Cytogenetics
Contributed by Mariel Bedell, DO and Mahmoud Aarabi, MD, PhD
Case Presentation
A toddler-aged female with no significant past medical history presents to the emergency department (ED) for a new onset neck mass in the setting of a recent streptococcus infection. Her infection was treated with amoxicillin with resolution of her symptoms until this morning when she woke up with a fever and a swollen neck. Her mother also describes that the patient appeared pale for the past week and experienced a nosebleed.
Vital signs examination shows mild tachycardia and a mild fever. Physical examination reveals bilateral tender cervical lymphadenopathy, splenomegaly, and skin pallor. A complete blood count with differential demonstrates pancytopenia and a predominating abnormal lymphoblastic population (Table 1). Blood cultures are negative.
| Lab | Result | Reference Range |
|---|---|---|
| White Blood Cells | 3.4 (L) | 5.0-17.0x10E+09/L |
| Red Blood Cells (RBC) | 1.06 (L) | 3.90-5.30x10E+12/L |
| Hemaglobin (Hb) | 3.2 (L) | 11.5 - 13.5 g/dL |
| Hematocrit | 9.6 (L) | 34.0-40.0% |
| Mean Corpuscular Volume | 90.7 (L) | 75.0-87.0 fL |
| Mean Corpuscular Hb (MCH) | 29.8 | 25.0 - 31.0 pg |
| MCH Concentration | 32.9 | 31.0 - 35.0 g/dL |
| RBC Distribution Width | 19.4 (H) | 11.8 - 15.2 % |
| Platelets | 8 (L) | 156-369x10E+09/L |
| Neutrophils | 2 (L) | 12-34% |
| Lymphocytes | 96 (H) | 45-75% |
| Blast Forms | 2% (H) |
A bone marrow biopsy is performed. Microscopy shows nearly 100% cellularity of the bone marrow with lymphoblastic predominance and decreased background trilineage hematopoiesis. Flow cytometry demonstrates an expanded abnormal B-lymphoblastic population positive for CD19, CD10, CD22, CD58, HLA-DR, and TdT and negative for myeloperoxidase, CD13, and surface light chains. Cytogenetic study results are summarized in Table 2. Fluorescence in situ hybridization (FISH) studies reveal an ETV6::RUNX1 gene rearrangement with loss of one ETV6 allele (Figure 1). Microarray studies confirmed loss of 12p, encompassing ETV gene, along with loss of 9p13.2, encompassing PAX5 gene, and a gain involving 20q (Figure 2). Karyotype studies are normal (46, XX).
| Test | Result |
|---|---|
| Karyotype | 46,XX |
| FISH | ETV6::RUNX1(84%) with loss of one ETV6 allele (80.6%) |
| Microarray | Losses involving 9p13.2 and 12p, gain involving 20q |
A. Interphase FISH using the fusion probes for ETV6 and RUNX1 loci reveals ETV6::RUTX1 fusion with loss of the second ETV6 allele. B. ETV6 and RUNX1 probe target locations on chromosomes 12 and 21, respectively. C. Visualization of chromosomes in metaphase FISH demonstrates ETV6 translocation to chromosome 21, resulting in a fusion signal, along with loss of the second ETV6 allele. FISH detected three RUNX1 signals, corresponding to one signal on a normal chromosome 21, and one split signal (chromosomes 12 and 21) due to the breakage of the RUNX1 probe.
Single copy losses are observed in the short arms of chromosomes 9 and 12, corresponding to the region containing PAX5 on chromosome 9 and ETV6 on chromosome 12 (bottom left and right insets). PAX5 is established as a likely secondary driver mutation in cases of B-ALL1. A single copy gain is noted within the long arm of chromosome 20, likely a secondary clonal change.