The Notation of Chromosome Structure

What is a Karyotype?

The results of genetic tests, specifically chromosome tests, are written according to the ISCN (International System for Human Cytogenetic Nomenclature) standards, and the shape, size, and number of chromosomes are presented as a "karyotype." In humans, a normal karyotype consists of 23 pairs of chromosomes: 22 pairs of autosomes and one pair of sex chromosomes, totaling 46 chromosomes.

General Principles of Notation

First, the total number of chromosomes, including sex chromosomes, is written, followed by the composition of the sex chromosomes separated by a comma. Females are represented as XX, and males as XY.

• Normal female: 46, XX
• Normal male: 46, XY

In cases of chromosome abnormalities, the notation starts with the abnormality in the sex chromosomes, followed by autosomal abnormalities in ascending order of chromosome numbers.

Numerical and Structural Abnormalities

Numerical abnormalities are indicated by placing a plus (+) or minus (−) sign before the affected chromosome to denote an increase or decrease in number.

Structural abnormalities are indicated by the abnormality symbol followed by the chromosome number in the first set of parentheses and the specific chromosome band in the second set of parentheses. Multiple chromosome numbers or bands are separated by a semicolon (;).

Symbols Used in Karyotype Notation (Main Ones)

• add: Additional material of unknown origin
• cen: Centromere
• c: Constitutional anomaly
• del: Deletion
• der: Derivative chromosome
• fra: Fragile site
• ins: Insertion
• inv: Inversion
• mar: Marker chromosome
• mat: Maternal origin
• p: Short arm of chromosome
• pat: Paternal origin
• q: Long arm of chromosome
• r: Ring chromosome
• rec: Recombinant chromosome
• t: Translocation
• ter: Terminal end of chromosome

Examples of Numerical Abnormalities

• Trisomy 21 (Down syndrome): 47, XX, +21
• Triploidy: 69, XXY

Examples of Structural Abnormalities

• Inversion of 14q11→q32 (chronic lymphocytic leukemia): 46, XY, inv(14)(q11q32)

Simplified and Detailed Notation

In addition to the simplified notation for structural abnormalities, a detailed notation method may be used for complex structural abnormalities.

A semicolon (;) indicates chromosome breakpoints, two colons (::) indicate breaks and rejoining, and an arrow (→) indicates the range of fragments. The terminal ends of chromosomes are denoted by "ter", with pter representing the short arm and qter representing the long arm, and the centromere is indicated as "cen". Descriptions of structural abnormalities start from the pter and end at the qter.

• Deletion of 5q13-q33
  • Simplified: 46, XX, del(5)(q13q33)
  • Detailed: 46, XX, del(5)(pter→q13::q33→qter)

Mosaicism and Chimerism

Mosaicism refers to a condition in which a single individual has two or more genetic lineages due to mutations or chromosome rearrangements, while chimerism refers to a condition where an individual has genetic material from different origins. Karyotype notation uses a slash (/) to indicate the two karyotypes, with "mos" for mosaicism and "chi" for chimerism written before the karyotype.

• Mosaicism with normal and trisomy 21 cells (Down syndrome): mos 46, XX/47, XX, +21

Derivative Chromosomes

Derivative chromosomes (der) are abnormal chromosomes resulting from inversions, deletions, or unbalanced translocations involving one or more chromosomes.

• Derivative chromosome from translocation between 1p32 and 3q21 and translocation between 1q25 and 11q13: 47, XY, t(1;11)(q25q13) + der(1)t(1;3)(p32;q21)

Recombinant Chromosomes

Recombinant chromosomes (rec) arise from meiotic crossover events involving carriers of structural chromosome abnormalities such as inversions and insertions.

• Recombinant chromosome from meiotic crossover in a female carrier of 2p21q31 inversion: 46, XX, rec(2)dup(2p)inv(2)(p21q31)mat

Ambiguous Chromosome Bands

Ambiguous Identification

Ambiguous numerical or structural abnormalities are indicated with a question mark (?).

• Possible loss of chromosome 21: 45, XX, −?21

Ambiguous Breakpoints or Chromosome Numbers

Ambiguous breakpoints or chromosome numbers are indicated with a tilde (~).

• Deletion in the region of 1q21-q24: 46, XY, del(1)(q21~24)

Two Possible Outcomes

When there are two possible outcomes, the notation uses "or".

• Additional material on chromosome 19 at either p13 or q13: 46, XX, add(19)(p13 or q13)

Incomplete Karyotype (inc)

When the quality of chromosome preparations is poor and analysis is incomplete, the karyotype is noted as incomplete (inc).

• Deletion on 1q21 with other possible abnormalities (inc; [ ] indicates the number of analyzed cells): 46, XX, del(1)(q21), inc[4]

Normal Variations

These are findings that are generally considered not to cause symptoms or affect fertility or offspring.

Variations in Length, Number, and Position

Variations in the length of heterochromatic regions (h), satellite stalks (stk), and satellites (s) are indicated by writing the chromosome or arm followed by h, stk, or s, and then indicating an increase (+) or decrease (−) in length. Changes in number and position are indicated by writing the chromosome and arm followed by h, stk, or s.

• Increase in the length of heterochromatin on chromosome 16q: 16qh+
• Decrease in the length of heterochromatin on the Y chromosome: Yqh−

Fragile Sites

Fragile sites are locations on chromosomes prone to structural abnormalities and are denoted by "fra".

• Fragile sites at 10q22.1 and 10q25.2: fra(10)(q22.1), fra(10)(q25.2)

Numerical Abnormalities

Sex Chromosome Abnormalities

• Klinefelter syndrome: 47, XXY
• Monosomy X (Turner syndrome): 45, X

Autosomal Abnormalities

• Trisomy 13 and 21: 48, XX, +13, +21
• Monosomy 22: 45,XX, -22

Uniparental Disomy (upd)

Uniparental disomy refers to the condition where both chromosomes or chromosome regions originate from one parent.

• Maternal uniparental disomy for chromosome 15: 46, XY, upd(15)mat