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Author: Janet M. Cowan, Ph.D.
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Introduction to Cytogenetics


Jorde, Carey, Bamshad & White: Medical Genetics, 3rd edition, C.V. Mosby Publishing, 2005.

  • Cell Cycle pp. 22-27
  • Chapter 6 p. 107


  1. Normal karyotype: number of chromosomes, basic nomenclature
  2. Typical indications for chromosome analysis in the newborn and adult. Examples of the findings
  3. Meiosis and the errors that can lead to trisomy/mis-segregation of balanced translocations

How to See Chromosomes

Chromosomes only visible as cells approach and pass through metaphase in cell cycle

What is seen is DUPLICATED chromosome

Normal human karyotype has 46 chromosomes - 22 pairs of autosomes and a pair of sex chromosomes

  • Female 46,XX
  • Male 46,XY

Karyotype Arrangement

Chromosomes have characteristic banding patterns created by trypsin and Giemsa

Chromosomes laid out in pairs, from largest (#1) to smallest (#21)

Arranged with short arm (p from French “petit”) going up, and long arm (q) going down

Chromosome movement via centromere

Karyotype Arrangement


International System for Human Cytogenetic Nomenclature (ISCN)

Karyotype components:

  • Number of chromosomes, sex, first change, second change, etc.
  • Sex chromosome changes are listed first and then others in numerical order


 p short arm
q long arm
+ additional chromosome
- missing chromosome
t translocation
del deletion
dup duplication
inv inversion
der derivative = structurally rearranged chromosome


Trisomy 21: 47,XY,+21

Trisomy 18: 47,XX,+18

Balanced translocation: 46,XX,t(3;5)(p21;q31)

Chromosomes listed in numerical order

Breakpoints listed in same order


Loss of one copy of a chromosome

45,X known

No other full monosomies reported

Loss of part of a chromosome = monosomy for small region

Example 1:



Three copies of a chromosome or part of a chromosome - normal chromosome number increased by 1 to 47



Three copies of EVERY chromosome - normal chromosome number increased by 23 to 69


Typical Newborn Presentation

Baby G is admitted to Neonatal Intensive Care Unit. Staff notes that baby has unusual features and call for Genetics consult. Genetics find the baby has: Hypotonia, protruding tongue, slanted palpebral fissures, small nose with low nasal bridge, small ears, short neck, relatively short metacarpals and phalanges in hands, wide gap between first and second toes (“sandal gap”)

In the Lab

0.25 – 0.5 ml blood added to 5 ml tissue culture medium (with fetal calf serum) Phytohemagglutinin (PHA) added to stimulate T-cells to divide. First harvest done after 48 hours

Fluorescence in Situ Hybridization (FISH)

Equivalent to doing a Southern blot on a slide

Put cells on slide, and add appropriate probe

Denature by heating at 95 degrees Celcius

Allow to reanneal for 4+ hours

FISH Probes

  • Single copy probes – disease specific regions such as trisomy 21 critical band
  • Centromeric probes - alpha satellite regions of chromosomes, used to count chromosomes
  • Paints - made from flow-sorted chromosomes, used to confirm translocations etc.

Back to the Blood in Culture - Harvest:

  1. Colchicine is added to disrupt mitotic spindle
  2. Hypotonic solution added to swell the cells
  3. Cells fixed
  4. Cell suspension dropped onto slides
  5. Slides are treated with trypsin solution and stained (G-banding)

Back to the Blood in Culture

How Does Trisomy 21 Happen?

  • Gametes form during meiosis
  • In meiosis 1 (MI) homologous chromosomes go to different daughter cells
  • In meiosis 2 (MII) each chromosome divides along its length and each chromatid goes to a daughter cell

How does Trisomy 21 Happen?

Frequency of Trisomy

Trisomy Frequency Parental Origin
47,Xx/Xy,+21 1 In 700 Mat MI>Mat MII 3:1
47,Xx/Xy,+18 1 In 6 – 8,000 Mat MI Or MII
47,Xx/Xy,+13 1 In 12,000 Mat MI Or MII

Typical Routine Adult Presentation

Mr. and Mrs. F, who are in their late 20’s, are referred to a fertility clinic because they have been married for 5 years, but have no children. Mrs. F has been pregnant four times, but all pregnancies have ended in miscarriage. As part of their workup, blood is sent for karyotype analysis. In the lab blood is cultured as before, but for 72 hours. Mr. F is found to have normal karyotype, 46,XY. Mrs. F is found to have apparently balanced translocation between chromosomes 10 and 11.

Adult Presentation

Mrs. F’s Karyotype 46,XX,t(10;11)(p15;q21)

  • Translocations = exchange of material between two or more chromosomes
  • Constitutional balanced translocation usually has no effect on phenotype
  • May result in infertility or history of spontaneous abortion
  • Constitutional translocations are present at birth in some or all of cells in body and most are unique to a family
  • Robertsonian translocations occur between acrocentric chromosomes (13/14/15/21/22) Results in loss of non-critical genes in the short arm regions of the chromosomes involved

Robertsonian translocation

Robertsonian Translocation

Count is decreased to 45: 45,XY,der(15;22)(q10;q10) or 45,XX,der(13;14)(q10;q10)

“q10” means that the break is in the centromere and the long arm is present

Frequency of Robertsonian Translocation Combinations

13 14 15 21 22
13 X 45% 3% 6% <1%
14 X 1% 36% <1%
15 X 3% 1%
21 X 4%

Translocations and Meiosis

  • Chromosomes pair along their lengths as far as possible making a four - armed figure
  • Centromeres of homologs repel each other and go to different daughter cells
  • Segregation errors may lead to combination of monosomy and trisomy

Possible Gametes

Mr. and Mrs. F decide to try to get pregnant one more time. Pregnancy ends in spontaneous loss, and tissue sent to the lab.

Karyotype of Fetus

Karyotype of Fetus


  • Unbalanced translocations will impact phenotype due to a mixture of monosomy and trisomy for the regions involved
  • Unbalanced translocations may be incompatible with life
  • Written as: 46,XX,der(5)t(5;8)(p13;q22)


  • Normal karyotype = 46 chromosomes. 22 pairs of chromosomes and 2 sex chromosomes (46,XX or 46,XY)
  • Chromosomes divided by the centromere into short (p) and long (q) arms
  • Each chromosome has a number of bands, each of which has been assigned a number
  • Karyotypes written using a system of nomenclature
  • Abbreviations used to describe changes such as t, der, dup, inv
  • Balanced constitutional rearrangements (translocation or inversion) do not alter phenotype and most are unique to a family
  • Unbalanced constitutional rearrangements result in duplication and deletion of material and are associated with changes in phenotype