Human Chromosome Nomenclature (ISCN)

Human Chromosome Nomenclature (ISCN)

5 sections · 25 min

01

Chromosome Morphology and G-Banding

Human somatic cells contain 46 chromosomes — 22 pairs of autosomes and one pair of sex chromosomes. Each chromosome has a characteristic size, centromere position, and banding pattern that allows unambiguous identification. G-banding (Giemsa staining after trypsin treatment) is the standard technique for cytogenetic analysis and produces the distinctive alternating light and dark band pattern used for karyotyping.

Key Points

  • Centromere position divides chromosomes into short arm (p, from French 'petit') and long arm (q)
  • Chromosome morphology by centromere position: metacentric (centromere central), submetacentric (centromere off-center), acrocentric (centromere near tip; chromosomes 13, 14, 15, 21, 22)
  • G-dark bands (AT-rich, gene-poor, late-replicating); G-light bands (GC-rich, gene-dense, early-replicating)
  • Standard clinical karyotype resolution: 400–550 bands; high-resolution banding: 550–850 bands; detects rearrangements ≥5–10 Mb

✦ Check Your Understanding

In ISCN band nomenclature, what does '7q11.23' specify?

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02

ISCN Karyotype Notation: The Basics

The International System for Human Cytogenomic Nomenclature (ISCN) provides a standardized framework for describing chromosomal findings. A complete karyotype description contains three mandatory components: the total chromosome number, the sex chromosome complement, and any abnormality or variant observed.

Key Points

  • Normal male: 46,XY — Normal female: 46,XX
  • Format: [total chromosome number],[sex chromosomes],[abnormalities]
  • Band nomenclature: chromosome number + arm (p/q) + region + band + sub-band (e.g., 7q11.23 = chromosome 7, long arm, region 1, band 1, sub-band 23)
  • Chromosome arms are divided from centromere outward: region 1, band 1 immediately flanks the centromere; band numbers increase toward the telomere

✦ Check Your Understanding

A karyotype is reported as 47,XY,+21. This represents:

Select an answer to reveal the explanation

03

Numerical and Structural Abnormalities

ISCN provides specific symbols and notation rules for all classes of chromosomal abnormalities. Numerical abnormalities (aneuploidy) change the total copy number of one or more chromosomes. Structural abnormalities rearrange chromosomal material without necessarily changing total chromosome count.

Key Points

  • Trisomy: extra chromosome indicated by '+': 47,XY,+21 = male trisomy 21 (Down syndrome)
  • Monosomy: missing chromosome indicated by '−': 45,X = Turner syndrome
  • Deletion: del(chromosome)(band range) — e.g., del(7)(q11.23q11.23) or del(7)(q11.23) for interstitial deletion
  • Duplication: dup; Inversion: inv; Translocation: t (balanced reciprocal) or der (derivative chromosome); Ring chromosome: r

✦ Check Your Understanding

Which ISCN symbol is used for a balanced reciprocal translocation between chromosomes 9 and 22?

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04

Mosaicism and Special Notations

Mosaicism — the presence of two or more chromosomally distinct cell populations in an individual — arises from a post-zygotic mutation. Mosaic findings require careful interpretation as clinical severity often correlates with the proportion of abnormal cells and the tissues affected.

Key Points

  • Mosaic notation: cell line 1[cell count]/cell line 2[cell count] — e.g., 45,X[12]/46,XX[18] = mosaic Turner syndrome
  • The cell count in brackets follows ISCN guidelines: minimum 20 metaphases analyzed for routine constitutional studies
  • Isodicentric chromosomes: idic — a single chromosome with two centromeres derived from one chromosome
  • Marker chromosomes: mar — small, structurally abnormal chromosome of uncertain origin; require FISH or array for characterization

✦ Check Your Understanding

A female patient's karyotype is reported as 45,X[12]/46,XX[18]. This indicates:

Select an answer to reveal the explanation

05

Array Cytogenomics: ISCN Notation for CNVs

Chromosomal microarray (CMA) and whole-genome sequencing generate copy number variant (CNV) data that must be described in standardized notation. ISCN 2020 introduced a comprehensive framework for reporting array findings using genome build coordinates alongside classic cytogenetic band nomenclature.

Key Points

  • Array ISCN format: arr[genome build] chromosomal band(start_coordinate_end_coordinate)×copy number
  • Example — 22q11.2 deletion: arr[GRCh38] 22q11.21(18,912,231_21,465,672)×1 (single copy = deletion in a diploid genome)
  • Duplication notation: ×3 for a single extra copy (3 total) in a diploid individual
  • Copy-neutral LOH (loss of heterozygosity = ROH or regions of homozygosity): hmz — indicates loss/absence of heterozygosity without copy number change; important for recessive disease and imprinting disorders

✦ Check Your Understanding

A chromosomal microarray report states: arr[GRCh38] 15q11.2q13.1(22,805,313_28,585,846)×1. This notation indicates:

Select an answer to reveal the explanation

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