This document discusses karyotyping and its applications. It begins with an overview of cytogenetics and the history of karyotyping. It then describes the different types of karyotyping including classic and digital karyotyping. The methodology section explains the process of karyotyping including chromosome staining techniques like Q-, G-, N-, and C-banding. Finally, the applications of karyotyping are discussed, such as detecting chromosomal abnormalities, aneuploidies, and genetic disorders. Karyotyping provides a genome-wide view of an individual's chromosomes and is useful for clinical diagnosis and research.

1. Karyotyping
Zahra Naz
Athar Hussain
Waqas Ahmad
By
Mphil-Biotechnology
(2nd semester)
National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan

2. • Cytogenetics
• History
• Karyotyping
• Types
• Methodology
• Staining techniques
• Applications
• Conclusion
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3. Cytogenetics
“Study of the structure and
properties of chromosomes,
chromosomal behaviour during
mitosis and meiosis, chromosomal
influence on the phenotype and the
factors that cause chromosomal
changes”
Rieger, R.; Michaelis, A.; Green, M.M. (1968), A glossary of genetics and cytogenetics: Classical and molecular, New York: Springer-Verlag
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4. History of Cytogenetics
1835 Hugo Von Mohl described cell division
1888 Von Waldeyer gave name chromosome
20th century- Golden era of genetics
1903 Johannsen coined the terms gene, genotype and phenotype
1982 Bloom and Carbon revealed molecular structure of centromere
Ferguson-Smith, M. A. (2015). History and evolution of cytogenetics. Molecular Cytogenetics 8, 19.6/18/2017 4

5. Karyotyping (A cytogenetic technique)
“Karyotyping is the process of pairing and ordering all the chromosomes of an
organism, thus providing a genome wide snapshot of an individual's
chromosomes (karyogram/ Idiogram)”
https://www.nature.com/scitable/topicpage/karyotyping-for-chromosomal-abnormalities-298
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6. Types of karyotyping
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7. Classic karyotype Cytogenetics
• Chromosome number and arrangement studies
• Smaller chromosomal aberrations are detected e.g. translocations
• Complex chromosomal rearrangements often remain hidden
Riegel, M. (2014). Human molecular cytogenetics: From cells to nucleotides. Genet. Mol. Biol. 37, 194-209.
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8. Digital karyotyping
• Based on quantitative analysis of DNA (DNA copy number)
• Detection by using short sequence tags (SST) (21 base pairs usually)
Wang, T.-L., Maierhofer, C., Speicher, M. R., Lengauer, C., Vogelstein, B., Kinzler, K. W., and Velculescu, V. E. (2002). Digital karyotyping.
Proceedings of the National Academy of Sciences of the United States of America 99, 16156.
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Chronic lymphocytic leukemia sample

9. Methodology
Redrawn: Image from https://infograph.venngage.com/p/219813/karyotype

10. Methods to position
chromosomes
http://learn.genetics.utah.edu/content/basics/readchromosomes/
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11. 1. On basis of size
www.shutterstock.com.279849302
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12. 2. On basis of banding
http://www.evolutionrevolution.eu/es/
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13. 3. On basis of position
of centromere
http://learn.genetics.utah.edu/content/basics/readchromosomes/
Group A: Large metacentric
Group B: Large submetacentric
Group C: Medium submetacentric (X)
Group D: Medium acrocentric
Group E: Short submetacentric
Group F: Short metacentric
Group G: Short acrocentric (Y)
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14. 6/18/2017 14
Results
https://www.mun.ca/biology/scarr/Human_Karyotype.html

15. http://www.rxlist.com/genetic_disease/article.htm
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16. Athar Hussain
Chromosome Banding

17. Introduction

18. Classification of Banding Techniques
Based on
GC and AT rich regions.
Constitutive Heterochromatin Region.
Always metaphase chromosomes whose size has condensed and whose
diameter is increased are used for chromosome banding studies after fixing
stage.
Wendy, A. B.,2001. Karyotype analysis and chromosome banding. Nature, 1-6.

19. The banding techniques fall into two principal groups:
• Bands, distributed along the length of the whole chromosome, such as G-,
Q-band
• Those that stain a number of specific bands.These include methods
which reveal centromeric bands, C-bands, and nucleolus organizer
regions, NOR's (at terminal regions of chromosomes).
Principle
Moore, C. M. and Best, R. G., 2002. Chromosome preparation and banding. Nature, 1-6.

20. Banding Techniques
Q
(Quinarcine)
G
(Giemsa)
N (NOR)
C
(Centromeric)
1958 1971 1973 1978
Casperson
et.al
Summer
et.al
Matsui &
Sasaki
Linde
&Laursen

21. 1.Q Banding
• Quinacrine mustard, an alkylating
agent, was the first chemical to band
chromosomes viewed under a
fluorescence microscope.
• Dark and light florescence
Ried, T., et.al ,1998. Chromosome painting : a useful art. Human Molecular Genetics, Vol(7),1619- 1626.

22. 1.Q Banding Techniques
Advantages
• Simple and Versatile.
• Used where G band is not
accepted.
• Used in study of chromosome
heteromorphism.
Disadvantages
• Tendency to fade during
examination.
 Photo-degradation .
UV light breaks the chemical
bond.

23. • It stain regions rich in adenine and
thymine.
• Standard G band staining techniques
allow between 400 and 600 bands to be
seen on metaphase chromosomes.
2.G Banding
• Methylene
Blue
• Eosin
• Azure B
Giemsa solution
https://en.wikipedia.org/wiki/Giemsa_stain

24. 2.G Banding Techniques
Chromosome
Weak Trypsin /
urea/ protease
Treated with
Giemsa
Banding pattern
To
denature
protein
Interaction of
the DNA with
thiazine & eosin
components of
stain with
Sulfar regions of
DNA
Methylene Azure+
Methylene Violet+
Methylene Blue+
Eosine
http://www.protocol-online.org/biology-forums/posts/15995.html

25. G Banding Techniques
Advantages
• Used in identification of bands
rich in Sulphur content.
• Used in the identification of
chromosomal abnormalities
• Gene Mapping.
Disadvantages
• Not used in plants.
• Required Pre-treatment by Salt
or proteolytic enzyme

26. G banding not used in Plants. Why????
• Human mitotic metaphase chromosome is 2.3 times shorter.
• Plant mitotic metaphase chromosome is 10 times more shorter than
human chromosome.
• Hence difficult to demonstrate the arrangement of bands at this level
of saturation with G banding technique.
Source: Greilhuber, J (1977). Why Plant chromosome do not
show G bands? .Theory of Applied Genetics, Vol 50(3): 121- 124.

27. • NOR-banding involves silver staining (silver nitrate solution) of the
"nucleolar organizing region", which contains rRNA genes.
• NOR region is highly condensed.
• It can neither be expressed to nor encode any protein
3. N(NOR) Banding

28. N Banding Techniques
Advantages
• Used in the identification of
nucleolar organizer region.
• Superior banding pattern for
plants.
Disadvantages
Time consuming both in
technique and reagent
preparation.

29. C (centromeric)-banding stains areas of heterochromatin, which
is tightly packed and repetitive DNA.
4. C Banding

30. C Banding Techniques
Advantages
• Identification of chromosomes
particularly in insects and plants.
• Identification of centromere position.
• Gene mapping.
Disadvantages
• C-banding methods do not permit
identification of every chromosome
in the somatic cell complement
Gupta ,P. K., 2012. Cytogenetics an advanced study, Chapter 1: 3-16.

31. Applications
Waqas Ahmad
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32. APPLICATIONS OF KARYOTYPING
• Detection of chromosomal aberration
• Identify loss and addition of chromosome
• Determine the risk of individual
• Detect aneuploidy
• Prebirth diagnosis of genetic diseases
• Gender identification
http://www.biotecharticles.com/Biology-Article/Karyotype-and-Its-Applications-in-Human-Health-2014.html

33. Diagnostic of different genetic Disorder in human
“Genetic disorder is a disease that is caused by an abnormality in an
individual's DNA”.
A. Autosomal Disorder
Autosomal Dominant
Autosomal Recessive
B. Allosomal Disorder
X- linked dominant
X- linked recessive
Y- linked
3. Mitochondrial Disorder
https://www.genome.gov/10001204/specific-genetic-disorders/

34. Mitochondrial disorder
• It is a disorder caused by mutations (or changes) in either
mitochondrial DNA or nuclear DNA
• These are only passed on from mother.
• 1:4000
https://www.genome.gov/10001204/specific-genetic-disorders/

35. Trisomy
• Three instances of a particular chromosome, instead of the normal two.
• Aged mothers
• High risk of aneuploidy chromosome
• Fertilization of an egg having aneuploidy chromosome result in fetus with
syndrome.
• Trisomy 21 (Down’s syndrome)
• Trisomy 18 (Edwards syndrome)
• Trisomy 13 (Patau syndrome)
https://www.genome.gov/10001204/specific-genetic-disorders/

36. Down Syndrome
• Down Syndrome also known as Trisomy 21, is a chromosomal
condition caused by the presence of all or part of an extra 21st chromosome.
• Non-disjunction during meiosis
• John Langdon Down (1866)
• Short height
• Severe mental deficiency with decline in the IQ with age
• Average IQ:50
• Brachycephaly with flat face and occiput
• Flat and low nasal bridge
https://www.genome.gov/10001204/specific-genetic-disorders/

37. Edward Syndrome
• Edward’s Syndrome also known as Trisomy 18 (T18)
or Trisomy E.
• 2nd most common disorder after down syndrome
• Mental deficiency
• Growth retardation
• Prominent occiput with elongated head
• Webbing of the neck
• Short sternum
• Micrognathia
http://syndrome.org/patau-syndrome/

38. Patau Syndrome
• A syndrome in which a patient had an additional chromosome on
position 13 due to non-disjunction of chromosomes during meiosis
• Patau syndrome 1 in 10,000 .
• Mental deficiency, Low birth weight, Abnormal development
of frontal lobe ,Hypoplasia of cerebellum etc
http://emedicine.medscape.com/article/947706-overview

39. Autosomal deletion
• An abnormality of DNA that involves missing
material.
• These can range from very small to very large
• The most common types of autosomal deletion
syndromes are:
• Wolf-Hirschhorn Syndrome
• Cri Du Chat
https://link.springer.com/chapter/10.1007/978-1-4613-0139-4_15

40. Autosomal deletion
2. CRI DU CHAT(5p deletion syndrome):
• Jerome Lejeune in 1963
• DELETION on the short arm of chromosome 5.
• Common in female
• Cries like a CAT
1. Wolf-Hirschhorn Syndrome (Pitt Syndrome ):
• Herbert L. Cooper(1961)
• DELETION of the short arm of chromosome 4
https://link.springer.com/chapter/10.1007/978-1-4613-0139-4_15

41. Allosomal disorder
Turner syndrome
1 X0=45
2 Extra skin on NECK
3 Infertile
4 Shorter than average
5 heart defects and kidney problems
https://ghr.nlm.nih.gov/condition/klinefelter-syndrome

42. Kleinfelter’s syndrome
1. XXY=47
2. A shortage of testosterone
3. Gynecomastia
4. reduced facial and body hair
5. Infertile
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43. Conclusion
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Q. & A.