ISCN Notation

Human cells typically contain 46 chromosomes which, when lined up in pairs and suitably stained, look like this under a microscope:

The staining process produces a predicable sequence of light and dark colored "bands" (of various lengths) containing DNA.

Abnormal banding patterns (eg. missing or re-arranged bands) may represent genetic abnormalities.

For each chromosome, bands are numbered in an orderly way:

Each chromosome has its own characteristic number and size of bands.

Geneticists describe normal arrangements using a terse notation that expresses the number of chromosomes present (46), along with the sex chromomes (XX or XY):

46,xy

This is called the "short" notation.

For more complicated arrangements (ie. abnormalities), it is useful to explicitly denote the chromosomes present, along with any abnormal banding patterns ("long" notation).

In the case of a normal male, that would be:

1 2 3 4 5 6 7 8 9 10111213141516171819202122x y
| | | | | | | | | | | | | | | | | | | | | | | |
| | | | | | | | | | | | | | | | | | | | | |
Sex model is male

Here each vertical bar | represents a single chromosome, and in the above example each type of sex chromosome has one of them.

But no new information is provided in this example, since nothing abnormal occured.

But suppose chromosomes 2 and 5 have "traded" bands in a female specimen, where all of the material in 2 above the band 2q21 has been switched with all of the material in 5 above 5q31.

Geneticist would describe this in short notation as:

46,xx,t(2;5)(q21;q31)

representing 46 chromosomes (two of which are x), along with a "translocation" occuring at the q21 band in 2 and q31 band of 3.

But how would you search for all specimens (including this one) where, say, the band q22 (above q21) of 2 is missing?

For that, you need the long form:

1 2 3 4 5 6 7 8 9 10111213141516171819202122x y
| | | | | | | | | | | | | | | | | | | | | | |
| | | | | | | | | | | | | | | | | | | | |
Cell observation is reciprocal translocation
Chromosome 2 is 2pter->2q21::5q31->5qter
Chromosome 5 is 5pter->5q31::2q21->2qter
Sex model is female
Exactly 1 whole copies of chromosome 2
Exactly 1 whole copies of chromosome 5
RTB(2,5) = balanced carrier of reciprocal translocation

Here, the notation:

2pter->2q21::5q31->5qter
5pter->5q31::2q21->2qter

explicitly describes the actual sequence of bands in the two aberrant chromosomes.

For example, it clearly shows that the band 2q22 is now present on the q arm of chromosome 5 (ie. within the material 2q21->2qter).

What this program does

This program converts short ISCN notation to its long form.