Cytogenetics, FISH, and PCR Testing for Hematopathology Samples

UT-Medical School at Houston, Pathology/ Last Revision on: 10/13/2017

 

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 green-top tube for

-Cytogenetics

 

-AML FISH Profile [RUNX1T1/RUNX1 t(8;21), PML-RARA t(15;17), RARA (17q21), inv(16), MLL (11q23)]

 

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

-BCR/ABL1

-FLT3 (ITD/TKD)

-AML Molecular Profile - 24 gene mutations by NGS (ASXL1, BCOR, CEBPA, CSF3R, DNMT3A, EZH2,IDH1, IDH2, KIT, KRAS, NPM1, NRAS, PHF6, PTPN11, RAD21, RUNX1, SF3B1, SRSF2, STAG2, TET2, TP53, U2AF1, WT1, ZRSR2)

 

-Quantitative PML/RARA for diagnostic and follow-up bone marrows with APL cases

-For AML cases with known t(8;21) or inv(16), typically by FISH from baseline BM, we will send for PCR with f/u BMs. Send a separate purple-top tube to Lab Corp,

ordered with a down-time test order slip; specifying the test to be sent to ARUP. Alert send-out section so that they can work on the approval process.

 

 

2. ALL

(a) Sample in green-top tube for

-Cytogenetics

-ALL FISH Profile [BCR-ABL t(9;22), MLL (11q23), ETV6- RUNX1 t(12;21), IGH (14q32), TCR alpha/delta (14q11). For pediatric acute lymphoblastic leukemia: includes CEP4 and CEP10]

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

-BCR/ABL1

 

3. CML

(a) Sample in green-top tube for

-Cytogenetics

-BCR/ABL by FISH

 

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

 

-Quantitative BCR/ABL1 (diagnostic and follow-up bone marrows)

 

 

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

 

4. PV

(a) Sample in green-top tube for

-Cytogenetics

(b) Sample in lavender tube for PCR: JAK2 V617F mutation (if negative reflex to JAK2 Exon 12 mutation)

 

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

(a) Sample in green-top tube for

 

-Cytogenetics

 

(b) Sample in lavender tube for MPN Molecular Profile (Next-gen seq): CALR, CSF3R, JAK2, MPL and SETBP1

 

6. Myeloid and Lymphoid Neoplasms with Eosinophilia

Sample in green-top tube for

-Cytogenetics

-FISH testing MPN-Eosinophilia panel: PDBGRα (4q12), PDGFRβ (5q32), FGFR1 (8p11)

 

7. PLASMA CELL MYELOMA

Sample in  green top tube for

-Cytogenetics

-Multiple Myeloma FISH Profile: CKS1B/CDKN2C (1p/1q), D5S630, D5S2064/EGR1 (5p/5q), 13q14/13q34, TP53 (17p13), IGH/FGFR3 t(4;14), IGH/CCND1 t(11;14), IGH/MAF t(14;16)

 

8. CLL

Sample in  green top tube for

-Cytogenetics

-CLL FISH Profile: 6q- (6p/6q21/6q23), ATM (11q22), +12 (12cen), 13q14/13q34, TP53 (17p13)

 

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

-IgVH mutation

 

9. MDS

Sample in  green top tube for

-Cytogenetics

-MDS FISH Profile: D5S630, D5S2064/EGR1 (5p/5q), D7S486 (7p11/ 7cen/ 7q31), +8 (8cen), D20S108 (20q)

 

10. Non-Hodgkin Lymphoma FISH Panel, if needed for diagnosis (unstained slides or paraffin block)

NHL FISH profile: BCL6 (3q27), 6q21/6q23, MYC (8q24), IGH/CCND1 t(11;14), IGH/BCL2 t(14;18), MALT1 (18q21)

 

11. Myeloid Molecular Profile, if needed for diagnosis of MDS; not universally adopted

Sample in lavender-top tube for Next-Gen Sequencing testing: ASXL1, BCOR, BRAF, CALR, CEBPA, CBL, CSF3R, DNMT3A, ETV6, EZH2, GATA2, GNAS, IDH1, IDH2, JAK2, KIT, KRAS, MPL, NF1, NPM1, NRAS, PDGFRa, PDGFRb, PHF6, PTPN11, RAD21, RUNX1, SETBP1, SF3B1, SMC1A, SMC3, SRSF2, STAG2, STAT3, STAT5b, TET2, TP53, U2AF1, WT1 and ZRSR2

12. LPL

Sample in lavender-top tube for PCR testing: MYD88

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SOLID TISSUE  (lymph node, bone marrow clot)

Note that decalcified bone marrow biopsy is not accepted

 

FISH sample for solid tissue:

-Unstained slides at 5 micron thickness

-Minimum 2 slides for each probe; add 2 extra slides

 

PCR sample for solid tissue:

-Unstained slides at 10 micron thickness

-Minimum 2 slides for each probe; add 2 extra slides

 

EBER sample for solid tissue (technical only, to be read by us):

-3 unstained slides at 5 micron thickness

 

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