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Analysis of Aberrations

The analysis of aberrations is done by excessive pattern matching in the "analyse" function of the Aberration class.

For quite all types of aberrations, a few features are common:

a leading plus sign indicates gain of an aberrant chromosome
a leading question mark indicates that the aberration is questionable
after the aberration proper, a multiplicator sign and multiplicators may follow
constitutional aberrations are marked with a "c"

After checking the common features above, the remaining aberration is compared to patterns specific for each type of aberration. First, the pattern checks for the "core" only, i.e. the symbol denoting the aberration and the respective chromosomes in parenthesis. If such a pattern matches, the aberration is regarded "identified". Next, another pattern will catch the break points. If no break points were found, the aberration is marked "non-expanded" but preliminarily valid. Otherwise, break points, SCCN qualitative and quantitative aberrations as well as fusions (in preparation) are calculated and the analyse function is left.

After each matching step, the matched part of the aberration description is removed. If the matchings do not consume up all of the original description, the aberration is assumed to contain an error.

If the aberration describes a derivative chromosome, the analysis is more complicated. After the original match of the der()-part, a collection of the aberrations following is established and these aberrations are analysed as described above. Then, the aberrations are introduced into the derivative chromosome.

A detailed description of the steps follows:

General Features

Removal of unnecessary parts

From the point of view of a human reader of an ISCN formula, additional spaces or the dot (".") between the second and third digit of a chromosomal band denomination may be useful in that they may render reading more easy. But from the view point of information, they are absolutely useless, since they do not confer any further information. Hence, all spaces and dots are removed from the description. This is also true for spaces and dots in positions which are not allowed in the ISCN manual (e.g. "46,XY,d el(1)(p 3.42 )" will be transformed into "46,XY,del(1)(p342)" and thus accepted as a correct description).

Indication of Gain or Loss

Next, an indication of gain or loss of a chromosome or an aberration may follow. This is determined by checking the first character of the description for "+" or "-".

Since not for every aberration a gain or loss can be accepted (e.g. +t(9;22)(q34;q11) is not acceptable because the aberration gives raise to two aberrant chromosomes), bogus indications have to be found out when the aberration core was identified.

Questioned Aberrations

Sometimes, it is unclear if the aberration is present at all. This is indicated by a question mark immediately before the symbol of the aberration.

Multiplicators

If an aberration is present more than once, its copy number is given at the end of the description. It is caught with the pattern "x(?<min>\d+)([\-\~](?<max>\d+))?$". A single value will be caught in the "min" group, while a range will fill both the "min" and the "max" group.

Constitutional aberrations

Constitutional aberrations are marked with a "c" at the end of the description before the multiplicators.

General bogus descriptions

After the above analyses, some general types of errors can be detected:

odd number of brackets
wrong chromosome number
not allowed characters (at this step, only digits, ";-~():>?" and "acdefhilmnpqrstuvXY" are acceptable)

Specific simple aberrations

Identifying the aberrations proper is done with pattern matching. The remaining aberration description is compared to a series of patterns until a specific aberration could be identified. Then, break points are searched for, and SCCN qualitative and quantitative aberrations as well as fusions (in preparation) are calculated.

The SCCN quantitative aberration depends on whether the aberrant chromosome replaces a normal chromosome or is additionally present.

Some of the patterns used for identifying special parts of the aberrations are as follows.

The chromosome number consists of either digits or one of XY; a leading question mark may indicate that the chromosome was not fully reliably identified during karyotype analysis. Hence the elementary pattern is "(?<numN>\??[\dXY]*)". It also allows for arbitrary combinations of XY and digits (e.g. "?Y2X") which must be identified later when break points are checked for existence.

Often bands are delimited by semicola. Here, a pattern catching everything upto the next semicolon is useful: "(?<bandN>[^\;]+)". Accordingly, the pattern for the last band before the closing bracket is "(?<bandN>[^\)]+)". These patterns will accept quite any bogus descriptions which will cause an error when a Band object is instantiated with.

A much more complicated pattern uses the structure of a band description. It starts with the notation of the arm (p or q) followed by a row of digits. If a range is given, an approximate sign ("~" or "-") followed by another row of digits may follow. Question marks may be sprinkled quite everywhere. This pattern is "(?<bandN>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)" and is useful when bands are not separated by semicola (e.g. with intrachromosomal insertions).

Whole chromosome gain or loss

The simplest aberration is the gain or loss of a whole chromosome. After the above analysis, the description was reduced to chromosome number only. Sometimes, if the gained or missing chromosome was not identified exactly, a question mark is added after the chromosome number, though the ISCN expects that question mark before it; this question mark at the wrong position is also accepted.

The pattern used is "^(?<num>[\dXY]+)(?<q>\??)$".

In contrast to the ISCN manual, multiplicators are accepted also for this type of aberrations (multiplicators were analysed above).

Translocations

Typically, translocations involve two chromosomes which exchange terminal fragments. Translocations involving upto ten chromosomes were found in the Mitelman database.

According to the ISCN manual, also interstitial fragments may be exchanged. When scanning several thousands of karyotypes for such a translocation, only one was found: t(2;4)(p15q23;p14q24) stemming from a publication from 1993, i.e. before ISCN 1995; and here, a centromere containing fragment would have to be exchanged. No karyotype showing a translocation of interstitial fragments between three chromosomes was discovered. The example given in the ISCN manual ("t(5;6)(q13q23;q15q23)") could not be found in the Mitelman database. Hence, doubts if such translocations do really exist may be advisable. Nonetheless, the enormous effort of dealing with exchanges of both terminal and interstitial fragments is done (see also "Discussion of ISCN").

Before ISCN 1995, the symbol "t" was also used for insertions. E.g. "t(11;14)(q13;q22q24)" would now be written "ins(11;14)(q13;q22q24)". This outdated style is not accepted by the analyse function.

A translocation cannot be gained ("+t..." is not acceptable). Translocations are balanced and thus do not yield gain or loss of chromosomal material.

The order of chromosomes in translocations is not cared about, e.g. "t(21;X)" instead of "t(X;21)" is also accepted.

Translocations involving two chromosomes

The basic pattern for identifying such aberrations is "^t$(?<num1>\??[\dXY]*)\;(?<num2>\??[\dXY]*)$", where "num1" will show up the first chromosome and "num2" the second chromosome.

Bands are then caught with the pattern "^$(?<band1>[^\;]+)\;(?<band2>[^$]+)\)$" which actually puts everything after the opening bracket upto the semicolon into group "band1" and everything after the semicolon upto the closing bracket into group "band2". If one of the groups contains more than one of "p" or "q", a translocation of an interstitial fragment is assumed. Here, each of the groups is matched to the pattern "^(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$" to receive the bands involved. Else, the groups already correspond to the bands.

Special care is taken during later analysis to ensure that the number of bands found is adequate and that the bands do really describe bands. Furthermore, in a translocation of terminal fragments, either both break points must be centromers or none of them.

Translocations involving three chromosomes

They are dealt with very similiar to the aberrations involving two chromosomes.

The basic pattern for identifying such aberrations is "^t$(?<num1>\??[\dXY]*)\;(?<num2>\??[\dXY]*)\;(?<num3>\??[\dXY]*)$", where "num1" will show up the first chromosome, and "num2" the second chromosome and "num3" the third chromosome.

Bands are caught with the pattern "^$(?<band1>[^\;]+)\;(?<band2>[^$]+)\;(?<band3>[^\)]+)\)$" and further analysed as described above.

Translocations involving more than three chromsosomes

For ease of programming, only translocations of terminal fragments are accepted for such translocations. For each number of chromosomes involved there is an extra section in the analyse function.

The basic pattern for such translocations is "^t$(?<num1>\??[\dXY]*)\;(?<num2>\??[\dXY]*)\;(?<num3>\??[\dXY]*)\;(?<num4>\??[\dXY]*)$" for a translocation involving four chromosomes. The block "(?<numN>\??[\dXY]*)\;" is repeated accordingly for higher numbers with adjusting the group numbers. The pattern for the bands is adjusted accordingly, but no care is taken of differentiating between terminal and interstitial fragments (in the latter case, an error would be raised).

This pattern is repeated for translocations upto ten chromosomes.

Deletions

Deletions may be terminal (only the start band is given) or interstitial (both start and end band have to be given).

The pattern for identifying the aberration is "^del$(?<num>[\?\dXY]+)$" with the "num" group catching a chromosome number consisting of digits, XY, or question marks.

Afterwards, bands are searched for with the pattern "^$(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$$". If the group "band2" stays empty, the deletion is assumed to be terminal, otherwise interstitial. Further calculation (SCCN etc.) must differentiate between these situations.

Furthermore, deletions of centromere spanning regions would give raise to acentromeric fragments which would be lost during cell divisions. Hence, in such cases the aberration must be marked invalid.

Additions

Material of unknown origin attached to a chromosome band and replacing the chromosomal material from that position is called addition.

The pattern for identifying the aberration proper is "^add$(?<num>[\?\dXY]+)$". The afflicted band is searched for with the pattern "$(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)$$".

Duplications

In a duplication, the chromosome and the start and end points are noted.

The pattern for identifying the aberration proper is "^dup$(?<num>[\?\dXY]+)$". The afflicted bands are searched for with the pattern "^$(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$$".

For the calculation of fusions, the order of the bands relative to the centromere is used to find out if the duplication was directed or inverted.

Dicentric chromosomes

In dicentric chromosomes, two chromosomes separated by a semicolon are given in the first pair of brackets, the bands separated by a semicolon follow in the second pair. Centromeres are not accepted as break points. Both chromosomes involved in a dicentric chromosome are replaced by it.

The pattern for identifying the aberration proper is "^dic$(?<num1>[\?\dXY]+)(\;(?<num2>[\?\dXY]+))?$". The afflicted bands are searched for with the pattern "^$(?<band1>[^\;]+)(\;(?<band2>[^$]+))?\)$".

When the dicentric chromosome replaces its normal chromosomes, two fragments are lost: those extending from the break points to the terminus of the same chromosomal arms. If the dicentric chromosome has been gained, two fragments have been gained: those extending from the break points via the centromere to the terminus of the opposite arm.

Isochromosomes

Isochromosomes are very simple for analysis: only one chromosome is named in the first pair of brackets, and the break point is either p10 or q10 (or questioned).

The pattern is "^i$(?<num>[\?\dXY]+)$$(?<band>\??[pq]10)$". I.e., isochromosomes are analysed in one step.

When the isochromosome replaces its normal chromosome, one fragment is lost (the other arm), and one fragment is gained (the arm the chromosome is made of). When the isochromosome is additionally present, no fragment is lost, but the arm the chromosome consists of is gained twice.

Iso-dicentric chromosomes

The notation structure of iso-dicentric chromosomes is almost as simple as that of isochromosomes, but they are analysed in two steps.

The pattern for identifying the aberration proper is "^idic$(?<num>[\?\dXY]+)$". The afflicted bands are searched for with the pattern "^$(?<band1>[^$]+)\)$". The centromere is by definition not a valid break point.

The isodicentric chromosome starts at the remaining terminus, extends via the centromere to the band denoted, and that part is duplicated and thus gained twice if the iso-dicentric chromosome is additionally present. The region from the denoted band upto its terminus has been lost once when the iso-dicentric chromosome replaces its normal chromosome.

Insertions

There are two types of insertion: intrachromosomal insertions (e.g. "ins(2)(p13q21q31)") taking place in one chromosome only, and interchromosomal insertions involving two chromosomes (e.g. "ins(5;2)(p14;q22q32"). All insertions are balanced, i.e. do not give raise to gains or losses by themselves; if an intrachromosomal insertion was gained, this is equivalent to the gain of the whole chromosome. If two chromosomes are involved, the gain of an insertion ("+ins...") is not defined because it gives raise to two aberrant chromosomes.

The pattern for identifying the aberration proper is "^ins$(?<num1>[\?\dXY]+)(\;(?<num2>[\?\dXY]+))?$". If only group "num1" is filled, it is an intrachromosomal insertion, when also group "num2" is filled, the insertion is interchromosomal.

The afflicted bands are searched for with the pattern "^$(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?);?(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band3>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$$".
Note that this pattern requires the presence of two bands only; if missing, the third band is assumed to be unknown and thus "?" (e.g. in "ins(5;?)(q13;?)" the second band is unknown and marked as such, so the third band being also unknown need not be denoted).
Also, the pattern regards the semicolon between the first and the second band as an optional character, regardless of the insertion type; i.e. in contrast to the ISCN manual the description will be accepted also when the semicolon is missing in interchromosomal aberrations or present in intrachromosomal insertions (e.g. "ins(5;2)(p14q22q32)" or "ins(2)(p13;q21q31)").

For fusions, the order of the second and third band relative to the centromere must be looked at.

Inversions

Inversions are described by the symbol "inv" followed by the relevant chromosome in the first pair of brackerts and the afflicted bands without semicolon in the second pair.

The pattern for identifying the aberration proper is "^inv$(?<num>[\?\dXY]+)$". The afflicted bands are searched for with the pattern "^$(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$$".

Inversions are balanced aberrations and thus do not yield gains or losses by themselfes. A gain of an inversion corresponds to the gain of the whole chromosome.

Ring chromosomes

Ring chromosomes whose composition was at least partially identified are a very complex topic. Generally, after the symbol "r" follow the chromosomes involved in ring formation in brackets separated by semicola, in the next pair of brackets their bands.

But not every chromosome involved needs to confer a centromere to the ring chromosome. If not marked "dic r" or "trc r", the ring chromosome is actually believed to be monocentric. But as can be proved with data from the Mitelman database, some of them are dicentric without being marked.

Monocentric ring chromosomes containing material of several chromosomes must be described as derivative chromosomes "der(a)r(a,b;c)...", where the centromere bearing chromosome need not be named first in the "r" clause.

The pattern for identifying the aberration proper is "^(dic)?r$(?<num1>[\?\dXY]+)(\;(?<num2>[\?\dXY]+))?(\;(?<num3>[\?\dXY]+))?$". It requires at least one chromosome and allows upto three chromosomes. A "trc r" would not be recognized, but that does not exist in the Mitelman database and thus is irrelevant.

Catching the band groups depends on the number of chromosomes found.

If there are three chromosomes, the primary pattern is "^$(?<band1>[^\;]+)\;(?<band2>[^$]+)\;(?<band3>[^\)]+)\)$", in a further step each group is matched to "^(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$". If a group contains a question mark only, both bands for that chromosome are thought to be unknown. Else if only one band for a chromosome was found, an error is raised. Since there are no tricentric ring chromosomes, such rings must be described as derivative chromosomes; SCCN data etc. must then be requested from that derivative chromosome.

With two chromosomes, the pattern is "^$(?<band1>[^\;]+)\;(?<band2>[^$]+)\)$" which is further analysed as with rings of three hcromosomes. Non-dicentric rings of such type must be described as derivative chromosomes, and SCCN data etc. has to be requested from that derivative chromosome. Dicentric ring chromosomes require the calculation of break points, fusions, SCCN qualitative and quantitative. If a dicentric ring replaces the normal chromosomes, all those fragments not denoted in the description are lost; if the ring is additionally present, both fragments denoted are gained.

If there is only one chromosome the pattern is "^$(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$$". Break points, fusions, SCCN qualitative and quantitative are calculated here.

Triplications

The formal description of triplications is simple. After the symbol "trp" follows the chromosome in brackets followed by the triplicated band in a second pair of brackets without separation by a semicolon.

The pattern for identifying the aberration proper is "^trp$(?<num>[\?\dXY]+)$". The bands are then caught with the pattern "^$(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$$".

For gains and losses, the triplicated fragment has been gained twice; if the triplication is additionally present, the whole (original) chromosome has additionally been gained once. As for fusions, the orientation of the triplicated fragment cannot be determined, hence both possible interpretations are taken, but marked questionable.

Idem Aberration

An "idem" aberration is generally ignored. Only when all karyotypes of a Karyotypes object are analysed, the "idem" term gets replaced with the appropriate aberrations.

Telomeric associations

Telomeric associations are denoted with the symbol "tas". In brackets follows a semicolon separated list of the chromosomes involved. The next pair of brackets shows the bands or band groups involved.

The pattern for identifying the aberration proper is "^tas$(?<num1>\??[\dXY]*)\;(?<num2>\??[\dXY]*)(\;(?<num3>\??[\dXY]*))?(\;(?<num4>\??[\dXY]*))?$" which allows for telomeric associations of upto 4 chromosomes requiring at least two chromosomes. Band groups are then caught with the pattern "^$(?<band1>[^\;]+)\;(?<band2>[^\;]+)(\;(?<band3>[^\;]+))?(\;(?<band4>[^\;]+))?$$" which also allows for upto 4 groups while requiring at least two groups.

If there are more than two chromosomes, the second band group must show two bands; if there are four chromosomes, also the third group must show two bands; other groups must show one band only.

SCCN qualitative aberrations are strightly calculated. The bands afflicted are not counted as break points, no gains are losses occured.

Homogeneously staining regions

Homogeneously staining regions may reside somewhere in a normal chromosome or at a break point in a derivative chromosome. After the symbol "hsr" follows the chromosome in brackets, then the band.

If it is located at the interface between two different chromosomes in a derivative chromosomes, both chromosomes and bands are noted.

The pattern for identifying the aberration proper is "^hsr$(?<num1>[\?\dXY]+)(\;(?<num2>[\?\dXY]+))?$" which requires at least one chromosome. The band(s) are then caught with the pattern "^$(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?);?(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$$". If two chromosomes were detected, two bands must be present, otherwise exactly one band.

Tricentric chromosomes

For the description of tricentric chromosomes, the symbol "trc" is used. In brackets follow the three chromosomes involved, separated by semicola. The band groups follow in the next pair of brackets separated by semicola; while the first and third group contain one band each, the second group shows two bands.

The pattern for identifying the aberration proper is "^trc$(?<num1>\??[\dXY]*)\;(?<num2>\??[\dXY]*)\;(?<num3>\??[\dXY]*)$". Band groups are caught with the pattern "^$(?<band1>[^\;]+)\;(?<band2>[^\;]+)\;(?<band3>[^\;]+)$$", the scond group being further analysed with "^(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$".

Break points, SCCN qualitative aberrations and fusions are calculated straight forward. For gains and losses, all fragments the tricentric chromosomes consists of are gained when the tricentric is additionally present. If it replaces its three normal chromosomes, the terminal fragment of the first chromosome, both terminal fragments of the second chromosome, and the terminal fragment of the third chromosome are losses.

Quadruplication

The formal description of quadruplications is simple. After the symbol "qdp" follows the chromosome in brackets followed by the quadruplicated band in a second pair of brackets without separation by a semicolon.

The pattern for identifying the aberration proper is "^qdp$(?<num>[\?\dXY]+)$". The bands are then caught with the pattern "^$(?<band1>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)(?<band2>\??[pq\?][\?\d]*([\-\~][\?\d]+)?)?$$".

For gains and losses, the quadruplicated fragment has been gained thrice; if the quadruplication is additionally present, the whole (original) chromosome has additionally been gained once. As for fusions, the orientation of the quadruplicated fragment cannot be determined, hence both possible interpretations are taken, but marked questionable; correct multiplicators cannot be given.

Complicated aberrations

Isoderivative Chromosomes

The notation of isoderivative chromosomes starts with the symbol "ider". The chromosome number follows in the first pair of brackets, the band in the second pair. Afterwards, a tail of other aberrations contributing to the isoderivative chromosome follows as with derivative chromosomes.

The pattern for identifying the aberration proper is "^ider$(?<num>[\?\dXY]+)$". The band is then caught with the pattern
"$(?<band>\??([pq]10)?)$".

Since the isomerization is the last step in the formation of an isoderivative chromosome, the aberration "ider(N)([pq]10)<aberrations>" is translated into the derivative chromosome "der(N)<aberrations>i(N)([pq]10)" and then analysed as a derivative chromosome (see next chapter).

Derivative chromosomes

The analysis of derivative chromosomes is by far the most complicated task.

For all derivative chromosomes, after the symbol "der" the centromere conferring chromosome(s) follow in brackets, separated by semicola. Hence, the pattern for identifying the aberration proper is "^der$(?<num1>\??[\dXY]*)(\;(?<num2>\??[\dXY]*))?(\;(?<num3>\??[\dXY]*))?$" which allows upto three chromosomes.

The following steps depend on the basic type of the derivative chromosome.

Detailed ISCN notation

A derivative chromosome may be notated in the detailed system of the ISCN. Then it must contain arrows or double colons. If such an item was found, this notation is assumed and the description of the aberration is passed to the constructor of the Chromosome class (see also Calculating Derivative Chromosomes).

Special notation of dicentric chromosomes / whole arm translocations

If derivative chromosomes are derived from a whole arm translocation (especially Robertsonian translocation) or a dicentric hromosome, the bands of the original aberration may follow in brackets directly after the der clause, e.g. "der(13;21)(q10;q10)" or "der(2;7)(q11;q36)", "der(2;8)(q3?1;q22)".

While in the ISCN manual, this type of notation is shown for Robertsonian translocations and other whole arm translocations only (pp.70f), cases describing dicentric chromosomes such way were discovered in the Mitelman database, e.g. Callet-Bauchu et al 1999, Leukemia, Case No. 1, or Giagounidis et al 2002, Ann Hematol, Cae No. 1.

Here, a chromosome object is instantiated with the first chromosome of the der clause, and then the formation of a dicentric chromosome is calculated.

If further aberrations are present in such a derivative chromosome, they are dealt with as in "normal" derivative chromosomes.

"Normal" derivative chromosomes

For all "normal" derivative chromosomes, a chromosome object is instantiated with the first chromosome of the der clause.

In the tail of remaining aberrations, the aberrations are searched for with the pattern "^\??\w+$[\?\dXY]+(\;[\?\dXY]+)*$($[pqor\?\d\;\-\~]+$)?". The pattern assumes that the aberration starts with its textual symbol (maybe with a question mark before it), and is followed by its chromosome(s) in brackets which may be separated by semicola. The bands of the aberration may be present or not. The pattern will take one aberration per loop.

If the pattern matched, an Aberration object is instantiated with the matched region. This aberration is analysed normally. If it is valid, it is stored in the collection of aberrations mcAberrations, otherwise the error description is taken from the aberration and analysis is aborted.

After looping through the tail of aberrations, the aberrations are introduced into the derivative chromosome instantiated above.

While most aberrations can be introduced straight forward, translocations need more consideration. Sometimes, the formation of a dicentric chromosome is meant. Hence, if the derivative chromosome is described with two centromere confering chromosomes, the derivative chromosome object is checked if it contains the acceptor band of the translocation and its second chromosome number equals the second chromosome number of the translocation, or alternatively if it contains the donor band of the translocation and its first chromosome number equals the first chromosome number of the translocation.

If the translocation was found to mean the formation of a dicentric chromosome, a dicentric is introduced instead.

In normal translocations, it may happen that the first chromosome of the der clause is not the first chromosome of the translocation term. If no aberration was introduced into the derivative chromosome object yet, a chromosome object is instantiated with the second chromosome of the der clause.

For all translocations, the fact is considered that the donor fragment could be named first in the t clause and thus chromosome and band ordering need to be rearranged for the introduction of the translocation.

Also with derivative chromosomes stemming from translocations involving three chromosomes, care must be taken to select the correct donor fragment.

The procedures for the introduction of aberrations into a derivative chromosome are described more closely in "Calculating Derivative Chromosomes".

Break points, gains and losses are then queried from the derivative chromosome object.