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AN75.1-5 | Principles of Genetics, Chromosomal Aberrations & Clinical Genetics — Part 2

Major Chromosomal Syndromes: Autosomal Trisomies

The NMC competency AN75.3 requires detailed knowledge of six chromosomal syndromes. We will cover each systematically.

Figure: Major Chromosomal Syndromes: Autosomal Trisomies

Down Syndrome (Trisomy 21) is the most common autosomal trisomy compatible with long-term survival, with an incidence of approximately 1 in 800-1,000 live births. Three cytogenetic mechanisms produce Down syndrome: (1) Free trisomy 21 (47,XX/XY,+21) — accounts for 95% of cases, caused by meiotic non-disjunction (predominantly maternal meiosis I). (2) Robertsonian translocation — approximately 4% of cases, most commonly rob(14;21); in one-third of translocation cases, a parent is a balanced carrier with significant recurrence risk. (3) Mosaicism (46,XX/XY // 47,XX/XY,+21) — approximately 1-2% of cases, with variable phenotype depending on the proportion of trisomic cells.

Clinical features include: craniofacial — brachycephaly (flat occiput), upslanting palpebral fissures, epicanthic folds, flat nasal bridge, small ears, Brushfield spots (white/grey specks on the iris periphery), protruding tongue (relative macroglossia due to small oral cavity), short neck with excess nuchal skin; limbs — single palmar crease (simian crease, present in ~45%), clinodactyly of the fifth finger (inward curving due to hypoplastic middle phalanx), wide gap between first and second toes ('sandal gap'); cardiac — congenital heart defects in 40-50% (endocardial cushion defect/AVSD is the most characteristic, also VSD, ASD, tetralogy of Fallot); gastrointestinal — duodenal atresia (double-bubble sign on antenatal ultrasound), Hirschsprung disease, imperforate anus; neurological — intellectual disability (IQ typically 25-50), hypotonia in infancy, early-onset Alzheimer disease (virtually universal neuropathological changes by age 40 due to triplication of the APP gene on chromosome 21); haematological — transient abnormal myelopoiesis (TAM) in neonates, increased risk of acute lymphoblastic leukaemia (ALL) and acute megakaryoblastic leukaemia; endocrine — hypothyroidism (15-20%), diabetes mellitus; musculoskeletal — atlantoaxial instability (important to screen before anaesthesia or contact sports).

Edward Syndrome (Trisomy 18) has an incidence of approximately 1 in 5,000-8,000 live births. It is the second most common autosomal trisomy at birth but is much more lethal than trisomy 21 — median survival is 5-15 days, with only 5-10% surviving beyond one year. There is a strong female preponderance (3:1 F:M ratio, likely due to preferential loss of male trisomy 18 foetuses). Clinical features include: severe intrauterine growth restriction, clenched fists with overlapping fingers (index finger overriding the middle, fifth finger overriding the fourth — a highly characteristic finding), prominent occiput, micrognathia, short sternum, rocker-bottom feet, congenital heart defects (particularly VSD and polyvalvular disease), renal malformations (horseshoe kidney), and severe intellectual disability. Prenatal detection is often possible through first-trimester combined screening (increased nuchal translucency, low PAPP-A, low free beta-hCG) or second-trimester maternal serum screening.

Patau Syndrome (Trisomy 13) has an incidence of approximately 1 in 10,000-20,000 live births. Median survival is 7-10 days. Clinical features reflect severe defects in midline structures: holoprosencephaly (failure of the forebrain to divide into two hemispheres, ranging from alobar to lobar types), midline facial defects including cyclopia (in severe holoprosencephaly), cleft lip and palate (often bilateral), microphthalmia or anophthalmia, scalp defects (cutis aplasia), postaxial polydactyly (extra digits on the ulnar/fibular side), congenital heart defects (VSD, ASD, dextrocardia), renal anomalies (polycystic kidneys), and cryptorchidism. The triad of holoprosencephaly (or related facial defects), postaxial polydactyly, and cardiac defects should immediately raise suspicion for trisomy 13.

Sex Chromosome Disorders: Turner and Klinefelter Syndromes

Turner Syndrome (45,X) affects approximately 1 in 2,500 live female births, making it the only monosomy compatible with postnatal survival (all autosomal monosomies are lethal in the first trimester). However, 99% of 45,X conceptuses abort spontaneously — Turner syndrome is found in approximately 10% of all first-trimester spontaneous abortions. The karyotype is 45,X in approximately 50% of cases; the remainder have mosaic karyotypes (45,X/46,XX most common), structural abnormalities of the X chromosome (isochromosome Xq, ring X, Xp or Xq deletion), or 45,X/46,XY mosaicism.

Figure: Sex Chromosome Disorders: Turner and Klinefelter Syndromes

Clinical features evolve with age. In the neonate: lymphoedema of the hands and feet (due to hypoplastic lymphatic channels), redundant nuchal skin (resolved cystic hygroma), and congenital heart defects. In childhood: short stature (adult height typically 140-148 cm without growth hormone treatment), broad chest with widely spaced nipples (shield chest), cubitus valgus (increased carrying angle of the arms), short fourth metacarpals, multiple pigmented naevi, and recurrent otitis media with sensorineural hearing loss. At puberty: primary amenorrhoea and absent breast development due to gonadal dysgenesis — the ovaries degenerate to fibrous streaks (streak gonads) lacking follicles, resulting in hypergonadotropic hypogonadism (elevated FSH and LH). Associated conditions: bicuspid aortic valve (15-30%, the most common cardiac finding), coarctation of the aorta (7-12%, almost pathognomonic when found in a female), horseshoe kidney (10%), autoimmune thyroiditis (Hashimoto's), celiac disease, and type 2 diabetes. Intelligence is normal, though there may be specific difficulties with visuospatial processing and mathematics.

Management includes: growth hormone therapy (starting in childhood to improve final height), oestrogen replacement therapy (initiated at age 12-13 to induce puberty, then combined with progesterone for endometrial protection), cardiac surveillance (baseline echocardiography and MRI for aortic root monitoring — risk of aortic dissection), renal ultrasound, thyroid function monitoring, and audiological assessment. With modern assisted reproduction (using donor oocytes), pregnancy is possible but carries increased cardiovascular risks requiring careful monitoring.

Klinefelter Syndrome (47,XXY) is the most common sex chromosome aneuploidy in males, with an incidence of approximately 1 in 600-700 live male births. It remains vastly underdiagnosed — an estimated 64-75% of affected individuals are never identified. The extra X chromosome arises from non-disjunction in either maternal meiosis I (most common), maternal meiosis II, or paternal meiosis I.

Clinical features are subtle before puberty — affected boys may be taller than average with relatively long legs and a tendency to language and learning difficulties. The full phenotype becomes apparent at puberty: hypogonadism with small, firm testes (typically <4 mL volume, compared to the normal adult range of 15-25 mL), gynaecomastia (breast development, present in ~40%), sparse facial and body hair, female pattern fat distribution, and infertility. The testes show progressive hyalinisation and fibrosis of the seminiferous tubules with absent or severely reduced spermatogenesis, while Leydig cell function is relatively preserved but insufficient — testosterone levels are low-normal to low, with elevated FSH and LH (hypergonadotropic hypogonadism). Intelligence is usually in the normal range, but verbal IQ may be lower than performance IQ, and there is an increased incidence of learning disabilities, attention difficulties, and psychosocial problems.

Associated conditions include: increased risk of breast cancer (20-50 times the male population risk, approaching female risk levels), osteoporosis (due to testosterone deficiency), metabolic syndrome and type 2 diabetes, venous thromboembolism, and autoimmune disorders (particularly SLE). Variants with additional X chromosomes (48,XXXY; 49,XXXXY) have more severe intellectual disability, more pronounced physical features, and skeletal abnormalities (radioulnar synostosis in 48,XXXY).

Management includes: testosterone replacement therapy (starting at puberty, continued lifelong — improves muscle mass, bone density, energy, mood, and secondary sexual characteristics), fertility counselling (testicular sperm extraction with ICSI is possible in some men, with success rates of 30-50%), breast cancer surveillance, bone density monitoring, and educational support for learning difficulties.

Prader-Willi Syndrome is caused by loss of function of paternally expressed genes in the 15q11.2-q13 region. Three mechanisms can produce this: (1) interstitial deletion of paternal 15q11-q13 (~70%), (2) maternal uniparental disomy of chromosome 15 (~25%), and (3) imprinting centre defects (~2-5%). Clinical features include severe neonatal hypotonia and feeding difficulties (often requiring tube feeding), followed by hyperphagia and obesity beginning at age 2-4 years, short stature, hypogonadism (cryptorchidism, delayed puberty), small hands and feet, characteristic facial features (almond-shaped eyes, narrow bifrontal diameter, thin upper lip), mild-to-moderate intellectual disability, and behavioural problems (temper tantrums, obsessive-compulsive behaviours, skin picking). Recurrence risk depends on the mechanism: negligible for de novo deletion, <1% for UPD, and potentially higher for imprinting centre mutations.

Genetic Variation, Diagnostic Techniques, and Genetic Counselling

Genetic variation (AN75.4) is the raw material for evolution and the basis of human individuality. Polymorphism refers to the occurrence of two or more alleles at a locus, where the rarest allele has a frequency greater than 1% in the population. Below this threshold, the rare variant is considered a mutation. This distinction is operational — both polymorphisms and mutations arise from the same molecular mechanisms (point mutations, insertions, deletions, repeat expansions) but differ in population frequency and typically in phenotypic effect. Polymorphisms are generally neutral or mildly beneficial (balanced polymorphism — e.g., sickle cell trait conferring malaria resistance), while mutations causing disease are maintained at lower frequencies by negative selection.

Figure: Genetic Variation, Diagnostic Techniques, and Genetic Counselling

Types of DNA sequence variation include: Single Nucleotide Polymorphisms (SNPs) — the most common type, occurring approximately once every 300 base pairs; they form the basis of genome-wide association studies (GWAS). Copy Number Variants (CNVs) — deletions or duplications of DNA segments ranging from 1 kilobase to several megabases. Microsatellites (Short Tandem Repeats, STRs) — repeating units of 2-6 nucleotides used in forensic identification and paternity testing. Insertion/deletion polymorphisms (indels) — small insertions or deletions. Variable Number Tandem Repeats (VNTRs/minisatellites) — repeating units of 10-100 nucleotides.

Mutation types include: point mutations (single nucleotide changes) — subdivided into missense (amino acid change), nonsense (premature stop codon), and silent/synonymous (no amino acid change); frameshift mutations (insertions or deletions not divisible by 3, shifting the reading frame); splice site mutations (affecting intron-exon boundaries); dynamic/trinucleotide repeat expansions (unstable repeats that expand across generations — e.g., CGG in fragile X, CAG in Huntington disease, CTG in myotonic dystrophy); large deletions/duplications (removing or duplicating entire exons or genes); and chromosomal rearrangements (covered earlier).

Diagnostic techniques (AN75.5):

Karyotyping is the standard cytogenetic technique for visualising chromosomes. Peripheral blood lymphocytes are cultured with phytohaemagglutinin (PHA) for 72 hours, arrested in metaphase with colchicine, treated with hypotonic solution to swell the cells, fixed, dropped onto slides, and stained. G-banding (Giemsa banding after trypsin digestion) produces a characteristic pattern of light and dark bands unique to each chromosome, with a resolution of approximately 5-10 Mb. Indications include: suspected chromosomal syndrome, ambiguous genitalia, recurrent pregnancy loss, infertility, and prenatal diagnosis.

Fluorescence In Situ Hybridisation (FISH) uses fluorescently labelled DNA probes that hybridise to complementary sequences on chromosomes. It can detect specific aneuploidies (using chromosome-specific probes), microdeletions (e.g., 22q11.2 deletion in DiGeorge syndrome), and translocations (using painting probes or locus-specific probes). FISH can be performed on interphase nuclei (no need for cell culture — results available within 24-48 hours) or metaphase spreads. Its resolution is approximately 100 kb — much better than karyotyping but limited to detecting only the specific abnormality targeted by the probe.

Polymerase Chain Reaction (PCR) is the foundational technique of molecular genetics. It amplifies a specific DNA sequence exponentially using: (1) two oligonucleotide primers flanking the target sequence, (2) thermostable DNA polymerase (Taq polymerase from Thermus aquaticus), (3) free deoxynucleotide triphosphates (dNTPs), and (4) repeated thermal cycling — denaturation (94-95°C), primer annealing (50-65°C), and extension (72°C). Each cycle doubles the target DNA, producing approximately 2^n copies after n cycles (typically 25-35 cycles). Variants include: RT-PCR (reverse transcriptase PCR for RNA analysis), real-time/quantitative PCR (qPCR — measuring amplification in real time using fluorescent reporters), multiplex PCR (simultaneous amplification of multiple targets), and allele-specific PCR (for detecting known point mutations).

DNA sequencing determines the exact nucleotide sequence of a DNA fragment. Sanger sequencing (dideoxy chain termination method) was the gold standard for decades and remains used for confirming specific mutations. Next-generation sequencing (NGS) has revolutionised genetic diagnostics, enabling: whole-exome sequencing (WES — sequencing all protein-coding regions, approximately 1.5% of the genome but containing ~85% of disease-causing mutations), whole-genome sequencing (WGS — complete genome coverage), and targeted gene panels (sequencing specific sets of genes associated with particular clinical phenotypes).

Genetic counselling (AN75.5) is the process of helping individuals and families understand and adapt to the medical, psychological, and familial implications of genetic contributions to disease. The core principles are: non-directive counselling (presenting information without recommending a specific course of action), informed consent (particularly for predictive genetic testing), confidentiality, and sensitivity to cultural and religious beliefs. In India, genetic counselling must navigate complex social dynamics including consanguinity, joint family structures, gender preferences, and stigma associated with genetic conditions. The National Guidelines for Gene Therapy Product Development and Clinical Trials (2019) and the Pre-Conception and Pre-Natal Diagnostic Techniques (PCPNDT) Act regulate prenatal genetic testing, with strict prohibitions on sex determination for non-medical purposes.