2013

ISCN

An International System for

Human Cytogenetic Nomenclature (2013)
Editors
Lisa G. Shaer
Jean McGowan-Jordan
Michael Schmid
Recommendations of the International Standing Committee on
Human Cytogenetic Nomenclature

This report should be cited in text as ISCN (2013).

The complete citation for reference lists is: ISCN (2013):
An International System for Human Cytogenetic Nomenclature,
L.G. Shaer, J. McGowan-Jordan, M. Schmid (eds); S. Karger, Basel 2013

Published in
collaboration with

Published in collaboration with Cytogenetic and Genome Research under the title ISCN 2013:
An International System for Human Cytogenetic Nomenclature (2013)
VI + 140 p. plus fold-out, 11 g., 4 tab., 2013
Although produced by the editors and publishers of Cytogenetic and Genome Research, this
publication is independent of the subscription.
Copies of ISCN 2013 can be ordered from the publishers:
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Library of Congress Cataloging-in-Publication Data

International Standing Committee on Human Cytogenetic Nomenclature.
ISCN 2013 : an international system for human cytogenetic nomenclature
(2013) / editors, Lisa G. Shaffer, Jean McGowan-Jordan, Michael Schmid.
p. ; cm.
International system for human cytogenetic nomenclature (2013)
Recommendations of the International Standing Committee on Human
Cytogenetic Nomenclature.
Published in collaboration with Cytogenetic and Genome Research.
Includes bibliographical references and index.
ISBN 978-3-318-02253-7 (soft cover : alk. paper)
I. Shaffer, Lisa G. II. McGowan-Jordan, Jean. III. Schmid, M. (Michael)
IV. Cytogenetic and genome research. V. Title. VI. Title: International
system for human cytogenetic nomenclature (2013).
[DNLM: 1. Cytogenetics--Terminology--English. QU 15]
611.01816--dc23
2012034067

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ISBN 9783318022537

Table of Contents

1
1.1
1.2
1.3
1.4
1.5

Historical Introduction .....................................................................

2
2.1
2.2
2.2.1
2.2.2
2.2.3
2.3
2.3.1
2.3.2
2.4
2.5

Normal Chromosomes .....................................................................

Introduction..........................................................................................
Chromosome Number and Morphology.....................................................
Non-Banding Techniques ........................................................................
Banding Techniques ...............................................................................
X- and Y-Chromatin ................................................................................
Chromosome Band Nomenclature ............................................................
Identication and Denition of Chromosome Landmarks, Regions, and Bands . .
Designation of Regions, Bands, and Sub-Bands ...........................................
High-Resolution Banding ........................................................................
Molecular Basis of Banding ......................................................................

6
6
6
6
7
8
9
9
10
12
15

Symbols and Abbreviated Terms ....................................................

36

4
4.1
4.2
4.3

Karyotype Designation ....................................................................

39
39
41

4.3.1
4.3.1.1
4.3.1.2
4.3.1.3
4.3.2
4.3.2.1
4.3.2.2
4.4
4.5

19561984............................................................................................
19851995............................................................................................
19962004............................................................................................
20052009............................................................................................
20102013............................................................................................

General Principles ..................................................................................

Specication of Breakpoints .....................................................................
Designating Structural Chromosome Aberrations by Breakpoints and
Band Composition .................................................................................
Short System for Designating Structural Chromosome Aberrations .................
Two-Break Rearrangements .....................................................................
Three-Break Rearrangements ...................................................................
Four-Break and More Complex Rearrangements ..........................................
Detailed System for Designating Structural Chromosome Aberrations.............
Additional Symbols ................................................................................
Designating the Band Composition of a Chromosome ..................................
Derivative Chromosomes ........................................................................
Recombinant Chromosomes ....................................................................

1
1
3
4
5
5

42
42
42
43
44
44
44
45
45
46

Uncertainty in Chromosome or Band Designation ........................

5
5.1
5.2
5.3
5.4

Questionable Identication .....................................................................

Uncertain Breakpoint Localization or Chromosome Number ..........................
Alternative Interpretation ........................................................................
Incomplete Karyotype ............................................................................

49
49
50
50
51

Order of Chromosome Abnormalities in the Karyotype ................

52

7
7.1
7.1.1
7.1.2
7.2

Normal Variable Chromosome Features .........................................

53
53
53
53
54

8
8.1
8.2
8.3
8.4

Numerical Chromosome Abnormalities..........................................

9
9.1
9.2
9.2.1
9.2.2
9.2.3
9.2.4
9.2.5
9.2.6
9.2.7
9.2.8
9.2.9
9.2.10
9.2.11
9.2.12
9.2.13
9.2.14
9.2.15
9.2.16
9.2.17
9.2.17.1
9.2.17.2
9.2.17.3
9.2.17.4
9.2.18
9.2.19
9.3

Structural Chromosome Rearrangements ......................................

Variation in Heterochromatic Segments, Satellite Stalks, and Satellites ............

Variation in Length .................................................................................
Variation in Number and Position .............................................................
Fragile Sites ..........................................................................................

General Principles ..................................................................................

Sex Chromosome Abnormalities ...............................................................
Autosomal Abnormalities ........................................................................
Uniparental Disomy................................................................................

General Principles ..................................................................................

Specication of Structural Rearrangements ................................................
Additional Material of Unknown Origin ......................................................
Deletions ..............................................................................................
Derivative Chromosomes ........................................................................
Dicentric Chromosomes ..........................................................................
Duplications .........................................................................................
Fission .................................................................................................
Fragile Sites ..........................................................................................
Homogeneously Staining Regions ............................................................
Insertions .............................................................................................
Inversions .............................................................................................
Isochromosomes ...................................................................................
Marker Chromosomes.............................................................................
Neocentromeres ....................................................................................
Quadruplications ...................................................................................
Ring Chromosomes ................................................................................
Telomeric Associations ...........................................................................
Translocations .......................................................................................
Reciprocal Translocations ........................................................................
Whole-Arm Translocations.......................................................................
Robertsonian Translocations ....................................................................
Jumping Translocations ..........................................................................
Tricentric Chromosomes .........................................................................
Triplications ..........................................................................................
Multiple Copies of Rearranged Chromosomes .............................................

IV

55
55
56
57
58
59
59
60
60
61
62
67
69
69
69
70
71
72
72
73
75
75
75
77
78
78
80
81
82
83
83
83

ISCN 2013

10
10.1
10.1.1
10.1.2
10.2
10.2.1
10.2.2
10.3

Chromosome Breakage....................................................................

11
11.1
11.1.1
11.1.2
11.1.3
11.1.4
11.1.5
11.1.6
11.2
11.3

Neoplasia ..........................................................................................

12
12.1
12.1.1
12.1.2

Meiotic Chromosomes .....................................................................

13
13.1
13.2
13.2.1
13.2.2
13.3
13.3.1
13.3.2
13.3.2.1
13.3.2.2
13.3.2.3
13.3.2.4
13.4
13.5
13.5.1

In situ Hybridization ........................................................................

13.6
13.7
13.8

Chromatid Aberrations ...........................................................................

Non-Banded Preparations .......................................................................
Banded Preparations ..............................................................................
Chromosome Aberrations .......................................................................
Non-Banded Preparations .......................................................................
Banded Preparations ..............................................................................
Scoring of Aberrations ............................................................................

Clones and Clonal Evolution ....................................................................

Denition of a Clone ...............................................................................
Clone Size.............................................................................................
Mainline ...............................................................................................
Stemline, Sideline and Clonal Evolution .....................................................
Composite Karyotype .............................................................................
Unrelated Clones ...................................................................................
Modal Number ......................................................................................
Constitutional Karyotype .........................................................................

Terminology .........................................................................................
Examples of Meiotic Nomenclature ...........................................................
Correlation between Meiotic Chromosomes and Mitotic Banding Patterns .......

Introduction..........................................................................................
Prophase/Metaphase in situ Hybridization (ish) ...........................................
Use of dim and enh ................................................................................
Subtelomeric Metaphase in situ Hybridization ............................................
Interphase/Nuclear in situ Hybridization (nuc ish) ........................................
Number of Signals..................................................................................
Relative Position of Signals ......................................................................
Single Fusion Probes ..............................................................................
Single Fusion with Extra Signal Probes .......................................................
Dual Fusion Probes ................................................................................
Break-Apart Probes ................................................................................
In situ Hybridization on Extended Chromatin/DNA Fibers (b ish) ...................
Reverse in situ Hybridization (rev ish) ........................................................
Chromosome Analyses Using Probes Derived from Sorted or Microdissected
Chromosomes .......................................................................................
Chromosome Comparative Genomic Hybridization (cgh) ..............................
Multi-Color Chromosome Painting ............................................................
Partial Chromosome Paints ......................................................................

Table of Contents

85
85
85
86
86
86
87
87
88
88
88
89
89
90
92
94
94
95
97
97
98
100
105
105
105
111
111
111
112
115
117
117
117
118
119
119
119
120
120
120

14
14.1
14.2
14.2.1
14.2.2

Microarrays .......................................................................................

15
15.1
15.2
15.3

Region-Specic Assays.....................................................................
Introduction..........................................................................................
Examples of RSA Nomenclature for Copy Number Detection .........................
Examples of RSA Nomenclature for Balanced Translocations or Fusion Genes . . .

129
129
129
130

16

References ........................................................................................

131

17

Members of the ISCN Standing Committee and Consultants ........

133

18

Appendix ..........................................................................................

135

19

Index .................................................................................................

137

Introduction..........................................................................................
Examples of Microarray Nomenclature .......................................................
Nomenclature Specic to SNP Arrays .........................................................
Complex Array Results ............................................................................

VI

121
121
122
127
128

ISCN 2013