Genetics, Chromosome Abnormalities

Development

Cytogenetics refers to the study of chromosomes. Although chromosomes have been recognized as the physical basis of inheritance for more than a century, the discipline of mammalian cytogenetics, as it is known today, emerged around the mid-1950s.[1] In 1956, the diploid number of chromosomes in human cells was established at 46 rather than the previously accepted 48.[1][2] By 1960, a technique for preparing chromosomes from cultured peripheral blood leukocytes had been developed.[3] This advancement allowed scientists to accurately describe aberrations in the normal human chromosome number and structure.  

Incidence of Chromosomal Abnormalities 

The development of karyotyping led to the identification of chromosome abnormalities in various conditions. Within 3 years, numerical chromosomal abnormalities were identified in Turner syndrome (45, X), Down syndrome (47, XX+21/47, XY+21), and Klinefelter syndrome (47, XXY). Subsequently, many additional numerical and structural chromosomal abnormalities were identified as techniques for chromosomal analysis advanced.[4][5]

Chromosomal abnormalities have been identified in approximately 0.5% to 1% of live-born infants and in nearly 5% of stillbirths. A higher incidence has also been reported in spontaneous abortions following assisted reproductive technologies.[6][7][8]

Classification of Chromosomal Abnormalities

Chromosomal abnormalities are broadly classified into numerical and structural abnormalities. 

Numerical abnormalities: Numerical abnormalities are considerably more common than structural ones and involve any deviation from the normal diploid number for a given species.

• Aneuploidy: Aneuploidy is an abnormality in the number of chromosomes in a cell resulting from the loss or duplication of one or more chromosomes. In humans, aneuploidy refers to any number of chromosomes other than the usual 46.[9][10]
  • Monosomy: Loss of one chromosome from a pair (2n − 1); for example, Turner syndrome (XO).
  • Trisomy: Presence of an extra copy of a chromosome (2n + 1); for example, Down syndrome (trisomy 21).

• Polyploidy: Polyploidy is a condition in which the entire set of chromosomes (haploid) is extra or missing.[11][12]

Structural abnormalities: Structural abnormalities involve the rearrangement of one or more chromosomes in the genome. Most structural aberrations result from the unequal exchange between chromosomes or the enzymatic misrepair of 2 chromosome breakages.[13] Examples include deletions, translocations, inversions, duplications, ring chromosomes, and isochromosomes (see Tables Structural Chromosomal Abnormalities and Numerical Chromosomal Abnormalities).

Table 1. Structural Chromosomal Abnormalities

Table 2. Numerical Chromosomal Abnormalities

Constitutional and Acquired Chromosomal Abnormalities

Chromosomal abnormalities may also be classified as constitutional or acquired.

Constitutional chromosomal abnormalities: These abnormalities, also known as inborn errors, are anomalies present in all tissues of a patient. These abnormalities may arise during gametogenesis or early embryogenesis, affecting all or a major portion of the organism's cells.[14]

The estimated incidence of constitutional chromosomal abnormalities is approximately 20% to 50% of all human conceptions, with more than 1000 distinct anomalies observed in live-born patients. An unbalanced anomaly may occur when certain genes are present in only 1 or 3 copies, rather than the typical 2. This genetic imbalance can result in a triad of clinical features: dysmorphia, psychomotor delay, or visceral malformations.[15]

Acquired chromosomal abnormalities: These abnormalities typically develop during adulthood and affect a single clone of cells, with a specific and localised distribution within the body. [14]

Cellular

Human somatic cells contain 46 chromosomes (2n), except for enucleate cells, such as red blood cells, and cell fragments, such as platelets. Human gamet cells (sperm and oocytes) contain 23 chromosomes (n).[16] Consequently, numerical chromosome abnormalities may occur in exact multiples of the haploid number (n), called euploidy, or in every other case.

Types of Cell Division

Cell division occurs in 2 forms: mitotic and meiotic.

Meiosis: Meiosis, also known as reduction division, is the process by which male and female gametes are formed. During spermatogenesis, male gametes (sperm) undergo 2 successive meiotic divisions: meiosis I and meiosis II.

• Meiosis I includes prophase I, metaphase I, anaphase I, and telophase I, followed by a brief resting phase called interkinesis.
• Meiosis II comprises prophase II, metaphase II, anaphase II, and telophase II.

These divisions result in haploid daughter cells containing half the chromosomal number of the parent cell.[17] Female gametes also undergo meiotic cell division, resulting in daughter cells of unequal size, each with a haploid chromosome number.[17] 

Mitosis: Mitotic cell division occurs in somatic cells and results in the formation of diploid daughter cells.[17]

Mechanisms of Aneuploidy

Aneuploidy most commonly results from failure of chromosome segregation during cell division, particularly during meiosis I or II. This outcome includes nondisjunction, premature disjunction, or anaphase lag, with nondisjunction being the most frequent mechanism.[13] Nondisjunction occurs when replicated chromosomes do not separate adequately during one of the two meiotic divisions, predominantly arising during meiosis I of oocyte formation rather than during spermatogenesis. As a result, the resulting germ cells contain either an extra chromosome or a missing copy of a chromosome.

Different consequences occur depending on which meiotic cycle is involved in nondisjunction. In meiosis I, the gamete contains 24 chromosomes from both the paternal and the maternal homologs. In meiosis II, the gamete still contains 24 chromosomes, but both copies exclusively derive from either the paternal or maternal homolog.[13] In contrast, sex chromosome aneuploidies typically have a different origin: paternal meiotic nondisjunction is responsible for at least 50% of cases.[14] 

Several factors are associated with human aneuploidies, including:

• Advanced maternal age
• Prior trisomy
• Aberrant recombination 
• Folic acid deficiency (to a lesser extent)
• Obesity
• Smoking
• Radiation [18] 

The rates of trisomy 21 increase nearly exponentially after 35 years of maternal age, rising in frequency from 10% to 20% to more than 60%.[16][19][20] 

If a new mutation occurs during embryogenesis or development (mitotic division), it may lead to mosaicism, defined as the presence of two or more karyotypically unequivocally distinct cell lineages within a single embryo.[20]

Aneuploidy is a general term used for an abnormal number of chromosomes, consisting of one or more extra or missing chromosomes.[16] Aneuploidy is the most prevalent chromosome abnormality in humans, developing in 5% to 10% of all pregnancies, and is the leading genetic cause of miscarriage and congenital defects.[18][21] Most aneuploidies are lethal; nonetheless, a limited number of viable syndromes exist. In contrast, polyploidy, the condition in which a cell has more than 2 sets of chromosomes, is uncommon in human embryos.[16] For example, triploidy (3 sets of chromosomes or 3N) may occur in up to 3% of all human conceptions. However, polyploidies, including monosomy, triploidy, tetraploidy, pentaploidy, and hexaploidy, are generally not compatible with life in humans.

Generally, an aneuploid chromosome set differs from the wild type by a small number of chromosomes, typically one. For example, trisomy (3 copies of a specific homologous chromosome or 2N + 1) is the most frequent constitutional chromosomal abnormality in humans.[14] Although extra copies have been identified for every chromosome, most are lethal during embryogenesis. Even the known viable clinical syndromes for trisomies are more frequently observed in spontaneous abortions than in live births.[14][16] 

Monosomies, defined as having a single nonhomologous set of chromosomes (2N − 1), are extremely rare in humans and are typically observed only in chromosomes 21 or X. The findings suggest that the effects of polyploidies arise from an imbalance of crucial gene products found on small, gene-poor chromosomes.[14][16]

Notably, numerical abnormalities of sex chromosomes have different implications than those involving autosomes. Aneuploidy in autosomes is less common than in sex chromosomes, and trisomies are generally tolerated better than monosomies.[1] This distinction explains why having an extra or missing sex chromosome is more compatible with life and may have only milder consequences (trisomy) or equally severe consequences (monosomy) compared to autosome aneuploidies.

Robertsonian Translocation

This chromosomal rearrangement involves the fusion of 2 acrocentric chromosomes at their centromeres, resulting in the loss of both short (p) arms and the formation of a single chromosome containing one centromere and the long (q) arms of both original chromosomes. Some individuals may carry this cytogenetic aberration and remain phenotypically normal, as the short arms of acrocentric chromosomes contain relatively small amounts of genetic material. The 2 retained long arms can often compensate for this loss. However, in certain cases, Robertsonian translocations can lead to genetic imbalances during gametogenesis, resulting in zygotes with aneuploidies such as trisomies or monosomies, which may cause significant phenotypic consequences, including Down syndrome. The estimated carrier frequency of Robertsonian translocations in the general population is approximately 1 in 1000.[13][16]

Testing

Over the past century, many new techniques have been developed for chromosome testing in cytogenetics.[22] The 2 principal methods for detecting chromosomal abnormalities are karyotyping and Fluorescence in situ hybridization (FISH).

Karyotyping

Traditionally, karyotyping is considered the definitive method for detecting chromosomal abnormalities because it accurately identifies fetal aneuploidies, structural rearrangements, and duplications and/or deletions greater than 5 Mb.[23] A karyotype is the entire set of chromosomes in an organism. In this process, cells are inoculated and cultured for 10 to 11 days at 37 °C, then treated with colchicine, a mitotic inhibitor that arrests cells in metaphase. After incubation and centrifugation, the medium is replaced with a hypo-osmotic solution to produce cell lysis. Finally, the sample is fixed on a glass slide, and chromosomes are stained with a specific dye, such as Giemsa stain, for analysis under a light microscope. The diagnosis rates for chorionic villus sampling and amniocentesis are 97.8% and 99.4%, respectively.[23]

However, this technique requires cells to be in metaphase. Only 24% to 36% of embryos produce metaphase cells of sufficient quality for accurate chromosome quantification, and fewer than 25% of these cases are sufficient for complete cell analysis.[24] Additionally, as cells need to be cultured, the entire process typically takes about 1 to 2 weeks.[16] Nevertheless, karyotyping of amniotic fluid samples remains the gold standard for diagnosing fetal aneuploidies.[23]

Fluorescence In Situ Hybridization

FISH uses fluorescently labeled DNA probes to assess the presence, location, and copy number of the complementary DNA sequence of interest within an individual's genome through hybridization.[16][23] Probes may be labeled either directly, by incorporating fluorescent nucleotides, or indirectly, by using nucleotides that act as haptens for fluorescently labeled antibodies. First, the sample is cultured to arrest in metaphase. Following incubation, hybridization, and washout to remove unbound probes, the sample is viewed under a fluorescence microscope. This technique is particularly advantageous as a relatively rapid diagnostic tool for detecting structural chromosomal abnormalities involving small DNA segments, such as microdeletions and translocations, as well as for detecting trisomies due to a more distinct fluorescent reading.[2][22][23] Furthermore, FISH has led to the development of several advanced cytogenetic techniques, including spectral karyotyping, multicolor FISH, and comparative genomic hybridization. These methods overcome some of the initial limitations of conventional FISH, such as restriction to a single probe, single color, or limited regions of analysis.[2][23]

Some chromosome abnormalities can be detected through cytogenetic diagnostics, but they may not be associated with clinical defects.[25]

Clinical Significance

Approximately 0.4% to 0.9% of newborns have chromosomal abnormalities, with about half of them having an abnormal phenotype.[14][19][26][27]

Autosomal Trisomies

Trisomy 13 (Patau syndrome):

• Incidence: Approximately 1 in 5000 to 1 in 16,000 live births (third most common autosomal trisomy)
• Karyotype: 47, XX or XY, +13
• Clinical features: Microcephaly, holoprosencephaly, microphthalmia, small or poorly developed eyes (anophthalmia or cyclopia), cleft lip and palate, polydactyly, rocker-bottom feet, congenital heart disease, cryptorchidism, brain or spinal cord abnormalities, weak muscle tone at birth, and severe intellectual disability.
• Prognosis: Miscarriage, stillbirth, or early death (median survival around 1 year).[13][16]

Trisomy 18 (Edwards syndrome):

• Incidence: Approximately 1 in 3000 to 1 in 5000  live births (second most common autosomal trisomy)
• Karyotype: 47, XX or XY, +18
• Clinical features: Low birth weight, microcephaly, micrognathia, low-set malformed ears, clenched fists with overlapping fingers, congenital heart and renal abnormalities, rocker-bottom feet, and severe intellectual disability.
• Prognosis: Miscarriage, stillbirth, or early death (median survival around 1 year).[13][16]

Trisomy 21 (Down syndrome):

• Incidence: Approximately 1 in 700 to 1 in 800 live births (most common autosomal trisomy)
• Karyotype: 47, XX or XY, +21
• Clinical features: Characteristic facial appearance (flat facies, prominent epicanthic folds, and flat occiput), Brushfield spot in irides, weak muscle tone at birth, single transverse palmar crease (simian crease), clinodactyly, congenital digestive and cardiac defects, intellectual disability, increased risk for leukemia, Alzheimer disease, and hearing and vision problems
• Prognosis: Approximately 75% of conceptions die in embryonic or fetal life. Nevertheless, if birth occurs, the prognosis is relatively good, with a median survival of about 47 years. Down syndrome is the most common aneuploidy that is compatible with long-term survival.
• Notes: Approximately 95% of patients with Down syndrome have trisomy 21. In contrast, 4% of cases result from Robertsonian translocation, and about 1% are due to mosaicism.[13][16][28]

Sex Chromosome Aneuploidies

Klinefelter syndrome:

• Incidence: 1 in 500 to 1 in 1000 male births
• Karyotype: Typically 47, XXY (>90%). However, other karyotypes have been described: 48, XXXY; 49, XXXXY; 46, XY/47, XXY (mosaicism)
• Clinical features: Increased height, long extremities, low upper/lower segment ratio, gynecomastia, reduced facial and body hair (female hair distribution), delayed and incomplete puberty, small testes (testicular atrophy), infertility, developmental delays (learning disabilities, delayed speech, and language development), and increased risk for breast cancer.
• Prognosis: Variable, depending on the severity of clinical manifestations and treatment; overall, fairly good. The life span is slightly reduced.[13][16]

Triple X syndrome:

• Incidence: Approximately 1 in 1000 female births
• Karyotype: 47, XXX
• Clinical features: Presents with increased height and risk of learning disabilities; delayed development of speech, language, and motor skills; weak muscle tone; behavioral and emotional difficulties; seizures; and kidney abnormalities. Some cases may seem phenotypically normal.
• Prognosis: Variable, depending on the severity of clinical manifestations and treatment; overall, fairly good.[13][16] 
• Notes: In this aneuploidy, X chromosomes are inactivated as Barr bodies. Therefore, 2 extra Barr bodies are present at karyotyping.

XYY syndrome:

• Incidence: Approximately 1 in 1000 male births
• Karyotype: 47, XYY
• Clinical features: Increased height and risk of learning disabilities; delayed development of speech, language, and motor skills; weak muscle tone; hand tremors; seizures; asthma; scoliosis; behavioral and emotional difficulties. As with triple X syndrome, some cases may seem phenotypically normal.
• Prognosis: Variable, depending on the severity of clinical manifestations and treatment; overall, fairly good.[13][16]

Turner syndrome:

• Incidence: Approximately 1 in 2000 to 1 in 2500 live female births; it is the most common sex chromosomal abnormality in females and the most common genetic cause of primary amenorrhea.
• Karyotype: 45, X accounts for 45% of cases because most zygotes cannot survive extrauterine life. Remaining cases have a mosaic karyotype (45, X/46, XX; 45, X/46, XY; or 45, X/47, XXX) or a structural abnormality (isochromosome, 46, Xi (Xq) or (Xp), or ring chromosome, 46, Xr (X)).
• Clinical features: Short stature, webbed neck, low posterior hairline, shield chest, amenorrhea, absence of puberty, the early loss of ovarian function (ovarian dysgenesis), infertility, skeletal abnormalities (cubitus valgus), lymphedema, and congenital kidney or heart disease (ie, horseshoe kidney and coarctation of the aorta).
• Prognosis: Variable, depending on the severity of clinical manifestations and treatment; overall, fairly good.[13][16][29]

Cytogenetic analysis of fetal cells requires samples from amniotic fluid, chorionic villi, or fetal blood, collected via invasive testing such as amniocentesis, chorionic villus sampling, or cordocentesis, respectively.[23] These methods pose a risk of miscarriage and other serious complications. However, some noninvasive genetic prenatal tests have been developed to allow even higher detection rates of aneuploidies in high-risk pregnancies. These noninvasive tests analyze cell-free DNA (cfDNA) in the maternal serum, as nearly 3% to 15% of cfDNA in the maternal blood is of fetal origin.[30] The utilization of cfDNA has increased enormously since its introduction in 2011. Although these techniques are limited to screening for common trisomies and carry a risk of test failure (2.6%-5.4%), they offer significant advantages over other methods and are likely to become widely adopted for prenatal screening in the future.[30] The detection of chromosomal aberrations early in pregnancy is crucial. Clinicians should discuss various medical options with parents to make an informed decision.[23]