What is cytogenetics?

It is a branch of genetic involving the study of the cell and the chromosomes in detail. The chromosomal studies include the grouping and numbering of chromosomes, studying their structures, their variations in numbers, and the related conditions. It involves the behavior of the chromosomes during the mitotic and the meiotic phases. Studying chromosomes involves various techniques. Conventional cytogenetic techniques include karyotyping and banding techniques. Molecular cytogenetic techniques involve modern tools to detect chromosomal aberrations. FISH, Array-CGH, and many others help in studying the chromosomes.

The human cytogenetics relates to the study of human chromosomes and the mechanisms and anomalies associated with the same. The plant and animal cytogenetics cover the study of the respective chromosomes and the conditions associated with the structural and numerical variations. The human chromosomes involve autosomes and sex chromosomes. The total complement of chromosomes includes 46 number of chromosomes. The study of every chromosome in detail includes revealing its structure, the banding pattern, the genes in every chromosome, the conditions associated with same, and overall functioning of the chromosome.

The human cytogenetics involves the study of human chromosomes and the anomalies associated with the same. Let us discuss the human chromosomes in detail.

Image 1: Chromosomes and cytogenetics

Human chromosomes:

The chromosomes occur in the nucleus. They consist of DNA compacted with histone proteins. The word chromatin indicates the strands of the chromosomal material in the interphase. It shows the presence of coiled and extended regions. There are two types of chromatin such as euchromatin and the heterochromatin. The euchromatin involves highly active DNA required for the transcription process. It stains lighter than the heterochromatin. Males possess X and Y chromosomes. The females possess two X chromosomes. The sizes and the shapes of the chromosomes vary as per the phase of the cell cycle. The size of the metaphase chromosome is 5mm. Chromosomes acquire different shapes during the anaphase such as the rods, V, J, T, or X shaped.

A metaphase chromosome reveals five main structural components such as the satellite, the telomere, the chromatids, the primary constriction, and the secondary constriction. The two symmetrical halves running parallel to one another indicate the chromatids. The ones adjacent to each other are known as sister chromatids. The primary constriction is also known as the centromere. It pins up the chromatids together. The centromere divides the chromosome into its respective arms. The short chromosomal arm is known as the p arm. The long chromosomal arm is known as the q arm. The secondary constriction or the nucleolar organizer region gets associated with the nucleolus and its formation. The position of the centromere is different for every chromosome.

Chromosome pair number	Group of the chromosome	Type of the chromosome based on its structure	Abnormalities associated with the structure or number
1	A	Metacentric	1p36 deletion syndrome
2	A	Submetacentric	2q37 deletion syndrome Cancers
3	A	Metacentric	3p deletion syndromes Microdeletion syndromes Cancers
4	B	Submetacentric	Cancers Wolf-Hirschhorn syndrome
5	B	Submetacentric	5q31.3 microdeletion syndrome  Cri-du-chat syndrome
6	C	Submetacentric	6q24-related transient neonatal diabetes mellitus  Cancers
7	C	Submetacentric	Russell-Silver syndrome Saethre-Chotzen syndrome Williams syndrome
8	C	Submetacentric	Recombinant 8 syndrome Trichorhinophalangeal syndrome type II
9	C	Submetacentric	Bladder cancer Chronic myeloid leukemia Kleefstra syndrome
10	C	Submetacentric	Cancers
11	C	Submetacentric	Jacobsen syndrome Neuroblastoma
12	C	Submetacentric	Pallister-Killian mosaic syndrome
13	D	Acrocentric	Retinoblastoma Trisomy 13
14	D	Acrocentric	FOXG1 syndrome Multiple myelomas Ring chromosome 14 syndrome
15	D	Acrocentric	Prader-Willi syndrome Angelman syndrome
16	E	Metacentric	16p11.2 deletion syndrome 16p11.2 duplication Rubinstein-Taybi syndrome
17	E	Submetacentric	17q12 deletion syndrome 17q12 duplication Acute promyelocytic leukemia Miller-Dieker syndrome Potocki-Lupski syndrome Smith-Magenis syndrome
18	E	Submetacentric	Tetrasomy 18p Trisomy 18
19	F	Metacentric	19p13.13 deletion syndrome
20	F	Metacentric	Alagille syndrome Cancers Ring chromosome 20 syndrome
21	G	Acrocentric	Down’s syndrome
22	G	Acrocentric	22q11.2 deletion syndrome 22q11.2 duplication 22q13.3 deletion syndrome Emanuel syndrome
X	-	Submetacentric	Klinefelter syndrome Triple X syndrome Turner syndrome X-linked acro gigantism
Y	-	Acrocentric	47, XYY syndrome 48, XXYY syndrome Y chromosome infertility

Karyotyping:

It helps in grouping the chromosomes from A to G. Human cells possess 22 pairs of autosomes (non-sex chromosomes). There are two sex chromosomes known as X and Y respectively. The procedure of karyotyping involves three main steps such as culturing the cells to get the chromosomes, banding or staining technique, and observation under the microscope followed by software analysis. After arranging the chromosomes in respective groups, they get analyzed for the presence or absence of the structural or numerical variations.

Image 2: Chromosome Banding

Chromosome banding:

The banding techniques help in identifying the dark and the light regions or chromosome bands. Various techniques exist in chromosome banding. The G-banding is the most commonly used technique. It involves treating the chromosomes with trypsin. The trypsin denatures the proteins present in the chromosome. The next step involves staining the chromosomes with Giemsa solution. The light and dark bands form due to this type of staining technique. Thus, it is possible to visualize them under the microscope. The Q banding method helps in staining the chromosomes with quinacrine mustard. The banding patterns mimic that of the G banding. The R-banding technique involves pre-heating of the chromosomes before staining with the Giemsa. It involves a reverse banding pattern as compared to the G banding. The Centromere and the secondary constriction regions get stained using C- banding.

Fluorescence in-situ hybridization:

The FISH technique utilizes a single-stranded DNA probe labeled with fluorescent labels. The single-stranded DNA probe gets annealed with the complementary target sequence on the chromosome. Hence, it detects the regions with similar sequences. Three main types of FISH probes include Centromeric probes, chromosome-specific unique sequence probes, and whole chromosome paint probes. The sequences found near the Centromeric regions show the presence of repetitive DNA. Also, the regions of centromere themselves show a large number of repetitive sequences. Thus, Centromeric probes help in identifying the sequences. The sub-microscopic deletions and duplications get identified using the chromosome-specific unique sequence probe. To visualize the entire chromosome, the cytogeneticists use whole chromosome paint probe. 

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