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Cytogenetics

Assign Test Priority

In a Clinical Cytogenetics laboratory, “Turnaround Time” (TAT) is measured in days or weeks rather than minutes or hours. Because the central limiting factor of the analysis is the biological growth rate of the cells in culture, the laboratory scientist cannot simply “speed up” the test in the same way a chemistry analyzer can be prioritized. Therefore, assigning test priority - or Triage - is a critical pre-analytical skill. The laboratory scientist must evaluate the clinical history, the specimen type, and the requested deadline to determine which cultures require modified harvesting schedules, extended work hours, or rapid preliminary reporting (such as STAT FISH) to affect immediate patient management

STAT / Emergency Priority

These are cases where the cytogenetic result will dictate an immediate, often irreversible, medical or surgical intervention. In these scenarios, the laboratory typically employs “short-term” culture techniques (24–48 hour harvests) or relies on rapid Interphase FISH to provide a preliminary answer while the standard culture grows

  • Newborns with Multiple Congenital Anomalies: A neonate born with ambiguous genitalia, life-threatening heart defects, or features suggestive of Trisomy 13 (Patau) or 18 (Edwards). The medical team needs to know whether to proceed with life-saving surgery or to move to palliative care. These samples are the highest priority in the constitutional section
  • Acute Promyelocytic Leukemia (APL): A medical emergency. If the pathologist suspects APL based on morphology (presence of Auer rods), the cytogenetics lab must confirm the presence of the t(15;17) translocation immediately. The detection of the PML:RARA fusion gene dictates the immediate administration of All-trans Retinoic Acid (ATRA) therapy, which is life-saving. This is typically handled via STAT FISH
  • Late Gestational Age Prenatal: Amniotic fluid received late in the pregnancy (e.g., >22 weeks). Because the legal window for pregnancy termination is closing or has closed (depending on jurisdiction), and because the result may determine the mode of delivery (C-section vs. vaginal), these cultures are expedited to ensure a result is available before delivery
  • Pre-Operative Cases: A patient with a renal mass or other solid tumor scheduled for surgery. The genetic result might determine the extent of the resection (partial vs. radical nephrectomy). The lab must coordinate to have results ready before the scheduled surgery date if possible

Urgent / Expedited Priority

These cases represent new diagnoses where treatment planning awaits the genetic classification, but the patient is currently stable. The goal is to minimize anxiety and hospital stay

  • New Leukemia Diagnoses (Non-APL): A new diagnosis of Acute Myeloid Leukemia (AML) or Acute Lymphoblastic Leukemia (ALL). The specific chromosomal abnormalities (e.g., deletion 5q, inversion 16, Philadelphia chromosome) will determine the chemotherapy regimen and risk stratification (favorable vs. unfavorable prognosis). While not a matter of hours like APL, these are prioritized over remission checks
  • Standard Prenatal Diagnosis: Routine amniocentesis or CVS. While not a medical emergency, the psychological burden on the parents is immense. These are prioritized to meet the standard of care (typically 7–10 days TAT) to allow for decision-making
  • Critical Bone Marrow Transplant Decisions: A patient nearing the day of transplant may need a “remission check” to ensure the donor cells are suitable or that the patient has cleared the leukemic clone before infusing new marrow

Routine Priority

These are cases where the diagnosis is essential for long-term management, genetic counseling, or prognosis, but a delay of a few days will not alter immediate medical care. These samples are processed according to standard batch protocols

  • Constitutional / Developmental Delay: A child or adult with intellectual disability, autism spectrum disorder, or dysmorphic features. The diagnosis helps with accessing social services and understanding recurrence risk, but there is no acute medical intervention pending. Note that Chromosomal Microarray (CMA) has largely replaced karyotyping for this indication, but karyotyping is still done for balanced translocations
  • Infertility and Recurrent Pregnancy Loss: Couples with a history of multiple miscarriages being evaluated for balanced translocations. The results are needed for future family planning, but there is no urgency
  • Solid Tumor Prognostics: In many solid tumors (e.g., lipoma vs. liposarcoma), the genetics provide confirmation of subtype or long-term prognosis. Because solid tissue cultures grow slowly (1–3 weeks), they are naturally lower priority than rapid-growing blood/marrow

Operational Strategies for Prioritization

Once priority is assigned, the laboratory scientist alters the workflow to meet the demand

  • Culture Modification
    • STAT: Setup multiple cultures and harvest the first one “early” (e.g., at 24 or 48 hours for bone marrow) to catch fast-dividing clones, even if the mitotic index is lower
    • Routine: Harvest at the standard optimal time (e.g., 72 hours for blood, 7–9 days for amnio) to maximize band resolution and cell yield
  • Laboratory scientist Assignment: STAT cases are often assigned to the most senior or experienced laboratory scientist s for analysis. This reduces the likelihood of ambiguous results that require re-analysis or consultation, thereby streamlining the reporting process
  • Preliminary Reporting: For high-priority cases, the laboratory often issues a “Preliminary Report.” For example, if a laboratory scientistspots a t(9;22) in the first two cells analyzed, a preliminary report is issued stating “Ph+ clone detected,” allowing the doctor to start Tyrosine Kinase Inhibitors immediately while the lab completes the full 20-cell count for the final report
  • Reflex Testing: Priority often dictates the “Reflex” algorithm. In a STAT newborn case, if the rapid FISH is positive for Trisomy 21, the lab may prioritize the Karyotype to determine if it is free trisomy (random) or a Robertsonian Translocation (heritable), as this impacts parental counseling immediately