Metaphase Chromosomes

The skill of the cytogeneticist lies in the ability to identify 46 distinct chromosomes by their unique banding patterns (“G-banding”) and to detect deviations from the norm. This pattern recognition requires memorizing the “landmarks” of the human genome

Chromosome Identification (The Groups)

Chromosomes are grouped (A–G) by size and centromere position

Group A (1–3): Large Metacentric

• Ch 1: The largest. Large block of heterochromatin near the centromere (1q12). p-arm ends in a dark cap; q-arm ends in a dark cap
• Ch 2: Large sub-metacentric. distinct banding pattern but no heterochromatic block
• Ch 3: Metacentric. Symmetrical. A bright central band in both p and q arms (3p14/3q21) makes it look like a “bow tie” or “dumbbell.”

Group B (4–5): Large Sub-Metacentric

• Differentiation: Hard to tell apart
  • Ch 4: p-arm is slightly smaller. q-arm has a distinctive light band (4q26). Overall stains lighter
  • Ch 5: q-arm has a distinct dark middle band (5q12). Overall stains darker

Group C (6–12 + X): Medium Sub-Metacentric (The “Difficult” Group)

• Ch 6: Distinctive clear band at 6p21 (HLA region)
• Ch 7: “Flat top.” The p-arm has a dark cap (7p22) followed by a light band (7p21) and a dark band (7p15)
• Ch 8: “Empty” looking. Generally stains lightly with poorly defined bands
• Ch 9: Often has a secondary constriction (heterochromatin) at 9q12
• Ch 10: Three distinct dark bands on the q-arm (proximal, middle, distal)
• Ch 11: Large dark block in the middle of the q-arm (11q14-22)
• Ch 12: Very long q-arm relative to p-arm. The centromere region is dark
• Ch X: Similar to 6 and 7. The q-arm has a distinct dark band at Xq21

Group D (13–15): Medium Acrocentric (Satellites)

• Ch 13: Wide, lightly stained q-arm. Distal q-arm is light
• Ch 14: Dark band near the centromere (14q12). Distal q-arm is dark
• Ch 15: The proximal half of the q-arm is dark; the distal half is light

Group E (16–18): Small Metacentric/Sub-Metacentric

• Ch 16: Metacentric. Large heterochromatin block at 16q12 (often polymorphic)
• Ch 17: Sub-metacentric. p-arm is very short and distinctively light
• Ch 18: Sub-metacentric. Densely stained (dark)

Group F (19–20): Small Metacentric

• Ch 19: Very light staining (GC-rich). Almost looks like a “ghost.”
• Ch 20: Very dark staining (AT-rich)

Group G (21–22 + Y): Small Acrocentric

• Ch 21: The smallest autosome. The q-arm is dark proximally and light distally
• Ch 22: The q-arm is dark and “boxy.”
• Ch Y: The p-arm is tiny. The q-arm is distinctive: the proximal half is Euchromatin (light), the distal half is Heterochromatin (dark/fuzzy)

Numerical Abnormalities (Mechanism & ID)

• Non-Disjunction: Failure of separation in Meiosis I or II
  • Trisomy 21: Three copies of the smallest G-group chromosome
  • Trisomy 18: Three copies of the dark E-group chromosome
  • XXY: A Y chromosome plus two X chromosomes (one active, one inactive/Barr body)
• Marker Chromosomes: Small fragments of unknown origin. They are counted as numerical abnormalities (e.g., 47,XY,+mar) until identified by FISH

Structural Abnormalities (Mechanism & ID)

Identifying structural defects requires spotting Asymmetry between homologs

• Deletions (del): One homolog is shorter than the other
  • Terminal: The end is missing. (e.g., del(5p) - the p-arm of one 5 is gone)
  • Interstitial: A band is missing from the middle. (e.g., del(13)(q14) - the light band in the middle of 13 is gone, causing the dark bands above and below to fuse)
• Translocations (t): Two chromosomes exchange pieces
  • Reciprocal: Two chromosomes look “weird.” For example, in t(8;21), one Chromosome 8 is too big (has a piece of 21), and one Chromosome 21 is too big (has a piece of 8)
  • Robertsonian: Two acrocentrics fuse. The total count drops to 45. A “single” large chromosome replaces two small ones (e.g., der(13;14))
• Inversions (inv): The banding sequence is flipped
  • Pericentric inv(16): The heterochromatin block of 16 flips to the p-arm, making the chromosome look distinctively asymmetrical compared to its homolog
• Isochromosomes (i): A chromosome divides horizontally instead of vertically at the centromere
  • i(17q): The resulting chromosome has two q-arms and zero p-arms. It looks like a perfectly symmetrical large metacentric chromosome (which 17 is not supposed to be)
• Ring Chromosomes (r): Both telomeres break off, and the sticky ends fuse
  • Identification: A circular chromosome. It is unstable and often lost during division

Key Recognition Tips

1. Look for Asymmetry: If the two Chromosome 9s don’t look identical (one is longer, or bands don’t align), investigate for structural defect
2. Check the Tips: Terminal deletions are subtle. Always check if the pter and qter (ends) are present
3. Count the Acrocentrics: There should be 10 (Pairs 13, 14, 15, 21, 22). If there are only 9, check for a Robertsonian translocation. If there are 11, check for Trisomy 21 or +mar