Cancer Cytogenetics Acute Myelogenous Leukemia/ Myelodysplastic Syndrome (AML/MDS) FISH Panel

Acute Myelogenous Leukemia (AML) is a disorder of myeloid cells which was historically categorized by the myeloid cell lineage involved, several of which showed recurrent balanced chromosomal rearrangements resulting in the creation of novel fusion proteins. Recent reclassification (Swerdlow et al. 2017) groups the recurrent rearrangements into a single category.  This FISH panel is designed to detect the most common, and/or prognostically-significant abnormalities in AML with recurrent genetic abnormalities and in therapy-related AML (Swerdlow et al. 2017).  Recurrent abnormalities are observed in the majority of AML cases. 

Myelodysplastic syndrome (MDS) describes a group of clonal haematopoietic disorders resulting in ineffective production of one or more of the myeloid cell lineages; risk for transformation to AML is increased.  MDS may occur de novo or may arise as a secondary malignancy associated with treatment.  This FISH panel is designed to detect the most common, and/or prognostically-significant abnormalities in MDS (Swerdlow et al. 2017). 

FISH studies are useful adjuncts to complete chromosome studies, particularly when following an abnormal clone, assessing relapse and progression, or when material is inadequate for chromosomal analysis.  

The AML/MDS FISH panel includes:

1. EGR1/5q33/5p15 locus-specific probes, to detect deletion of chromosome 5q or monosomy 5.
2. D7S486/CEP 7 locus specific probes, to detect deletion of chromosome 7q or monosomy 7.
3. MLL break-apart probe, to detect MLL (11q23.1-23.3) disruption.
4. BCR/ABL + ASS dual-fusion probe, to detect t(9;22) and variants.
5. PML/RARA dual-fusion probe, to detect t(15;17) and variants.
6. RUNX1T1/RUNX1 (aka ETO/AML1) dual-fusion probe, to detect t(8;21) and variants.
7. CBFB/MYH11dual-fusion probe, to detect inv(16) or t(16;16).
8. DEK/NUP214 dual-fusion probe, to detect t(6;9) and variants.
9. GATA2/MECOM dual-fusion probe, to detect t(3;3) and variants.
10. NUP98 break-apart probe, to detect NUP98 (11p15.4-15.5) disruption.
11. D20S108/20qtel probe set, to detect monosomy 20 and 20q deletion.
12. CEP 8, to detect trisomy 8.
13. TP53/NF1 locus-specific probe, to detect monosomy 17 and deletion of TP53 (17p13.1).
14. ETV6 break-apart probe, to detect ETV6 (12p13.2) disruption.

Note:  Reflex testing may include MLLT3/MLL t(9;11), AFF1 break-apart, MLL/MLLT1 t(11;19), and/or RUNX1 break-apart when relevant.  Additional charges may apply.

Note:  Interphase FISH analysis is not intended to stand alone, but rather to provide supplemental information to routine cytogenetic studies.

Slides are prepared per standard protocols and 100-200 interphase cells are scored per probe.

*Please note: it is our laboratory policy to analyze at least one metaphase cell from every hybridization if possible, including both normal and abnormal cells if both exist.

Bone Marrow:Shortly before aspiration, add 0.2 cc of Sodium Heparin (1,000 units/ml) to tube of transport medium (please contact lab to arrange for transport medium to be sent).Add at least 1 cc of bone marrow aspirate to the tube and suspend well.Allow no clots to form.
Bone marrow smears:Provide 10 slides
Blood:May be used if bone marrow is inaspirable and blasts (.5%) are present.Send in Sodium Heparin tube.

• Adult - 3-5 mL drawn into a GREEN top sodium heparin vacutainer tube or into a pre-heparinized plastic syringe (use 0.2 cc sodium heparin, 1000 unit/mL).Do NOT use lithium heparin.
• Child - 1-2 mL, as above.
• Infant - 1-2 mL, as above.
• Keep at room temperature and transport to laboratory as soon as possible.
• Contact Client Services at (855) 535-1522 for supplies and instructions.

Bone core biopsy: May also provide cells in cases where marrow is severely packed.Send in transport medium with Sodium Heparin.
FFPE Slides: Specimen Requirements:**

• If sending slides, please include H&E stained slide cut from same block
• Preferred slice thickness is 4-5 microns on positively charged slides. 
• Please submit 12-20 slides.  Store at room temperature.
• Contact Client Services at (855) 535-1522 for shipping supplies and instructions
• **Note: cutoffs for copy number probes are insensitive to low-level mosaicism

Lymph node or tumor: Tumor specimens of at least 0.5 cm³ (up to 3 inches in diameter) are immediately collected with sterile methods into closable containers with sterile transport medium.* Needle biopsies will be accepted, but are often difficult to grow.Deliver the specimen in transport medium to the laboratory within a day, if possible, with decreased success rates as specimens are delayed in transit.Protect sample from temperature extremes during shipping.

*Sterile Ringer’s solution, either lactated or non-lactated and sterile isotonic saline are alternatives, if no complete RPMI is available.  Contact Client Services for more information on media requirements.

It is preferable to collect the specimen before initiation of chemotherapy in the patient.  Tumor samples should be selected from viable areas, with as little normal or necrotic material as possible. 

Unacceptable specimens are acellular, necrotic specimens, septic specimens, specimens in fixative or frozen, or specimens collected more than one week previously.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES.  Please include detailed clinical information.

Mon-Sat

5-10 days: Contact Lab at 855-KDL-1LAB (535-1522) - Time varies depending on number and type of tests performed.

• Keep specimen at room temperature during transit. 
• Do not use the cold pack provided in the KDL shipping kit. 
• Ship the specimen overnight express, using the FedEx priority overnight label provided. 
• The specimen must arrive at the lab no more than 24 hours after collection.

1. Swerdlow et al. (Eds.): WHO Classification of Tumors of Haematopoietic and Lymphoid Tissues. IARC: Lyon 2017
2. De Braekeleer et al. 2012 Leuk Res 36, doi: 10.1016/j.leukres.2012.04.010; Haferlach et al. 2012 Genes Chrom Cancer 51, doi: 10.1002/gcc.21918