Jump to ContentJump to Main Navigation
Contents

Human Chromosomes

Chapter:
Nomenclature
Author(s):

Harriet S. Meyer

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 reports4-6 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).

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 Symbolsa

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 Symbolsa

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.Find This Resource

    2. Mueller RF, Young ID. Emery’s Medical Genetics. New York, NY: Churchill Livingstone; 2001.Find This Resource

      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.Find This Resource

              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.Find This Resource

                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.

                Previous | Next