Hematopathology Send-out Tests to NeoGenomics

UT-Medical School at Houston, Pathology/ Last Revision on: 12/20/2024

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Flow Cytometry (T, technical only)

-For new acute leukemia cases: Extended L/L Panel (31 markers)

-For new cases with suspected diagnosis: Standard L/L Panel (24 markers) with appropriate Add-on Tubes

(Note that appropriate Add-on Panels may be automatically added by technical personnel if abnormal cell subsets are detected)

-For samples from Surgical Path/Cytopath: T&B Tissue Panel with appropriate Add-on Tubes (such as Plasma Cell)

-For PNH: High Sensitivity PNH

-For MRD in B-ALL: B-ALL MRD (G, only Global option is available)

-Sample pickup by NeoGenomics: twice daily M-F (noon and 5:45-6:15 pm). Besides these pickups, STAT pickup can be done by calling 866.776.5907 (option 3, giving client account number: 17336 for Memorial Hermann-TMC). Put sample in usual flow sample box at lab window.

-Local Houston flow cytometry lab, operating Monday-Sat: 7256 South Sam Houston Parkway West, Suite 300 Houston, TX 77085; phone 866 776 5907

Cytogenetics, FISH, and PCR/NGS (G, global)

NOTES: for patient already in remission, we will just order tests to cover known positive abnormalities from previous diagnostic bone marrow (translocations, mutations, etc). Only for patients still refractory or with relapse we would order all tests as for new cases to cover any genomic evolution that yield new abnormalities.

1.AML

(a) Sample in dark green-top tube for

-Oncology Chromosome Analysis

-AML Std FISH Panel:

-BCR/ABL1 by FISH

(b) Sample in lavender-top tube for:

- Neotype AML Express (NGS):TAT 3-5 days

DNA Sequencing: SNVs/InDels (38 genes): ABL1, ASXL1, BCOR, BRAF, CALR, CBL, CEBPA, CSF3R, DDX41, DNMT3A, ETV6, EZH2, FLT3, GATA2, HRAS, IDH1, IDH2, JAK2, KIT, KRAS, MPL, NF1, NPM1, NRAS, PHF6, PPM1D, PRPF8, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, TET2, TP53, U2AF1, WT1, ZRSR2

RNA Sequencing: Fusions (9 genes): ABL1, KAT6A, KMT2A, MECOM, MYH11, NUP98, NUP214, RUNX1, RARA

-PML-RARA Translocation, t(15;17) (Quantitative PML/RARA) for follow-up bone marrows with APL cases

-RUNX1-RUNX1T1 (AML1-ETO) Translocation, t(8;21), quantitative PCR testing. For AML cases with known t(8;21) or inv(16), typically by FISH from baseline BM

-Note: for difficult APL cases, call Neogenomics to request for a STAT FISH testing for the PML/RARA component. It can be done on the same day of Neogenomics receiving the sample in their lab. The other FISH tests in the AML panel can be completed later. Note STAT along with MD contact name and phone number to receive STAT results.

2A. Adult B cell ALL

(a) Sample in green-top tube for

-Oncology Chromosome Analysis

-For bcr-abl1-like ALL: ALL, Ph-like [PDGFRb (5q32), BCR/ABL1-ASS1 t(9;22), JAK2 (9p24.1), EPOR (19p13.2) and CRLF2 (Xp22.33/Yp11.32)]

Note: STAT FISH testing is available by request for BCR-ABL1. Note STAT along with MD contact name and phone number to receive STAT results.

b) Sample in lavender-top tube:

-BCR/ABL1 Standard p210,p190 (quant PCR for known case with bcr/abl1)

-ClonoSEQ B-cell clonality (ID) for 1^st BM; ClonoSEQ B-cell tracking for follow-up BM

2B. Adult T cell ALL

(a) Sample in green-top tube for

-Oncology Chromosome Analysis

-To Mayo for TALPF (pedi FISH, <31 years old) or TALAF (adult FISH, >/=31 years old).

(b) Sample in purple top to:

-NeoGenomics for NOTCH1 mutation analysis

-ClonoSEQ T-cell clonality (ID) for 1^st BM; ClonoSEQ T-cell tracking for follow-up BM

2C. Pediatric B cell ALL

(a) Sample in green-top tube for

-Oncology Chromosome Analysis

-For bcr-abl1-like ALL: ALL, Ph-like [PDGFRb (5q32), BCR/ABL1-ASS1 t(9;22), JAK2 (9p24.1), EPOR (19p13.2) and CRLF2 (Xp22.33/Yp11.32)]

Note: STAT FISH testing is available by request for BCR-ABL1. Note STAT along with MD contact name and phone number to receive STAT results.

b) Sample in lavender-top tube for

-BCR/ABL1 Standard p210,p190 (quant PCR for known case with bcr/abl1)

-ClonoSEQ B-cell clonality (ID) for 1^st BM; ClonoSEQ B-cell tracking for follow-up BM

-NeoTYPE ALL Profile

-B cell ALL MRD by flow cytometry (global) for follow-up BM

2D. Pediatric T cell ALL

(a) Sample in green-top tube for

-Oncology Chromosome Analysis

-To Mayo for TALPF (pedi FISH, <31 years old)

(b) Sample in purple top

-To NeoGenomics for NOTCH1 mutation analysis

-ClonoSEQ T-cell clonality (ID) for 1^st BM; ClonoSEQ T-cell tracking for follow-up BM

-MRD T cell ALL by flow cytometry to PhenoPath (Requisitions are in the hemepath signout room)

3. CML

(a) Sample in green-top tube for

-Oncology Chromosome Analysis

(b) Sample in lavender-top tube for quantitative PCR testing:

-BCR/ABL1 Standard p210,p190 (diagnostic and follow-up bone marrows)

(c) For detection of resistance to Imatinib Mesylate if clinically indicated: Abl1 Kinase Domain (Gleevec Resistance), sample in purple-top tube for PCR

4. PV

(a) Sample in green-top tube for

-Oncology Chromosome Analysis

(b) Sample in lavender tube for PCR: JAK2 V617F qualitative (check box if negative reflex to JAK2 Exon 12-14 mutation )

5. ET, PM, MPN-NOS, MPN/MDS

(a) Sample in green-top tube for

-Oncology Chromosome Analysis

-MPN FISH panel: PDGFRa, CHIC2, FIP1L1 (4q12) | PDGFRb (5q33) | FGFR1 (8p11) | BCR/ABL1 t(9;22) including ASS1 (9q34)

(b) Sample in lavender tube for MPN Extended Reflex Panel:

JAK2 V617F, JAK2 Exon 12-14, CALR exon 9, and MPL exon 10.

6. Myeloid and Lymphoid Neoplasms with Eosinophilia

Sample in green-top tube for

-Oncology Chromosome Analysis

-Eosinophilia FISH profile: PDGFRa, CHIC2, FIP1L1 (4q12) | PDGFRb (5q33) | FGFR1 (8p11) | CBFB inv(16), t(16;16) |

7. PLASMA CELL MYELOMA

Sample in green top tube for

-Oncology Chromosome Analysis

8. CLL

(a) Sample in green top tube for

-Oncology Chromosome Analysis

(b) Sample in lavender-top (baseline bone marrow only) for

-IgVH Hypermutation analysis

9. MDS (incl Cytopenia)

Sample in green top tube for

-Oncology Chromosome Analysis

Sample in lavender-top

-Neotype MDS/CMML Profile (NGS):

ASXL1, BCOR, BCORL1, BRAF, CALR, CBL, CEBPA, CUX1, DDX41, DNMT3A, ETNK1, ETV6, EZH2, FLT3, GATA2, GNB1, HRAS, IDH1, IDH2, JAK2, KIT, KRAS, MPL, NF1, NPM1, NRAS, PDGFRA, PHF6, PIGA, PPM1D, PTEN, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, STAT3, STAT5B, TET2, TP53, U2AF1, WT1, and ZRSR2

10. B cell Non-Hodgkin Lymphoma FISH Panel, if needed for diagnosis

(bone marrow aspirate or unstained slides of bone marrow clot)

-Low grade B cell: Low grade/small B cell lymphoma FISH panel: BCL6 (3q27) | CCND1/IgH t(11;14) IgH/BCL2 t(14;18) | MALT1 (18q21)

-High grade B cell: High grade/large B cell lymphoma FISH panel: BCL6 (3q27) | MYC (8q24) | BCL2 (18q21) |. Note that this B-NHL High Grade FISH profile is needed for large B cell lymphoma that meets one or more of the following criteria:

11. LPL

Sample in lavender-top tube for PCR testing: MYD88

12. HCL

(a) Sample in green top tube for

-Oncology Chromosome Analysis

(b) Sample in lavender-top for PCR

-BRAF

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SOLID TISSUE (lymph node, bone marrow clot)

Note that decalcified bone marrow biopsy is not accepted

(A) FISH sample for solid tissue:

-Unstained slides at 5 micron thickness