Karyotyping

A karyotype (or karyogram) is a digital image representation of the entire genome of an individual, where the chromosomes from a single metaphase cell are arranged and classified systematically.
Chromosomes are paired and ordered according to internationally accepted standard conventions based on their length (with chromosome 1 being the longest and 22 the smallest), banding pattern, and the position of the centromere.
Based on centromere position, chromosomes are categorized as metacentric (centromere in the middle), submetacentric (centromere distant from the center), and acrocentric (centromere at the end).
The primary purpose of conventional karyotyping is to evaluate the genome for numerical chromosomal abnormalities (aneuploidies or polyploidies) and large structural chromosomal rearrangements.

Chromosomes are always prepared from actively dividing cells.
Common tissue sources include peripheral blood lymphocytes, skin fibroblasts (from skin biopsies), bone marrow aspirates, tumor biopsies, and fetal tissues such as chorionic villi and amniotic fluid.
The process is labor-intensive and involves initially culturing the cells, with or without stimulation.
The dividing cells are artificially arrested in mitosis, typically during metaphase or prometaphase, by adding a chemical agent such as colecimid or colchicine.
The arrested cells are then subjected to a hypotonic solution, which disrupts the nuclear cell membrane and allows for proper dispersion of the chromosomes.
Following fixation, the slide preparations are stained to produce a unique, recognizable banding pattern for each chromosome pair.
The most widely utilized staining method is GTG banding (G bands by trypsin using Giemsa), which yields a specific sequence of dark (G-positive) and light (G-negative) bands along the length of the chromosomes.
A standard metaphase chromosome spread typically provides a resolution of 450 to 550 bands, allowing the detection of anomalies larger than approximately 5 Megabases (Mb).
High-resolution chromosome analysis utilizes prometaphase or prophase chromosomes that are less condensed, offering 550 to 850 bands, which aids in detecting smaller structural abnormalities.

While chromosomal microarray (CMA) has largely replaced karyotyping as the first-tier diagnostic test for unexplained intellectual disability, autism spectrum disorder, and multiple congenital anomalies, karyotyping remains a critical diagnostic tool in specific clinical scenarios.

Category	Specific Indications
Suspected Aneuploidy	Clinical features of Down syndrome (Trisomy 21), Edwards syndrome (Trisomy 18), Patau syndrome (Trisomy 13), Turner syndrome (45,X), or Klinefelter syndrome (47,XXY).
Reproductive & Endocrine	Ambiguous genitalia, disorders of sexual differentiation, primary amenorrhea, and infertility.
Family History	Recurrent pregnancy losses ($\geq$3), prior history of stillbirths and neonatal deaths, or a family history of a known/suspected balanced structural chromosomal rearrangement.
Oncology	Surveillance and diagnosis of specific solid tumors and leukemias (using bone marrow aspirates) to determine remission or relapse.
Instability Syndromes	Evaluation for chromosome breakage syndromes (e.g., Fanconi anemia, Bloom syndrome, Ataxia-telangiectasia).

According to the International System for Human Cytogenetic Nomenclature (ISCN), a karyotype description begins with the total number of chromosomes, followed by the sex chromosome constitution, and finally any structural abnormalities.
A normal female karyotype is designated as 46,XX and a normal male karyotype as 46,XY.

Abbreviation / Symbol	Meaning	Example / Clinical Translation
+ or -	Gain or loss of a whole chromosome	47,XX,+21 (Female with Trisomy 21)
del	Deletion of a chromosome segment	46,XY,del(5p) (Male with deletion of the short arm of chromosome 5, seen in Cri-du-chat syndrome)
t	Translocation (exchange of material between chromosomes)	t(2;8)(q33;q24.1) (Reciprocal translocation between long arms of chromosomes 2 and 8)
inv	Inversion of a chromosome segment	46,XY,inv(2)(p21q31) (Male with a pericentric inversion on chromosome 2)
mos or /	Mosaicism (presence of distinct cell lines)	mos 45,X/46,XX (Turner syndrome mosaicism)

Advantages: Karyotyping represents the entire genome and is the standard procedure for identifying recognizable numerical aneuploidies.
Crucially, it is the only test that can detect structurally balanced chromosomal rearrangements, such as balanced reciprocal translocations, Robertsonian translocations, and inversions, which do not involve a net gain or loss of genetic material and are thus missed by CMA.
Limitations: Conventional karyotyping suffers from a limited resolution (approximately 5 Mb), meaning it cannot detect microdeletions, microduplications, or single-gene point mutations.
Additionally, the procedure is slow due to the requisite cell culture phase and may fail to detect low-level somatic mosaicism.