Cytogenetics, FISH, and PCR
Testing for Hematopathology Samples
UT-Medical School at Houston,
Pathology/
Last Revision on: 7/14/2020
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
-Oncology Chromosome Analysis
-Rapid AML Therapeutic Panel (under Molecular Genetics):
(i)Sanger sequencing (6 genes): FLT3 (ITD and TKD), NPM1, CEBPA,
IDH1/IDH2, and TP53
(ii)FISH
probes: 5q-, -5 (5p15, 5q31, 5q33) | 7q-, -7 (Cen 7, 7q22, 7q31) |
RUNX1/RUNX1T1 (ETO/AML1) t(8;21) | MLL (11q23) | PML/RARA t(15;17) | CBFB
inv(16), t(16;16) | 17p- (TP53 17p13.1, NF1 17q11.2)
(b) Sample in lavender-top tube for quantitative PCR testing:
-BCR/ABL1 Standard p210,p190
-PML-RARA
Translocation, t(15;17) (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 Quantitative PCR with
f/u BMs; i.e. RUNX1-RUNX1T1 (AML1-ETO) Translocation, t(8;21). Send specimen (purple-top
tube) for this.
-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.
2. ALL
(a)
Sample in green-top tube for
-Oncology Chromosome Analysis
-For adult: ALL, Adult FISH Panel [TCF3/PBX1
(E2A/PBX1) t(1;19) | Trisomy or Tetrasomy 4, 6, 10, 17 (Cen 4, Cen 6, Cen 10,
Cen 17) | MYC (8q24) | BCR/ABL1/ASS1 t(9;22) | MLL (11q23) | IgH (14q32) |]
-For pediatric: ALL, Pediatric FISH Panel [TCF3/PBX1 (E2A/PBX1)
t(1;19) | Trisomy or Tetrasomy 4, 6, 10, 17 (Cen 4, Cen 6, Cen 10, Cen 17) |
MYC (8q24) | BCR/ABL1/ASS1 t(9;22) | MLL (11q23) | ETV6/RUNX1 (TEL/AML1)
t(12;21) | IgH (14q32)]. Note that we need to write
down name of this test in request slip.
-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 processing 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 quantitative PCR testing:
-BCR/ABL1 Standard p210,p190
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
-Plasma cell myeloma FISH panel [1p-, 1q+, iso(1q): CDKN2C (1p32), CKS1B (1q21) | +5, hyperdiploidy (5p15) | +9, hyperdiploidy
(9q22) | +15, hyperdiploidy (15q22) | 13q- (13q14,
13q34) | IgH (14q32) | 17p- (TP53 17p13.1, NF1
17q11.2)]; check “with reflex to IgH Complex if positive [FGFR3/IgH
t(4;14) | CCND1/IgH t(11;14) | IgH/MAF
t(14;16) | IgH/MAFB t(14;20)],
8. CLL
(a) Sample
in green top tube for
-Oncology Chromosome Analysis
-CLL FISH Profile: 6q- [SEC63 (6q21), MYB (6q23)] |
ATM (11q22.3) | p53 (17p13.1) | Trisomy 12 (Cen 12) | 13q-/-13 (13q14, 13q34) |
CCND1/IgH t(11;14)
(b) Sample
in lavender-top (baseline bone marrow only) for
-IgVH Hypermutation analysis
9. MDS
Sample
in green top tube for
-Oncology Chromosome Analysis
-MDS FISH standard panel: 5q-, -5 (5p15, 5q31, 5q33)
| 7q-, -7 (Cen 7, 7q22, 7q31) | Trisomy 8 (Cen 8) | MLL (11q23) | 20q- (20q12,
20qter)
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:
(a)
Ki67
≥70%
(b)
Germinal
center type (based on Hans algorithm with IHCs)
(c)
Positive cMyc by IHC (≥40% of cells)
These
cases also need to have the following IHCs: bcl2, bcl6, cMyc
to report double/triple expressors
11. (Neotype)
Myeloid Profile, if needed for
diagnosis of MDS; not universally adopted
Sample in lavender-top tube for Next-Gen
Sequencing testing:
ABL1, ASXL1, ATRX,
BCOR, BCORL1, BRAF, CALR, CBL, CBLB, CBLC, CDKN2A, CEBPA, CSF3R, CUX1, DNMT3A,
DDX41, ETNK1, ETV6, EZH2, FBXW7, FLT3, GATA1, GATA2, GNAS, GNB1, HRAS, IDH1,
IDH2, IKZF1, JAK2 including V617F and Exons 12+14, JAK3, KDM6A, KIT, KRAS, MLL,
MPL, MYD88, NF1, NOTCH1, NPM1, NRAS, PDGFRA, PHF6, PML, PPM1D, PTEN, PTPN11,
RAD21, RUNX1, SETBP1, SF3B1, SH2B3, SMC1A, SMC3, SRSF2, STAG2, STAT3, STAT5B,
TET2, TP53, U2AF1, WT1, ZRSR2.
12. LPL
Sample
in lavender-top tube for PCR testing: MYD88
13. HCL
(a) Sample
in green top tube for
-Oncology Chromosome Analysis
(b) Sample
in lavender-top for PCR
-BRAF
++++++++++++++++++++++++++++++++++++++++++++++
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
-Minimum
2 slides for each probe; add 2 extra slides
(B) PCR sample for solid tissue:
-Unstained
slides at 10 micron thickness
-Minimum
2 slides for each probe; add 2 extra slides
(C) EBER sample for solid tissue (technical
only, to be read by us):
-3
unstained slides at 5 micron thickness
+++++++++++++++++++++++++++++++++++++++++++++
NEOGENOMICS
Account
Number: 17336
·
Account Name: Memorial Hermann – Texas Medical Center
·
Client Service Phone: 866.776.5907, option 3 and email: client.services@neogenomics.com
·
Client Service Fax: 239.690.4237
·
NeoLink Online Portal Access: https://neolink.neogenomics.com/APvX/security/login.aspx
·
Test Menu Link: www.neogenomics.com/test-menu
·
Requisition Forms:
o
Heme: https://www.neogenomics.com/sites/default/files/Requisition/Neo-Hematopathology-Requisition.pdf
o
Solid Tumor: https://www.neogenomics.com/sites/default/files/2020-06/Neo_Solid-Tumor-Req_062620_Final_FF.pdf
o
IHC: https://www.neogenomics.com/sites/default/files/2019-07/Neo-IHC-Req.PDF