Test Directory

• EGR1 , 5p15.3/5q31.2 Deletion
• 7q22/7q31.2 Deletion
• 8cen, 8p11.1-q11.1
• 20q12/20q13.1 Deletion
• KMT2A (MLL) , 11q23.3 Rearrangement
• TP53, 17p13/CEN17 Deletion
• ETV6 , 12p13 Rearrangement

EGR1, 5p15.3/5q31.2 Deletion Probe

An interstitial deletion of chromosome 5, del(5q), is associated with myelodysplastic syndrome (MDS)/myeloproliferative disorder (MPD) and acute myelogenous leukemia (AML). Deletion of 5q can be observed in both de novo and therapy related AML. It is also seen as monosomy 5. In AML, 5q deletion is usually associated with a complex karyotype. The prognosis of AML with 5q-/-5 is generally unfavorable, associated with rapid disease progression and poor outcome and survival, especially when it is seen as a part of complex karyotype. Deletions of the long arm of chromosome 5 could vary considerably, and involvement of all bands between 5q11 and 5q33~q34 have been identified. The frequent loss of 5q suggests that important tumor suppressor genes map to this genomic segment. The so-called “5q- syndrome” associated with isolated deletion of chromosome 5 in MDS is a favorable prognostic indicator. In contrast, complex karyotypes with deletion of chromosome 5 in MDS are associated with an adverse outcome. Deletion of 5q or monosomy 5 in AML, with or without other chromosome changes, is also associated with a poor prognosis. Other chromosome changes commonly occurring with 5q- are monosomy 7/7q-, trisomy 8, and 20q-. These changes can be detected by using individual FISH probes or as part of the MDS probe panel. FISH for abnormalities of chromosome 5 can be performed on interphase or metaphase cells.

7q22/7q31.2 Deletion Probe

-7/7q- seen in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML); they may occur de novo or be secondary to an exposure to chemical mutagens or to chemotherapy treatments with alkylating agents; may probably also be secondary to immunosuppressive therapy for severe aplastic anemia. Deletion (7q) is always interstitial; cluster of breakpoints in 7q11 to 7q36, with two common minimal zones in q22 and in q32-34. FISH for abnormalities of chromosome 7 can be performed on interphase or metaphase cells.

8cen, 8p11.1-q11.1 Probe

Trisomy 8 is seen in myelodysplastic syndromes (MDS): refractory anemia (RA), refractory anemia with ring sideroblasts (RARS), refractory anemia with excess of blasts in transformation (RAEBT), chronic myelomonocytic leukemia (CMML). +8 is a rare anomaly in lymphoid malignancies (90% of +8 occur in myeloid malignancies); found in about 5% of acute lymphocytic leukemia (ALL). Progression from myelodysplastic syndrome (MDS) towards acute myelogenous leukemia (AML) would occur in about half cases of +8 solely. FISH for abnormalities of chromosome 8 can be performed on interphase or metaphase cells.

20q12/20q13.1 Deletion Probe

Deletion 20q is seen in a very large spectrum of hematological malignancies such as myelodysplastic syndromes (MDS), acute myeloid leukemias (AML), polycythemia vera (PV) and chronic neutrophilic leukemia. An interstitial or terminal deletion of the long arm of chromosome 20 (20q-) has been described as the second most frequent sole clonal structural abnormality (5 %) behind t(9.22). In MDS, 20q- alone is associated with a good prognosis regarding survival and potential for AML evolution, as defined by the International Prognostic Scoring System (IPSS) for MDS prognosis. In de novo acute leukemia, a poor response to treatment and a reduced survival is observed. In myeloproliferative disorders, the presence of 20q does not appear to adversely affect survival. Other chromosome changes commonly occurring with deletion 20q are monosomy 5/5q-, monosomy 7/7q-, and trisomy 8. FISH can detect this abnormality in either interphase or metaphase cells.

MLL (KMT2A), 11q23.3 Breakapart Probe- Rearrangement

Mixed-lineage leukemia (MLL) abnormalities are frequently found in infant leukemias and therapy-related leukemias. Acute myeloid leukemia (AML) with lysine methyltransferase 2A (KMT2A) rearrangement is a myeloid neoplasm in which the KMT2A locus on chromosome 11q23.3 is fused with any of several partner genes. KMT2A gene rearrangements result from deletions, duplications, inversions, and translocations at the 11q23 locus. More than 80 fusion partners have been described in KMT2A rearranged AML. Overall, MLLT3, AFDN, ELL, and MLLT10 are most commonly implicated in KMT2A-rearranged AML, resulting from the translocations t(9;11)(p22;q23), t(6;11)(q27;q23), t(11;19)(p13.1;q23), and t(10;11)(p12;q23), respectively. As compared to AML with normal karyotype, the presence of KMT2A rearrangement is associated with a lower mutation burden. Adult patients predominantly have mutations in genes encoding the RAS pathway (NRAS, KRAS and PTPN11). FLT3 tyrosine kinase domain mutations (TKD), as well as mutations in RUNX1, TET2, PLCG2 and ZRSR2, have also been described. Mutations in NRAS, KRAS, PTPN11 and FLT3-TKD often occur at low (<20%) variant allele fractions indicating a subclonal nature. Mutations in DNMT3A, NPM1, CEBPA and FLT3 internal tandem duplication are uncommon. FISH can detect this abnormality in either interphase or metaphase cells.

TP53, 17p13/17cen, 17p11.1-q11.1 Deletion Probe

The tumor protein 53 ,P53 (TP53) Deletion is a fluorescence in situ hybridization (FISH) Test used to detect deletion of the P53 (TP53) region on chromosome 17 at location 17p13 in fixed bone marrow specimens from patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). The test is indicated under revised diagnostic criteria for myeloid neoplasms (MN) issued by the International Consensus Classification (ICC) and the World Health Organization (WHO) recommended major change pertaining to TP53-mutated (TP53mut) MN. and in conjunction with other clinicopathological criteria.

ETV6, 12p13 Breakapart Probe-Rearrangement

Description:

Deregulation of the ETV6 gene through translocation, deletion or somatic mutation is recurrent in myeloid malignancies. By metaphase cytogenetics (MC), approximately 1% of patients with acute myelogenous leukemia (AML) and 0.6% of patients with myelodysplastic syndrome (MDS) have deletion of part of 12p13.2 Mapping studies place ETV6 within the smallest commonly deleted region.

Specimen Types: Bone Marrow Aspirate or Leukemic Whole Blood

Preferred Collection Container: Green Top (Sodium Heparin)

Alternate Collection Container: Lavender Top (EDTA)

Desired Specimen Volume: 3 - 5 mL

Minimum Acceptable Volume: 1 mL

• Lithium heparin is not acceptable.
• Specimens must be collected in a sterile collection container.

Each specimen must be accompanied by a requisition form, script, electronic order or physician note. Each order must indicate the reason for testing (diagnosis).

• Transport to the laboratory at room temperature.
• Store specimen as whole blood, in original tube, at room temperature and deliver to lab within 24 hours.
• If specimen cannot be delivered within 24 hours, store in refrigerator. Do not freeze specimen.
• Specimens collected on the weekends must be refrigerated upon arrival at HNL Lab Medicine.

• Specimen frozen
• Specimen arriving without any form of patient identification (unlabeled)
• Specimen with attached needles
• Specimen arriving with broken or leaking collection tube
• Unfixed specimen treated with fixative

EGR1, 5p15.3/5q31.2 Deletion Probe

In a normal cell, the expected signal pattern is two red signals and two green signals. In an abnormal cell containing the deletion, the expected signal pattern is one red signal and two green signals.

7q22/7q31.2 Deletion Probe

In a normal cell, the expected signal pattern is two red signals and two green signals. In an abnormal cell containing the deletion, the expected signal pattern is one red signal and two green signals or one red signal and one green signal.

8cen, 8p11.1-q11.1 Probe

In a normal cell the expected signal pattern is two aqua signals. Abnormal cells containing trisomy 8, have a three aqua signal pattern.

20q12/20q13.1 Deletion Probe

In a normal cell, the expected signal pattern is two red signals and two green signals. In an abnormal cell containing the deletion, the expected signal pattern is one red signal and two green signals or one red signal and one green signal.

KMT2A (MLL), 11q23.3 Breakapart Probe- Rearrangement

In a normal cell, the expected signal pattern is two fused signals. In an abnormal cell containing a rearrangement, the expected signal pattern is one red signal, one green signal, and one fused signal.

TP53, 17p13/17cen Deletion Probe

In a normal cell, the expected signal pattern is two red signals and two green signals. In an abnormal cell containing the deletion, the expected signal pattern is one red signal and two green signals or one red signal and one green signal.

ETV6, 12p13 Breakapart Probe- Rearrangement,

In a normal cell, the expected signal pattern is two fused signals. In an abnormal cell with a rearrangement, the expected signal pattern is one red signal, one green signal, and one fused signal.

• FISH MDS Panel
• Myelodysplastic Syndrome
• Myelodysplastic Panel