[BioC] SKY/CGH data. How do I interpret it.

[Luzie U. Wingen]

Hi Peri,

On Tue, Dec 28, 2004 at 08:19:45AM -0800, S Peri wrote:
>  i am trying to make sense of CGH/SKY data. Can any
> one who had worked with this kind of data help me to
> understand the logic of this kind of representation of
> the karyotype. How can I interpret the deletions and

> additions. Apologies, if this question is out of place
> here, but I did not find any other place where most
> bioinformatics people visit.
This is not so much bioinformatics but cytogenetics.

The logic of the representation should follow the "International System for
human cytogenetic nomenclature (1995)" or ISCN 1995.
You have to read the whole book to understand all the important details:
ISCN (1995): An International System for Human Cytogenetic Nomenclature, Mitelman, F (ed); S. Karger, Basel, 1995.
See: http://www.iscn1995.org/index.php
There is also a Karyotype Syntax Checker which tells you, if you used the
nomenclature correctly - what is not the case with your karyotype.

> Karyotype:
> 55-90<3n->,X,-X,-X,-1,del(1)(p11),-2,t(2;11)(q32;q23),der(2)t(2;11)(q32;q23),der(3;15)(q10;q10),
> +der(3;15)(q10;q10),-4,del(5)(q13),+der(5;8)(p10;q10),+der(5;8)(p10;p10)del(8)(q22),
> +der(5;6)(p10;q10),+der(5)t(5;11)(?;q2?4)del(11)(q12),+6,idic(6)(q11),ace(6),+7,
> -7,?inv(7)(p14;q21),+8,+8,+8,-9,+del(9)(q11),-10,der(11)t(2;11)(q32;q23)del(11)(p11),
> der(?11)t(5;11)(?;p11)t(11;21)(q23;?),der(11)t(11;18)(q24;?),+der(11)t(11;18)(q24;?)t(16;18)(?;?),
> +der(?11)t(11;21)(q23;?)del(11)(p11),-12,-13,-13,-14,-14,der(14)t(5;14)(?;p11),der(14;17)(q10;p10),
> -15,der(15)t(15;16),-16,i(17)(p10),i(17)(q10),+19,-19,der(19)t(5;19)(q13;q13),+20,
> +21,-21,+22
To get some rough ideas how things work:
The starting number tells you how many chromosomes were found in your
preparation of the cell nucleus.
Thats 55-90 in your case (I believe this is problematic as one karyotype should
be described and not a summary of several karyotypes, but with cancer cells you
may not know which is the important one).
The number is then followed by the number of sex chromosomes (One X found, as
three were expected (triploid karyotype), two are missing (-X,-X).
Then the autosomes are listed which show aberrations.
That can be either a loss (signified by a minus symbol before the number, e.g.
-1 means one chromosome 1 is missing (as here a 3n karyotype is presumed there
should be 6 present and only 5 are found ...) or a gain (signified by a +).
Other aberrations are 
deletions of parts of the chromosome (del(1)(p11) would mean that cytoband p11 is deleted 
	(or the whole arm from there?) from one chromosome 1)
translocations (meaning a material swap between two chromosomes at indicated cytobands)
etc.

The used abbreviations can be found at:
http://cgap.nci.nih.gov/Chromosomes/ISCNSymbols

I guess you better cooperate with some cytogenetic specialist if you have to
look a lot into such complex karyotypes.

Luzie

-- 
Luzie U. Wingen, Institut fuer Zell- und Molekularpathologie,
Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover,
Tel.: (+49) 0511-532-4669, Fax: -4521, Email: wingen.luzie at mh-hannover.de