MGD 4.1 Chromosomal abnormalities

Chromosomes: structure and basic concepts

• A chromosome consists of proteins and one long molecule of DNA.

• Each chromosome has a short arm (p) and a long arm (q) connected by a centromere.

• A chromatid is one of two identical halves of a replicated chromosome.

• Before cell division (M phase), chromosomes replicate (S phase) so that each daughter cell receives a complete set of chromosomes.

• In humans, a diploid cell has 46 chromosomes: $22$ pairs of autosomes and $1$ pair of sex chromosomes (total $46$).

Karyotype, karyogram, and ideogram

• A karyotype is the actual picture of an individual’s collection of chromosomes.
• A karyotype is a preparation of the complete set of metaphase chromosomes in cells, sorted by length, centromere location, and other features.
• A karyogram is the arrangement of the whole set of chromosomes in pairs by size and centromere position.
• Distinction:
  • Karyotype describes chromosome number and their appearance.
  • Karyogram is the visual arrangement of the chromosomes in pairs by size and centromere position.
• Reference formats: the standard reporting uses the diploid number and sex chromosomes, e.g. $46,\,XX$ (normal female) or $46,\,XY$ (normal male).

Chromosome ideogram and banding

• A chromosome ideogram is a graphical representation of chromosomes.
• GTG/G-banding (Giemsa staining) produces visible karyotypes by staining condensed chromosomes.
• Dark and light bands are numbered according to international convention: ISCN 2013.
• Giemsa (G-banding) is a nucleic acid stain used in cytogenetics.

Karyotyping: process and sources

• Karyotyping is the process of pairing and ordering all the chromosomes of an individual.
• It detects changes in chromosome number and structural changes (deletions, duplications, translocations, inversions).
• Karyotypes are prepared from mitotic cells arrested in metaphase or prometaphase when chromosomes are most condensed.
• Possible tissue sources: peripheral blood, skin biopsy, tumour biopsies, or bone marrow (cancer).
• For prenatal diagnosis, sources include amniotic fluid or chorionic villus samples.

Indications for karyotyping

1) Prenatal screening:

• Down syndrome, especially with maternal age > $35$ years.
• Family history of chromosomal abnormalities.
• Abnormal ultrasound scan of the fetus.

2) Birth defects:

• Malformations.
• Mental or developmental impairment.

3) Abnormal sexual development:

• Klinefelter syndrome (47,XXY), Turner syndrome (45,X).

4) Infertility; recurrent fetal loss.

5) Leukemia and other cancers.

Chromosomal abnormalities: overview

• Polyploidy: possession of more than two complete sets of chromosomes.
• Aneuploidy: abnormal number of chromosomes for autosomes or sex chromosomes.
• Chromosomal mutations (structural):
  • Deletion
  • Duplication
  • Inversion
  • Insertion
  • Translocation

Polyploidy

• Definition: polyploidy is the heritable condition of possessing more than two complete sets of chromosomes.

• Most polyploids have an even number of chromosome sets; the most common in plants is tetraploidy (4n).

• Polyploids are common in plants, some fish, and amphibians; often fit and well adapted.

• In some animal tissues, polyploidy can occur in otherwise diploid organisms (endopolyploidy, e.g., human muscle tissues).

• Example: many strawberry species and hybrids can be diploid (2n), tetraploid (4n), pentaploid (5n), hexaploid (6n), etc.

• In humans, true polyploidy is lethal or extremely rare; triploidy ($69$ chromosomes) and tetraploidy ($92$ chromosomes) occur in pregnancies and miscarriages.

• Triploidy is usually due to polyspermy (one egg fertilised by more than one sperm) and occurs in about $2 ext{-}3\%$ of all pregnancies and ~$15\%$ of miscarriages.

• Complete tetraploidy is rarer but observed in about $1 ext{-}2\%$ of early miscarriages.

• Why polyploidy can be lethal: abnormal chromosome sets disrupt normal cell function.

• Examples (species): strawberries can be ddifferent ploidies; in humans, polyploidy is generally not compatible with life.

Aneuploidy

• Definition: presence of an abnormal number of chromosomes in a cell (usually one more or one less).

• It is the most common and clinically significant human chromosome abnormality, occurring in at least $3 ext{-}4\%$ of all clinically recognised pregnancies.

• In humans, the most common aneuploidies are trisomies (three copies of a chromosome), representing about $0.3\%$ of all live births.

• With few exceptions, trisomies are not compatible with life; trisomies account for about $35\%$ of spontaneous abortions.

• Most common mechanism: nondisjunction during meiosis (failure of homologous chromosomes or sister chromatids to separate properly).

• Maternal meiosis I is the most likely stage because oocytes can be arrested in prophase I for decades.

• The risk of trisomy increases with maternal age; women > $35$ are routinely offered testing for fetal chromosome abnormalities.

Autosomal trisomies: viable examples

• Viable autosomal trisomies are limited to a few chromosomes:
  • Trisomy $21$: Down syndrome (viable)
  • Trisomy $18$: Edwards syndrome (viable, but severe)
  • Trisomy $13$: Patau syndrome (viable to a limited extent)
• Trisomy $21$ is the only viable autosomal trisomy with the smallest predicted protein-coding content on chromosome $21$ (except the Y chromosome), making the perturbation less severe.
• Trisomy 21 is most commonly caused by full trisomy; mosaic and translocation variants exist.
• Down syndrome karyotype: $47,\,XX,+21$ or $47,\,XY,+21$.
• Trisomy 21 affected individuals have characteristic facial features and increased risk of certain health issues.

Down syndrome: clinical features and epidemiology

• Karyotype: $47,\,XX,+21$ or $47,\,XY,+21$ (and mosaic/translocation variants exist).
• Incidence: about $1/800\text{ to }1/1000$ live births (more common in males: approximately 1.15:1).
• Distinct facial features: flattened face, small head, short neck, protruding tongue, upward slanting palpebral fissures, small ears, poor muscle tone.
• Hands/feet: broad, short hands with a single palmar crease; short fingers; small hands/feet; excess flexibility.
• Iris: Brushfield spots (tiny white spots).
• Growth and development: intellectual disability (IQ ~$35${-}70).
• Health associations: congenital heart disease, higher risk of haematological malignancies (ALL risk ~10x higher), hypothyroidism, GI issues (e.g., constipation due to lack of nerves in colon), infertility (males infertile, females reduced fertility), eye and hearing disorders.

Edwards syndrome: clinical and epidemiology

• Karyotype: $47,\,XX,+18$ (or $47,\,XY,+18$).
• Incidence: around $1/6000$ live births; ~80% of affected individuals are female.
• Typical lifespan: $5 ext{-}15$ days, with $5 ext{-}10\%$ surviving beyond 1 year.
• Population data (2019, England and Wales): 95 live births with Edwards’ syndrome; mortality rate ~$98.1\%$ in the same year.
• Features: intrauterine growth retardation; low birth weight; potential heart defects and other organ abnormalities; severe intellectual disability; weak cry and limited response to sound.

Patau syndrome: clinical features and epidemiology

• Karyotype: $47,\,XY,+13$ (or $47,\,XX,+13$).
• Incidence: about $1/10{,}000 ext{ to }1/21{,}700$ live births.
• Survival: $5 ext{-}10\%$ live past the first year; a small percentage reach early adulthood.
• Features: multiple congenital abnormalities including severe intellectual disability, congenital heart defects, brain or spinal cord abnormalities, microphthalmia (very small eyes), low-set ears, polydactyly (extra fingers/toes), cleft lip/palate, hypotonia.

Sex chromosome aneuploidies and X inactivation

• Humans tolerate extra sex chromosomes better than extra autosomes due to X inactivation and the small gene content on the Y chromosome.
• Affected individuals typically show reduced sexual development and fertility, but may have normal life spans and responsive symptoms to hormone therapies.
• Common conditions:
  • Turner syndrome: $45,X$
  • Triple X syndrome: $47,XXX$
  • Klinefelter syndrome: $47,XXY$
  • XYY syndrome: $47,XYY$

X chromosome inactivation (Lyonization)

• X inactivation is a random transcriptional silencing of one of the two X chromosomes in female cells during development.
• Inactivation is stable; the same X chromosome remains inactive in all progeny cells.
• Result: females are a mosaic of cells with either the maternally inherited or paternally inherited X silenced.
• Barr body: an inactive X chromosome visible as a dense chromatin body in the nucleus.

Turner syndrome: 45,X

• Epidemiology: the most common sex chromosome abnormality in females; occurs in $1/2000$ to $1/2500$ live female births (roughly 10% of miscarriages are 45,X).
• Proportion with lifespan extending beyond infancy is low; some may reach early adulthood.
• Common congenital features: multiple anatomical abnormalities; high risk for cardiovascular and kidney issues; short stature; incomplete pubertal development without hormone therapy.
• Symptoms:
  • Short stature
  • Delayed or absent sexual development (no breast development; absent or irregular menses; small ovaries; potential need for hormone therapy)
  • Cardiovascular problems (bicuspid aortic valve, coarctation of the aorta, aortic arch elongation, hypertension)
  • Kidney defects in about $30\%$ to $40\%$ of individuals
  • Hearing problems (hearing loss in >$50\%$ in adulthood)
  • No mental retardation typically

Triple X syndrome: 47,XXX

• Incidence: about $1/1000$ live births; most are undiagnosed.
• X inactivation: two of the three X chromosomes are inactivated, leaving one active.
• Phenotype: highly variable; many have no noticeable effects or only mild symptoms.
• Common feature: taller than average height.
• Sometimes more significant symptoms occur, varying among individuals.

Klinefelter syndrome: 47,XXY

• Incidence: about $1/500\text{ to }1/1000$ live male births.
• Onset: symptoms typically appear after puberty.
• Common physical features: taller, less muscular body; gynecomastia (breast tissue development).
• Management: sex hormone therapy and surgical options as needed.

XYY syndrome: 47,XYY

• Incidence: about $1/1000$ live male births.
• Phenotype: not really a syndrome; often near-normal phenotype.
• Characteristics: increased growth rate in early childhood (about +7 cm taller than average) and normal testosterone levels and fertility.
• IQ: typically within normal range but on average ~10 to 15 points lower than siblings.
• Noted in popular media but lacks convincing evidence of a higher rate of criminal behavior.

Chromosomal translocations and related concepts

• Chromosomes can break and reattach to other chromosomes; breakpoints often lie between genes, so a balanced translocation carrier typically has a full gene complement and no phenotype.
• However, there is a risk of passing on derivative chromosomes to offspring, which can result in unbalanced offspring with phenotypic abnormalities.

Robertsonian translocation

• Formed by breakage of two acrocentric chromosomes (nos. 13, 14, 15, 21, 22) near their centromeres, with fusion of their long arms.
• Resulting total chromosome number is reduced to $45$.
• Carriers are usually phenotypically normal since there is no net loss of essential genetic material.
• Incidence in the population is about $1/1000$, with the most common fusion being between chromosomes $13$ and $14$.

Philadelphia chromosome and therapy implications

• Philadelphia chromosome results from a reciprocal translocation between chromosomes $9$ and $22$: $t(9;22)(q34;q11)$.
• This translocation creates the BCR-ABL fusion gene, encoding an oncogenic protein.
• Therapy: BCR-ABL tyrosine-kinase inhibitors (TKIs) are first-line therapy for most patients with chronic myeloid leukemia (CML).

Deletions and other mutations

• Deletion example: deletion of the short arm of chromosome $17p$ (17p) is found in $5 ext{-}8\%$ of chronic lymphocytic leukemia (CLL) patients and is associated with rapid disease progression and poor response to treatment.

Visualising chromosomes: FISH and beyond

• Fluorescence in situ hybridization (FISH) uses fluorescent probes to detect specific DNA sequences on chromosomes.

• Example: a fluorescent signal marks a specific locus; multiple probes can be used simultaneously to order segments relative to one another.

• Interphase FISH can detect chromosomal abnormalities in non-dividing cells.

• Applications: Charcot–Marie–Tooth syndrome duplication (evident as three signals for a locus), Philadelphia chromosome (green and red signals).

• Spectral karyotyping (SKY) and multicolor-FISH (M-FISH):

  • Paint each human chromosome in one of 24 colors.
  • Probe mixtures are hybridized and detected using multiple fluorescence filters.
  • M-FISH is a 24-color karyotyping technique and the method of choice for studying complex interchromosomal rearrangements.
  • Process involves metaphase chromosome preparations and labeling of chromosome-painting probes.
  • 24 chromosome painting probes plus Cot-1 DNA are used.
  • There is a 24-color scheme to distinguish all chromosomes.

Aneuploidy visual summaries

• Common examples shown: Down Syndrome, Klinefelter Syndrome, Turner Syndrome.

Summary (key takeaways)

• Chromosomes vary in shape and size; they come in pairs with characteristic banding patterns and identifiable features.
• Karyotyping can identify chromosomal abnormalities from a small cell sample.
• Large-scale chromosomal abnormalities are usually lethal; smaller-scale abnormalities can be viable but cause varying phenotypes.
• Automated visualization techniques (FISH, SKY, M-FISH) enable efficient screening and complex rearrangement analysis.

Notation quick reference

• Normal human karyotype formats: $46,\,XX$ or $46,\,XY$.
• Autosomal trisomies can be denoted as $46,\,XX,+21$, $46,\,XY,+21$, etc.
• Monosomy: e.g., Turner syndrome $45,X$.
• Translocations: $t(9;22)(q34;q11)$ (Philadelphia chromosome).
• Deletions: $17p$ deletion.
• Polyploidy: $3n, 4n$ (triploidy, tetraploidy) corresponding to $69$ or $92$ chromosomes respectively.