Cytogenetics
Learning objectives
- LO 1Describe what a normal chromosome is made of, how it is identified, and why chromosome analysis is used clinically.
- LO 2Compare mitosis and meiosis, and predict the chromosomes that result when either goes wrong.
- LO 3Recognize the common abnormalities in the number of autosomes and sex chromosomes.
- LO 4Name the kinds of structural chromosome changes and what each does to offspring.
- LO 5Define chromosomal mosaicism and explain how it arises.
- LO 6Explain confined placental mosaicism and why it matters for prenatal testing.
MAPBig-picture map of chromosome abnormalities
LO 1Normal chromosomes
Q1. What is a normal human chromosome set?
- 46 chromosomes = 23 pairs: 22 pairs of autosomes + 1 pair of sex chromosomes (XX or XY)
- ≈20,000 genes spread over 400–1,000 visible bands → one band ≠ one gene; each band holds hundreds of genes
Trap
A visible band is a large stretch of DNA. A deletion of one band removes many genes, which is why even "small" visible deletions cause syndromes.
Q2. What are the parts of a chromosome?
| Telomere | Centromere | |
|---|---|---|
| Where | Caps the ends of each arm | Primary constriction between p and q |
| Job | Seals chromatin; prevents fusion with other chromosomes | Site where the spindle attaches and pulls chromatids to opposite poles |
| Sequence | Always TTAGGG, repeated hundreds to thousands of times | Highly repetitive, but unique to each chromosome |
| Euchromatin | Heterochromatin | |
|---|---|---|
| Packing | Less condensed | More condensed |
| DNA | Coding (active genes) | Mostly noncoding |
| Where | Chromosome arms | Around centromeres and the distal Y |
Memory tool
p = petite (short arm); q comes next in the alphabet (long arm). Euchromatin = "truly" active; heterochromatin = "different," packed away.
Step 1
Acrocentric chromosomes (centromere near one end, tiny p arms): 13, 14, 15, 21, 22. Only these form Robertsonian translocations. Telomerase keeps telomeres long in stem and cancer cells.
Q3. How are chromosomes analyzed, and when is it used?
- Analysis uses cells in metaphase, when chromosomes are most condensed and line up
- Cells are grown, arrested in metaphase, spread and G-banded → karyotype
- Meiotic cells are extremely hard to prepare, so meiosis is studied indirectly
- Standard G-banding misses changes under ≈5 Mb; use high-resolution banding, FISH or chromosomal microarray
| Clinical use | Example |
|---|---|
| Suspected aneuploidy | Down, Turner, Klinefelter features |
| Malformations / developmental delay | Unexplained birth defects |
| Reproductive problems | Recurrent miscarriage, infertility (look for balanced translocations) |
| Prenatal testing | CVS, amniocentesis |
| Cancer | Leukemia translocations |
In-house exam
Know why chromosomes are studied at metaphase and why meiotic chromosomes are rarely studied directly.
Q4. What do the terms and karyotype notation mean?
Numerical
- Haploid = n (23)
- Triploid = 3n (69)
- Tetraploid = 4n (92)
- Aneuploid: trisomy 2n+1; monosomy 2n−1
Structural
- Deletion = partial monosomy
- Duplication = partial trisomy
- Also translocation, inversion, ring, isochromosome
| Karyotype | Meaning |
|---|---|
| 47,XY,+21 | Male with trisomy 21 |
| 45,X | Turner syndrome |
| 46/47,+21 | Mosaic: normal and trisomy 21 cell lines |
| 45,XY,der(14;21)(q10;q10) | Balanced Robertsonian 14;21 carrier (45 chromosomes) |
| 46,XX,t(7;21)(q21;q11.2) | Balanced reciprocal translocation carrier |
| 46,XY,der(21)t(7;21)(q21;q11.2) | Unbalanced: inherited only the derivative 21 |
ApplyLO 1 application questions
A1Why can't a single G-band deletion be described as a single-gene disorder?
A2A child has features of a microdeletion syndrome but a normal G-banded karyotype. Next test?
LO 2Mitosis, meiosis and nondisjunction
Q1. What happens in mitosis?
Purpose: make identical, diploid daughter cells for growth and replacing dying cells.
| Phase | Key event |
|---|---|
| Interphase (G1, S, G2) | Growth; DNA copied in S phase |
| Prophase | Chromosomes condense; spindle and centrioles form |
| Prometaphase | Nuclear membrane disappears |
| Metaphase | Chromosomes line up on the metaphase plate (stage used for analysis) |
| Anaphase | Centromeres divide; sister chromatids pulled to opposite poles |
| Telophase | Cytokinesis; nuclear membrane reforms; chromosomes decondense |
Memory tool
PMAT: Prophase, Metaphase (Middle), Anaphase (Apart), Telophase (Two). Prometaphase sits between P and M.
Q2. What happens in meiosis, and why are there two divisions?
Occurs in germ cells only. Purpose: make haploid eggs and sperm with new gene combinations through independent assortment and recombination.
| Stage | What happens | Chromosomes per cell |
|---|---|---|
| Start | DNA replicated | 46, each with 2 chromatids |
| Meiosis I | Homologs pair; recombination in prophase I (synaptonemal complex, crossing over); independent assortment; homologs separate = reduction division | 23, each with 2 chromatids |
| Meiosis II | Like mitosis: sister chromatids separate | 23, each with 1 chromatid |
One crossover produces two parental-type and two recombinant gametes.
High yield
Meiosis I separates homologs; meiosis II separates sister chromatids. Every nondisjunction question depends on this.
Q3. How does meiosis differ in males and females?
| Males | Females | |
|---|---|---|
| Products | All 4 become sperm | 1 mature oocyte + 2 polar bodies |
| Cytoplasm | Divided evenly | Divided unequally |
| Starts | Puberty, after many mitotic divisions | Fetal life, after fewer mitotic divisions |
| Timing | Continuous, done in weeks | Arrested in prophase I before birth; resumes each cycle at ovulation; arrests in metaphase II; completed only after fertilization |
Analogy — the paused movie
Each oocyte is a movie paused at the same scene (prophase I) for 12–45 years. The longer the pause, the more likely the chromosomes come apart wrongly when "play" is pressed. That is why nondisjunction rises with maternal age.
Q4. How do mitosis and meiosis compare overall?
| Meiosis ("reduce") | Mitosis ("split") |
|---|---|
| Two divisions | One division |
| Germ cells | Somatic cells |
| Homologous chromosomes pair | Homologs act independently |
| Daughter cells haploid | Daughter cells diploid |
| Daughter cells have new assortments of parental chromosomes | Identical daughter cells |
Q5. What happens when chromosomes fail to separate (nondisjunction)?
Nondisjunction = failure of chromosomes to separate. It is the mechanism of aneuploidy and happens most often in meiosis I of oogenesis.
| Meiosis I error | Meiosis II error | |
|---|---|---|
| What fails | Homologs don't separate | Sister chromatids don't separate |
| Gametes | All 4 abnormal: 2 with both homologs (n+1), 2 with none (n−1) | 2 normal, 1 with two identical copies (n+1), 1 with none (n−1) |
| After fertilization | Trisomy or monosomy | Normal, trisomy or monosomy |
Step 1
A meiosis I error gives a gamete with both different homologs (heterodisomy); a meiosis II error gives two identical copies (isodisomy). If the zygote later loses the extra copy ("trisomy rescue"), it can be left with uniparental disomy (both copies from one parent), a cause of Prader-Willi syndrome.
In-house exam
Be able to draw nondisjunction in MI vs MII and state the gametes from each.
ApplyLO 2 application questions
A1A nondisjunction leaves half of the gametes normal. Which division failed?
A2Why are female eggs more prone to nondisjunction than sperm?
LO 3Numerical abnormalities
Q1. How common is aneuploidy, and which kinds survive?
- Most common and clinically significant chromosome disorder: >3–4% of recognized pregnancies
- Trisomy can occur for any chromosome but is rarely viable (21, 18, 13 and sex chromosomes are the survivors)
- Monosomy of a whole chromosome is always lethal, except monosomy X
- Mechanism: nondisjunction, most often maternal meiosis I
High yield
The only viable full monosomy is 45,X (Turner).
Q2. What do autosomal abnormalities have in common?
- Developmental delay / intellectual disability
- Facial features that look more like others with the syndrome than like family members
- Growth delay
- Congenital malformations
Q3. How do the three viable autosomal trisomies compare?
| Trisomy 21 (Down) | Trisomy 18 (Edwards) | Trisomy 13 (Patau) | |
|---|---|---|---|
| Face / body | Low nasal root, upslanting palpebral fissures, round cheeks, downturned mouth, short neck, flat occiput | Prenatal growth deficiency; clenched hands with overlapping fingers, small jaw, prominent occiput | Midline defects: oral clefts, spina bifida, omphalocele; microphthalmia |
| Heart | 40% congenital heart defect | Congenital heart defects (VSD) | Congenital heart defects |
| Other | 15–20× ↑ leukemia risk | — | — |
| Intellect | Moderate–severe disability | Profound | Profound |
| Survival | Into adulthood | 95% miscarried; 50% die in first weeks; 5% reach 1 year | 95% miscarried; 5% of those born reach 1 year |
Trisomy 21
- Upslanting fissures, flat face, low nasal root
Trisomy 18
- Clenched hands, overlapping fingers, growth deficiency
Trisomy 13
- Cleft lip/palate, small eyes, polydactyly
Memory tool
Match the number to a milestone age: Drinking age 21 (Down), Election (voting) age 18 (Edwards), Puberty at 13 (Patau). D-E-P in order of decreasing number.
In-house exam
Down syndrome causes: ≈95% meiotic nondisjunction (maternal age), ≈4% Robertsonian translocation (higher recurrence if a parent carries it), ≈2% mosaicism (milder).
Step 1
- Down: AV septal defect (endocardial cushion), duodenal atresia ("double bubble"), Hirschsprung, single palmar crease, sandal gap, early-onset Alzheimer (APP on chr 21), ALL and AML (megakaryoblastic); 1st-trimester ↑ nuchal translucency, ↓ PAPP-A, ↑ hCG; quad screen ↓ AFP, ↑ hCG, ↓ estriol, ↑ inhibin A.
- Edwards: rocker-bottom feet, clenched fists with overlapping fingers, micrognathia; quad screen ↓ AFP, ↓ hCG, ↓ estriol, normal/↓ inhibin.
- Patau: holoprosencephaly, cleft lip/palate, polydactyly, cutis aplasia, microphthalmia; ↓ PAPP-A, ↓ hCG.
Q4. Why are sex chromosome abnormalities milder than autosomal ones?
- The Y has few active genes (<50), mostly for gonadal and genital development
- X inactivation (Lyon hypothesis): when more than one X is present, all but one are inactivated early in development and seen as Barr bodies. Which X is silenced is random in each early cell, so females are naturally mosaic
Step 1
Number of Barr bodies = number of X chromosomes − 1. 47,XXY has one Barr body; 45,X has none.
Q5. What are the main sex chromosome syndromes?
| Turner | Klinefelter | 47,XXX | 47,XYY | |
|---|---|---|---|---|
| Karyotype | Most often 45,X | Most often 47,XXY | 47,XXX | 47,XYY |
| Height | Short (proportionate) | Tall, disproportionately long limbs | Taller than average | Taller than average |
| Gonads | Ovarian dysgenesis, sexual infantilism | Small testes, sterile (seminiferous tubule atrophy) | Premature ovarian failure | Usually normal |
| Other | Webbed neck, low hairline, broad shield chest, congenital heart defects | Gynecomastia in ⅓; IQ 10–15 points below siblings | Lower IQ than sibs | Hyperactivity, ADD, learning disabilities; lower IQ than sibs |
| Overall | — | — | Relatively benign; usually chromosomally normal offspring | |
Turner (45,X)
- Short, broad shield chest, sexual infantilism
Klinefelter (47,XXY)
- Tall, long limbs, gynecomastia, small testes
Step 1
- Turner: most common cause of primary amenorrhea; bicuspid aortic valve, coarctation, horseshoe kidney, lymphedema / cystic hygroma at birth; streak ovaries → ↓ estrogen, ↑ FSH/LH. Often arises from loss of the paternal X; not maternal-age related.
- Klinefelter: hypergonadotropic hypogonadism (↓ testosterone, ↑ FSH/LH, ↓ inhibin, ↑ estrogen); most common chromosomal cause of male infertility.
ApplyLO 3 application questions
A1A newborn with clenched fists, overlapping fingers and a VSD. Most likely karyotype and outlook?
A2A tall 17-year-old boy with small firm testes, gynecomastia and learning difficulties. Karyotype and Barr bodies?
A3Why can a woman with 47,XXX look nearly normal while trisomy 18 is lethal?
LO 4Structural abnormalities
Q1. What is a Robertsonian translocation?
- Whole-arm exchange between two acrocentric chromosomes (13, 14, 15, 21, 22)
- Breaks occur in the short arms; the two long arms fuse at the centromere; the short arms (no essential genes, repeated elsewhere) are lost
- Most common: t(13;14)
- Balanced carrier: 45 chromosomes (healthy). Unbalanced: 46 chromosomes (extra long arm = translocation trisomy)
- Carrier females pass on unbalanced forms more often than carrier males
- ≈4% of Down syndrome is from a Robertsonian translocation
Formation
- Short arms break off; long arms join
Balanced vs unbalanced
- Balanced: 45 chromosomes, normal gene dose
- Unbalanced: 46 chromosomes, three copies of 21q
Trap
A Down syndrome child with 46 chromosomes has a translocation, not standard trisomy. Test the parents: if one is a balanced carrier (45 chromosomes), the recurrence risk is far higher than the age-based risk.
Step 1
A carrier of der(21;21) (Robertsonian between the two 21s) can only produce trisomy 21 or monosomy 21 conceptions: 100% of live births have Down syndrome.
Q2. What is a reciprocal translocation, and what happens to the carrier's children?
- Exchange of segments between two (usually nonhomologous) chromosomes; any translocation that is not Robertsonian
- Mostly family-specific, not recurrent
- Balanced: 46 chromosomes; ≈70% inherited. Unbalanced: 46 (rarely 47)
- In meiosis, the four chromosomes pair as a cross-shaped quadrivalent
| Segregation | Gametes |
|---|---|
| Alternate | One normal + one balanced (all genes present, just swapped) |
| Adjacent-1 | Two unbalanced: partial trisomy of one segment + partial monosomy of the other |
| Adjacent-2 | Unbalanced (less common) |
Phenotype of the unbalanced child depends on the size of the unbalanced segment, the genes involved, and whether the imbalance is mainly monosomic (worse) or trisomic.
In-house exam
Example: mother 46,XX,t(7;21)(q21;q11.2) (balanced) → fetus 46,XY,der(21)t(7;21)(q21;q11.2) (unbalanced: partial trisomy 7q + partial monosomy 21q). A chromosome count alone can't tell balanced from unbalanced reciprocal translocations: both are 46.
Step 1
Balanced translocation carriers present with recurrent miscarriage or infertility. Acquired reciprocal translocations drive cancers: t(9;22) CML, t(15;17) APL, t(8;14) Burkitt, t(14;18) follicular lymphoma.
Q3. What kinds of deletions are there?
| Type | Breaks | Result |
|---|---|---|
| Terminal | 1 | Loss of a chromosome end |
| Interstitial | 2 | Loss of a middle segment |
| Ring | 2 | Both ends (and telomeres) lost; broken ends fuse into a ring with the centromere |
Microdeletions
- Usually <5 Mb → can be missed by G-banding
- Seen with high-resolution chromosomes (sometimes), FISH, or chromosomal microarray
- Example: DiGeorge / velocardiofacial syndrome (22q11.2)
Step 1
- 22q11.2 (DiGeorge): CATCH-22: cleft palate, abnormal facies, thymic aplasia (T-cell deficiency), cardiac (conotruncal) defects, hypocalcemia (no parathyroids).
- Cri-du-chat: 5p deletion; cat-like cry, VSD. Williams: 7q11.23 (elastin); elfin face, hypercalcemia, very friendly, supravalvular aortic stenosis.
Q4. What is an isochromosome?
- The centromere divides across (transversely) instead of lengthwise → one chromosome with two identical p arms and one with two identical q arms
- Result: trisomy for one arm and monosomy for the other
- Most common: i(Xq), a Turner syndrome variant. Less common: i(21q), i(9p), i(12p)
Step 1
i(12p) is the marker of testicular germ cell tumors.
Q5. What are inversions, and why do they matter only for offspring?
| Paracentric | Pericentric | |
|---|---|---|
| Definition | 2 breaks in one arm; segment flips; centromere not included | 2 breaks on either side of the centromere; segment with centromere flips (centromere position can change) |
| Carrier | Usually healthy (balanced; nothing lost) | |
| Meiosis | Homologs form an inversion loop to pair | |
| Crossover in loop | Dicentric and acentric chromosomes → nonviable | Duplication/deletion (unbalanced) recombinants → affected offspring |
Memory tool
PERIcentric = includes the centromere (peri = around it). PARAcentric = alongside, on one arm only.
ApplyLO 4 application questions
A1A child with Down syndrome has 46 chromosomes. Her healthy mother has 45. Explain.
A2A couple has three miscarriages. The husband's karyotype is 46,XY,t(2;5)(q21;q31). Why the losses?
A3A woman with Turner features has 46 chromosomes: one normal X and one X with two long arms. Abnormality?
LO 5Chromosomal mosaicism
Q1. What is mosaicism?
The presence, in one person or tissue, of at least two cell lines with different karyotypes, all derived from a single zygote. Example: 46,XX/47,XX,+21.
Trap
Mosaicism comes from one zygote. Two cell lines from two zygotes (fused twins) is chimerism.
Q2. How does mosaicism arise?
| Route | Start | Event | Result |
|---|---|---|---|
| Mitotic nondisjunction (autosome) | Normal 46 zygote | Nondisjunction in an early mitosis → 47,+21 and 45,−21 cells; the monosomic line dies | 46/47,+21; mostly normal cells |
| Mitotic nondisjunction (sex chromosome) | Normal 46,XX zygote | Both products viable | 45,X / 46,XX / 47,XXX (three lines) |
| Meiotic nondisjunction + trisomy rescue | 47,+21 zygote | Anaphase lag: one extra 21 is lost in a later division | 46/47,+21; mostly abnormal cells |
High yield
The earlier the error in development, the more tissues carry the abnormal line. Starting from a trisomic zygote leaves most cells abnormal.
Q3. What does mosaicism look like in a patient?
- Usually a milder phenotype than the full trisomy
- Uneven spread of abnormal cells → asymmetric body shape or appearance
- Often hypo- or hyperpigmented skin patches
- A normal blood karyotype doesn't rule it out; test another tissue (e.g., skin)
Step 1
Pigment streaks follow lines of Blaschko. Trisomy rescue can leave uniparental disomy (both copies of a chromosome from one parent) → imprinting disorders.
ApplyLO 5 application questions
A1A girl has mild Down features and streaky skin pigmentation; her blood shows 46/47,+21 with 20% abnormal cells. Most likely mechanism?
A2A woman has 45,X/46,XX/47,XXX cells. How did three lines arise?
LO 6Confined placental mosaicism
Q1. What is confined placental mosaicism (CPM)?
- An abnormal (often trisomic) cell line found in the placenta but not the fetus
- Detected in 1–2% of CVS samples (chorionic villus sampling tests placental tissue)
- Possible patterns after an early error:
- Mosaic in both placenta and fetus
- Abnormal line only in the placenta (CPM)
- Abnormal line only in the fetus
- Placenta aneuploid, fetus normal (trisomy rescued in the fetal lineage)
Analogy — the packaging vs the product
CVS samples the box (placenta), not the product (fetus). A dented box doesn't mean a broken product, so an abnormal CVS result must be checked in fetal cells.
Q2. What do you do when CVS shows mosaicism?
- Confirm in fetal cells with amniocentesis (amniotic fluid cells come from the fetus)
- Detailed ultrasound for growth and anomalies
- Counsel: CPM can still cause placental dysfunction / growth restriction, and a rescued fetus may have uniparental disomy
In-house exam
Know the number: CPM in 1–2% of CVS, and that it is a discrepancy between placenta and fetus.
ApplyLO 6 application questions
A1CVS at 11 weeks shows 46,XX/47,XX,+16 mosaicism. Ultrasound is normal. Next step?
IDImage ID
Image 1 — child
Image 2 — infant
Image 3 — infant
Image 4 — adult
Image 5 — adult
Image 6 — karyotype
Image 7 — diagram
Image 8 — diagram
MCQExam-style questions
1A newborn has Down syndrome. Karyotype is 47,XY,+21. What is the most likely mechanism?
2A child with Down syndrome has 46 chromosomes. The phenotypically normal mother has 45 chromosomes. What is the mother's karyotype most likely to show?
3Which statement about whole-chromosome monosomy is correct?
4Nondisjunction occurs in one meiotic division and produces two normal gametes, one with two identical copies of a chromosome and one with none. Which division failed?
5A newborn has a cleft lip and palate, microphthalmia, omphalocele and a heart defect. Which karyotype is most likely?
6A 15-year-old girl has short stature, a webbed neck, a broad chest and no breast development. Which finding is expected?
7Why are sex chromosome aneuploidies usually milder than autosomal ones?
8A healthy man with recurrent pregnancy loss has 46 chromosomes with a segment of 2q exchanged for a segment of 7p. In meiosis, which segregation gives a normal or balanced gamete?
9A deletion removes both ends of a chromosome, and the broken ends join. What forms?
10A girl has mild Down features, asymmetric growth and streaky pigmentation. Blood karyotype: 46,XX[16]/47,XX,+21[4]. Best explanation?
11CVS shows trisomy 2 in 30% of cells; amniocentesis shows a normal fetal karyotype. This is:
12A carrier of a pericentric inversion has a child with a duplication of one segment and a deletion of another on the same chromosome. How did this happen?
!Numbers that differ between in-house and Step 1
| Item | In-house | Step 1 / board review |
|---|---|---|
| Microdeletion size | Usually <5 Mb; missed by G-banding (notes phrase it as "needs >5 Mb to be seen") | Below the ≈5–10 Mb resolution of G-banding → FISH/microarray |
| Down syndrome causes | ≈95% nondisjunction · ≈4% Robertsonian · ≈2% mosaic | ≈95% · ≈4% · ≈1% |
| Down heart defect | 40% congenital heart defect | ≈40–50%; AV septal defect most typical |
| Trisomy 18 heart defect | VSD | VSD (and others) |
| Trisomy 13 | Midline defects, microphthalmia | Also holoprosencephaly, polydactyly, cutis aplasia |
| Aneuploidy frequency | >3–4% of recognized pregnancies | ≈5% of pregnancies; ≈50% of first-trimester losses |