1

MEDICAL CYTOGENETICS

edited by

Hon Fong L. Mark

Brown University School of Medicine

Rhode Island Department of Health

Providence, and

KRAM Corporation

Barrington, Rhode Island

Summarized from chapters 2 and 3

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Contents INTRODUCTION ............................................................................................................................... 4

NORMAL VARIATIONS ..................................................................................................................... 7

SHAPES OF CHROMOSOMES ........................................................................................................... 7

Other Chromosome Attributes.................................................................................................... 8

CHROMOSOME BANDING AND IDENTIFICATION ............................................................................ 9

Chromosome Regions and Band Designations ............................................................................ 9

Karyotype Descriptions ............................................................................................................. 19

NUMERICAL ABNORMALITIES OF CHROMOSOMES ...................................................................... 20

A. Sex Chromosome Aneuploidies ............................................................................................ 20

1. Constitutional Sex Chromosome Aneuploidies ................................................................. 20

2. Acquired Sex Chromosome Aneuploidies ......................................................................... 20

B. Autosome Aneuploidies ........................................................................................................ 21

C. Mosaics and Chimeras ........................................................................................................... 21

D. Uniparental Disomy (upd) ..................................................................................................... 22

STRUCTURAL CHROMOSOME ABNORMALITIES ............................................................................ 23

A. Additional Material, Origin Unknown ................................................................................... 23

B. Deletion ................................................................................................................................. 24

1. Terminal Deletions ............................................................................................................ 24

2. interstitial Deletions .......................................................................................................... 24

C. Derivative and Recombinant Chromosomes ......................................................................... 24

1. Derivative Chromosomes .................................................................................................. 24

2. Recombinant Chromosomes ............................................................................................. 25

D. Insertions............................................................................................................................... 25

1 Insertion Within a Chromosome ........................................................................................ 26

2. Insertion Involving Two Chromosomes ............................................................................. 26

E. Inversions ............................................................................................................................... 26

1. Paracentric Inversion ......................................................................................................... 26

2. Pericentric Inversion .......................................................................................................... 26

F. Isochromosomes .................................................................................................................... 26

1. lsodicentric Chromosomes ................................................................................................ 27

G. Marker Chromosomes .......................................................................................................... 27

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H. Ring Chromosomes ............................................................................................................... 27

I. Translocations ........................................................................................................................ 27

1. Reciprocal Translocations .................................................................................................. 28

2. Whole-Arm Translocations ................................................................................................ 29

3. Robertsonian Translocations ............................................................................................. 29

NEOPLASM, CLONES, AND CLONAL EVOLUTION........................................................................... 30

A. Clones .................................................................................................................................... 30

1. Mainline ............................................................................................................................. 31

2. Stemline and Sideline ........................................................................................................ 31

B. Clonal Evolution-Related Clones ........................................................................................... 31

C. Unrelated Clones ................................................................................................................... 31

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INTRODUCTION The history of human cytogenetics began with the discovery of the correct diploid

chromosome number (46) in man.

Of the 46 chromosomes in a normal human somatic cell, 44 are autosomes and 2 are sex

chromosomes (XX in a female and XY in a male).

A. B.

Figure 1: (a) The normal human female chromosome complement. (b) The normal

human male chromosome complement.

The normal human chromosome complement is shown in Fig. 1a (female) and Fig. 1b

(male). This orderly display of an organism's chromosomes by shape, size (starting with

the largest chromosome), and banding pattern is called a karyotype. Present karyotypes

are GTG-banded karyotypes, derived from metaphases on slides that are treated with

trypsin and stained with Giemsa, a Romanowsky stain, to produce a series of distinctive

transverse bands spaced along the entire chromosome complement (the G-banding

pattern). Banding is used to identify individual chromosomes unambiguously. It is

especially critical for distinguishing chromosomes of similar sizes and shapes. The

different kinds of banding and the various methods employed to induce banding are

discussed later.

Prior to the banding era, chromosomes from nonbanded (or solid-stained) metaphase

cells were karyotyped based on size and position of the centromere. Such a nonbanded

karyotype is shown in Fig. 2. During the prebanding era, other features, such as prominent

satellites and secondary constrictions, were often utilized as well.

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Figure 2: Nonbanded male karyotype.

With the advent of banding in the late 1960s and early 1970s, each chromosome in the

human genome could be identified unambiguously. Based on the unique chromosome

bands, cytogeneticists all over the world were able to identify abnormalities in the

structure as well as the number of chromosomes.

It has been observed that the uniform initial reaction of trainees, when they are handed

the first metaphase for karyotyping, is that the task is nearly impossible to perform: “One

chromosome looks just like another.’’ Proficiency in manual karyotyping needs diligence

and practice. Table 1 gives a tested protocol for identifying each and every chromosome

on a GTG-banded metaphase.

With the availability of instantaneous automated karyotyping system it is usually easier

to perform semimanual karyotyping via instructions of the technologists than to let the

computer do the job entirely by itself and then to correct its many mistakes.

Table1: Morphologic Characteristics of Individual Human Chromosomes

Chromosome Group Morphologic characteristics

1 A The largest metacentric chromosome.

2 A The largest submetacentric chromosome.

3 A The second largest metacentric chromosome

4 B A large submetacentric chromosome. Its arm ratio is approximately 4: 1. It has a small dark band below the centromere.

5 C It is the same size and shape as chromosome 4. It has a large dark band in the middle of the long arm.

6 C The largest of the C group. It has a submedian centromere and a large light area in the middle of the short arm.

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7 C A medium-sized submetacentric chromosome. It has two dark bands in the long arm and a dark band near the tip of the short arm.

8 C A medium-sized submetacentric chromosome. It is the least distinguishable of the C group. It has a dark band near the end of the long arm.

9 C It looks similar to chromosome 7, but is smaller and has less distinct bands. A secondary constriction can sometimes be seen near the centromere on the long arm of chromosome 9.

10 C It has three dark bands in the long arm. The band near the centromere is much darker than the other two.

11 C It has a large dark band in the middle of the long arm.

12 C It has a large dark band in the middle of the long arm. The short arm is noticeably shorter than the short arm of chromosome 11.

13 D An acrocentric chromosome with a dark lower half.

14 D An acrocentric chromosome. It has two dark bands: one near the centromere and the other near the end of the long arm.

15 D An acrocentric chromosome. It is the lightest stained of the D group. It has a small dark band in the middle of the long arm.

16 E The most metacentric of the E group Chromosomes. It is the same size as the D group. It has a dark band at the Centromere.

17 E It is the same size as chromosome 16, but is more submetacentric. It has a large light area in the long arm and a dark band at the end.

18 E It is slightly smaller than chromosome 17. It is mostly dark. It has an occasional noticeably dark band near the centromere.

19 F A small metacentric chromosome with a dark band at the centromere.

20 F A small metacentric chromosome that is grayish.

21 G A small acrocentric chromosome with a dark band

22 G A small acrocentric chromosome that is grayish.

X C It is almost as large as chromosome 6. It has two distinguishing dark bands: one in the middle of the short arm and the other in the long arm.

Y G Although usually the same size as chromosomes 21 and 22, it does not possess satellites and is morphologically distinct.

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NORMAL VARIATIONS Normal variations are called polymorphic variants, polymorphisms, or heteromorphic

variants. Some of the uses of these cytogenetically distinguishable normal variants

include the following:

Use as markers for population studies.

Determination of the origin of nondisjunction.

Paternity determination.

Detection of maternal contamination in amniotic fluid cultures.

Establishment of the origin of ovarian teratomas.

Determination of the zygosity of twins.

Determination of the origin of certain deleted or translocated chromosomes.

In follow-up studies in bone marrow transplantation (BMT), although the Y

chromosome may be a better marker in sex-mismatched BMTs.

Examples of polymorphisms include the large dark heterochromatic block below the

centromere in the long arm of chromosome 1 that varies in size from individual to

individual but is constant from cell to cell within an individual. Another human

chromosomal polymorphism is the pericentric inversion of chromosome 9.

SHAPES OF CHROMOSOMES The shapes of chromosomes are illustrated in Fig. 2.

Metacentric chromosomes have centromeres that lie near the centers of the

chromosomes.

Submetacentric chromosomes contain centromeres in off-center locations on the

chromosomes. The short arm of the chromosome is called p (for petit) arm,

whereas the long arm is called the q arm (Fig. 4).

Acrocentric chromosomes have very short p arms. These chromosomes usually

end in structures called satellites, which are connected to the main structure of

the chromosome by stalks.

Telocentrics are chromosomes that lack short arms. These chromosomes do not

exist in humans.

Chromosomes are grouped by size and position of the centromere. For historic reasons,

however, chromosome 21 is shorter than chromosome 22. The human Y chromosome is

similar in size and shape to chromosomes 21 and 22, but it lacks satellites and has

consistent, albeit subtle, characteristic features such as morphology of the long arm.

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Figure 3: Shapes of chromosomes.

Figure 4: Chromosome landmarks.

Other Chromosome Attributes

The modal chromosome number is the number of chromosomes per cell most often

encountered in the metaphases scored from a sample. The modal chromosome number

in a normal human individual is the diploid number of 46. Due to artifacts of the

technique, chromosomes are sometimes lost on the slide. This is termed random loss. An

International System for Human Cytogenetic Nomenclature defines random loss as the

loss of the same chromosome in no more than two metaphase cells. Loss of a particular

chromosome is considered to be significant if it is encountered in three or more cells.

The arm ratio, q/p, is the length of the long arm divided by the length of the short arm.

The centromere index, expressed as a percentage, is the length of the short arm divided

by the total length of the chromosome, p/(p + q). The relative length, expressed as a

percentage, is the length of that individual chromosome divided by the total haploid

lengths of all the chromosomes in the human genome. Alternative approaches to

estimating relative lengths have been proposed in the literature.

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When chromosomes are stained with a chromatin stain, such as Giemsa or Wright’s stain,

they do not produce bands. Nevertheless, they can be classified into 7 groups based on

the size and centromere position. The letters A-G were assigned to the groups.

Group A (1 -3) Large metacentric or near metacentric chromosomes

distinguishable from one another by the size and the position

of the centromere

Group B (4-5) Largest of the submetacentric chromosomes

Group C (6-12 and X) Medium-sized submetacentric chromosomes (most difficult

to distinguish from one another)

Group D (13-15) Larger acrocentric chromosomes with usually polymorphic

satellites on the short arms

Group E (16-18) Shorter metacentric or submetacentric chromosomes

Group F (19-20) Smallest of the metacentric chromosomes

Group G (21-22 and Y) Smaller acrocentric chromosomes usually with polymorphic

satellites; Y chromosome can be distinguished from the rest of

the G group chromosomes by its lack of satellites and usually

darkly stained heterochromatic long arm

CHROMOSOME BANDING AND IDENTIFICATION When chromosome preparations are treated with dilute solutions of proteolytic enzymes

(trypsin, pepsin, etc.) or salt solutions, (2XSSC) and treated with a chromatin stain, such

as Giemsa, there appeared alternating dark and lightly stained demarcations called bands

which can be seen along the length of each chromosome. The banding patterns produced

are unique to each chromosome pair, thus enabling the identification of individual

chromosomes as well as their regions. Methods commonly used to produce these

discriminative banding patterns include Giemsa or G-banding, quinacrine mustard or Q-

banding, reverse or R-banding, and constitutive heterochromatin or C-banding, each

with its own attributes. The most frequently used methods for routine cytogenetic

analysis are the G- and Q-bands. R-banding and C-banding are occasionally used to

delineate specific abnormalities.

Chromosome Regions and Band Designations

The recommendations of “Paris Conference (1971): Standardization in Human

Cytogenetics’’ provided a diagrammatic representation of banding patterns, elucidating

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the typical band morphology for each chromosome, which came to be known as an

ideogram. The Paris Conference (1971) introduced a numbering system helpful in

designating specific bands and regions while describing a structural abnormality. A partial

list of recommended symbols and abbreviations appears in the following table.

Selected List of Symbols and Abbreviations Used in Karyotype Designations"

Abbreviation Explanation

add Additional material, origin unknown

( or ) Arrow from or to

[ ]square brackets Number of cells in each clone

cen Centromere

chi Chimera

single colon (:) Break

double colon (::) Break and reunion

comma (,) Separates chromosome number from sex chromosome and

also separates chromosome abnormalities

del Deletion

de novo A chromosome abnormality which has not been inherited

der Derivative chromosome

dic Dicentric

dmin Double minute

dup Duplication

fiS Fission

fra Fragile site

h Heterochromatin

i Isochromosome

inv Inversion

ins Insertion

mar Marker chromosome

mat Maternal origin

minus sign (-) Designates loss

mos Mosaic

multiplication sign (X) Multiple copies

P Short arm

Pat Paternal origin

Ph Philadelphia chromosome

plus sign (+) Gain

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q Long arm

question mark (?) Questionable identification

r Ring chromosome

rcp Reciprocal

rec Recombinant chromosome

rob Robertsonian translocation

s Satellite

/ slant line Separates cell lines and clones

semicolon (;) Separates altered chromosomes and breakpoints in

structural rearrangements involving more than one

chromosome

stk Satellite stalk

t Translocation

UPd Uniparental disomy

The most recent ideogram of human chromosomes depicting the regions and bands at

three different resolutions as revealed by the G-banded method is shown in Fig. 2.

The centromere cen divides a chromosome into a short p arm and a long q arm. Each

chromosome arm is divided into regions. This division is based on certain landmarks

present on each chromosome.

By definition, a landmark is a consistent and distinct morphologic area of a chromosome

that aids in the identification of a chromosome.

A region is an area that lies between two landmarks. The regions are numbered in

increasing order starting from the centromere and moving toward the telomere on both

arms. The two regions immediately adjacent to the centromere are designated as 1, the

next distal as 2, and so on. The regions are divided into bands and the bands into

subbands. A band is that part of a chromosome which is distinctly different from the

adjacent area by virtue of being lighter or darker in staining intensity. Sequential

numbering of chromosome arms and bands helps to make the designation of specific

bands easy. For example, the terminal band on the long arm of chromosome 2 can be

written as 2q37, for chromosome 2, long arm, region 3, band 7.

For descriptive purposes, the centromere is divided arbitrarily into two parts. The region

between the middle of the centromere and the first band on the short arm (cen p11 or

p11.1) is designated p10. Similarly, the region between the middle of the centromere and

the first band on the long arm (cen q11 or q11.1) is designated q10. The designations

p10 and q10 allow us to describe isochromosomes, whole-arm translocations, and

Robertsonian translocations more accurately.

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13

14

15

16

17

18

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Figure 2 Ideograms of G-banding patterns for normal human chromosomes at three

different resolutions. The left, center, and right at 450, 550, and 850 band levels,

respectively. (Reproduced with permission from S. Karger, ISCN 1995).

Karyotype Descriptions

The nomenclature for a karyotype follows certain basic rules. When designating a

karyotype, the first item specified is the total number of chromosomes, including the sex

chromosomes present in that cell, followed by a comma (,) and the sex chromosomes, in

that order. Thus a normal female karyotype is written as 46,XX and a normal male

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karyotype as 46,XY. The format is a continuous string of characters, without a space

between characters.

A chromosome abnormality, when present, follows the sex chromosome designation

along with an abbreviation or symbol denoting the abnormality (see Table 3). With a

series of hypothetical cases, we will further illustrate the use of ISCN (1995) in the

following pages.

NUMERICAL ABNORMALITIES OF CHROMOSOMES All numerical abnormalities (aneuploidies) in a karyotype are presented in increasing

order of the chromosome number except for the sex chromosomes. Among sex

chromosomes, X will precede Y. In describing aneuploidy involving more than one

chromosome, the lower number chromosome will be placed first. As a general principle,

aneuploidies are written by using the symbols plus (+) and minus (-). However, there are

some subtle but distinct differences in the nomenclature for aneuploidies involving

autosomes and sex chromosomes as well as for constitutional and acquired aneuploidies.

The following examples will help clarify the differences.

A. Sex Chromosome Aneuploidies

Sex chromosome aneuploidies can be constitutional (congenital) or acquired. ISCN (1995)

has provided special ways to distinguish between the two. Shown below are some

examples of constitutional and acquired sex chromosome aneuploidies.

1. Constitutional Sex Chromosome Aneuploidies

45,X X monosomy as seen in Turner syndrome

47,XXY Typical karyotype seen in Klinefelter syndrome

47,XXX A female with three X chromosomes

48,XXYY Variant of Klinefelter syndrome with two X and two Y chromosomes

2. Acquired Sex Chromosome Aneuploidies

Acquired sex chromosome aneuploidies are presented by using the symbols plus (+) or

minus (-). When presenting a case with both constitutional and acquired sex chromosome

anomalies, the letter c (for constitutional) is placed after the sex chromosome

complement which was seen constitutionally. However, it is not necessary to use c if the

constitutional sex chromosome complement is normal. The following examples show

both scenarios.

45,X,-X A normal female with two X chromosomes and with the loss of one

of the X chromosomes in her tumor cells.

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47,XX,+X A normal female with two X chromosomes and gain of an extra X

chromosome

in her tumor cells.

45,X,-Y A normal male with XY chromosomes and loss of the Y

chromosome in his tumor cells.

48,XY,+X,+Y A normal male with an acquired X and Y chromosomes in his tumor

cells.

48,XXYc,+X A patient with Klinefelter syndrome with an acquired X

chromosome in his tumor cells. The small letter c is placed next to

XXY to show that constitutional sex chromosome complement of

the patient is XXY and not XXXY.

46,Xc,+X A Turner syndrome patient (45,X) with gain of an X chromosome in

her tumor cells

B. Autosome Aneuploidies

The autosome aneuploidies, both constitutional and acquired, are described by simply

placing a + or - sign before the chromosome in question. When both constitutional and

acquired aneuploidies are seen together, place letter c after the chromosome which is

involved in constitutional aneuploidy.

47,XY, + 18 Male with trisomy 18

48,XX,+ 18,+21 Female with both trisomy 18 and trisomy 21

45,XY,-21 Male with monosomy 21

46,XY, + 21c, -21 Male trisomy 21 patient with loss of a chromosome 21 in his tumor

cells

48,XX, + 8, +21c Female trisomy 21 patient with gain of a chromosome 8 in her

tumor cells

C. Mosaics and Chimeras

An individual with two or more cell types differing in chromosome number or structure is

either a mosaic or a chimera. If the two cell types in a specific instance originated from a

single zygote, the individual is a mosaic (mas). If the cell types originated from two or

more zygotes, the individual is a chimera (chi). When designating mosaic or chimeric

karyotypes, a slant line (/) is used to separate the cell types. The actual number of cells

detected in each clone is given within square brackets [ ]. Usages such as percentage and

ratios should be avoided in the karyotype, but may be used in the text.

When two or more cell lines are present and the cell lines are unrelated, the largest clone

is recorded first, the next largest second, and so on. When two or more related abnormal

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cell lines are seen, they are written in order of increasing complexity. In all situations, the

normal cell line is always given last.

mos 45,X[4]/46,XX[16] A mosaic with two cell lines. An analysis of 20 cells

showed that this individual has 4 cells with 45,X and

16 cells with 46,XX karyotypes.

mos 45,X[5]/47,XYY[5]/46,XY[10] A mosaic with three cell lines including normal. Note

that the normal cell line is given last.

mos 47,XX,+13 [15]/46,XX[5] A mosaic with trisomy 13 and normal cell lines. In a

chimera where the two cell lines are normal 46,XX or

46,XY and they are represented in equal proportion,

any one of them may be listed first. If one cell line is

larger than the other, the larger clone is listed first.

chi 46,XX[10]/46,XY[10] A chimera with female and male cells in equal

number.

chi 47,XX, + 2 1 [15]/46,XY [5] A chimera with female and male cell lines. The

female cell line shows trisomy 21, while the male cell

line is normal.

chi 69,XXX[20]/46,XY[5] A chimera with triploid-diploid cell lines. The triploid

line is female, while the diploid line is male.

D. Uniparental Disomy (upd)

In upd, which is also a numerical abnormality, both members of a specific chromosome

pair are inherited from the same parent. Examples include some patients with Angelman

and Prader-Willi syndromes.

46,XY,upd( 15)pat Male karyotype with uniparental disomy for

paternally derived chromosome 15.

46,XY,upd(22)pat[10]/47,XY,+22[6] Mosaic male karyotype with one cell line with upd

for a paternally derived 22

and the other with trisomy 22. Here, both cell

lines are abnormal and therefore

the largest is recorded first.

46,XX,upd pat Paternal upd for all 23 pairs of chromosomes, as

may be seen in complete

hydatidiform moles.

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46,XY,upd pat A complete hydatidiform mole with XY sex

chromosomes (very rare). All 46 chromosomes

are paternally derived.

46,XX,upd mat

Maternal upd as may be seen in ovarian

teratoma. All 46 chromosomes are maternally

derived.

STRUCTURAL CHROMOSOME ABNORMALITIES As stated previously, all abnormalities are presented in increasing order of chromosome

number. However, when the X and Y chromosomes are involved in structural

rearrangements they are listed first, with X: always before Y. When designating an

abnormality which is limited to a single chromosome, the abbreviation of the abnormality

is given and then the number of the chromosome is written within parentheses, such as,

de1(2), ins(4), dup(5), and r(X:). If two or more chromosomes are involved in a

rearrangement, such as in a translocation, a semicolon (;) separates each

chromosome. Some examples are t(3;4), t(2;3;4), or t(15;17). The chromosome arm and

the breakpoint for the chromosomes involved are separated by a semicolon within a

second set of parentheses. The chromosome number that is entered first is usually the

one with the smallest number, unless a sex chromosome is involved. In such an event the

sex chromosome is always designated first, e.g., t(X:;l) or t(Y,15). If in the same cell a

specific chromosome is involved in both a numerical and a structural rearrangement, the

numerical abnormality is designated first, e.g., +13,der(13;14). The chromosome

nomenclature may be written in two different ways, namely, the short form and the long

form. The long form allows better understanding of the karyotype by way of suggesting

the chromosome region present in a karyotype and designating the bands where the

break: and the reunion occur. In rare situations, particularly in structural rearrangements,

the long form may be the only way to show where and how the rearrangement occurred.

However, most practicing clinical cytogeneticists use the short form to report their results

since it is concise and brief. Cytogenetic reports must contain description of the

rearrangements in words, particularly in reporting abnormal

karyotypes. This is an essential element of the laboratory report because the consumers

of the report, most often, are not scientists. Following are a few examples of using short

and long forms of nomenclature.

A. Additional Material, Origin Unknown

When additional chromosome material is attached to a chromosome, usually its origin is

not identifiable through conventional banding methods. This is especially true if the

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abnormality is subtle and originates de novo. The abbreviation add is then used to record

the rearrangement:

46,XX,add( 17)(p13) Short form

46,XX,add(17)(?::p13qter) Long form

Additional material of unknown origin is attached to chromosome 17 band 17p13.

Here the type of rearrangement that resulted in the abnormality is also unknown.

46,XX,add(9)(q22) Short form

46,XX,add(9)(pterq22::?) Long form

Additional material of unknown origin attached to band 9q22. It is assumed that

the chromosome region 9q22+qter is deleted and replaced by the added material.

B. Deletion

A deletion is an aberration in which a part of a chromosome is lost. Deletions can be either

terminal or interstitial.

1. Terminal Deletions

46,XY7dell() (q32) Short form

46,XY,del( l)(pter+q32:) Long form

A karyotype with terminal deletion of chromosome 1. A single colon (:) indicates a break

at lq32 and deletion of the region distal to it. The remaining chromosome consisting of

regions lpter to lq32 is present in the cell. (The terminal regions of the short and long

arms of a chromosome are designated by pter and qter, respectively).

2. interstitial Deletions

46,XY,del(1)(p2lp32) Short form

46,XY,del( 1)(pterp21 ::p32qter) Long form

A break and reunion represented by a double colon (::) occurred at bands lp32 and lp21. The segment between the two breakpoints is deleted.

C. Derivative and Recombinant Chromosomes

1. Derivative Chromosomes

A structurally rearranged chromosome generated by events involving two or more

chromosomes or due to multiple events within a single chromosome is a derivative

chromosome. Thus, each unbalanced product of a translocation event is a derivative

chromosome and is designated by the abbreviation der. The identity of the Centromere

in a derivative chromosome determines its chromosome number. For example, der(3)

indicates that this derivative chromosome has the chromosome 3 centromere.

46,XY,der(3)t(3;6)(p21;q23)

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The derivative chromosome 3 in this example resulted from an adjacent 1 segregation of a balanced translocation between the short arm of a chromosome 3 at band p21 and the long arm of a chromosome 6 at band q23. The modal number of 46 chromosomes in this example indicates that there are two normal chromosomes 6. The der(3) replaces one normal chromosome 3. This unbalanced karyotype shows loss (monosomy) of region 3p21+pter and gain (trisomy) of 6q23+qter.

45,XY,der(3)t(3;6)(p21;q23),-6 The der(3) is same as in the above example and replaces one of the normal chromosome 3. However, there is only one normal chromosome 6 in the cell, the result of a 3: 1 segregation. Note that the chromosome number in a cell is critical in understanding the nomenclature. Also note that the -6 is placed at the end of the karyotype. This unbalanced karyotype represents monosomy for the 3p21 to the pter region of chromosome 3 and monosomy for the 6pter to the 6q23 region of chromosome 6.

47,XY7+der(3)t(3;6)(p21;q23)mat The der(3) is the same as in the first example. As a result of 3:1 segregation, the mother contributed a normal 3 and the derivative 3. The father contributed a normal 3 as well. The patient is therefore trisomic for both 3p21+qter and 6q23+qter.

2. Recombinant Chromosomes

A recombinant chromosome is also a structurally rearranged chromosome. It arises from

meiotic crossing over between two homologous chromosomes in a heterozygote: one a

structurally rearranged chromosome and the other a normal homolog. Recombinant

chromosomes commonly arise due to crossing over within the limits of the inversion in

an inversion heterozygote.

46,XY,inv(3)(p21q32) A pericentric inversion of a chromosome 3 is designated above. During meiosis, crossing over within the inverted segment could result in two recombinant chromosomes.

46,XY,rec(3)dup(3p)inv(3)(p2lq32) Duplication from 3pter to 3p21 and deletion from 3q32 to 3qter.

46,XY,rec(3)dup(3q)inv(3)(p2lq23) Duplication of 3q23 to qter and deletion from 3p21 to 3pter.

D. Insertions

An insertion is a structural rearrangement wherein a part of a chromosome is inserted

into a new place on a chromosome. Insertions can be within a chromosome or between

two chromosomes, and can be direct or inverted.

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1 Insertion Within a Chromosome

46,XX,ins(3)(p21q27q32) This represents a direct insertion within a chromosome. The long arm segments between band 3q27 and 3q32 have been inserted into the short arm of the same chromosome at band 3p21.

2. Insertion Involving Two Chromosomes

46,XX,ins(4;9)(q31;ql2q13) The long arm segments between bands 9q12 and 9q13 have been inserted into the long arm of chromosome 4 at band q31. The recipient chromosome is always specified first, regardless of the chromosome number.

E. Inversions

A chromosomal aberration in which a portion (segment) of a chromosome is reversed in

orientation. Inversions are of two types. Paracentric inversions involve only one arm of a

chromosome, while pericentric inversions involve both arms of a chromosome.

1. Paracentric Inversion

46,XY,inv(3)(q21q27) A break and a reunion occurred at bands 3q21 and 3q27 (long arm) of a chromosome 3. The interlying segment was reattached with its bands in an inverted sequence.

2. Pericentric Inversion

46,XY,inv(2)(p21q31) A break and a reunion occurred at bands 2p21 in the short arm and 2q31 in the long arm of a chromosome 2. The interlying segment was reattached with its bands in an inverted sequence.

F. Isochromosomes

An abnormal chromosome with duplication of one of the arms (as a result of a misdivision

of the centromere) resulting in a metacentric chromosome with identical gene sequences

on both arms is referred to as an isochromosome. In the karyotype the isochromosome

is abbreviated as i. When the nature of the centromere is not known (monocentric or

dicentric), the breakpoint in an isochromosome is assigned to the arbitrary centromeric

bands p 10 and q10 depending upon whether the isochromosome consists of the short

arm or the long arm. The use of p10 and q10 will be further demonstrated under

Robertsonian translocations and whole arm translocations.

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46,XX,i(18)(p10) An isochromosome for the short arm of a chromosome 18. The breakpoint is assigned to p 10.

46,XX,i(18)(q10) An isochromosome for the long m of a chromosome 18. The breakpoint is assigned to q10.

1. lsodicentric Chromosomes

Unlike the isochromosome, the isodicentric chromosome contains two copies of the same

centromeres. One of the two centromeres is usually inactive. Designated by idic, the

breakpoints in isodicentric chromosomes are usually on the band adjacent to the

centromere on the opposite arm.

46,XX,idic( 18)(ql1.2) An isodicentric chromosome for the entire short arm of chromosome 18 as well as for the long m region between the centromere and the band 18q11.2.

G. Marker Chromosomes

Marker chromosomes mar are structurally abnormal chromosomes of which no part can

be identified. If any part of such a marker is identifiable it is no longer a marker but a

derivative chromosome. The presence of a mar in a karyotype is always recorded by a

plus (+) sign.

47,XY,+mar A male karyotype with a marker chromosome.

48,XY, + 2mar A male karyotype with two marker chromosomes.

48,XY,t(5;12)(q13;pl2),+21,+mar A male karyotype with a t(5;12), an extra chromosome 21 and a marker chromosome.

H. Ring Chromosomes

A structurally abnormal chromosome as a result of two breaks, one on the short arm and

one on the long arm. The broken ends are attached to form a ring configuration. The net

result is deletions of the terminal ends of both arms.

46,X,r(X) A female karyotype with only one normal X chromosome and a ring X chromosome with no information on breakpoints.

46,Xr(X)(p22q24) A female karyotype with one noma1 X chromosome and a ring X chromosome with breakage and reunion at bands Xp22 and Sq24.

I. Translocations

The interchange or transfer of chromosomal segments between two chromosomes

is defined as a translocation.

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1. Reciprocal Translocations

If the translocation involves a mutual exchange of segments between two chromosomes,

it is a reciprocal translocation. To describe a reciprocal translocation the abbreviation rcp

or the letter t can be used. The latter is more often used. In translocations involving two

chromosomes, the autosome with the lowest number is specified first. If an X or Y

chromosome is involved in the translocation, the X or Y is specified first, in preference to

the autosomes. If the translocation involves three or more chromosomes, the same rule

applies. However, in such rearrangements the first chromosome will be the one with the

lowest number (or sex chromosome), the second chrornosome specified will be the one

that received the segment from the first, and so on.

46,XX,t(7; 10)(q22;q24) Breakage and reunion occurred at bands 7q22 and lOq24. The segments distal to these bands were interchanged. The translocation event has not altered the total DNA content of this cell. Therefore, the translocation is cytogenetically balanced.

46,X7t(X;1)(p21;q32) Breakage and reunion occurred at bands Xp21 and lq32. The segments distal to these bands were interchanged. The translocation is balanced. As per the general rules, the X chromosome is specified first.

46,X7t(Y;15)(q11.23;q21.2) Breakage and reunion occurred at subbands Yql 1.23 and 15q21.2. The segments distal to these subbands were interchanged. This translocation is cytogenetically balanced. Here again, the sex chromosome is specified first.

46,XY,t(9;22)(q34;q11.2) Breakage and reunion occurred at bands 9q34 and 22q11.2. The segments distal to these bands have been interchanged. This represents the typical translocation resulting in the Philadelphia (Ph) chromosome.

46,XX,t(1;7;4)(q32;p15;q21) This is an example of a translocation involving three chromosomes. The segment on chromosome 1 distal to lq32 has been translocated onto chromosome 7 at band 7 p15, the segment on chromosome 7 distal to 7p15 has been translocated onto band 4q21, and the segment on chromosome 4 distal to 4q21 has been translocated onto chromosome 1 at lq32. The translocation is cytogenetically balanced.

The general principles also apply to designating translocations involving more than three

chromosomes.

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2. Whole-Arm Translocations

Whole-arm translocation is also a type of reciprocal translocation in which the entire arms

of two nonacrocentric chromosomes are interchanged. Such rearrangements are

described by assigning the breakpoints to the arbitrary centromeric region designated as

p10 and q10. The breakpoint p10 is assigned to the chromosome with the lower number

of the two chromosomes involved or the sex chromosome. Consequently, the second

chromosome will have a breakpoint at q10. This assignment is particularly useful in

describing whole-arm translocations in which the nature of the centromere is not known.

46,XX,t(3;8)(p10;q10)

A balanced whole-arm translocation between chromosome 3 and chromosome 8. In this example the short arm of chromosome 3 and the long arm of chromosome 8 have been fused. Reciprocally, the long arm of chromosome 3 has fused with the short arm of chromosome 8. However, it need not be written in the karyotype. The modal number 46 is also indicative of the presence of the reciprocal product. Which abnormal chromosome carries the centromere of 3 or 8 is not known. The karyotype is apparently balanced.

46,XX,t(3;8)(p10;p10) Balanced whole-arm translocation in which the short arms of chromosomes 3 and 8 and the long arms of chromosome 3 and 8 have been fused.

45,X,der(X;3)(p10;q10) A derivative chromosome consisting of the short arm of X and the long arm of 3. The reciprocal product consisting of the long arm of X and the short arm of 3 is missing. Note: the total chromosome number is 45, suggesting the loss of the reciprocal product. The net result is monosomy for the entire long arm of X and the entire short arm of 3.

47,XX,+der(X;3)(p10;q10) This karyotype has an extra derivative chromosome consisting of the short arm of X and the long arm of 3 (same as in the previous example). Also present are two normal X chromosomes and two normal chromosomes 3. The net result is trisomy for the entire short arm of X and the entire long arm of 3.

3. Robertsonian Translocations

Robertsonian translocations originate through centric fusion of the long arms of

acrocentric chromosomes consisting of pairs 13, 14, 15, 21, and 22. Since Robertsonian

translocations are also whole-arm translocations, they can be described adequately using

the same nomenclature approach as for whole arm translocations. In a Robertsonian

translocation, the short arms of the chromosomes involved are lost. In the translocation

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heterozygote the loss of short arms is not known to be causally related to an abnormal

phenotype. However, in order to maintain uniformity in the nomenclature, a

Robertsonian translocation product is considered to be a “derivative chromosome” and

therefore the symbol der is used. For historical reasons, the abbreviation rob may also be

used.

45,XX,der(13;14)(q10;q10) A balanced Robertsonian translocation occurred between the long arm of a chromosome 13 and the long arm of a 14. As a result, the chromosome number was reduced to 45. The origin of the centromere nature is unknown. Breakage and reunion have occurred at bands 13q10 and 14q10. This derivative chromosome has replaced one chromosome 13 and one chromosome 14. There is no need to indicate the missing chromosomes because the chromosome number is reduced to 45. The karyotype now contains one normal 13, one normal 14, and the der(13;14). The short arms of the 13 and 14 are lost, which is not associated with an adverse clinical outcome.

46,XX,+13,der(13;14)(q10;q10) A derivative chromosome consisting of the long arms of a 13 and a 14, same as in the above example. However, in this karyotype there are two normal 13 and one normal 14. The additional 13 is shown by the designation + 13. In this example a 13 is involved in both numerical and structural abnormalities. In such instances the numerical abnormality is designated before the structural abnormality.

NEOPLASM, CLONES, AND CLONAL EVOLUTION All principles dictating the nomenclature are identical to both constitutional and acquired

changes. However, some unusual situations and circumstances apply uniquely to

acquired chromosome changes. We will define some of the terminology used in the

description of acquired changes. We will also give some examples of complex

chromosome rearrangements not usually seen in constitutional karyotypes.

A. Clones

A clone is defined as a cell population derived from a single progenitor. In acquired

chromosome changes, a clone is defined as two cells with the same structural aberration.

In numerical aberrations, a trisomic clone must have at least two cells with the same extra

chromosome; for a monosomy clone, a minimum of three cells must show the loss of the

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same chromosome. A clone is not necessarily homogeneous, since subclones may

develop during evolution.

1. Mainline

The mainline is the most frequent chromosome complement of a tumor cell population.

It is a quantitative term and does not indicate the sequence of origin, such as primary

versus secondary.

46,XX,t(9;22)(q34;ql1.2)[3]/47,XX,+8,t(9;22)(q34;ql1.2)[17] In the above karyotype, the clone with 47 chromosomes is the mainline, even though it is likely that the basic or the primary clone was the one with 46 chromosomes.

2. Stemline and Sideline

The stemline ( SE ) is the most basic clone of a tumor cell population. All additional

subclones are termed sidelines (sdl).

46,XX,t(9;22)(q34;ql1.2)[3]/47,XX,+8,t(9;22)(q34;ql1.2)[17]/48,XX,+8, t(9;22)(q34;ql1.2),+ 19[12] In the above example, the clone with 46 chromosomes is the stemline and the clones with 47 and 48 chromosomes are the sidelines. The clone with 47 Human Cytogenetic Nomenclature chromosomes is the mainline since the largest number of cells show that karyotype.

B. Clonal Evolution-Related Clones

Cytogenetically related clones are presented in the order of increasing complexity as far

as possible, regardless of the size of the clone. This means that the stemline is presented

first, followed by the subclones in the order of increasing complexity.

46,XX,t(8;21)(q22;q22)[12]/45,X-X,t(8;21)(q22;q22)[19]/46,X,-X,+8,t(8;21)(q22;q22)[5] In tumors with related clones such as the one above, the term idem may be used followed by the additional changes. The idem can replace only the stemline, which is usually given first. Example: 46,XX,t(8;21)(q22;q22)[12]/45,-X,idem[19]/46,- X,+8,idern[5]

C. Unrelated Clones

Clones with completely unrelated aberrations are presented according to their size, the

largest first, then the second largest, and so on. The normal diploid clone is always

presented last.

46,XX,t(8;21)(q22;q22)[10]/47,XX,+8[6]/45,XX,i(8)(q10)[4]

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If a tumor contains both related and unrelated clones, the related clones are written first in the order of increasing complexity, followed by the unrelated clones in order of decreasing size.

Numerous other more complex structural karyotypic changes may be encountered. These

cases are rather rare and are not addressed here. However, one can easily extrapolate

from the basic principles eluded to earlier and throughout this chapter and arrive at the

proper nomenclature.