AMA Manual of Style (10th edition ed.) : A Guide for Authors and Editors

AMA Manual of Style Committee

Publisher:: Oxford University Press

Print Publication Date:: Mar 2007

Print ISBN-13:: 9780195176339

Published to AMA Manual of Style:: Apr 2009

DOI:: 10.1093/jama/9780195176339.001.0001

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Human Chromosomes

Chapter:: Nomenclature
Author(s):: Harriet S. Meyer

15.6.4 Human Chromosomes

Chromosomes are dark-staining, threadlike structures in the cell nucleus composed of DNA and chromatin that carry genetic information (definition after Nussbaum et al¹ and Mueller and Young²).

Formalized standard nomenclature for human chromosomes dates from 1960 and, since 1978, has been known as the International System for Human Cytogenetic Nomenclature (ISCN).

Material in this section is based on recommendations in ISCN 2005.³ Earlier reports^4-6 have also been consulted.

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:

Group	Chromosomes
A	1-3
B	4, 5
C	6-12, X
D	13-15
E	16-18
F	19, 20
G	21, 22, Y

A chromosome may be referred to by number or by group:

chromosome 14

a D group chromosome

Chromosome Bands.

Chromosome bands are elicited by special staining methods; terms in the left-hand column need not be expanded:

Banding Pattern	Technique
Q-banding, Q bands	quinacrine
G-banding, G bands	Giemsa
R-banding, R bands	reverse Giemsa
C-banding, C bands	constitutive heterochromatin
T-banding, T bands	telomeric
NOR	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:

Abbreviation	Expansion
QF	Q bands by fluorescence
QFQ	Q bands by fluorescence using quinacrine
CBG	C bands by barium hydroxide using Giemsa stain
Ag-NOR	NOR staining, silver nitrate technique

Chromosomes contain short and long arms, which are joined at the centromere (Figure 5).

Figure 5. Diagram of chromosome 7 at different levels of resolution showing bands and subbands (reprinted from ISBN 20053 by permission of S Karger AG, Basel, Switzerland).

Figure 5. Diagram of chromosome 7 at different levels of resolution showing bands and subbands (reprinted from ISBN 2005³ by permission of S Karger AG, Basel, Switzerland).

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:

17p	short arm of chromosome 17
3q	long arm of chromosome 3
Xq	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:

Acceptable:	chromosome arm 17p; short arm of 17; 17p
Not:	chromosome 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:

4q3	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:

11q23	chromosome 11, long arm, band 23 (region 2, band 3)
11q23.3	band in above subdivided, resulting in subband 23.3
20p11.23	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.

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,XX	46 chromosomes (2 each of chromosomes 1–22 and 2 X chromosomes in human female karyotype)
46,XY	46 chromosomes (2 each of chromosomes 1–22, 1 X and 1 Y in human male karyotype)
45,X	45 chromosomes, 1 X chromosome (Turner syndrome)
47,XXY	47 chromosomes, 2 X chromosomes, 1 Y (Klinefelter syndrome)
47,XYY	47 chromosomes, 1 X, 2 Y chromosomes
69,XXX	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:

45,X/46,XX

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

47,XX,Þ21 (female)

47,XY,Þ21 (male)

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

48,XX,Þ8,Þ21c

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:

mos 45,X/46,XY

chi 46,XX/46,XY

Brackets indicate the number of cells observed in a clone:

chi 46,XX[25]/46,XY[10]X

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:

46,XY[3]//

//46,XX[17]

46,XY[3]//46,XX[17]

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:

MI,23,XY

MI,24,X,Y

Chromosome Rearrangements.

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 Symbols^a

Abbreviation/Symbol	Explanation
AI	first meiotic anaphase
AII	second meiotic anaphase
ace	acentric fragment
add	additional material of unknown origin
arr	array
b	break
c	constitutional anomaly
cen	centromere
cgh	comparative genomic hybridization
chi	chimera
chr (cs [1985])	chromosome
cht (ct [1985])	chromatid
cp	composite karyotype
cx	complex chromatid interchanges
del	deletion
der	derivative
dia	diakinesis
dic	dicentric
dim	diminished
dip	diplotene
dir	direct
dis	distal
dit	dictyotene
dmin	double minute
dn (de novo [1995])	chromosome abnormality not inherited
dup	duplication
e	exchange
end	endoreduplication
enh	enhanced
fem	female
fis	fission
fra	fragile site
g	gap
h	heterochromatin
hsr	homogeneously staining region
i	isochromosome
idem	stemline karyotype in subclones
ider	isoderivative
idic	isodicentric
inc	incomplete karyotype
ins	insertion
inv	inversion or inverted
ish	in situ hybridization
lep	leptotene
MI	first meiotic metaphase
MII	second meiotic metaphase
mal	male
mar	marker chromosome
mat	maternal origin
med	medial
min	minute acentric fragment
ml	mainline
mn	modal number
mos	mosaic
neo	neocentromere
nuc	nuclear
oom	oogonial metaphase
or	alternative interpretation
p	short arm
PI	first meiotic prophase
pac	pachytene
pat	paternal origin
pcc	premature chromosome condensation
pcd	premature centromere division
prx	proximal
ps	satellited short arm
psu	pseudo-
pvz	pulverization
q	long arm
qdp	quadruplication
qr	quadriradial
qs	satellited long arm
r	ring chromosome
rcp	reciprocal
rea	rearrangement
rec	recombinant chromosome
rev	reverse
rob	robertsonian translocation
roman numerals
I	univalent
II	bivalent
III	trivalent
IV	quadrivalent
s	satellite
sce	sister chromatid exchange
sct	secondary constriction
sdl	sideline
sl	stemline
spm	spermatogonial metaphase
stk	satellite stalk
subtel	subtelomeric region
t	translocation
tan	tandem
tas	telomeric association ter terminal end of chromosome or telomere (tel [1995])
tr	triradial
trc (tri [1985])	tricentric
trp	triplication
upd	uniparental disomy
var (v [1995], var [1985])	variant or variable region
xma	chiasma(ta)
zyg	zygotene
:	break
::	break and reunion
;	separates chromosomes and chromosome bands in structural rearrangements involving 2 or more chromosomes
→	from-to
+	gain
−	loss
∼	intervals and boundaries in a chromosome segment
<>	angle brackets for ploidy
[]	square brackets for number of cells
=	number of chiasmata
×	multiple copies
?	questionable identification
/	separates clones
//	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:

chte	chromatid exchange

Three-letter symbols combined are set with a space:

cht del	chromatid deletion
psu dic	pseudodicentric

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:

short:

46,XY,t(2;5)(q21;q31)

long:

46,XY,t(2;5)(2pter→2q21::5q31→5qter;5pter→5q31::2q21→2qter)

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.

Order. 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).

t(X;13)(q27;q12)

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:

inv(2)(p21q31)

inversion in chromosome 2

Exceptions to numerical order convey special conditions; for example, when a piece of one chromosome is inserted into another (3-break rearrangement), the recipient chromosome precedes the donor:

ins(5;2)(p14;q21q31)

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:

+14	entire chromosome 14 gained

A plus sign following p or q and the chromosome number indicates an addition to that chromosome:

14p+	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:

Shorter Term	Karyotype Term
14p+	add(14)(p13)
14q+	add(14)(q32)

For example:

the 14q+ cytogenetic abnormality was found to be add(14)(q32).

A minus sign preceding a chromosome signifies loss of the entire chromosome:

−5	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:

Text	Karyotype
5q−	del(5)(q13q31)

A deletion of the entire long arm of a chromosome should not be expressed in text with a minus sign.

del(5q)

(not 5q−)

(Use more specific terms in karyotypes.)

Punctuation

Parentheses: the number of the affected chromosome follows the rearrangement symbol in parentheses:

inv(2)

inversion in chromosome 2

Details of the aberration follow in a second set of parentheses:

inv(2)(p13p24)

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:

t(2;5)(q21;q31)

translocation involving breaks at 2q21 and 5q31
Comma: Commas separate the number of chromosomes, sex chromosomes, and each term describing an abnormality:

46,XX,r(18)(p11q22)

female karyotype with ring chromosome 18 with ends joined at bands p11 and q22

Underlining. In different clones within the same karyotype, an underline (underbar) distinguishes homologous aberrations of the same chromosome:

46,XX,der(1)t(1;3)(p34;q21)/46,XX,der(1)t(1;3)(p34;q21)

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.

Or. 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)

Spacing. 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”).

Long Karyotypes. 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)[12]/45,idem, −X[19]/46,idem, −X,+8[5]/47,idem, X,+8,+9[8]

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 Symbols^a

Abbreviation/Symbol	Explanation
amp	amplified signal
arr	array
cgh	comparative genomic hybridization
con	connected signals
dim	diminished signal intensity
enh	enhanced signal intensity
fib ish	extended chromatin/DNA fiber in situ hybridization
FISH	fluorescence in situ hybridization
ish	in situ hybridization
nuc ish	nuclear or interphase in situ hybridization
pcp	partial chromosome paint
rev ish	reverse in situ hybridization
sep	separated signals
subtel	subtelomeric
wcp	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:

46,XY.ish del(22)(q11.2q11.2)(D22S75−)

47,XY,+mar.ish der(8)(D8Z1+)

(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

47,XX,+mar

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:

der(1)t(1;3)(p32;q21)t(1;11)(q25;q13)

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:

der(22)t(9;22)(q34;q11.2)

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).

References

1. Nussbaum RL, McInnes RR, Willard HF. Thompson & Thompson Genetics in Medicine. 6th rev reprint ed. Philadelphia, PA: Saunders; 2004.
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2. Mueller RF, Young ID. Emery’s Medical Genetics. New York, NY: Churchill Livingstone; 2001.
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3. Shaffer LG, Tommerup N, eds. ISCN 2005: An International System for Human Cyto-genetic Nomenclature (2005). Basel, Switzerland: S Karger AG; 2005.
Find This Resource

4. Mitelman F, ed. ISCN 1995: An International System for Human Cytogenetic Nomenclature 1995. Basel, Switzerland: S Karger AG; 1995.
Find This Resource

5. Mitelman F, ed. ISCN (1991): Guidelines for Cancer Cytogenetics: Supplement to an International System for Human Cytogenetic Nomenclature. Basel, Switzerland: S Karger AG; 1991.
Find This Resource

6. Harnden DG, Klinger HP, eds. ISCN (1985): An International System for Human Cytogenetic Nomenclature. Basel, Switzerland: S Karger AG; 1985.
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7. Qumsiyeh MB, Yilmaz Y. Molecular biology of cancer: cytogenetics. In: DeVita VT Jr, Hellman S, Rosenberg SA, eds. Cancer: Principles and Practice of Oncology. 7th ed. Philadelphia, PA: Lippincott Williams & Wilkins; 2005:34-43.
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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.

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