Kasey Altman Test Management
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.
|Tests Performed||Tissue Source|
|10/28/20 Weill Punch bx|
|10/29/20 Weill Surgical bx|
|11/6/20 MSK Inguinal bx|
|3/10/21 MSK Surgical bx|
|SAMPLE RECEIVED||REPORT DATE||TESTS||Tumor %||FINDINGS||SAMPLE USED||ID NUMBER||ADDITIONAL FINDINGS|
|11/6/2020||11/23/20||FoundationOne HEME||MS STABLE, MYCN ampl., PAX3-FOX01||10/29/20 Weill Surgical bx||Specimen ID S20-30315 A2|
|11/18/2020||11/26/20||Archer Fusion||PAX3-FOX01||11/6/20 MSK Inguinal bx||(MSK:S20-62313/3-1 GYN, DOP:11/6/2020, 15 USS and 1 H&E)|
|11/19/20||12/11/20||MSK IMPACT (1 of 2)||MSS, MYCN fc 3.6||11/6/20 MSK Inguinal bx||?|
|1/27/21||2/10/21||Tempus WES||x||FAILED||10/28/20 Weill Punch bx||Specimen from Weill - S2030053 A1 (10/28/20 Date of Weill punch bx) no TL number signed out since DNA and RNA failed TL-21-16E71A|
|2/27/21||3/24/21||Tempus WES (1 of 2) only DNA portion successful; RNA failed||80%||AR, MYCN||11/6/20 MSK Inguinal bx||MSK#TS-196840.2.LN Tempus (number may be wrong# TL-21-6F08AF)|
|3/22/21||4/12/21||MSK Impact (2 of 2)||MYCN fc 59.1 TET2, TP53, *see additional to right||3/10/21 MSK Surgical bx||*GPS2, TP53 mutation & deletion, FANCC, CARM1, SMARCA4|
|4/21/21||5/11/21||Tempus RNA (transcriptome)||90%||ERBB3, CCNE1 overexpressed||3/10/21 MSK Surgical bx||case S21-15486, block 2. (MSK id) DNA seq on Mem. #TS-196840.2.LN. ***here's correct TL number from Tempus:TL-21-8BF105- was same as 3/24 WES DNA portion = TL-21-6F08AF|
|6/2/21||6/14/21||FoundationONE Liquid CDx||NO REPORTABLE ALTERATIONS||Blood Sample taken 6/1/21||For TRACK trial; order #1109238-01|
|??? Tom T. says TL-21-8BF105 is the RNA seq from inguinal nov 2020?? Ask Tempus|
|6/20/21 (in system 6/22)||7/14/21||Tempus WES (2 of 2) only DNA portion||60%||TP53, MYCN, (CXXC1 unknown 83% VAF)||3/10/21 MSK Surgical bx||case S21-15486, block 2_3;Report # TL-21-KAQMT3IR ( internal id TL-489579)|
|8/9/21||Guardant cfDNA||Neg for MYCN and TP53|
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)
|8 ug N DNA|
|8.6 ug T1 DNA|
|4 ug T2 DNA|
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
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).
|Date added||Test||Provider||Contact||Suggested by||Info|
|6/8/21||Fruit fly model||Vivant||Nahuel Villegasfirstname.lastname@example.org||Nahuel Villegas|
Whole Genome Sequencing
|Exact Science/Ashion||Rebecca Owens|
|Lenny Wexler/ Michael Ortiz MSK|
(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)
|Razelle Kurzrock, Rick Stanton,|
|6/16/21||CCTDI analysis||(share BAM files)||Charles Kelleremail@example.com||Charles Keller|
|6/16/21||Comprehensive IHC||UT Houston||Dr. Robert Brown|
|Charles Keller & Bill Passman(?)|
713-500-5342. Specialist pathologist creates comprehensive and elegant IHC panels
Dr. Wexler doesn't see value
|Christian Seitz (if +, GD-2 CAR T)|
|6/24/21||Digital PCR||Stefano Pacifico|
Plasma free amino acid panel
|MSK or Labcorp||Xiyan Li (Filctricine)|
(make sure includes cystine - https://www.labcorp.com/tests/700068/amino-acid-profile-quantitative-plasma
|7/16/21||DNA Breakpoint in cfDNA||Need to identify||Javed Khan|
First map DNA Breakpoint then surveille in cfDNA liquid biopsy; Update: 8/3/21 - Lenny Wexler believes commercial cfDNA sufficient to surveil mutant TP53