ISCN- International System for Human Chromosome Nomenclature for Karyotyping

ISCN- International System for Human Chromosome Nomenclature was developed to denote various chromosomal anomalies to make results conclusive universally. 

The manual of denotation is based on the outcomes of 1977’s standing committee met in Stockholm. 

Karyotyping is a manual process to perform as well as to make and interpret results. Unlike other techniques a vast portion of the whole process is performed by human hands. 

Therefore in order to make results conclusively worldwide, scientists have developed a unique system to interpret results. 

In the present article, we are going to discuss the ISCN system of karyotyping nomenclature and related aberrations. We will also discuss how to interpret the complex results of karyotyping. 

Group of human chromosomes: 

Scientists have categorized chromosomes based on their size, shape and location of centromere into 7 broader groups. 

The group A chromosomes are larger metacentric chromosomes and bigger in size than other chromosomes. Chromosomes 1, 2 and 3 are larger metacentric. 

The group B chromosomes are larger submetacentric chromosomes whose two arms are not equal, the p arm is shorter than the q. Note that the group B chromosomes are hard to distinguish. 

Chromosomes 4 and 5 are larger metacentric. 

The group C chromosomes are smaller metacentric chromosomes. Banding is needed to identify this group of chromosomes. Chromosomes 6, 7, 8, 9, 10, 11, 12and X are smaller metacentric. 

The group D chromosomes are medium-sized acrocentric chromosomes whose p arm is absent, instead, a satellite is present. Chromosomes 13, 14 and 15 are included in group D. 

16, 17 and 18 are group D chromosomes which are relatively smaller and shorter metacentric or submetacentric. 

Group E chromosomes are short metacentric which are chromosomes 19 and 20. 

The group G chromosomes are smaller and short acrocentric chromosomes. Chromosomes 21, 22 and Y are included in this category. 

Common symbols and abbreviations in karyotyping: 

Symbol or abbreviationDescription
Arrow →From → To
: (single colon)Break 
:: (double colon)Break and reunion
rRing chromosome
aceAcentric fragment
robRobertsonian translocation
derDerived chromosome
dicDicentric chromosome
hSecondary constriction
marMarker chromosome
matMaternal origin
qLong chromosome arm
pShort chromosome arm
patPaternal origin
phPhiladelphia chromosome
rRing chromosome
recRecombinant chromosome
varVariable chromosome region
sceSister chromatin exchange
tanTandem translocation
terTerminal (chromosome ends)

Abbreviations used in banding techniques

GTGG-bands by Giemsa trypsin Giemsa 
G- banding Giemsa trypsin Giemsa banding
QQuinacrine bands
CCentromeric bands
QFQQ-bands by fluorescence using quinacrine
GFHQ- bands by fluorescence using Hoechst 33258
GAGG-bands by acetic saline using Giemsa
CBGC-bands by barium hydroxide using Giemsa
RBAR-bands by BrdU using Giemsa
RHGR-bands by heating using Giemsa
RFAR-band by fluorescence using acridine orange

These are some of the common cytogenetics and karyotyping abbreviations designed by the ISCN and used in the clinical cytogenetics widely. 

Now let’s see some of the examples of karyotyping indications and how to interpret it. 

We will start with some easy examples and gradually increases the complexity of the results:

46, XX- 23 pairs of female chromosomes 

46, XY- 23 pairs of male chromosomes

46, XX, 4p-

Let us decode the symbols. 4p- the short arm of chromosome 4, ‘-’ deletion. 

Deletion of the p arm of chromosome 4 in the female sample. 

46, XX, del(5p): 

Deletion of the short p arm of the chromosome 5 in the female sample. 

46, Y fra(X)(q)

Fragile X chromosome in the male. 


Trisomy 21 in the male sample


Deletion on the long q arm at position q21 of chromosome 1 in the female sample. 


Here the inv- inversion occurs on the same arm and centromere is not involved means, it is a paracentric inversion. 

The present karyotype is of male with the paracentric inversion on the p arm of chromosome 2. 


Pericentric inversion between the p and q arm of the chromosome 2. 


Ring chromosome of X in the male. 

Now take a look at some complex karyotype results: 

46,XY,inv(2)(pter→p21::q31→p21::q31→qter) comment below and let me know what you think about this karyotype? I will answer it later. 

Related articles:

How does the ISCN work? 

The international system of chromosomal nomenclature and indications is a working committee created to make a streamline result format for the medical karyotyping. 

Though periodically review committee’s had to review the annotations and to remove the gaps and complexity in the results. 

Practically, the entire nomenclature system is based on the size, shape and location of the centromere of a chromosome. 

The location of the centromere of every chromosome, the length of the p arm and q arm and the number of bands on different chromosomes are taken into consideration in order to interpret the results and study the chromosomes. 

The chromosome bands are broadly divided into three categories; very low-resolution bands, good resolution bands and high-resolution bands. 

Usually, 300 bands, 550 bands and 1000 bands on each chromosome are considered very low-resolution bands, good low-resolution bands and high-resolution bands.

To study numerical chromosomal alterations, low-resolution banding is enough, however, to study minor copy number variations like deletion, duplication or translocation high-resolution banding is employed. 


I think this is enough for a newbie to learn the nomenclature of chromosomes. We will discuss cancer cytogenetics and karyotyping elsewhere. 
For more related articles stay connected with our blog.

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