sarcoma
59:00has the same alterations as
59:02any other pleomorphic sarcoma.
59:04So if you look at this,
59:06so on the left you have pleomorphic
59:08rhabdom and then you have
59:10undifferential pleomorphic sarcoma,
59:12pleomorphic liposarcoma.
59:13Here it looks pretty much the same.
59:16So pleomorphic rhabdom has the same genomics,
59:21the same signature and any other adult
59:24theomorphic sarcoma and just supported
59:27the fact that these are included in the
59:31therapeutic bracket of pleomorphic sarcoma.
59:33So if you ask a sarcoma medical
59:35oncologist how you treat pleomorphic
59:37crap that they will say like any
59:40other pleomorphic sarcoma,
59:42not with Embryon Arab the
59:44protocol which makes sense.
59:46However,
59:46it is our role to make sure we
59:50distinguish the two of them.
59:51So final thoughts if we need any.
59:56I hope I convinced you giving you so many
01:00:01examples about the wide application of
01:00:03NGS beyond diagnosis and classification.
01:00:06And the last point here is that our role
01:00:10as pathologist seems to be evolving.
01:00:13A lot during the NGS era and
01:00:17it's advisable if you ask me to
01:00:20keep an active role in,
01:00:22you know,
01:00:23incorporating and interpreting all
01:00:25these NGS tests and putting together
01:00:28with the remaining of the findings for,
01:00:31you know,
01:00:31an improved diagnosis and a better
01:00:34management for these patients.
01:00:35Thank you very much.
01:00:51Any questions?
01:00:55I guess I was very clear,
01:01:04are these affiliations
01:01:05detectable or liquid files?
01:01:09Very good question.
01:01:11So we have a similar panel with IMPACT.
01:01:15IMPACT has 500 genes we call MSK Access,
01:01:19which does the sequencing from
01:01:22the circulating DNA includes
01:01:24I believe 70 something genes.
01:01:27It's not very reliable,
01:01:29it's not very accurate.
01:01:31So I guess if you're looking
01:01:33at a specific alteration like
01:01:34just you look at kits, you know,
01:01:37this may work well in the blood if
01:01:39you know exactly what you're after,
01:01:41but not not for these genomically
01:01:43complex circle ones.
01:01:47See, I do have a question.
01:01:53You mentioned earlier reverse morphology
01:01:56with the genomic data, NGS data,
01:01:59then you go back and look at the tumor.
01:02:03Do you think that the NGS data should be
01:02:08signed out by the surgeon pathologist?
01:02:14I, I think it should be signed
01:02:16about the molecular pathologist to
01:02:18make sure that everything you know,
01:02:20the quality control and everything
01:02:22and then to be discussed the results
01:02:25in like a molecular tumor board.
01:02:26And I think that's what we are missing.
01:02:29We missed this link. I agree with you.
01:02:31That's very important to kind
01:02:32of put together.
01:02:33I mean, you know,
01:02:34doesn't make sense with what we see and
01:02:37a lot of time it makes sense and then
01:02:39they trigger us to do additional tests
01:02:41that we didn't even think about that right.
01:02:43So I gave a number of examples here,
01:02:47but I truly think they should be signed on
01:02:49by molecular pathologists that would know,
01:02:52you know, the pitfalls all the.
01:02:54So there's
01:02:57a question in chat that's you've been
01:03:00settled in the collation so far.
01:03:04Yeah, it's used, but not, not great,
01:03:06no, at least the cases I've sent
01:03:09to methylation in our department,
01:03:12maybe because I send zebras
01:03:14so usually say no match.
01:03:17So actually I've not been sending much.
01:03:19I mean, I, I have a question.
01:03:21I mean, the, the workup takes a long time,
01:03:24right? So I'm a drastic guy.
01:03:26I get questions from my own
01:03:28colleagues more or less the same day
01:03:30that you've got the whole answer.
01:03:33These these workups take a long time.
01:03:35And every time there's a typical workflow,
01:03:37you get a biopsy, say London's
01:03:39going to sell something or other,
01:03:40you get a reflection,
01:03:41and then you spend your time working it up.
01:03:43Yeah, that's sort of the way it works.
01:03:45And then you don't have that issue
01:03:47about how fast you have to work.
01:03:48You've got, you know,
01:03:49you can work, take a month,
01:03:51and it's not a big deal. Yes,
01:03:56I mean it depends. As I said,
01:03:57we cannot activate these NGS tests.
01:04:00It's all by clinician.
01:04:01So we just emailed them.
01:04:03I said hey, you know,
01:04:04I don't know what this is,
01:04:06please get consent,
01:04:07get blood from the patient so we,
01:04:09we can activate the NGS right away.
01:04:12I will sign out the biopsy,
01:04:13you know, if I if I think it's,
01:04:15you know, high grade or whatever,
01:04:17I would say undifferentiated and then
01:04:20the classification will be done on the
01:04:22resection or I will suggest material if
01:04:25it's from outside to do Archer or whatever,
01:04:28if it's monomorphic Archer,
01:04:30if it's piomorphic NGS.
01:04:32But yeah, I mean,
01:04:33everybody wants to the result the same day,
01:04:37but and even the resection,
01:04:39I sign it out and then impact,
01:04:41you know, comes back in a month later.
01:04:43And I always say that make
01:04:45fun of myself said, you know,
01:04:47my diagnosis is as good as, you know,
01:04:49one month because then then I'll
01:04:51have the results of the NGS.
01:04:53And then I may have to, yeah,
01:04:55reconsider my diagnosis,
01:04:56which, you know,
01:04:57happens as I showed you couple of times.
01:05:00But this, this is great.
01:05:01You know,
01:05:02these are finally some objective tools.
01:05:04Some some sometimes doesn't all make sense,
01:05:06but most of the time if they find
01:05:09an alterations or a fusion and we
01:05:12confirm by immuno chemistry, it's real.
01:05:14So we, you know,
01:05:16we changed the diagnosis.
01:05:20Finally some questions. Yeah,
01:05:23I just wanted to come back to the question,
01:05:25some of the stuff you mentioned about
01:05:28GIST and actually one question kind
01:05:29of came up with Rob's point for the
01:05:32GIST and she asked do you do that?
01:05:34Do you need a clinician order for that or
01:05:36do you do that in her complexity manner?
01:05:38I cannot, I cannot. It's just a patient
01:05:41need to be consent to draw blood.
01:05:43So and because you see Mati Nibben,
01:05:47you know TKI, they do it on every case.
01:05:49I don't have to tell them that the GIST
01:05:52sarcoma oncologist are outstanding.
01:05:54So I don't have to tell them.
01:05:56But yes, it's being done on every
01:05:59case and with the normal gram that you
01:06:02described that incorporates the genomic
01:06:05data is I don't know if I missed it.
01:06:07Maybe you shouldn't,
01:06:08but is that could be look at
01:06:10that anywhere or is that posted
01:06:12anywhere on the it's published,
01:06:13so published you can cut
01:06:15it and I'm just kidding.
01:06:17Yeah, it's published, Yeah,
01:06:19it's published last year and we also have
01:06:23recently done a similar one in Lyle.
01:06:26Yeah.
01:06:26One
01:06:30thing that I think some of the patients,
01:06:32any paths might not be pick up from
01:06:34our like hard scale.
01:06:40Yeah, that's the hardest part because
01:06:43most of the commercially available,
01:06:45they don't provide them and even
01:06:48even within our own departments,
01:06:51different molecular pathologists
01:06:53use different thresholds.
01:06:55So it may depend.
01:06:56So a lot of the studies
01:06:58that we do copy number,
01:06:59we had to go back to the raw data to
01:07:02make sure that everything is accurate.
01:07:04So you're perfectly right.
01:07:07This is still very subjective field,
01:07:11you know, to report the arm
01:07:14level copy number changes
01:07:18also because our clinicians don't
01:07:20really care that much, you know,
01:07:22they're all after mutations,
01:07:23fusions, you know,
01:07:24so then maybe it's not so much,
01:07:26you know, detail or is no, no,
01:07:28no certain standards that are being applied.
01:07:32I don't know what what's the situation here?
01:07:35And signing out molecular, but
01:07:39right, yeah, most commercial the same.
01:07:42They are not reported.
01:07:44So when we we did the the the
01:07:48prognostication in LYO, LYO is a disease.
01:07:51Lyo is a disease of copy number, right.
01:07:55It's not necessarily like just,
01:07:57it's truly you have to have very good data.
01:08:00So we were not able to find a,
01:08:03a validation cohort.
01:08:04So in the end, we have to take from
01:08:08like the Genie project of ACR,
01:08:11get all the raw data,
01:08:13redo our own copy number in order for us
01:08:15to be able to compare with the impact.
01:08:18So it was really very, very hard.
01:08:22I don't know,
01:08:23maybe in the future they will standardize
01:08:26this better and maybe will come
01:08:28from if the clinicians require it.
01:08:33I just want to thank you for coming.
01:08:34I really enjoyed it.
01:08:37I remember signing out with you and
01:08:39one of the first things you said to
01:08:41me was is there blood in the system?
01:08:43And now I can see why that was such
01:08:46an important question for for me to.
01:08:47Yeah, I can't.
01:08:48Yeah, I'm sure the fellows think I'm crazy.
01:08:52You know, every, you know,
01:08:53like we are looking at the slides and
01:08:54said is there blood in the system?
01:08:56Like why? It's like this question,
01:08:58so very
01:09:02important question. I'm
01:09:11just so thank you.
01:09:12Thank you so much. Oh, OK.
01:09:13OK. Let me, let me just.
01:09:15Yeah, it's my great honor. OK.
01:09:21I just want to give this award.
01:09:22OK, guys, could you stay for two seconds?
01:09:25I'm going to make it short.
01:09:26All right? OK, Don't worry.
01:09:28Don't worry.
01:09:29I have to do it officially.
01:09:30All right,
01:09:32So it's my great pleasure
01:09:33and honor to present the
01:09:36Doctor McAllister Actorship
01:09:38Award to our today's speaker,
01:09:39Doctor Antonescu,
01:09:41on behalf of the entire department.
01:09:43So just briefly about Doctor McAllister.
01:09:46He was a graduate of a Yale College.
01:09:48Then he went to John Hopkins
01:09:50where he graduated from Med school
01:09:52and finished his residency there as well,
01:09:55and actually came back here as the chief
01:09:58of surgical pathology for the Memorial
01:10:00unit of the Yale New Haven Hospital
01:10:02for 25 years from 1953 to 1978.
01:10:08He was regarded as one of the
01:10:11best diagnosticians, educator,
01:10:12great mentor, advisor,
01:10:15and friend to many students, residents,
01:10:19and all colleagues in in our hospital
01:10:21system. So I think you really truly
01:10:24represent what this lectureship award
01:10:27is for and we are very grateful
01:10:29that you came to us today.
01:10:29So thank you so much. So
01:10:31this is, it's not big, but it's from heart.