Babak Nami

1. Introduction1. Introduction

The discovery of the chromosomal etiology of any abnormalities likes Downsyndrome, Turner syndrome, Klinefelter syndrome, etc was irregular to classifyand give an account them. The need for guidelines and standardization ofterminology thus become imperative, therefore hold some internationalconferences on human chromosome nomenclature:

2. Human chromosomes• There is 46 chromosomes in a normal human somatic cell. Of them 44 are autosomes

and 2 are sex chromosomes.• The autosomes are assigned in descending order of length, size and centromere

position of each pair. Sex chromosomes assign at last.• In a normal male the sex chromosomes are XY, and in a normal female ,they are XX.

• According to Chicago conference chromosomes in the centromere position classified into three basic categories:

Metacentric: a chromosome whit its centromere placed in middle

Sub-metacentric: a chromosome whit its centromere placed closer to one end of it

Acrocentric: a chromosome whit its centromere placed almost one end of it

3. Chromosomes Identification3. Chromosomes Identification

Identification of individual chromosomes and chromosome regions for extracted chromosomes at metaphase late become possible with banding techniques:

3.1. G-banding: there is refers to staining by Giemsa after digesting the chromosomes with trypsin. In this pattern dark bands in a light background are available. This method will normally produce 300-400 bands in a normal, human genome and is using routinely in USA, Canada and many countries.

3.2. Q-banding: utilize quinacrine mustard or similar matters and fluorescencemicroscope for appearing light bands. Note these bands conform on dark bands microscope for appearing light bands. Note these bands conform on dark bands in G-banding pattern.

3.3. R-banding: is the reverse of G-banding (the R stands for "reverse"). The dark regions are euchromatic (guanine-cytosine rich regions) and the bright regions are heterochromatic (thymine-adenine rich regions).This method is useful to observe bands that don’t sufficiently stained in G and Q banding. R-banding is a standard method for distinguish any chromosome abnormality at the European countries like France especially.

3.4. C-banding: Staining centromeric region and ‘Constitutive heterochromatin’ is basis matter in this method.

G-banding pattern

Q-banding patternQ-banding pattern

Normal 46,XY male karyotype. Characteristic G-banding (top) and fluorescent Q-banding (bottom). The same cell was used for both methodologies to demonstrate the complementary banding patterns.

4. Chromosomes Description4. Chromosomes Description

4.1. Chromosomes Arms: Each chromosome divided by the centromere into a short or ‘p’ arm (from the French petit) and a long or ‘q’ arm (from the French queue). Region from centromere to end of p arm called “p10”, and from the centromere to end of q arm called “q10”:

4.2. Chromosomes regions: Each chromosome arm is divided into regions. This division is based on certain landmarks present on each chromosomes. A region is an area that lies between two landmarks.

The two regions immediately adjacent to the centromere are designated as “1” (p1 and q1), the next distal as “2”, and so on.

4.3. Chromosomes bands and subbands: Regions are divided into bands and the bands into subbands. A band is that part of a chromosome that is distincly different from the adjacent area by virtue of being lighter or darker in staining intensity.• Each band defined as a numbered and after a related region number.• subband defined as a number after a dot sign that pointed after related band • subband defined as a number after a dot sign that pointed after related band number

Example:The terminal band in the long arm of chromosome 2 can be written as :

2q37To mean chromosome 2, long arm, region 3, band 7 and is referred to as

“Two q Three Seven”not

“Two q Thirty-seven”

2q24.3Chromosome: 2Arm: Long(q)Region: 2Band: 4Subband: 3

2q24.3Chromosome: 2Arm: Long(q)Region: 2Band: 4Subband: 3Subband: 3Subband: 3

5. Karyotype Descriptions5. Karyotype Descriptions

1. A normal female karyotype is written as 46,XX and normal male karyotype as 46,XY

Note: the characters are contiguous, without space between items. 2. Sex chromosome abnormalities are describe first, following by autosomal changes in numerical order. For each chromosome described, numerical changes are listed before structural abnormalities.

6. Nomenclature of chromosomes abnormalities6. Nomenclature of chromosomes abnormalities

There are two groups of abnormalities discussed about chromosomes:

6.1. Numerical abnormalities of chromosomes:The term “numerical abnormalities” refers to changes in the number of

chromosomes by gain or loss of chromosome(s). This is called Aneoploidy too(an abnormal number of chromosomes), and occurs when an individual ismissing either a chromosome from a pair (monosomy) or has more than twochromosomes of a pair (Trisomy, Tetrasomy, etc).

6.2. Structural chromosome abnormalities:When the chromosome's structure is altered. This can take several forms:

• Deletions• Duplications• Translocations• Inversions• Rings• Isochromosomes

Aneoploidies involving the sex chromosomesAneoploidies involving the sex chromosomes

• Constitutional: (5% of whole pregnancies)

45,X Classical monosomy X or Turner syndrome

47,XXY Classical Klinefelter syndrome47,XXX A female with three X chromosomes48,XXYY Variant of klinefelter syndrome

• Acquired: (Certain leukemias and solid tumors)

45,X,-X

(Normal female with two X chromosomes but with the loss of one X in her tumor cells)

47,XX,+X(Normal female with two X chromosomes and gain of an extra X in her tumor cells)

48,XY,+X,+Y(This is describes a male with acquired X and Y chromosomes his tumor)

48,XXYc,+X(Here, we have a patient with klinefelter syndrome who has an acquired X chromosome in his tumor cells. The letter “c” is placed next to XXY to show that the patient’s sex chromosome complement is XXY and not XY or XXXX )

Numerical Abnormalities of the AutosomesNumerical Abnormalities of the Autosomes

In this matter the exception that (+) and (-) signs are used to designate constitutionals.

47,XY,+18 Male with trisomy 1848,XX,+18+21 Female with both trisomy 18 and trisomy 2145,XY,-21 Male with monosomy 2145,XY,-21 Male with monosomy 2146,XY,+21c,-21 Male trisomy 21 patient with loss of one chromosome 21 in his tumor cells48,XX,+21c,+21 Female with trisomy 21 and gain of an additional chromosome 21 an her tumor cells

Mosaics and ChimerasMosaics and Chimeras

An individual with two or more cell types, differing in chromosome number or structure is either a mosaic or a chimera.

Mosaic: the cell types originated from a single zygote.Chimera: the cell types originated from two or more zygote that subsequently fused.

• In designating mosaic or chimera karyotype, a slash (/) is used to separate the cell lines. separate the cell lines.

• The actual number of cells detected in each clone can be given within [ ].

• The largest clone is recorded first, then the next largest, and so on.

• Whenever a normal cell line is present, it is always recorded last, irrespective of the number of normal cells detected.

mos 45,X[4]/46,XX[16]

This is Turner mosaic with two cell lines.

mos 45,X[4]/46,XX[16]

This is Turner mosaic with two cell lines.

mos 45,X[4]/46,XX[16]

Analysis of 20 cells (4+16) showed that this individual has 4 cells that are 45,X and 16 cells are 46,XX.

Analysis of 20 cells (4+16) showed that this individual has 4 cells that are 45,X and 16 cells are 46,XX.

Mos 45,X[5]/47,XYY[5]/46,XY[10]This represents a mosaic with three cell lines.

In a chimera where the two cell lines are normal (46,XX and 46,XY) and both are present in equal proportions, either one of them can be listed first. If one cell line is larger clone is listed first.

chi 46,XX[10]/46,XY[10]This describes a chimera with female and male cells in equal number.

chi 47,XX+21[15]/46,XY[5]chi 47,XX+21[15]/46,XY[5]This is a chimera with both female and male cell lines. The female cell line shows trisomy 21, whereas the male cell line is normal.

chi 69,XXX[20]/46,XY[5]This represents a chimera with triploud and diploid cell lines. The triploid line is XXX, whereas the diploid line is XY.

Note: Use of the abbreviations “chi” and “mos” is optional, as the presence of chimerism or mosaicism is usually evident from the karyotype.

Structural chromosome abnormalities Structural chromosome abnormalities

These abnormalities are less common in comparison with aneoploidy, accurse in 1 case of 375 alive births.

• Involved chromosome number in parentheses [e.g. r(X), del(2), ins(4), dup(5)].

• If two or more chromosomes are involved in a rearrangement, as with translocation, a semicolon (;) is used to separate chromosome numbers within parentheses [e.g. t(3;4), t(2;5;10)].parentheses [e.g. t(3;4), t(2;5;10)].

• Chromosome are listed in numerical order unless a sex chromosome is involved [e.g. t(X;1) 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,t(13;14)].

Additional Material, Origin Unknown (add)Additional Material, Origin Unknown (add)

When a chromosome has additional material attached to it, the origin of this material might not be identifiable with conventional banding methods.To represent the abbreviation “add” (from the Latin additio) is used.

46,XX,add(17)(p13)46,XX,add(17)(p13)Additional material of unknown origin is attached to chromosome 17 at band p13

46,XX,add(9)(q22)Additional material of unknown origin attached to chromosome 9 at q22

Deletions (del)Deletions (del)

This is an aberration in which a part of a chromosome is lost.Deletions can be either terminal, where all chromosomal material from the breakpoint on is lost, or interstitial, in which an interstitial section of one arm is missing.

• Terminal Deletions

46,XY,del,(1)(q32) (short form)

46,XY,del(1)(pter q32) (long form)

This karyotype describes a terminal deletion involving the long arm of chromosome 1, the colon present in the long form indicates a break at band 1q32 and deletion of the region distal to it. The rest of the chromosome, from 1 pter to 1q32, is present.

• Interstitial Deletions

46,XY,del(1)(p21p32) (short form)

46,XY,del(1)(pter p21::p32 qter) (long form)

Breakage and reunion are represented in the long form by double colon (::).Here, this occurred involving bands 1q21 and 1p32 segment between them has been deleted.

Derivative Chromosomes (der)Derivative Chromosomes (der)

A structurally rearranged chromosome generated by events involving two or more chromosomes or the result of multiple events within a single chromosome is a derivative chromosome. Thus, each unbalanced product of a translocation event is a derivative chromosome.The identify of a derivative chromosome is determined by its centromere.

46,XY,der(3)t(3;6)(p21;q23)The derivative chromosome 3 in this karyotype is the result of a translocation between the short arm of chromosome 3 at band p21 and the long arm of chromosome 6 at band q23. The der(3) replaces one normal chromosome 3, and both chromosomes 6 band q23. The der(3) replaces one normal chromosome 3, and both chromosomes 6 are normal. This unbalanced karyotype results in monosomy (loss) of region 3p21 pter and trisomy (gain) of 6q23 pter. This karyotype is the product of adjacent-1 segregation.

45,XY,der(3)t(3;6)(p21;q23),-6the der(3) is same as in the above example and again replaces one of the normal chromosomes 3. However, there is only one normal chromosome 6 in the case, resulting in monosomy for both 3p21 pter and 6pter q23. This is the result of 3:1 segregation.

Recombinant Chromosomes (rec)Recombinant Chromosomes (rec)

Recombinant chromosomes are also structurally rearranged chromosomes. They arise de novo from meiotic crossing-over between homologous chromosomes when one is structurally abnormal.

46,XY,rec(3)dup(3p)inv(3)(p21q27)One normal chromosome 3 has been replaced by a recombinant chromosome 3. The segment 3q21 pter is duplicated, and the segment from 3q27 qter is deleted. The key to interpreting this karyotype is “dup(3p)”; dup indicates a duplication.

Fragile Sites (fra)Fragile Sites (fra)

A male would be described as 46,Y,fra(X)(q27.3), and a female would be 46,X,fra(X)(q27.3). Other fragile sites are described in the same way for example: 46,XY,fra(12)(q13.1)

Insertions (ins)Insertions (ins)

An insertion is a structural rearrangement in which a part of a chromosome is typically insertitially repositioned into a different area of the karyorype. Insertion can occur within a chromosome or between two chromosomes.

• Insertion Within a Chromosome

46,XX,ins(3)(p21q27q32)This represents a direct insertion. The long arm segment between bands 3q32 has broken away and been inserted into the short arm of the same chromosome at band p21.NOTE: the orientation of the inverted segment has no changed (i.e., band q27 is still proximal to the centromer relative to band q32)

• Insertion Between Two Chromosomes

46,XX,ins(4;9)(q31;q12q13)The long arm segment between bands 9q12 and 9q13 has been inserted, in its original orientation, into the long arm of chromosome 4 at band q31.

Inversions (inv)Inversions (inv)

A chromosomal aberration in which a segment of a chromosome is reversed in orientation but not relocated is called an inversion.

• Paracentric Inversions:Involve only one arm of a chromosome.

• Precentric Inversions:Involve both arms of a chromosome and therefore, include the centromere.

Examples:Examples:46,XY,inv(3)(p21q31)

Break and reunion occurred at band q21 and q27 in long arm of chromosome 3. The segment lying between these breakpoints has been reattached with its bands in reverse (inverted) order.

46.XY,inv(2)(p21q31)Break and reunion occurred at bands p21 (short arm) and q31 (long arm) of chromosome 2. The segment between these bans, including the centromere, was reattached with its bands in inverted order

Isochromosomes (i)Isochromosomes (i)

An abnormal chromosome in which one arm is duplicatedThe breakpoint in an isochromosome is assigned to the centromer, at band p10 or q10, depending on which arm is duplicated:

46,XX,i(18)(p10)This describes an isochromosome for the short arm of chromosome 18, as evident by assigning the breakpoint to band p10.

46,XX,i(18)(q10)This describes an isochromosome for the long arm of a chromosome 18; the creakpoint is assigned to q10.

Isodicentric Chromosomes (idic)Isodicentric Chromosomes (idic)

Isodicentric chromosomes contine two copies of the same centromer (unlike isochromosomes).One of two centromeres might be inactive, in which case the chromosome is pseudodicentric (psudic).The breakpoints in isodicentric chromosomes are usually on the band The breakpoints in isodicentric chromosomes are usually on the band adjacent to the centromere on the opposite arm:

46,XX,idic(18)(q11.2)Here, we have an isodicentric chromosome compired of two copies of the entire short arm of chromosome 18, two copies of the centromere, and two copies of the small potion of the long arm between the centromere and band q11.2

Isodicentric chromosome 15 [idic(15)] (right). Two normal copies chromosome 15, one chromosome comes from the mother and the other from the father (left)

Marker Chromosomes (mar)Marker Chromosomes (mar)

Marker chromosomes are supernumerary, structuarally abnormal chromosomes of which no part can be identified.If any part of such a chromosome is identifiable, it is not a marker but a derivative chromosome.The presence of a “mar” in a karyotype is always by a plus (+) sign.

47,XY,+marThis is a male karyotype with a marker chromosome.

48,XY,+2marThis is a male karyotype with two marker chromosomes.

48,XY,t(5;12)(q13;p12),+21,+marThis discribes a male karyotype with a translocation involving chromosomes 5 and 12, an extra chromosome 21, and a markerchromosome.

Ring chromosomes (r)

A structurally abnormal chromosome with two breaks, one on short arm and one the long arm, in which the broken ends are attached to from a circular configuration is a ring chromosome. The net result is deletion of at least the terminal ends arms, and potentially more (most) of either or both arms.

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

46,X,r(X)(p22q24)This describe a female karyotype with one normal X chromosome and a ring X chromosome with break and reunion at band p22 and q24. the material distal to both breakpoints is lost.

FusionFusion

Deleted Genetic Material

Deleted Genetic Material

Deleted Genetic Material

Deleted Genetic Material