ISCN Error Analysis
Errors in ISCN formulae are very prevalent: some 10% of the karyotypes in the Mitelman database contain errors. Most of them are due to insufficient statements. Very often, break points are denoted which do not exist.
Apart from such errors based on sloppiness or typos, there are errors caused by a lack of grasp. It is not very easy to understand the ISCN, it is often unsystematic, and more complicated rearrangements cannot be expressed with it (se also: ISCN Discussion).
Hence, during the analysis of karyotypes, the CyDAS software generates a series of error messages; if there are several errors in one karyotype, only the first error will be explained. We tried to render the error messages generally comprehensible, so that a skillful reader could grasp the type of error and how to correct it. This page is intended to offer further support to grasp the type of the error and to remove it.
- The band does not exist
This is quite the most common error at all: a break point was given which does not exist.
Though that error might look like a typo, transposed digits, or something like that, we think it can be attributed to ignorance of the correct denomination of the chromosomal bands: in many cases, approaches to get to a correct band description by simple transpositions fail, e.g. 8q34: neither 8q43 nor 8p34 do exist. With 7q12, we could believe that 7q21 was meant, but of course it could be 7q11.2.
Check the band numbers by help of ideograms, as can be found e.g. in the ISCN manual on pages 14-21; these ideograms are also the basis for the Online-Ideograms and Online-Karyograms if the CyDAS site.
- No break points found for aberration
- An error occured when trying to expand element
- Aberration element ... was expanded to ... and then found non-valid.
Once upon a time, it was a very difficult task to determine which one of the chromosomes was affected by an aberration. Hence, the ISCN formally allows to name the affected chromosome alone without the affected band. But such aberrations are useless for further analysis.
Often the author knows the breakpoints, but because they are generally
known he does not write them down. That's extremely common with the Philadelphia
translocation which is just described by t(9;22) instead of t(9;22)(q34;q11).
If the breakpoints were specified at another investigation of the same patient, or somewhere else in the same publication, these breakpoints are not repeated. For the software, the situation is clear: the breakpoints are missing, the data are useless for further analysis.
The CyDAS desk top application offers the function "Edit - Breakpoint Search" which automatically adds breakpoints for the cases described above; it must be called explicitly. It is not available with the internet applications.
Generally, the software searches for breakpoints in other clones of the same karyotype, i.e. if several clones are separated by slashes ("/") in the formula. During this serach for break points, errors may occur or erroneous aberrations may be created, thus giving raise to the latter error messages.
By the way, there are only two sites in the ISCN manual stating explicitly
that breakpoints need not be repeated:
An example is on p. 57 shwoing a karyotype with a Philadelphia translocation and an extra Philadelphia chromosome: 47,XX,t(9;22)(q34;q11),+der(22)t(9;22) "The breakpoints in the extra der(22) need not be repeated." I.e. the rearrangement giving raise to the derivative chromosome was denoted in the same clone, and the type of rearrangement including the affected chromosomes was still repeated.
The other site is an example on clonal evolution on p. 80 in the context of the "idem" symbol.
Whenever breakpoints are known, the must be written in the ISCN formula. The omission of the repetition of break points which is acceptable according to the ISCN (but by far not so often as is done!) should be generally avoided.
- Cannot find aberrations for (iso)derivative chromosome
- An error occured when trying to expand element
- Aberration element ... was expanded to ... and then found non-valid.
When describing a derivative chromosome, the denomination of the chromosome is followed by all aberrations involved in the generation of the derivative chromosome or by its band composition. The latter statments are often omitted.
With a karyotype 47,XX,t(9;22)(q34;q11),+der(22) it may be clear to the author that the "der(22)" means "der(22)t(9;22)(q34;q11)". But how is a software expected to guess that? It could also mean "der(22)add(22)(p11)del(22)(p11)".
With polyclonal karyotypes, the CyDAS software tries to find the aberrations from other clones. With 47,XX,t(9;22)(q34;q11),+der(22)t(9;22)(q34;q11)/48,XX,+8,t(9;22)(q34;q11),+der(22), such an expansion works. With 45,XX,-9,der(22)t(9;22)(q34;q11),der(22)t(9;22)add(22)(p11)/46,XX,+8,-9,der(22), a surely correct expansion is no more possible. During such expansions errors may occur or erroneous aberrations may be generated, thus giving raise to the latter error messages.
When writing down derivative chromosomes, all the aberration involved in the generation of the derivative chromosome must be denoted (including the break points of these aberrations), or the band composition.
- Second band for duplication (triplication, translocation,...) missing
Most rearrangements do not occur at a single site only, but they involve two or more sites on the genome. A translaocation involves at least two chromosomes, hence a breakpoint for each chromosome is required (with translocations of interstitial fragments, it's even two breakpoints per chromosome). An inversion inverts a fragment of a chromosome, hence both a start and an end point for that fragment are required. A duplication duplicates a fragment, and accordingly also here both a start and an end point are required.
Even if the fragment involved is very small only and does not extend over the borders of a chromosomal band, two breakpoints are required! A duplication of Xq21 is written dup(X)(q21q21) but not dup(X)(q21).
By the way, there is quite some difference between a del(5)(q13) and a del(5)(q13q13): the former describes a terminal deletion of the q arm from band 5q13 upto the q terminus, the latter one describes an interstital deletion of a tiny fragment residing inside band 5q13 but keeping all the rest. Since both notations per se are correct - but with such extremely different meaning! - the CyDAS software cannot generate a useful error message here.
If a rearrangement involves an interstiatial fragment, both the start and the end point of that fragment must be written, also when both break points reside in the same chromosomal band.
No symbol of the ISCN faces such frequent abuse as does the "t" for translocations. And that abuse already starts in the ISCN manual: the generation of dicentric chromosomes is not dentoted with the intended symbol "dic" but with that "t" when a derivative chromosome is described. Further authors found even more ways of abuse, some of them are to be explained here.
- A translocation cannot be gained or lost:
- An insertion cannot be gained or lost
- A Telomeric Association cannot be gained or lost
A tarnslocation gives raise to (at least) two derivative chromosome: a t(9;22)(q34;q11) causes both derivative chromosomes der(9)t(9;22)(q34;q11) and der(22)t(9;22)(q34;q11). But what was meant, if a +t(9;22)(q34;q11) was written? Is it the gain of both derivative chromosomes?
When scrutinizing some examples from the Mitelman database, we can deduce that a "+t" should mean the gain of a dicentric chromosome, i.e. a "+dic" is meant. Especially from the given chromosome count can be deduced that only one chromosome was gained.
Chadduck et al 1991, Pediatr Neurosurg, Case 1
since the dicentric chromosome replaces a chromosome 2 and 12 each.
Similarly, a gain of an insertion or a telomeric association does not make sense.
Depending on the situation, a gain of the involved derivative chromosome(s) ("+der,+der") must be denoted, or a dicentric chromosome ("dic").
- For a translocation of an interstitial fragment, two break points per chromosome must be given
Translocation may exchange not only terminal fragments (i.e. fragments
starting at the breakpoint and extending upto the terminus of the same
chromosomal arm), but also fragments which do not extend to the terminus
but to a second breakpoint only ("interstitial fragment"). The ISCN manual
shows an example:
Here, the fragment 5q13q23 of chromosome 5 was replaced with the fragment 6q15q23, and vice versa. Because fragments are exchanged, both start and end points of each fragment must be denoted.
There are also translocations involving three chromosomes ("three way
translocations"). An example from the ISCN manual is
Here, the f ragment 2p21pter moved to band 7q22 and replcaes all the chromosomal material from there upto theq terminus of chromosome 7. That region 7q22qter in turn moved to band 5q23 and replaces everything from there upto the q terminus of chromosome 5. The latter region 5q23qter finally moved to band 2p21 and replaces the fragment 2p21pter.
Very often, descriptions are encountered with two bands (i.e. a frgament)
for one chromosome of the three chromosomes (and one band each for the
other two chromosomes). E.g.
Jin et al 1995, Cancer Res, Case 43
It cannot be a normal three way translocation because then there was only one band for chromosome 10 (i.e. either 10p11 or 10q26). Nor can it be a translocation of interstital fragments because then also the chromosomes 7 and 15 required two bands each.
From communication with other cytogeneticists, we deduce that some people
want to state that the chromosome for which two bands were given was involved
in two translocations which were written as one term. That means for the
above example that there occured the translocations t(7;10)(q11;p11)
t(10;15)(q26;p11) which both involved the same chromosome
Hence, the derivative chromosome 10 suffered two aberrations, and ought to be denoted correctly as: der(10)t(7;10)(q11;p11)t(10;15)(q26;p11). Accordingly, both the other involved chromosomes 7 and 15 must be denoted as derivative chromosomes: der(7)t(7;10)(q11;p11), der(15)t(10;15)(q26;p11).
The corrected formula then is:
If a translocation of interstital fragments (i.e. fragments which do not extend upto the terminus of the chromosome arm) is meant, two breakpoints (start and end point) must be given for each fragment.
But if there are two distinct translocations which both involve one common chromosome, all three involved chromosomes must be written as derivative chromosomes with the aberrations involved in their respective genereation.
- In a translocation between two chromosomes, either both break points must be centromers or none
- The centromere is not a valid break point for the formation of a dicentric chromosome when the other break point is not a centromere
Whole chromosome arms can be translocated. In such cases, the break points are assigned to the centromeres, i.e. to p10 oder q10, and "mixed" centromeres are created from the original chromosomes.
If the chromosomal break occured not exactly in the centromere but close by it, the next band has to be denoted, i.e. p11 or q11 (or more excatly, e.g. p11.1). Here, we must consider if the centromere was part of the translocated fragment thus generating a dicentric chromosome which must be dentoed with a "dic" symbol, or not.
A translocation of a whole chromosomal arm exactly from its centromere to a position on an other chromosome outside the centromere does not make sense: either the break was just behind the centromere generating a chromosome which contains the centromere of the other translocation partner only, or the break was just before the centromere thus translocating a small portion of the other arm also and generating a dicentric chromosome (such translocations are always non-balanced because an acentric fragment remains which will be lost during the following cell divisions).
- van Echten et al 1995, Genes Chromosomes Cancer, Case 30
- Singh et al 2001, Laryngoscope, Case 1
This is an unbalanced translocation, the derivative chromosome is described mono-centric. Hence the breakpoint for chromosome 8 is likely to be p11: +der(8)t(8;12)(p11;p11).
Also this translocation is described unbalanced and monocentric. Chromosomal material from the q arm of chromosome 13 was translocated to band 8p21. Hence it is: +der(8)t(8;13)(p21;q11).
Check if the breakpoint is really exactly inside the centromere: then both breakpoints are centromeres. Otherwise, the breakpoint of one translocation partner was close by the centromere and must be denoted accordingly (with the other translocation partner, the break was also close by the centromere or farther distal); you must differentiate between reciprocal (balanced) translocations and dicentric chromosomes.
- No known symbol for the description of the type of aberration was found, or the ISCN grammar was not observed
- Invalid aberration description
- Aberration element ... contains invalid character(s)
Aberrations are analysed by a pattern matching approach step by step, checking for one type of aberration in each step. If such pattern matching failed to identify the type of aberration, the former message is issued; i.e. the message describes several types of errors which are not more closely differentiated.
These are mainly two types of errors:
A non-existing symbol was used for the description of an aberration.
The cause might be a typo, e.g. writting ibs instead of ins.
In some case, the search pattern already requires a specific breakpoint description, e.g. for isomerisation. An isomerization can only occur at a centromere, i.e. the band must described as p10 or q10. If p11 was named instead (iso-dimerisation), the isomerisation could not be discovered.
Sometimes, wrong symbols or notations can be intercepted at an earlier stage: if they contain characters which are not part of any symbol. Here, the latter message is issued.
If some characters remain after the analysis of an aberration, that
aberration is criticised as invalid. Often just a comma is missing which
separates this aberration from the next aberration in the ISCN formula;
then these two aberrations are regarded as one aberration which could no
more be analysed correctly.
Warning: with a derivative chromosome being the first aberration, such a composite term could be analysed as a correctly described term!
But often, there is a general lack of knowledge of the ISCN, as can be proved with the CyDAS log files:
- 46,xy,del (q34.3)
- 46,xy,del 9q34
- der6 t(6;12)(q23;q13)
- der ring(20;22)(q?q?;q10q12)
Even worse are those cases, where we cannot find out what the authors wanted to express, even when thinking long about their descriptions. Again, a few examples from the CyDAS log files:
- t(13:17) 14 q12
Check the spelling of the symbol for the rearrangement and adhere to the grammar of the ISCN; if needed, add a comma separating distinct aberrations.
- An error occured while constructing a derivative chromosome
- Addition not possible because the band is missing in chromosome
- Deletion not possible because the band is missing in chromosome
- The first chromosome does not contain the band for the formation of a dicentric chromosome
- Duplication not possible because the band is missing in chromosome.
- Acceptor Band for Insertion not found in Chromosome.
- Start Band for Insertion not found in Donor Chromosome.
- End Band for Inversion not found in Chromosome.
- The acceptor chromosome does not contain the acceptor band for translocation.
- and some other similiar messages
If a chromosome faced two or more rearrangements, it must be described as a derivative chromosome.
Many cytogeneticists believe that the detailled ISCN notation is no more valid and then try to describe a highly aberrant chromosome using the short notation (that opinion is definitley wrong!). Often it is sufficient to write down all the aberrations which generated the derivative chromosome after the "der" symbol; but a number of cases remains when that short notation fails (see ISCN Discussion).
More often, the overview seems to get lost with such chromosomes, and hence some bands are assigned wrongly.
The CyDAS software calculates a derivative chromosome step by step, introducing the aberrations one at a time in the order given. Often the software discovers that a band which is required for a rearrangement (a breakpoint) is not present in the chromosome.
- Gibas et al 1986, Cancer Genet Cytogenet, Case 5
- Gorunova et al 1998, Genes Chromosomes Cancer, Case 17
- Gorunova et al 1998, Genes Chromosomes Cancer, Case 9
- Becher et al 1990, Cancer Genet Cytogenet, Case 6
At first, der(11;13)t(11;13)(p13;q14) is calculated to der(11;13)(11qter->11p13::13q14->13pter). The t(11;15)(p15;q12) requires band 11p15, which is no longer present.
Since a +der(13)t(11;13)(q14;p13) is described with the same case, a permutation of the bands can be assumed.
At first, der(7;9)t(7;9)(q22;p13) is calculated to der(7;9)(7pter->7q22::9p13->9qter). The duplication dup(7)(q36q22) requires bands 7q36 and 7q22, but band 7q36 is no longer present.
At first, der(15)t(6;15)(p11;p11) is calculated to der(15)(15qter->15p11::6p11->6pter). The addition add(16)(p13) requires band 16p13, which cannot be present at all. We may assume that a comma (before add(16)(p13)) is missing.
At first, der(4)t(4;9)(q31;q34) is calculated to der(4)(4pter->4q31::9q34->9qter). The translocation t(3;9)(q27;q22) requires band 9q22, which is no longer present.
Since a der(9)t(4;9)(q31;q22)... is described with the same case, we can assume that the bands of chromsome 9 were permuted in the translocations.
If you cannot determine the aberrations which generated the derivative
chromosome, simply write down the band composition of the chromosome (i.e.
the detailled notation).
If the rearrangements can be determined, check the derivative chromosome by drawing an ideogram for it, e.g. using the Online-Ideograms or the Online-Karyograms of the CyDAS site.
Non-sense Descriptions of Derivative Chromosomes
- A subterm in the description of a derivative chromosome could not be identified as a rearrangement
With a derivative chromosome, either its band composition or the aberrations generating it must be denoted. Very often, we can find notations showing a band description after the "der" symbol, e.g. der(3)(p?), der(7)(q?), der(10)(p?), der(14)(q?), etc.
Because such notations are very common, we must assume that is not (always) a typo which mutated a deletion ("del") into a derivative chromsome.
More likely, the authors wanted to tell that they identified a chromosome which has some deviation, and that they also could narrow down the site where the deviation is located.
Maybe the authors wanted to express that chromosomal material of unknown origin replaces the material from that sit upto the terminus of the same chromsome arm. That is the hallmark of an addition which is to be described with the symbol "add". E.g. add(14)(q?) instead of der(14)(q?).
It is also possible that chromosomal material of unknown origin is located at that position, followed thereafter with the normal rest of the chromosome arm. That is called an insertion of unknown material, which is described with the symbol "ins". E.g. ins(3;?)(p?;?) instead of der(3)(p?).
The situation is more complicated if the origin of the derivative chromosome proper is not clear (i.e. if we cannot determine the origin of teh centromere), but when we can determine that somewhere material of the chromosome denoted follows, and maybe thereafter again unknown material. Such an aberration is a gain of a derivative chromosome of unknown origin with a translocation or an insertion. E.g. der(?)t(7;?)(q?;?) stands for a der(?)(?->?cen->?::7q?->7qter), or der(?)ins(?;14)(?;q?q?) stands for a der(?)(?->?cen->?::14q?->14q?::?).
Try to find out if it is an addition or an insertion of unknown material, or if its is a chromosome of unknown (centromeric) origin containing some identifiable material (see above), then describe the derivative chromosome accordingly.