Launched in the early 1970s, banding methods allow for the identification of chromosomes not only by length and centromere position, but also by their unique banding properties. Figure 3.1 illustrates the characteristic size, centromere position, and G-banding banding pattern for each human chromosome pair. The commonly used G-, Q-, and R-banding techniques show bands distributed along the entire chromosome, whereas the C-, T-, or NOR-banding techniques are used to identify specific chromosome structures that are heritable features (Table 3.1; see also Chap. 4). To identify each chromosome in the human karyotype, it is important to be familiar with the characteristic morphological features or landmarks of each chromosome, such as the telomeres that cap the ends of the chromosomes, the centromere or “primary constriction” that divides a chromosome into two arms, and certain defined bands (Fig. 3.2). The symbols p and q are used to designate the short and long arms, respectively. Convention places the short arm or “p” (from the French petite) arm at the top in diagrammatic representations and the long or “q” arm at the bottom. Characteristic regions and bands within a given chromosome are observed when banding techniques are used. Chromosome regions refer to those areas lying between two distinct landmarks and are divided into bands. For example, the long arm of chromosome 7 has three regions: 7q1, 7q2, and 7q3 (Fig. 3.2). These regions are further subdivided into bands. A band is defined as a part of the chromosome that is clearly distinguishable from its adjacent segments based on its staining properties.

As a general rule, a chromosome band contains ∼5–10 megabases (Mb) of DNA. “High-resolution” cytogenetic techniques (see Chap. 4) produce elongated chromosomes that allow further refinement of karyotypic aberrations by subdividing bands into smaller sub-bands. Banding resolution and patterns may vary depending on the banding method employed (Table 3.1), so it is important to state the level of banding resolution and banding method employed on the final report when describing a cytogenetic result. The gene content of chromosome bands is also variable and, in general, reflects functionality.

Giemsa or G-banding is the most common banding method employed in North American cytogenetics laboratories. G-dark (positive) bands are AT rich, gene poor, and late replicating. The early replicating G-light (negative) bands are GC rich, gene rich, and late replicating. Reverse or R-banding shows this banding pattern in reverse (i.e., reversal of light and dark G-bands). However, the numbering of the bands is identical with both banding methods. Additional banding/staining methods are used to detect specific chromosome regions or abnormalities. For example, centromeric and pericentromeric DNA are comprised of alpha-satellite and various other families of repetitive satellite DNA, which are easily visualized using constitutive heterochromatin (C-banding) methods. C-banding is particularly useful when identifying the morphologically variable heterochromatin regions of the Y chromosome and chromosomes 1, 9, and 16. The short arms of the acrocentric chromosomes house the ribosomal RNA gene clusters in the nucleolar organizing regions (NORs), which form the nucleolus of the cell. NORs are detected by silver-based NOR staining. Finally, telomeres are comprised of (TTAGGG)_n mini-satellite repeats that stain darkly with T-banding. Technical details of the various chromosome banding methods may be found in Chap. 4.

Figure 3.3 shows the idiograms or diagrammatic representations of the G-banding patterns for normal human chromosomes 1 and 13 at five successive levels of resolution. The centromere itself is designated as “10,” with the part adjacent to the short arm as “p10” and the part adjacent to the long arm as “q10.” The bands and regions are numbered outward from the centromere to the telomeres. Four distinct chromosome units—the chromosome number, the chromosome arm, the region number, and the band number within a region—are needed to describe a precise location within a specific chromosome. For example, 7q34 refers to chromosome 7, long arm, region 3, band 4 (Fig. 3.2). This is referred to as “seven q three four,” NOT “seven q thirty-four.” If “high-resolution” banding is used, the band may be further subdivided using a decimal point after the band designation. Having a copy of the human chromosome idiograms and a reference set of well-banded karyotypes representing the banding methods and banding level of resolution routinely employed by the laboratory is helpful.

Karyotype descriptions convey the total number of chromosomes, the sex chromosome complement, and a description of any chromosome abnormalities present. The correct use of punctuation in the nomenclature string brings structure and meaning to the description. Table 3.2 provides a quick reference guide of the conventional cytogenetic ISCN punctuation symbols and their meaning.

The description of any human karyotype begins with two basic components separated by a comma; the total number of chromosomes is listed first, followed by the sex chromosome complement. Thus, a normal male karyotype is written as 46,XY, and a normal female karyotype is designated as 46,XX.

There are a few additional basic rules to describing chromosome aberrations:

The following are examples using these basic guidelines; refer also to each specific section below for additional information:

This is a female with a balanced paracentric inversion (an inversion involving a single chromosome arm) of the long arm of chromosome 3. One break occurred at band 3q21 and the other at 3q26.2. The chromosome segment between those breakpoints is present but inverted 180°. There are no spaces after any commas in the description, and there is no semicolon in the second set of parentheses because the aberration affects a single chromosome. When normal chromosomes are replaced by structurally altered chromosomes, there is no need to record the normal chromosome as missing. In this case, the nomenclature implies that one morphologically normal chromosome 3 and one inv(3q) are present in this XX karyotype with 46 chromosomes. See also “Inversions” later.

This is a male karyotype showing a balanced translocation between the X chromosome and chromosome 9. The breakpoints for this translocation are Xp22.3 and 9q22, respectively. The chromosomal segments distal to these breakpoints have been exchanged. Note that the normal sex chromosome in this example is written before the X chromosome aberration. Semicolons are present in both sets of parentheses because two chromosomes are involved.

This is a female karyotype in which material from the long arm of chromosome 2 between bands q22 and q32 (donor chromosome) is inserted into the long arm of chromosome 5 at band q13 (receptor chromosome). This is a direct insertion because the original orientation of the inserted segment has been maintained in its new position; that is, band 2q22 remains more proximal, or closer, to the centromere than band 2q31. If the insertion were inverted in the receptor chromosome 5, the ISCN would be written as ins(5;2)(q13;q32q22), indicating that band 2q22 is now more distal to the centromere than band 2q32.

These denote the same aberration, a translocation involving an X chromosome and chromosome 18, in either a female or male, respectively. The normal sex chromosome is listed before the rearranged one.

If both the X and Y chromosome are involved in aberrations, the abnormality involving the X chromosome is listed before that of the Y chromosome.

This describes a mosaic karyotype with one cell line showing a single X chromosome in 25 cells and a second cell line with a normal female (XX) sex chromosome complement in 15 cells. Note the use of a space between mos and the chromosome number and the (optional) use of square brackets to indicate the number of cells in each cell line. See also “Mosaicism and Chimerism” later.

This is a female with two different aberrations involving chromosome 8. The numerical aberration is listed before the structural aberration.

This male patient has two clones; these are separated by a slant line (/). The first clone of 16 cells shows a translocation between the long arms of chromosomes 9 and 22, with breaks at bands 9q34.1 and 22q11.2, respectively. The segments distal to the breakpoints have been exchanged (Fig. 3.4). The second clone of four cells shows gain of chromosome 8 as the sole clonal aberration. The abnormalities observed in the first clone are not seen in the second clone and vice versa. This situation is seen in neoplasia; see “Describing Cancer Karyotypes” later.

Constitutional and acquired (neoplastic) karyotypes may show a tremendous range of structural abnormalities. ISCN allows for both an abbreviated or short system as well as a detailed system of nomenclature. Whenever possible, use of the short system is strongly encouraged; all examples to this point are written in this way. Using the short system, the chromosome number, sex chromosome complement, type of rearrangement, the chromosome(s) involved, and the breakpoints are indicated. However, complex rearrangements, especially structural aberrations with multiple gains and losses or involving multiple chromosomes, may necessitate the use of a detailed system that describes the involved chromosomes from end to end. The detailed system is particularly useful when describing complex acquired aberrations in malignant disorders.

The rules used in the short system are retained in the detailed system with one exception. Instead of writing the breakpoints within the last parentheses, an abbreviated description of the band composition of the rearranged chromosome(s) starting from the end of the short arm (pter) and proceeding to the end of the long arm (qter) is specified, that is, the bands are identified in the order in which they occur in the derivative chromosome. In the detailed system, a single colon denotes a break, a double colon denotes breakage and reunion, and an arrow indicates “from→to.” If there are doubts as to whether to use the short or detailed system, first write the short system and determine if the aberration(s) can be accurately drawn as described in the nomenclature string. If the abnormalities cannot be correctly visualized using the short system, the detailed system should be used. The detailed system was devised to be flexible; therefore, if only one of several chromosome aberrations requires the use of the detailed system, it is acceptable to combine the short and detailed systems to describe the karyotype. Table 3.4 lists the most common structural aberrations found in human karyotypes with interpretation of the findings and examples of how to write them in both the short and detailed systems.

Gains and losses of whole chromosomes in the karyotype string are usually denoted by the use of either a plus (+) or minus (−) sign before the aberrant chromosome; for example, 47,XY,+21. The exception is the sex chromosomes in constitutional studies, where sex chromosome gains and losses are indicated by listing the chromosome(s) present (e.g., 45,X or 47,XXY) without use of plus or minus signs. Acquired sex chromosome aberrations are written with plus and minus signs (see “Describing Cancer Karyotypes” later).

Ploidy refers to the number of sets of chromosomes present. Thus, diploid refers to the normal situation of two sets of each chromosome (e.g., 46,XX or 46,XY). A haploid, triploid, or tetraploid karyotype is evident from the chromosome number; for example, 23,X, 69,XXY, or 92,XXYY, respectively. If additional chromosome changes are evident, these are expressed in relation to the appropriate ploidy level. The ploidy levels most commonly used in human karyotyping, most often in acquired diseases, are:

This represents a near-haploid karyotype with two copies of chromosomes 4 and 10 and single copies of all other chromosomes.

This describes a near-triploid karyotype with four copies of chromosome 13 and three copies of all other chromo­somes.

This represents a near-tetraploid karyotype with three copies of chromosomes 2 and 5, five copies of chromosomes 8 and 21, and four copies of all other chromosomes.

For more complex ploidy changes, please refer to ISCN [2].

At times, the biology of the study or the chromosome number will vary between two ploidy levels. Because precise communication of the karyotypic data is key, these cases may be written with the ploidy level in angle brackets “< >” immediately after the chromosome number and before the sex chromosome complement. For example, high hyperdiploidy, a favorable finding in pediatric acute lymphoblastic leukemia (ALL), may be written relative to 2n ploidy even though it represents a near-triploid clone; for example, 59<2n>,XX,+X,+4,+5,+6,+10,+10,+14,+14,+17,+17,+18,+18,+21.

Endoreduplication (end) is a special form of duplication of the genome without mitosis, giving rise to four-stranded chromosomes at prophase and metaphase. Endoreduplication should be written as end 46,XY. Note the space after the triplet and before the chromosome number.

Abbreviations are used to specify structural abnormalities (see Table 3.4) and precede the chromosome(s) involved in the aberration in the nomenclature string.