Formalized standard nomenclature for human chromosomes dates from 1960 and, since 1978, has been known as the International System for Human Cytogenetic Nomenclature (ISCN).
Human chromosomes are numbered from largest to smallest1 from 1 to 22. There are 2 additional chromosomes, X and Y. The numbered chromosomes are known as autosomes, X and Y as the sex chromosomes. Chromosomes stained using techniques that do not produce bands are grouped based on similar size and centromere position, as follows:
21, 22, Y
A chromosome may be referred to by number or by group:
a D group chromosome
Q-banding, Q bands
G-banding, G bands
R-banding, R bands
C-banding, C bands
T-banding, T bands
nucleolar organizing regions
Banding technique codes of several letters provide more information about the banding method. These abbreviations must be expanded, but the letters in the list above (Q, G, R, C, T, NOR) within those terms need not be expanded:
Q bands by fluorescence
Q bands by fluorescence using quinacrine
C bands by barium hydroxide using Giemsa stain
NOR staining, silver nitrate technique
Chromosomes contain short and long arms, which are joined at the centromere (Figure 5).
The short arm is designated by p, for petit, and the long arm by the next letter of the alphabet, q.7 Arm designations follow the chromosome number:
short arm of chromosome 17
long arm of chromosome 3
long arm of the X chromosome
Expressions such as those on the left need not be expanded. It is incorrect to refer to chromosome arms as chromosomes:
chromosome arm 17p; short arm of 17; 17p
Regions are determined by major chromosome band landmarks. Chromosome arms contain 1 to 4 regions, numbered outward from the centromere. The region number follows the p or the q:
region 3 of long arm of chromosome 4
The regions are divided into bands, also numbered outward from the centromere. Bands have subdivisions or subbands. The band number follows the region number, and the subband number follows a period after the band number. When a subband is further subdivided, the sub-subband number follows the subband number without a period or other intervening punctuation:
chromosome 11, long arm, band 23 (region 2, band 3)
band in above subdivided, resulting in subband 23.3
chromosome 20, short arm, sub-subband 11.23 (region 1, band 1, subband 2, sub-subband 3)
It is correct usage to refer to the above expressions as “band 11q23,” “band 11q23.3,” and “band 20p11.23.”
The centromere is designated band 10, as in the following:
p10 (portion of centromere facing short arm)
q10 (portion of centromere facing long arm)
Visualization of genomic information by chromosome region in humans and other organisms is available at the National Center for Biotechnology Information Map Viewer.8
Karyotype is the chromosome complement of an individual, tissue, or cell line. Karyotype is expressed as the number of chromosomes in a cell including the sex chromosomes, a description of the sex chromosome composition, and, whenever applicable, any chromosome abnormality.
The karyogram and the idiogram are graphic representations of karyotype. The karyogram is “a systemized array of the chromosomes” that has been prepared using methods such as photomicrography. An idiogram is “diagrammatic representation of the karyotype.”3(p6)
In karyotype expressions, the sex chromosomes, which should always be spec-ified, are separated from the number of chromosomes by a comma, as in the following examples:
46 chromosomes (2 each of chromosomes 1–22 and 2 X chromosomes in human female karyotype)
46 chromosomes (2 each of chromosomes 1–22, 1 X and 1 Y in human male karyotype)
45 chromosomes, 1 X chromosome (Turner syndrome)
47 chromosomes, 2 X chromosomes, 1 Y (Klinefelter syndrome)
47 chromosomes, 1 X, 2 Y chromosomes
3 each of chromosomes 1–22 and X
A virgule is used to indicate more than 1 karyotype in an individual, tumor, cell line, and so on:
Descriptions of autosomal chromosome abnormalities are presented after the sex chromosomes and listed in numerical order irrespective of aberration type, separated from the sex chromosomes by a comma. For instance, the karyotype of a person with trisomy 21 (Down syndrome) with an extra chromosome 21 is specified as
A karyotype description may contain both constitutional and acquired elements. For instance, the karyotype of a tumor cell from a person with trisomy 21 could show both the constitutional anomaly and an acquired neoplastic anomaly, eg, an acquired extra chromosome 8, and would be expressed as
The lowercase c specifies that the trisomy 21 is constitutional, as distinguished from the acquired trisomy 8.
An individual with more than 1 karyotypic clone may have a mosaic (single-cell origin) karyotype or a chimera (multicell origin) karyotype, which should be spec-ified with a 3-letter abbreviation at first mention of the karyotype, eg:
Brackets indicate the number of cells observed in a clone:
A double slant (virgule), used in chimeras resulting from bone marrow transplants, separates recipient and donor cell lines. Recipient karyotype precedes the double slant, donor karyotype follows the double slant, and either or both may be specified, eg:
For details on order in such expressions, consult ISCN 2005.
Meiotic karyotypes may begin with a term such as MI and contain a haploid or near-haploid number of chromosomes, and may or may not have a comma between X and Y:
The abbreviations and symbols in Table 6 are used in descriptions of chromosomes, including chromosome rearrangements. The table is adapted from ISCN 2005.3 Former designations based on ISCN 1995 and ISCN 1985 appear in parentheses. (A short online version of the information in Table 6 is available through the Cancer Genome Anatomy Project.9)
Table 6. Chromosome Rearrangement Abbreviations and Symbolsa
first meiotic anaphase
second meiotic anaphase
additional material of unknown origin
comparative genomic hybridization
chr (cs )
cht (ct )
complex chromatid interchanges
dn (de novo )
chromosome abnormality not inherited
homogeneously staining region
stemline karyotype in subclones
inversion or inverted
in situ hybridization
first meiotic metaphase
second meiotic metaphase
minute acentric fragment
first meiotic prophase
premature chromosome condensation
premature centromere division
satellited short arm
satellited long arm
sister chromatid exchange
telomeric association ter terminal end of chromosome or telomere (tel )
trc (tri )
var (v , var )
variant or variable region
break and reunion
separates chromosomes and chromosome bands in structural rearrangements involving 2 or more chromosomes
intervals and boundaries in a chromosome segment
angle brackets for ploidy
square brackets for number of cells
number of chiasmata
separates chimeric clones
a Adapted by permission of S Karger AG, Basel, Switzerland.
Single-letter abbreviations combined with other abbreviations are set closed up, eg:
Three-letter symbols combined are set with a space:
The symbols in the list of chromosomes from ISCN 2005 are part of an efficient shorthand that describes the exact changes in a karyotype containing rearranged chromosomes. In publications that range beyond the field of cytogenetics, the symbols should always be defined.
Chromosome rearrangement terms can be written using a “short system” or short form. Complex abnormalities are designated by the more specific “detailed system” or long form. The detailed form uses symbols such as arrows to describe individual derivative chromosomes resulting from complex rearrangements (even the short system can result in a complex expression), eg:
The complete nomenclature, formulated for consistency in the description of chromosomal rearrangements, is detailed in ISCN 2005.3 The following sections contain terms that illustrate some of the basic principles of the ISCN. Terms such as these may stand alone or may be part of longer expressions such as those above.
For aberrations involving more than 1 chromosome, the sex chromosome appears first, then other chromosomes in numerical order (or, less commonly, in group order if only group is specified).
translocation involving bands Xq27 and 13q12
For 2 breaks in the same chromosome, the short arm precedes the long arm, and there is no internal punctuation, eg:
inversion in chromosome 2
insertion of portion of long arm of chromosome 2 into short arm of chromosome 5
Plus and Minus Signs
A plus sign preceding a chromosome indicates addition of the entire chromosome:
entire chromosome 14 gained
A plus sign following p or q and the chromosome number indicates an addition to that chromosome:
addition to 14p
Such a term is ambiguous; it might refer to one of many possible specific additions to 14p of an individual karyotype, to an unknown addition to 14p, or to additions to 14p in general. A term like 14p+ may be used after context has been provided. In the case of karyotype descriptions, this means using more specific terms incorporating symbols such as add, der, and ins:
the 14q+ cytogenetic abnormality was found to be add(14)(q32).
A minus sign preceding a chromosome signifies loss of the entire chromosome:
all of chromosome 5 missing
A minus sign following a chromosome arm signifies loss from that arm, but this should be reserved for text, while more specific notation is used in karyotype descriptions, eg:
A deletion of the entire long arm of a chromosome should not be expressed in text with a minus sign.
▪ Parentheses: the number of the affected chromosome follows the rearrangement symbol in parentheses:
inversion in chromosome 2
Details of the aberration follow in a second set of parentheses:
inversion in chromosome 2 involving bands 13 and 24 of the short arm
▪ Semicolon: In rearrangements involving 2 or more chromosomes, a semicolon is used:
translocation involving breaks at 2q21 and 5q31
▪ Comma: Commas separate the number of chromosomes, sex chromosomes, and each term describing an abnormality:
female karyotype with ring chromosome 18 with ends joined at bands p11 and q22
In different clones within the same karyotype, an underline (underbar) distinguishes homologous aberrations of the same chromosome:
In manuscripts, authors should indicate that the underline is intended, so that it will not be set as italics, per typographic convention, in the published version.
This word indicates “alternative interpretations of an aberration”3(p50) or alternative results (for instance, breaks appearing in consecutive bands using different techniques):
add(19)(p13 or q13)
add(10)(q22 or q23)
As seen in previous examples, there is no spacing between the elements of a karyotype description (except following mos and chi, between 2 or more 3-letter abbreviations [eg, cht del, rev ish enh], and before and after “or”).
Multiline karyotypes carry over from 1 line of text to the next with no punctuation other than that of the original expression (eg, no hyphen at the end of the first line), as in the following tumor karyotype:
46,XX,t(8;21)(q22;q22)/45,idem, −X/46,idem, −X,+8/47,idem, X,+8,+9
In Situ Hybridization.
Style for terms describing karyotypes identified by means of this technique alone or along with cytogenetic analysis (traditional karyotyping techniques) is similar to that described above (see also 15.6.1, Nucleic Acids and Amino Acids). Some symbol meanings may differ. Table 7 is adapted from ISCN 2005.3
Table 7. In Situ Hybridization Abbreviations and Symbolsa
comparative genomic hybridization
diminished signal intensity
enhanced signal intensity
extended chromatin/DNA fiber in situ hybridization
fluorescence in situ hybridization
in situ hybridization
nuclear or interphase in situ hybridization
partial chromosome paint
reverse in situ hybridization
whole chromosome paint
separates probes on different derivative chromosomes
[period] separates cytogenetic observations from results of in situ hybridization or array-based cgh
present on a specific chromosome
duplication on a specific chromosome
absent on a specific chromosome
precedes number of signals seen
a Adapted by permission of S Karger AG, Basel, Switzerland.
Examples are as follows:
(D22S75 refers to the probe for the DNA segment sequence D22S75; see 15.6.2, Human Gene Nomenclature.)
Marker Chromosomes, Derivative Chromosomes, and the Philadelphia Chromosome.
A marker chromosome “is a structurally abnormal chromosome in which no part can be identified”3(p73) and might be included in a karyotype as in
A structurally abnormal chromosome in which any part can be recognized is considered a derivative chromosome, defined as “a structurally rearranged chromosome generated by a rearrangement involving two or more chromosomes or by multiple aberrations within a single chromosome.”3(p62)
A derivative chromosome is specified in parentheses, followed by the aberrations involved in the generation of the derivative chromosome. The aberrations are not separated by a comma. For instance:
signifies a derivative chromosome 1 generated by 2 translocations, one involving the short arm with a breakpoint in 1p32 and the other involving the long arm with a breakpoint in 1q25.
Philadelphia chromosome is the name given to a particular derivative chromo-some found in chronic myelogenous leukemia and some types of acute leukemia. The Philadelphia chromosome can be abbreviated as “Ph chromosome” or, if clear in context, “Ph.” Appendages, as in Ph1, Ph1, Ph1, or Ph′, are not necessary, and Ph is the preferred form. The Ph chromosome is the derivative chromosome 22 resulting from the translocation t(9;22)(q34;q11) and may be described as follows:
The Ph chromosome is the result of a rearrangement that juxtaposes the oncogene ABL with the breakpoint cluster region gene BCR (see 15.6.2, Human Gene Nomenclature, and 15.6.3, Oncogenes and Tumor Suppressor Genes).
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8. NCBI Map Viewer. http://www.ncbi.nlm.nih.gov/mapview/. Accessed April 21, 2006.
9. ISCN abbreviated terms and symbols. The Cancer Genome Anatomy Project. http://cgap.nci.nih.gov/Chromosomes/ISCNSymbols. Accessed April 21, 2006.