Kasey Altman Test Management

Testing Principles

Tissue is a scarce commodity to be managed frugally.

Liquid biopsies are non-invasive, useful to monitor progress, and should be taken frequently.

Choose the most encompassing sequencing, including RNA if possible, versus a limited gene panel.

To save tissue, don't run redundant tests.

Refuse all tests that are optional and don't return results to the patient.

Have a process in place for reporting results; ensure Delsee & Kasey receive results in real-time as well as copies going to all key members of the care team. Avoid needing to reverse engineer and going back to manually request any results.

7/23/21 UPDATE from MSK - TISSUE AVAILABILITY (Thank you, Dr. Matt Hanna):

Based on the available images I can review:

First block does not have a lot of tissue left (~0.5x0.1 mm),

Second block had IMPACT tested on it still has a reasonable amount of tissue in it.

Another block had additional testing on it and I do not have an up to date idea of how much tissue is left,

The remaining four blocks did not have additional testing and all have sufficient tissue

for immunohistochemistry (IHC) or molecular testing if indicated. The tissue is

embedded in a paraffin wax and usually is processed as unstained slides for

additional testing (IHC requires an unstained slide, molecular testing usually uses the

tissue on unstained slides to be scraped off for further processing)

6/18/21 STATUS ON MSK TISSUE AVAILABILITY (Thank you, Dr. Wexler):

Remaining banked “tissue”; waiting for additional information on the(FFPE) material and on the 2 cell-free DNA (cfDNA)

N is the normal DNA extracted from your “normal” peripheral blood cells (Peripheral Blood Mononuclear Cells).

T1 (November lymph node) and T2 (March perianal biopsy) are the 2 tumor samples we obtained at MSKCC.

T3 was also tissue from the March perianal biopsy which was requested and resubmitted in an attempt to get RNA data. It is still not clear to us (MSK) why it failed (two completely independent methods, one of which was done manually)

ug is an abbreviation for micrograms

ng is an abbreviation for nanograms (1000 nanograms = 1 microgram)

160ng T3 RNA (probably contaminated or otherwise unusable)

DNA and RNA samples are available to be used for other applications, including pickup to ship to an outside facility. Not known how much of the above material (specifically the 4 micrograms of T2 DNA) was used to send to Tempus this week.

Possible Additional Testing Options

Testing priority:

Tissue staining by IHC or immunofluorescence such that tissue slides can then be sent off for gene sequencing (re-use of slides already stained). Secure digital images of the H&E- and any/all IHC-stained slides if at all possible (e.g. via John Iafrate; See #4 below)

The pathologist should determine tumor cell count per slide/block before necessarily sending the requisite # of slides to sequencing companies (i.e. they should discuss directly with the company before sending with rationale why they are sending less than requested if the sample has a lot of tumor cells in it).

Digitize H&E and any IHC slides for future analyses or exploratory algorithmic studies (e.g. immune score, TIL count, etc.). These slides can be stored freely, without identifiers, in the PathPresenter public library slide box

Reserve ⅓ of tissue for future use by the patient for uses yet to be determined. Establish this up-front with the physician and pathologists.

Mind the consent language on any forms involving use/ownership of your tissue. Request a conversation with hospital administration if needed. Request to have in hand well in advance for review.

For digital pathology slide scanning, please scan a whole slide image ideally at 40x magnification. Scanners typically used are Phillips, Leica's Aperio, Hamamatsu, etc. It may have to be done in a research lab if they do not have a digital pathology workflow (which most centers do not...yet).

Whole Genome Sequencing

Darwin's OncoTarget/OncoTreat

(Test to consider if tissue bx in future) https://www.pathology.columbia.edu/diagnostic-specialties/personalized-genomic-medicine/oncology-testing/darwin-oncotarget-tm-oncotreat

Insight - (formerly AdvanceSM)

Jensed2@LabCorp.com

https://www.statnews.com/2021/06/15/why-two-scientific-powerhouses-are-teaming-up-to-tackle-rare-cancers-long-overlooked-in-research/

https://www.cc-tdi.org/current_research/needle-from-the-haystack-repurposed-drug-for-rhabdomyosarcoma/

robert.brown@uth.tmc.edu

713-500-5342. Specialist pathologist creates comprehensive and elegant IHC panels

Dr. Wexler doesn't see value

https://www.linkedin.com/in/christian-seitz-424612a0/?originalSubdomain=de

Plasma free amino acid panel

(make sure includes cystine - https://www.labcorp.com/tests/700068/amino-acid-profile-quantitative-plasma

First map DNA Breakpoint then surveille in cfDNA liquid biopsy; Update: 8/3/21 - Lenny Wexler believes commercial cfDNA sufficient to surveil mutant TP53