Genetic and Cytological

mapping of
chromosomes

Guided by;
Presented & prepared Dr.N.N Singh
by: Dr.(Mrs.)V.R.Brave
Dr. Neelakshi Singh Dr. G.Sreedhar
MDS-II yr Dr. Ritika Caroli
 CONTENTS
•Introduction
•Terminologies
•Genetic Symbols
•Human Chromosomes
-Chromosomal Nomenclature
-Banding Pattern
•Genetic Mapping
•Cytological Mapping
•Types Of Genetic Disease
•Implications In Oral Disease
•Investigations In Genetic Disease
•Future Trends
•Summary
•Conclusion
•Bibliography
 INTRODUCTION
The science of heredity or genetics is the study of two
contradictory aspects of nature: heredity and variation. The
process of transmission of characters from one generation
to next by sexual or asexual reproduction is called
inheritance or heredity.

The heredity and variations play an important role in the

formation of new species. The biological science which
deals with the mechanism of heredity and causes of
variations in living beings is known as GENETICS. The word
genetics was derived from the Greek root gen which means
to become or to grow into and it was coined by Bateson in
1906 for the study of physiology of heredity and variation.
• The cultural evolution of
human beings is strongly
influenced by the
knowledge of hereditary
phenomena of early man.
Despite the long standing
concern with heredity and
the practice of selective
breeding, it was not until
the discovery of Mendel’s
laws that we are able to
explain the actual basis for
inheritance. Gregor Mendel
In more recent years , BIOTECHNOLOGY have led
to the creation of special genetically engineered
strains of bacteria or fungi that carry specific gene
from unrelated organism (human). Further, the
most exciting and alarming application of genetic
knowledge is to human species itself. One can
now diagnose hereditary or genetic disease before
or soon after birth and in some cases we can
provide secondary treatment.

The diagrammatic, graphical representation of

relative distances between linked genes of a
chromosome is called LINKAGE OR GENETIC
MAP. Because, such a linkage or genetic map is
the outcome of crossing over studies, is also called
as cross over map.
 TERMINOLOGIES
Gene: The fundamental physical and
functional unit of heredity, which
carries information from one generation
to the next ;a segment of DNA,
composed of a transcribed region and a
regulatory sequence, that make
possible transcription.

Homozygous :the organism having

two similar genes for a particular
character in a homologous pair of
chromosomes is known as homozygous
or genetically pure for that character.

Heterozygous :an individual

containing both dominant and recessive
genes or traits or characters of a allelic
pair is known as heterozygous or
hybrid.
Allele : one of two or more
forms that can exist at a
single gene locus,
distinguished by their
differing effects on
phenotype. Alleles are
genes controlling the same
characteristic (e.g hair
colour) but producing
different effects(black or
red )and occupying
corresponding positions on
homologus chromosomes.

Carrier :a heterozygous
individual. An individual
who possesses a mutant
allele but does not express
it in the phenotype
because of a dominant
allelic partner, e.g, an
individual of genotype Aa
is a carrier of a if there is
complete dominance of A
Gene mutation :
change in the structure
of a gene.

Linkage: the
occurrence of different
genes on the same
chromosome
 Linkage group: all of the genes located physically on a
given chromosome.

Linkage map: a chromosome map; an abstract map of

chromosomal loci, based on recombinant frequencies.

Oncogene :a gene that induces uncontrolled cellular

proliferation, they can be either cellular or viral in origin.

Mutation: a spontaneous permanent change in a gene or

chromosome which usually produces a detectable defect in
the organism concerned and transmitted to the offsprings.
Candidate gene:

A candidate gene is a gene, located in a chromosome

region suspected of being involved in the expression of
a trait such as a disease, whose protein product
suggests that it could be the gene in question. A
candidate gene can also be identified by association
with the phenotype and by linkage analysis to a region
of the genome.
Pedigree: a family tree, drawn with
standard genetic symbols, showing
inheritance patterns for specific
phenotypic characters
Symbols used in constructing a
pedigree:
Autosome : the chromosomes
which are not associated with sex
chromosomes.

Chromosome :the nucleoprotein

structure which are generally more
or less rod like during nuclear
division. Genes are arranged on
chromosomes in a linear fashion.
Before DNA replication ,each
chromosome consist of a single DNA
molecule plus protein and is called
as chromatid.
After replication, each
chromosome consist of two identical
molecules of DNA plus protein, and
called as sister chromatid.
Centromere : the chromosomal
locus which regulates the
movement of chromosomes
during meiosis and mitosis. The
centromere is defined by specific
DNA sequence plus protein that
can bind to them.

Chromatin : DNA plus the

protein that package in within the
cell nucleus.
• CROSSING OVER:
It is a process that produces new combinations of genes by
interchanging of corresponding segments between non-sister
chromatids of homologous chromosomes.
The chromatins resluting from such interchanges of chromosomal parts
are known as cross overs.
Crrosing over occurs at two level:
(i) Chromosomal crossing over(gross chromosome)
(ii) genetic recombination(DNA level)
The frequency of crossing over appear to be closely related to physical
distance between genes on chromosomes and serves as a tool in
constructing genetic maps of chromosomes.
Satellite DNA consists of very large arrays of tandemly
repeating, non-coding DNA. Satellite DNA is the main component of
functional centromeres, and form the main structural constituent of
heterochromatin.The name "satellite DNA" refers to how repetitions of
a short DNA sequence tend to produce a different frequency of the
nucleotides adenine, cytosine, guanine and thymine, and thus have a
different density from bulk DNA - such that they form a second or
'satellite' band when genomic DNA is separated on a density gradient
Telomere: specialized structure at
either end of the chromosome that
ensures complete replication of the
chromosome ends and protects the
ends within the cell.

Locus : the position or place on a

chromosome occupied by a
particular gene or one of its allele.

Meiosis :it is the reduction division

in which the diploid or somatic
chromosome numbers rare
reduced to half and often produce
haploid gametes.

Mitosis: process of cell division,

whereby the genetic material is
precisely divided and two new
chromosome set identical to the
original are generated.
Phenotype :the appearance or discernible character of an
individual, which is dependent on its genetic makeup usually
expressed in words, eg. tall ,dwarf.

Genotype :the genetic make up or constitution of an

individual, with reference to the traits under consideration,
usually expressed by a symbol, eg, +,DD (tall), dd(short),etc

Karyotype :the entire chromosome complement of an

individual or cell, as seen during mitotic metaphase.
•Cytogenetics: it provides the cytological
explanations of different genetical principles.

• Genetic engineering: array of techniques that

facilitate the manipulation and duplication of
pieces of DNA for industrial, medical and research
purpose.
Autosomal dominant inheritance: the second
copy of the gene on the homologus chromosome
cannot compensate for the mutated copy:
-consecutive generations are affected
-half of offspring are affected, male=female
-unaffected individual cannot transmit the disease.
Autosomal recessive inheritance: the second
copy of the gene on the homologus chromosome
compensates for the mutated copy:
-half of the children of unaffected carriers will be
carriers.
-if both parents are carrier, then one quarter of
their offspring are affected ,and one half are
carrier.
-usually only one generation is affected
X-linked: a second copy of the gene is only present in
females,in X linked recessive disease only males are
affected, unaffected female carriers transmit the disease.
Half of carrier female offspring inherit mutation-males are
affected and females are carriers. Affected males cannot
transmit the disease to their sons, but all of their
daughters are carrier. X linked diseases are occasionally
dominant.
SYMBOLS IN GENETICS
An organism with diploid cell(2n) has paired chromosomes
and out of two contrasting characters each chromosome
contains only one gene or trait for a single character.
According to classical method of symbolization, the
dominant character is expressed in capital letters for eg–tall
character is represented as ‘T’ and the recessive character
by ‘t’.
In modern genetic literature one more method called “wild
type symbolism” is widely used-when one phenotype is
more common in occurrence, then its alternative
phenotype, and “mutant type” for least occurrence. In this
the symbol (+) is used to indicate the normal allele for wild
type.
Symbols
 HUMAN CHROMOSOME:
Tijo And Levan,1956 cultured somatic cells from
fibroblast of human embryos and counted the
human chromosome no as 46. Our genetic
information is stored in 23 pairs of chromosomes
that vary widely in size and shape.

Chromosome 1 is the largest and is over three

times bigger than chromosome 22. The 23rd pair of
chromosomes are two special chromosomes, X and
Y, that determine our sex. Females have a pair of X
chromosomes (46, XX), whereas males have one X
and one Y chromosomes (46, XY).
Chromosomes are made of DNA, and
genes are special units of
chromosomal DNA. Each chromosome
is a very long molecule, so it needs to
be wrapped tightly around proteins
for efficient packaging. Near the
center of each chromosome is its
centromere, a narrow region that
divides the chromosome into a long
arm (q) and a short arm (p).
We can further divide the
chromosomes using special
stains that produce stripes
known as a banding pattern.
Each chromosome has a distinct
banding pattern, and each band
is numbered to help identify a
particular region of a
chromosome. This method of
mapping a gene to a particular
band of the chromosome is
called CYTOGENETIC
MAPPING.
NOMENCLATURE
To facilitate identification of the individual bands, by
convention each chromosome is divided into regions by the
centromere, the chromosome ends, and certain easily
identifiable bands. The
regions are numbered sequentially outward from the
centromere toward each end of the chromosome, and within
each region the bands are also numbered outward from the
centromere.
Therefore, by specifying the number of the chromosome, the
arm symbol, the region number, and the band number within
that region, the precise identification of a specific band can be
made:

for example, 5pl4 indicates chromosome 5, short arm,

region1, band4 .
When the chromosomes are not
normal, the abnormality involved is
specified. For example, an extra or
missing chromosome is indicated by a
plus or minus sign followed by the
number of the chromosome involved.
Thus, 47,XY,+21 denotes 47
chromosomes, male sex
chromosomes, with an extra
chromosome21.
An increase or decrease in the length of a
chromosome arm is indicated by a plus or minus
sign placed after the symbol for the chromosome
arm involved: for example, 46,XY,5p- denotes
46chromosomes, male sex chromosomes, and
loss from the short arm of one chromosome
number 5;

46,XX,21q+ denotes 46 chromosomes, female

sex chromosomes and increase in the length of
the long arm of a chromosome number21.
46,XY,t(11;22)(q23;q11) denotes a male
karyotype with a reciprocal translocation
between
a chromosome 11 and a chromosome 22, with
one break point in the long arm of chromosome
11 at region 2, band 3 and the other in the long
arm of chromosome 22 at region 1, band 1. The
nomenclature 46,XX,del(5)(p14) denotes a
female karyotype with a deletion from a
chromosome 5 with the break point in the short
arm at region 1, band4.
Chromosomes can be segregated into three groups
on the basis of centromere location, an important
identifying chromosomal feature.The distal ends of

each chromosome are termed as telomeres.

A metacentric chromosome is one in which the
centromere is located in the middle of the
chromosome and includes chromosomes 1,3,16,19
and 20.
An acrocentric chromosome is
one in which the centomere is
located near the end of the
chromosome and include
chromosome 13,14,15,21 and
22.

The remainder of the

chromosomes are
known as
submetacentric with
centromeres located in
between the middle and
the end.
 CLASSIFICATION OF CHROMOSOME
The human metaphase chromosomes were first classified by Denver
IN 1960.To follow this classification,each of the 22 pairs of autosomes
has been numbered from 1 to 22 according to their decreasing size.

Patau 1960 divided them into seven groups:

A group: 1 to 3 pairs- Metacentric
B gruop:4 to 5 pairs- Submetacentric
C group:6 to 12 pairs-Submetacentric
D group:13 to 15 pairs-Acrocentric
E group:16 to 18 pairs-Submetacentric(16 is
metacentric)
F group:19 to20 pairs-Metacentric
G group:21 to 22 pairs-Acrocentric

In males,group G contain a variable Y chromosome which lacks

satellites.The X chromosome is a member of group C and can be
identified by special banding method.
Chromosomal banding
patterns
Before the banding era, chromosomes appeared as
solid, dark linear structures. In 1970s, new
techniques were developed that produced unique
alternating light and dark staining patterns for each
chromosome, called bands. The most commonly
used banding technique is Geimsa banding (giemsa
stain) or G-banding. One band represents
approximately 5 to 10x106 basepairs(bp) of DNA.
Banding pattern of an
individual chromosomes
as revealed by the
fluorescent and Giemsa
staining.
A uniform system of designating bands
produced with different staining techniques
in human chromosomes was introduced in
conference at Paris in 1971.Such a system is
necessary for various purposes: designating
breakpoints in structurally aberrant,
rearranged or deleted chromosomes and
defining the location of genes on
chromosomes.
The principal techniques that demonstrate
the different classes of bands are G-,Q-,R-
BANDING. All use the same principle of
chromatin denaturation or enzymatic
digestion followed by the incorporation of a
DNA specific dye.
BANDING METHOD------ DEFINITION

C- methods that demonstrate “constitutive

heterochromatin”. C band is a unit of chromatin stained by
these methods.
• Constitutive heterochromatin comprises approx.20% of human
genome and is composed of satellite and non satellite repetitive DNA
sequence.
• This form of chromatin stains dark in nondividing interphase cells and
remain condensed and are called chromocenters.
• In humans, C-bands are located at all centromeres and the distal
long arm of Y chromosome.C-bands also vary in position with respect
to the centromere and are classified in this basis into 5 levels:
• NI-no inversion
• MIN-partial inversion minor
• HI-half inversion
• MAJ-partial inversion major
• CI-complete inversion
C-banding have no clinical significance,but because they are inherited
from parent to child they can be used as familial markers.
Q- methods using fluorescent dyes like quinacrine mustard or
quinacrine to demonstrate bands along the chromosome
called Q bands.
• This dye binds to DNA by intercalation or by external ionic binding.
• This method was introduced by Caperson and coworkers in 1968and
is the oldest of the modern banding technique,as well one of the
simplest and versatile.
• It can be demonstrated throughout the length of the human
chromosome and were the basis of the standard description of the
banded huiman karyotype.
• Chromosome preparation are stained in a solution dye,monted in an
appropriate aqueous fluid and viewed with a fluorescence
microscope.
• Two types of Q Bands in human chromosomes:euchromatic &
heterochromatic.Most of the variation is in band size but in some
chromosomes there is also variation in brightness.
G-techniques that demonstrate bands along the
chromosomes
using a Geimsa dye mixture,with G banding three types of
chromatin can be identified- euchromatin, centromeric and
intercalary heterochromatin.
• It is most widely used banding technique,they draw attention to
specific feature of chromosomes such as heterochromatin.The fields
of application of G banding are defining karyotypes and locating
breakpoints in clinical conditions,in cancer cells,in evolutionary
studies and in gene mapping.

• The treatment consists of exposure of chromosome to a salt solution

at 60°C or to trypsin to denature the chromosomal proteins.

• The bands produced are believed to reflect both the structural

composition and function of the chromosomes.

• Adenine and thymidine(A+T)rich segments of DNA which appear to

contain few transcribed genes and late replicating in the S
phase,correspond to dark G bands or brightly fluorescing Q bands.
 Marker chromosomes
• Chromosomes whose exact origin cannot be identified.

• They may have segments that do not band with the G banding
technique but instead show a uniform and intermediate level of
staining with Geimsa after treatment that produced a typical G
banding pattern elsewhere on the chromosome. These distinctive
segments are called homogeneously staining regions ,or HSR.
R- the reverse Giemsa staining method which gives patterns
opposite in staining intensity to those obtained by G
banding.
• In this technique,the chromosome preparation that were heated in
phosphate buffer at 87° C and then stained with Giemsa.
• The stained chromosome in R banding showed a pattern
complementary to G and Q banding ,only disadvantage was of pale
staining and so phase microscopy was required to examine.The
addition of ACRIDINE ORANGE solved this problem.
• R bands contain most of the genes are G +C rich and replicate early
in the S phase.
• One of the biggest advantage of R banding is that the ends of the
chromosomes(termini) are strongly stained and is of great benefit in
studying translocations or other structural anamolies involving the
distal ends of chromosomes.
 Nuclear Organizer Region (NOR) Banding

Other banding techniques uses the Feulgen stain (F bands)

and one can selectively stain the nucleolar region(N Bands)
which are located in the satellite of chromosome no
13,14,15,21,22.
• Specific chromosomal regions that form and maintain the nucleoli are
called nuclear organizer regions (NORs).

• These regions are located on the stalks of acrocentric chromosomes.

• They can be stained by use of Giemsa Stain (N- BANDING) or Silver
Impregnation(Ag-NOR Banding).

• It is useful for the detection of heritable polymorphisms.

• Furthermore ,NOR activity in human male meiosis and in malignant
cells can be evaluated .
GENETICMAPPING:
When one knows all the genes, linkage groups and
number of linkage groups of species, it becomes
possible for him that by adopting the crossing over
as a tool, he may determine the relative distances
between the genes in a linkage group and also their
order and may give diagrammatic representation of
chromosomes showing the gens as points separated
by distances proportional to the amount of crossing
over. Such a representation of relative distances
between linked genes of a chromosome is called
linkage or genetic map.
 CONTENTS
•Introduction
•Terminologies
•Genetic Symbols
•Human Chromosomes
-Chromosomal Nomenclature
-Banding Pattern
•Genetic Mapping
•Cytological Mapping
•Types Of Genetic Disease
•Implications In Oral Disease
•Investigations In Genetic Disease
•Future Trends
•Conclusion
•Summary
•Bibliography
What is genetic mapping?
Developing new and better tools to make gene hunts faster, cheaper
and practical for any scientist was a primary goal of the Human
Genome Project (HGP).

One of these tools is genetic mapping, the first step in isolating a

gene. Genetic mapping - also called linkage mapping - can offer firm
evidence that a disease transmitted from parent to child is linked to
one or more genes. It also provides clues about which chromosome
contains the gene and precisely where it lies on that chromosome.
Construction of MAP
1.Determination of linkage groups
2. Determination of Map Distance
3. Determination of Gene Order
4. Combining Map segments
1.Determination of linkage groups
First the exact no of chromosomes of the particular
species has to be known, then total no of genes of that
species by undergoing hybridization experiments in
between wild and mutant strains. By this technique only,it
can easily be determined that how many phenotypic traits
remain always together or linked and consequently their
genes during course of inheritance. Thus, different linkage
groups of a species can be worked upon.
2. Determination of Map Distance
• The intergene distance on the chromosome cannot be measured in
the customary units employed in light microscopy, geneticists use an
arbitrary unit to measure the map unit, to describe the distance
between linked genes. A map unit is equal to1 percent of cross
over(recombinants)that is it represents the linear distance along the
chromosome for which a recombination frequency of 1 percent is
observed. These distances can also be expressed in morgan units,
one morgan unit represents 100 percent cross over.
• 1% crossover can be expressed as 1centimorgan(1cM)
• It is now possible to calculate the size of gene, as well as distances
separating them, and to photograph genes in the electron
microscope.
• The percentage of crossing over between two linked genes is
calculated by test crosses-
-two point test cross
-three point test cross
3. Detremination of Gene Order
• After determining the relative distances between the genes of a
linkage group, it becomes easy to place genes in three proper linear
order. For example, if the linear order of three genes ABC is to be
determined, then these three genes may be in any one of three
different orders depending upon that which gene is in the middle.
• The relative distances and ordering of genes in a linkage group are
determined in separate segments by two point test crosses or three
point crosses, as the case may be.

4. Combining Map segments

• Finally, the different segments of maps of a complete chromosomes
are combined to form a complete genetic map of 100 centimorgans
long for a chromosome.
• Interference and Coincidence
• In higher organism it is found that one chaisma formation redices the
probability of another chaisma formation in an immediately adjacent
region of the chromosome, probably because of physical inability of
the chromatids to bend back upon themselves within ceratin minimum
distances.The tendency of one cross over to interfere with the other
crossover is called interference. The strength of interference varies
in different segments of chromosomes and is usually expressed in
terms of coefficient of coincidence.

• Coefficient of coincidence= % observed double crossover

% expected double crossover
• The coincidence is the complement of interference, so:
• Coincidence+ interference=1.0
When interference is 1, no double crossover will be observed and
coincidence becomes zero. When ,interference decreases,
coincidence increases. Coincidence value varies from 0 and 1.
CHROMOSOME, PHYSICAL OR
CYTOLOGICAL MAPPING
It has been found that linkage map distances
between genes are not necessarily proportional to
physical linear measurements. Special cytological
techniques have been used to determine the
physical locations of a gene in a chromosome.
Localization has been accomplished by identifying a
gene locus with relation to some visible landmark
such as a chromosome or cross bands. In this
process the polytene chromosome of salivary gland
of Drosophilla have been found very useful.
Difference between genetic and
cytological mapping

The frequency of crossover usually varies in

different segments of chromosomes but is
highly predictable even between any two
gene loci. Therefore, the actual physical
distance between linked genes bear no
direct relationship to the map distance
calculated on the basis of crossover
percentage.
However the linear order of genes is
identical in both the maps.
• How do researchers create a genetic map?
• To produce a genetic map, researchers collect blood or tissue
samples from family members where a certain disease or trait is
prevalent. Using various laboratory techniques, the scientists isolate
DNA from these samples and examine it for the unique patterns of
bases seen only in family members who have the disease or trait.
These characteristic molecular patterns are referred to as
polymorphisms, or markers.
• The more DNA markers there are on a genetic map, the more likely it
is that one will be closely linked to a disease gene - and the easier it
will be for researchers to zero-in on that gene. One of the first major
achievements of the HGP was to develop dense maps of markers
spaced evenly across the entire collection of human DNA.
• What are genetic markers?
• Markers themselves usually consist of DNA that does not contain a
gene, however they can tell a researcher the identity of the person a
DNA sample came from. This makes markers extremely valuable for
tracking inheritance of traits through generations of a family, and
markers have also proven useful in criminal investigations and other
forensic applications.
• Although there are several different types of genetic markers, the
type most used on genetic maps today is known as a microsatellite
map. However, maps of even higher resolution are being constructed
using single-nucleotide polymorphisms, or SNPs (pronounced
"snips"). Both types of markers are easy to use with automated
laboratory equipment, so researchers can rapidly map a disease or
trait in a large number of family members.
• The development of high-resolution, easy-to-use genetic
maps, coupled with the HGP's successful sequencing
and physical mapping of the entire human genome, has
revolutionized genetics research. The improved quality of
genetic data has reduced the time required to identify a
gene from a period of years to, in many cases, a matter
of months or even weeks. Genetic mapping data
generated by the HGP's laboratories is freely accessible
to scientists through databases maintained by the
National Institutes of Health and the National Library of
Medicine's
National Center for Biotechnology Information
(NCBI) [ncbi.nlm.nih.gov].
Each human is estimated to have approx. 30000 to 40000
different genes. Alterations in these genes, or in combination
of them, can produce genetic disorders. These genetic
disorders are classified into several major groups:

1.CHROMOSOMAL DISORDERS, in which entire

chromosomes(or large segments of them) are missing,
duplicated or otherwise altered. These disorders include
disease such as Down Syndrome and Turner Syndrome.
2.Disorders in which single genes are altered; these
are often termed “mendelian’ conditions, or
SINGLE GENE DISORDER such as cystic fibrosis,
sickle cell disease and haemophillia.

3.MULTIFACTORIAL DISORDERS, which result

from a combination of multiple genetic and
environmental causes. Many birth defects such as
cleft lip and /or palate as well as adult disorders like
heart disease and diabetes.
4.MITOCHONDRIAL DISORDERS, a relatively
small number of diseases caused by alterations in
the small cytoplasmic mitochondrial chromosome.
Classification of human
chromosome abnomalies

Numerical abnormalties:

The no. of chromosomes in a normal haploid gamete is 23

or N. A diploid complement is the equivalent of 46
chromosomes or 2N. Euploid refers to exact multiple of N;
for example, triploid complement or 3N ,would contain 69
chromosomes and a tetraploid complement or 4N would
consist of 92 chromosomes.
I.EUPLOIDY
A. Triploidy
B. Tetraploidy

Incomplete triploid embryo with upper

lip midline cleft
II.ANEUPLOIDY
A. Monosomies
B. Trisomies
C. Tetrasomies
D. Pentasomies

indicates a noneuploid state such as

loss of a single chromosome
monosomy ,the gain of a single
chromosome,trisomy. A chromosome
complement with two extra identical Trisomy 21 male fetus, at
chromosomes is tetrasomic.The most 16 developmental week-
common mechanism responsible for Showing simian crease.
clinodactyly of fifth finger
aneuploidy is nondisjunction or the and mild posterior nuchal
failure of chromosomes to separate edema
normally during cell division.It can
occur in the first or second stage of
meiosis or in mitosis.
III.REARRANGEMENTS
A. Translocations
1.Robertsonian
2.Reciprocal
3.Complex

They are most common type

of rearrangements.They result
when all or parts of two or
more chromosome become
integrated into a single
chromosome.
 Inversion
• There are two types of inversions,paracentric and
pericentric.Paracentric inversion occurs when there are two breaks
on one arm of a single chromosome and the chromosomal segment
between those two breaks is reconstituted at 180°.It does not
involve the centromere.Perecentric does involve the centromere,in
this one break occurs on one chromosomal arm and the other break
on the other chromosomal arm of a single chromosome.Carriers of
either type of inversion are usually phenotypically normal because
typically all of the genetic material is retained(balanced);such
material is simply rearranged differently.
B. Inversion
1.Paracentric 2.Pericentric
• C. Insertions:In genetics an insertion (also called an insertion mutation)
is the addition of one or more nucleotide base pairs into a DNA sequence.
This can often happen in microsatellite regions due to the DNA polymerase
slipping. Insertions can be anywhere in size from one base pair incorrectly
inserted into a DNA sequence to a section of one chromosome inserted into
another.
• On a chromosome level, an insertion refers to the insertion of a larger
sequence into a chromosome. This can happen due to unequal crossover
during meiosis
1.within a chromosome
a. direct
b. inverted
2.between two chromosomes
a. direct
b. inverted
 DELETION & DUPLICATION
• A deletion is the loss of a chromosomal segment.If distal end of the
chromosome is lost ,it is called as terminal deletion,requiring only
one chromosomal break.If the loss is within the chromosome ,it is
called as interstitial deletion, requiring two chromosomal
breaks.Deletions may arise as a result of (1) chromosomal breakage
with loss of the acentric fragment (2) abnormal translocation
segmentation or inversion recombination (3)unequal crossing over
between sister chromatid or misaligned homologous chromosomes.
• Duplication results in partial trisomy for the involved chromosomal
segment.Similar to deletions,duplications may arise as a
consequence of unequal crossing over between sister chromatids or
misaligned homologous chromosome.
D. Deletions
1.Terminal
2.Interstitial
 E. Isochromosomes

Isochromosome arise a
result of a transverse instead
of a longitudinal split of the
centromere during meiosis or
mitosis or as the
consequence of a
translocation adjacent to the
centromere of one
chromosomal arm to its
homolog.
 F. Ring Chromosome
• They are formed when a break occurs on each arm of a
chromosome followed by fusion of the exposed ends to create a
circular structure. The distal fragments are lost because they lack a
centromere. They may also arise as the result of telomere-to-
telomere fusion. A ring chromosome originating from this mode
loses little if any chromatin.
• In mitosis ring chromosomes are often unstable, undergoing sister
chromatid exchange and generating smaller or larger rings.
• Individuals with ring chromosomes may be severely mentally
retarded with multiple congenital anomalies or only mildly delayed
or clinically normal. The phenotypic variability depends upon how
much the chromosomal material is lost in the formation of ring.
 IV.MOSAICISM
Mosacism can be defined as the presence in the individual or tissue,of two or
more cell lines that differ in their genetic constitution but are derived from
a single zygote,that is they have same genetic origin.
Chromosome mosaicism occur genrally due to non disjunction in an early
embryonic mitotic division with the persistent of more than one cell line.
For eg. 2 chromatids of no. 21 chromosome failed to separate at second mitotic
division in a human zygote,this would result in 4 cell zygote having 2 cells
with 46 chromosomes,one cell with 47 chromosome(trisomy 21) and one
cell with 45 chromosome(monosomy 21)

Type I,chromosome abnormal cell line is

confined to trophoblast only
Type II to villous stroma
Type III both trophoblast and
extraembryonic stroma are different from
the fetus
 AUTOSOMAL ABNORMALITY
• Down syndrome(trisomy 21) Approximately 95% of affected
individuals have regular trisomy 21 (47,XX or XY, +21); the
remainder have trisomy 21 mosaicism or a translocation between
chromosome 21 and another chromosome, in addition to two
normal chromosomes 21.
 TRISOMY 13 PATAU SYNDROME
• Over 80% of trisomy-13 individuals have regular trisomy, and the remainder
have a translocation involving a chromosome-13 or trisomy-13 mosaicism.
Loss of a chromosome segment has a greater effect on the phenotype than
does a gain. Consequently, monosomy is seen far less frequently than
trisomy and, in fact, monosomy 21 is the only undisputed complete
monosomy described in liveborn infants. There are also rare cases of
mosaic monosomics, and a variety of partial monosomies occurring as a
consequence of structural rearrangement.

Trisomy 13,severe bilateral

cleft lip and palate
TRISOMY 18 (EDWARD SYNDROME)

Female fetus ,at 14

developmental week.
Note the typical positioning
of hand and rocker
bottom feet.
 CRI DU CHAT SYNDROME

Microcephaly,hypertelorism,
down slanting palpebral
fissures,low set ears and
micrognathia.
 SEX CHROMOSOME ABNORMALITY

TURNER SYNDROME
KLEINFELTER
SYNDROME
 CRANIOFACIAL MALFORMAIONS &
CHROMOSOMAL ABERRATION
MAXILLARY HYPOPLASIA: 18q-;21; XXXX; XXXXX; XXXXY

ANAMOLIES OF MANDIBLE
1.Hypoplasia(micrognathia);1q+;4p-;5p-;+8;+9;10q+;11q++13;13q-;
+18;18p-;21q-;triploidy;XO;XXXX
2.Prognathism : 4p+;+21;XXXXX;XXXXY

ANAMOLIES OF THE MOUTH

1.short or absent philtrum :4p-;5p-;9p+;13
2. Microstomia: r(6); +18
3. Macrostomia :3p+;4p+;18p-;+20
4.cleft lip ± cleft palate : 1q+;4p-;5p-;9p+;13;+18;18q-;+21;21q-;triploidy
5.isolated cleft palate:3p+;4p-;7q+;10q+;11p+;+13;13q-;+18;18q-;r(18);
+21;21q-;22q+;triploidy;XO;XXXXY
ANAMOLIES OF DENTITION

1.Hypodontia : +21
2.Microdontia: +20,+21;triploidy;XO
3.Macrodontia; =21;XYY
4.Peg shaped lateral incisors:+21;XXXXY
5.Syndontia;+21
6.Enamel hypocalcification:+21

ANAMOLIES OF TONGUE

1.Macroglossia: 7q+;+20(pallister in 1976);+21;triploidy

2.Bifid tongue: +13

3.Fissured tongue: +21

GENETIC DISEASE,
AND THEIR
LOCUS
I. Developmental disturbances of Oral & Paraoral structures
DISEASE GENETIC LOCUS
Deletion in chromosome
Van Der Woude syndrome
band 1q32,band 17p11

Cleft lip/palate-ectodermal
PVRL1(11q23-q24)
dysplasia syndrome

Branchio –oto renal syndrome

EYA1(8q13.3)
type 1
Hay wells syndrome TP73L(3q27)
LADDs(levy-hollister FGFR2(10q26),FGFR3(4p16.3)
syndrome) FGF10(5p13-p12)
Oral –facial-digital
CXORF5(Xp22.3-p22)
syndrome,type 1

Rubinstein –Taybi syndrome CREBBP(16p13.3),EP300(22q13)

Weyers acrofacial dysostosis EVC(4p16)

Witkop tooth and nail

MSX1(4p16.1)
syndrome
Hereditary intestinal
Germline mutation STK11(band 19p13.3)
polyposis syndrome

Amelogenesis Imperfecta DXS85 at Xp22

Dentinogenesis DSPP on chromosome 4

Imperfecta,type 1 4q21.3
II. Benign & Malignant Tumors Of Oral Cavity
TUMORS GENETIC LOCUS
Chromosomal aberrations
Keratoacanthoma Gain on 8q,1p,9q
Deletion on 3p,9q,19p,19q
Leiomyoma t(12;14)(q14-15;q23-24)
Lipoma Rearrangement of 12q,13q,6p
Lipoblastoma 8q11-13
Fibrosarcoma t(12;15)(p13;q25)
Synovial sarcoma t(X;18)(p11;q11)
Liposarcoma t(12;16)(q13;p11.2)
Chromosomal translocation involving
Hemangioendothelioma chromosome 1 and 3
t(1;3)(p36.3;q25)
t(12;19)
Hemangiopericytoma
t(13;22)
Chromosome 22band q12
Ewing sarcoma Other 11 & 21
t(11;22)(q24;q12)
Osteosarcoma d13q14
Synovial sarcoma t(X;18)(p11;q11)
Non Hodgkin lymphoma t(14;18)(q32;q21)
 t of c-myc oncogene from chromosome
8 to either immunoglobulin heavy
Burkitt’s lymphoma chain-chromosome 14[t(8;14)] or one
light chain loci on chromosome
2[t(8;2)]or chromosome 22[t(8;22)]
t(11;14),t(14;8),t(8;14)
Multiple Myeloma
other 6q-,7q-,5q-,t(9;22),17q+
Losses in chromosome 13,chromosome
Solitary Plasma cell
1p,chromosome 14q and gain in
Myeloma
chromosome 19p,9q,1q
13q14-q21loss
Leiomyosarcoma
5p14 gain
Loss of heterozygosity of chromosome
Rhabdomyosarcoma 11p15
Embryonal t (2;13)(q37;q14)on chromosome 13
Alveolar and either PAX 3gene on chromosome
2 or PAX 7 gene on chromosome 1
Alveolar soft part sarcoma 17q25 and Xp11.2
Neurofibroma 22q12.1
 III. Tumors of Salivary Gland
Pleomorphic Adenoma 12q13-15
Putative gene PLAG1
mapped to chromosome 8q12
t(3;8)(p21;q12)

IV. Cyst and tumors of Odontogenic origin

Jaw cyst-Basal cell
9q22.3-q31
nevus,Bifid Rib syndrome
 V. Diseases of Bones and Joints
COL1A1 on chromosome band
Osteogenesis imperfecta 17q21 and COL1A2 on band
7q22.1
FBN1 gene on chromosome
Marfan syndrome
15,bands q15-q23

Achondrogenesis Unknown locus

Type IA(Fraccaro-Houston- Mutation of DDST
Harris type) (distrophic dysplasia sulfate
Type IB transporter)
Hypophosphatasia ALPL on band1p36.1-34
Pyknodystosis 1q21
Mutation in GNAS1 gene
Fibrous dysplasia
20q13.2
Cherubism 4p16.3
Vitamin D resistant Rickets
X-linked Mutation in PEX gene Xp22.1
AD 12p13
 Crouzon disease Mutation of FGFR-2 gene
Mandibulofacial dysostosis 5q32-q33.1
Apert syndrome 10q25-q26
Achondroplasia 4p16.3

Chondroectodermal
4p16.1
dysplasia

Cleidocranial dysplasia 6921

Tricho-dento-osseous
17q21.3-q22
syndrome
 VI. Blood disease
Polycythemia Vera d of 20q,13q,5q,7q trisomy 8,9,1q
Chediak Higashi syndrome 1q42-43
Wiskott –Aldrich syndrome Xp11.22-23
12q(v WF gene)
Von Willebrand disease
mutation,insertion or deletion

VII. Diseases of Skin

Ectodermal dysplasia
X linked hypohidrotic Xq-12-q13.1
Hidrotic ED GJB6 on 13q
Psoriasis 19q13,17q25 and 1q21
Pachyonychia Congenita Ch 17
ATP2A2
Karatosis follicularis
12q23-24.1
Incontinentia Mutated X

VIII. Diseases of nerves & muscle

Mild restricted Muscular
4q35
Dystrophy
CANCER:

Cancer is a genetic disease resulting from deviations of the normal

genetic mechanisms that regulate cell growth.These deviations
manifest themselves in many different ways including alterations of
the normal chromosomal complement.These changes can be
numerical or structural.

• Chronic myelogenous leukemia was the first neoplastic disease to be

associated with a specific chromosomal abnormality.This was shorter
than normal chromosome (Philadelphia or Ph chromosome).
Translocations are common not only in the leukemias
but also in mesenchymal neoplasms(sarcomas),where
they are often the sole karyotyping change.Anomolous
juxtaposition of gentic material can occur as the result
of translocation generating a chimeric gene.These
altered genes and abnormal protein production are
believed to be responsible for the induction of abnormal
cellular proliferation, referred as oncogenes.
The chromosomal abnormalities observed in cancer are often
multiple and complex e.g lipoma.
Cytogenetic analysis has provided insight into the
histopathogenesis of certain type of neoplasm for which the
derivation was previously unknown.eg Ewing sarcoma has
been shown a functionally identical chromosomal rearrangement
involving chromosomes 11 and 22 with peripheral
neuroepithelioma and Askin tumor ,indicating a common
mechanism of oncogenesis and a similar tissue origin.
 Genetic alteration in SCC of head and neck

Normal Mucosa Precursor Lesion Dysplasia

(ch9ploss) (3p,17p loss) (11q,13q,14q loss

p53 mutation)

Invasion Carcinoma In Situ

(6p,8,4q loss)

Courtesy WHO 2003

CLINICAL IMPLICATION
 INVESTIGATIONS
• Detecting chromosomal abnormalities
• The loss of part of a chromosome or deletion may be either
microscopic and visible using standard chromosome preparations.

• KARYOTYPING
For karyotyping of human chromosomes venous blood is taken and
blood leucocytes are stimulated to divide by mitosis in vitro by the
addition of phytohaemagglutinin. Colchicine is added to arrest cell
division at metaphase stage.It is further treated with saline which
results in swelling of cells and dispersal and better clarity for
counting and morphological study. Therafter, the material is stained
for eg by Giemsa to demonstrate the banding pattern of
chromosome. Finally,a suitable metaphase spread is photographed
through a high power microscope. The individual chromosome are
cut and then arranged in orderly fashion in homologous pairs, to
produce a standard arrangement.
Other samples which can be used
At submicroscopic level where special techniques are required for
identification.The most useful investigation is fluorescent in situ
hybridization(FISH).
• Hybridization refers to the bindig or annealing of complementary
DNA or RNA sequences.This approach permits the detection of
specific nuclei acid sequences in morphologically preserved
chromosomes,cells or tissue sections.
• FISH can be performed on cytologoical specimens such as cytologic
touch preparation and on surgically obtained pathological
specimens such as paraffin embedded tissue sections.
• Knowledge of the histologic derivation of an aneuploid cell is
important in developing novel therapeutic modalities that could
selectively target the neoplastic population within a specific
malignancy.
The use of whole genome arrays (DNA chips) will revolutionize
chromosome analysis in the future and allow rapid detection of gain or
loss of DNA in individuals in whom a karyotype is normal but symptoms
and signs suggest underlying genetic cause.These chips also called as
MICRO ARRAYS contain thousand of miniature probes i.e.short
sequences of DNA which are complementary to known sequences in
the normal genome.Each probe is embedded in one of thousands of
miniature wells on the chips.The patient sample is hybridized to the
chip and positive and negative results for each probe are typically read
off using a robot which detects fluorescent labels inserted in the DNA.
• Gene linkage
• The polymorphism in the normal genome can be mapped
using SNP or variations in the fragments of DNA
fragments generated with restriction enzymes . The
comparison of map in affected and unaffected individuals
allows identification of locus of DNA where the
responsible genes reside. The confidence of linkage with
diseases in question is influenced by the number of
subjects studied, the strength of the gene on disease.
• The confidence can be expressed as LoD (likelihood of
disequilibrium) score, which is –log10 of the probability (p
value) of linkage ,LoD score of >3 (p<0.001) is taken as
statistically significant .
• DNA sequence analysis
• PCR can amplify virtually any gene sequence for
analysis by gel electrophoresis or by automated DNA
sequencing.
• Prenatal testing
• Direct invasive testing of pregnancy for specific condition
usually one severe enough to cause infant death or severe
disability where a positive result will be used to decide about
termination of pregnancy .

Method used in prenatal testing

Test Gestation Comments
Ultrasound 1st trimester onwards Increased nuchal translucency for trisomie
and Turner ,NTDs,CHD
Chorionic villus
biopsy From 10-12 week 2% risk of miscarriage,used for early
chromosomal,DNA and biochemical
analysis; a specialized test

Amniocentesis From 14 week <1% risk of miscarriage, used for early

-fluid chromosomal,DNA and biochemical
-cells analysis, e.g. α-fetoprotein for NTD

Cordocentesis From 19 week 2-3% risk of miscarriage,specialized test

used for chromosomal & DNA analysis.
AMNIOCENTESIS
CHORIONIC VILLUS
SAMPLING
 Indications

• Advanced maternal age

• Previous child with detectable chromosomal abnormality
or parent with chromosomal abnormality such as
balanced translocation
• Parent or child with genetic diseases
• Abnormal antenatal scan
 FUTURE TRENDS

• Pharmacogenomics: the science of dissecting the genetic

determinants of drug kinetics and effects using information from the
human genome is called pharmacogenomics. Recently,it has been
recognized that a large series of polymorphic genes are involved in
drug absorption, distribution, tissue effects and metabolism, for ex a
large family of cytochrome P450 genes, mostly expressed in liver,
determine the metabolism of a host of specific drug.

• Polymorphism in these and other drug metabolic genes determine

the persistence of drug and therefore, should provide information
about dosages and toxicity.
• Gene therapy: the human genome project prospects the
gene therapy raised over the last decade or more has to
be fully realized.To date experiments to replace or repair
mutated genes have met with very limited success. Most
notable have been approaches to replace defective genes
in inherited human immunodeficiency syndromes. Genetic
engineering of a patient bone marrow cells can be
undertaken in vitro and the resulting reengineered bone
marrow transplanted back. Initial positive finding in the
treatment of severe combine immunodeficiency
syndrome(p72) have been tempered more recently with
the development of leukemia like conditions.
• Stem cell therapy: stem cells, primitive cells with the possibility of
both self renewal and differentiation. Broadly these come in two
categories
1) embryonal stem cells derived from early blastocyte,
2) adult stem cell present in differentiated tissues.

• Much of the excitement and controversies surrounds embryonal

stem cells which are derived from human embryos left over from in
vitro fertilizations programmes. In mammalians human model
species such cells can be taken and used to regenerate
differentiated tissue cells such as in heart and brain.

• These cells have the ability to produce any cell in the body and
proliferate rapidly in culture and so could be used refashion
damaged organs.
CONCLUSION
 CONCLUSION
• During the past decades, considerable efforts have been expending
on detecting gene loci that contribute to susceptibility for dental
agenesis. However the success in such genetic identification
attempts has been limited, and most of the fundamental questions
relating to the genetic epidemiology of dental agenesis remain
unanswered. In contrast to what has been found for monogenic traits
the results related to complex traits often have been rather
inconsistent.
Cytogenetic analysis is not a panacea for histopathology, but it is a
powerful adjunct that can complement conventional microscopy in
the formulation of an accurate diagnosis.
 SUMMARY
• The human genome consists of approximately 3 billion base pair,
some genetic disorders of nuclear DNA and 16000 base pairs of
mitochondrial DNA encoding upward of 30,000 genes.
• Genes are organized into introns and exons. Introns are spliced out
of the mature messenger RNA. Elements that control gene
expression are located adjacent to the genes they control.
• Three major patterns of Mendelian genetic transmissions are known:
autosomal dominant, autosomal recessive and sex linked.
• Some disorders occur with increased frequency in families but do not
display classic mendelian transmission; these are said to display
multifactorial inheritance.
• Aside from single gene disorders ,some genetic disorders occur as a
result of abnormalities of chromosome number or structure.
• The ability to isolate cloned genes has had enormous impact on our
understanding of the molecular basis of human genetic disorders.
• Molecular techniques now exist that allow diagnosis of some genetic
disorders, either by direct detection of mutations or by genetic
linkage analysis.
• Genetic counselling involves familiarizing a family with the medical
facts about the disorder, the role of heredity, options available for
dealing with genetic risks and helping the family adjust to dealing
with the disorder.
• A no. of methods of prenatal diagnosis exist, including chorionic
villus sampling and amniocentesis, both of which provide fetal cells
for genetic diagnosis.
• Genetic evaluation and screening will have a greater importance in
the evaluation and treatment of a number of disorders of the head
and neck, including hereditary hearing loss and head and neck
cancer.
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Thank you