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Cytogenetics

Cultural Artifacts, Instability Syndromes, Normal Variants

Not everything seen under the microscope is a disease. The cytogeneticist must skillfully differentiate between True Pathology, Harmless Variants, Instability Syndromes (DNA repair defects), and Laboratory Artifacts. Misidentifying these categories leads to false-positive diagnoses and unnecessary patient anxiety or treatment

Cultural Artifacts (Pseudomosaicism)

These are chromosomal abnormalities that arise in vitro (in the flask/dish) during the culture process and are not present in the patient

  • Definition: An abnormality found in a single cell (or a single colony in amniocytes) that is not reproduced in other cells/cultures
  • Common Examples
    • Broken Cells (Random Loss): A cell with 45 chromosomes because one “rolled away” during harvest. If the missing chromosome is different in every cell (e.g., -C, then -E, then -G), it is technical
    • The “7/14” Translocation: In lymphocyte cultures, rearrangements between Chromosomes 7 and 14 (e.g., t(7;14)) are a common artifact related to V(D)J recombination in T-cells reacting to the mitogen (PHA). It is clinically insignificant
    • Culture Shock: Older cultures (>10 days) or those exposed to temperature fluctuations often develop random trisomies (e.g., +2) or endoreduplication (4N cells)
  • Resolution: Apply the rules of clonality. If the abnormality is restricted to a single cell/colony and not seen in the second culture vessel, it is dismissed as an artifact

Chromosomal Instability Syndromes

These are rare inherited disorders caused by defects in DNA repair mechanisms. The chromosomes are “fragile” and break spontaneously. The cytogenetic diagnosis relies on provoking this breakage using stress agents

  • Fanconi Anemia (FA)
    • Defect: DNA crosslink repair (FANC genes)
    • Assay: Culture cells with Mitomycin C (MMC): or DEB (Diepoxybutane)
    • Finding: Massive chromosomal carnage - radial figures (triradials/quadriradials) and multiple breaks
  • Bloom Syndrome
    • Defect: Helicase (BLM)
    • Assay: Bromodeoxyuridine (BrdU) incorporation
    • Finding: Increased Sister Chromatid Exchange (SCE). The chromosomes look like “harlequin” patterns with excessive swapping between sister chromatids
  • Ataxia Telangiectasia (AT)
    • Defect: Double-strand break repair (ATM)
    • Finding: Spontaneous translocations involving Chromosomes 7 and 14 (immune genes) in lymphocytes
  • ICF Syndrome
    • Finding: Instability of the Centromeric regions of chromosomes 1, 9, and 16. They appear “puffed” or de-condensed

Normal Variants (Heteromorphisms)

The human genome contains regions of repetitive DNA (Heterochromatin) that vary in size and staining intensity between individuals. These variations are inherited, stable, and phenotypically harmless. They are “fingerprints,” not defects

  • Pericentric Inversion of 9 [inv(9)(p11q13)]
    • The most common variant (1-2% of population). The heterochromatin block flips to the p-arm
    • Reporting: It is considered a normal variant and is often not even included in the ISCN abnormal string (or noted as a polymorphism). It does not cause infertility or miscarriage
  • Variable Heterochromatin (qh+ / qh-)
    • Chromosomes 1, 9, 16, and Y have large blocks of constitutive heterochromatin near the centromere (q12 band)
    • 1qh+, 9qh+, 16qh+, Yqh+: These regions can be massive (doubling the arm length) or tiny. They are benign
  • Acrocentric Satellites (ps+ / pss)
    • The short arms (p-arms) of D and G group chromosomes (13, 14, 15, 21, 22) contain rDNA stalks and satellites
    • Giant Satellites (ps+): Large knobs on top
    • Double Satellites (pss): Two knobs
    • Stalk length (pstk+): Long necks
    • Clinical: All benign. However, a “satellite” on a non-acrocentric chromosome (e.g., sat(17)) is a translocation, not a variant
  • Y Chromosome Length
    • The Y chromosome distal q-arm is heterochromatin. A “Long Y” or “Short Y” is a normal familial trait with no impact on fertility

Clinical Implication of Variants

  • Paternity Testing (Historical): Before DNA microsatellites, these variants (e.g., “Dad has a huge 16qh+ and so does the baby”) were used to prove paternity
  • Bone Marrow Transplant
    • If the donor has an inv(9) and the recipient does not, the inv(9) serves as a perfect marker to track Chimerism: (engraftment success)

Summary Checklist

  • Is it in multiple cells?: (No = Artifact)
  • Is it a known variant?: (inv(9), 1qh+, 21ps+ = Benign)
  • Is there breakage?: (Radials/Breaks = Check for Instability Syndrome)
  • Is it t(7;14)?: (Likely culture artifact in lymphocytes)