Medical Genetics

01 Molecular Genetics Essentials

Medical genetics is the branch of medicine dealing with the diagnosis and management of hereditary disorders. A firm understanding of molecular biology — from DNA structure through protein synthesis — is the foundation upon which all clinical genetics rests. The human genome contains approximately 3.2 billion base pairs distributed across 23 pairs of chromosomes (22 autosomal pairs and 1 pair of sex chromosomes), encoding roughly 20,000–25,000 protein-coding genes.

DNA Structure & Replication

Deoxyribonucleic acid (DNA) is a double-stranded helix composed of nucleotide subunits, each consisting of a deoxyribose sugar, a phosphate group, and one of four nitrogenous bases: adenine (A), thymine (T), guanine (G), and cytosine (C). Base pairing follows Watson-Crick rules: A pairs with T (2 hydrogen bonds), G pairs with C (3 hydrogen bonds). The two strands run antiparallel (5′→3′ and 3′→5′). DNA replication is semiconservative — each daughter molecule contains one original and one newly synthesized strand. Key enzymes include helicase (unwinds), primase (RNA primer), DNA polymerase III (synthesis, 5′→3′ only), and DNA ligase (joins Okazaki fragments on the lagging strand).

Gene Structure

A typical human gene consists of: promoter (upstream regulatory region, often containing a TATA box ~25 bp upstream of the transcription start site), exons (protein-coding sequences that are retained in mature mRNA), introns (intervening non-coding sequences removed by splicing), and 3′ untranslated region (UTR) with a polyadenylation signal. Enhancers and silencers may be located thousands of base pairs away and regulate transcription by looping to interact with the promoter complex. The average human gene has ~8 exons, but individual genes vary enormously — the dystrophin gene (DMD) has 79 exons spanning 2.4 Mb, making it the largest known human gene.

Transcription & Translation

Transcription occurs in the nucleus: RNA polymerase II synthesizes a pre-mRNA complementary to the template (antisense) DNA strand, reading 3′→5′ and synthesizing 5′→3′. Post-transcriptional modifications include 5′ capping (7-methylguanosine), splicing (removal of introns by the spliceosome at GT-AG splice sites), and 3′ polyadenylation. The mature mRNA is exported to the cytoplasm for translation by ribosomes. Translation proceeds in codons (triplets of nucleotides); the start codon is AUG (methionine), and the three stop codons are UAA, UAG, UGA. Transfer RNA (tRNA) molecules carry specific amino acids matched to codons via their anticodon loops.

Types of Mutations

02 Chromosome Structure & Karyotype Notation

Humans have 46 chromosomes: 22 pairs of autosomes (numbered 1–22 by size) and one pair of sex chromosomes (XX in females, XY in males). Each chromosome consists of a single, continuous DNA molecule wrapped around histone proteins forming nucleosomes, which further compact into chromatin and ultimately the visible chromosome during cell division.

Chromosome Architecture

Key structural landmarks: the centromere divides the chromosome into a short arm (p, for "petit") and a long arm (q). Based on centromere position, chromosomes are classified as metacentric (centromere near center — chromosomes 1, 3, 16, 19, 20), submetacentric (centromere off-center — most chromosomes), or acrocentric (centromere near the end — chromosomes 13, 14, 15, 21, 22). The telomeres are repetitive TTAGGG sequences at chromosome ends that protect against degradation and shorten with each cell division (relevant to aging and cancer biology). Acrocentric chromosomes have satellite stalks containing ribosomal RNA genes — these are clinically significant because they can participate in Robertsonian translocations.

Karyotype Notation (ISCN)

Karyotypes follow the International System for Human Cytogenomic Nomenclature (ISCN). The standard format is: total chromosome number, sex chromosomes, abnormality.

Cell Division

Mitosis produces two genetically identical diploid daughter cells (for somatic growth and repair). Meiosis produces four haploid gametes and is unique for two features critical to genetic diversity: crossing over (homologous recombination during meiosis I) and independent assortment of homologous chromosomes. Errors in meiosis cause nondisjunction — failure of homologs (meiosis I) or sister chromatids (meiosis II) to separate — resulting in aneuploidy (trisomy or monosomy) in the offspring. Nondisjunction in meiosis I produces gametes with both homologs (one disomic, one nullisomic); nondisjunction in meiosis II produces one disomic gamete with identical copies, one nullisomic, and two normal.

03 Inheritance Patterns

Understanding the patterns by which genetic traits are transmitted through families is essential for genetic counseling, risk assessment, and family planning. The major Mendelian and non-Mendelian patterns are described below.

Autosomal Dominant (AD)

Only one mutant allele needed for disease expression. Each affected individual has a 50% chance of passing the mutation to each offspring, regardless of sex. Key features: vertical transmission (appears in every generation), male-to-male transmission possible (distinguishes from X-linked), variable expressivity (different features/severity among carriers of same mutation), reduced penetrance (some carriers never manifest disease). New mutations (de novo) are common, especially for conditions reducing reproductive fitness (e.g., achondroplasia — ~80% de novo). Examples: Marfan syndrome, neurofibromatosis type 1, Huntington disease, familial hypercholesterolemia, ADPKD.

Autosomal Recessive (AR)

Two mutant alleles required (homozygous or compound heterozygous). Carrier parents (heterozygous) have a 25% risk per pregnancy of an affected child, 50% carriers, 25% unaffected non-carriers. Key features: horizontal pattern (siblings affected, parents unaffected), increased incidence with consanguinity, often involves enzyme deficiencies (loss of function). Examples: cystic fibrosis, sickle cell disease, PKU, Tay-Sachs, spinal muscular atrophy.

X-Linked Recessive (XLR)

Gene on X chromosome; primarily males affected (hemizygous). Carrier females are usually unaffected but may show mild manifestations due to skewed X-inactivation. Key features: no male-to-male transmission (father passes Y to sons), affected males related through carrier females, all daughters of affected males are obligate carriers. Carrier mother has 50% chance of affected sons and 50% chance of carrier daughters. Examples: Duchenne muscular dystrophy, hemophilia A and B, G6PD deficiency, Fabry disease.

X-Linked Dominant (XLD)

Affects both males and females with one mutant allele on X, but often more severe or lethal in males. Affected females transmit to 50% of sons and 50% of daughters; affected males transmit to all daughters and no sons. Examples: Rett syndrome (MECP2 — almost exclusively in females; lethal in most males), Incontinentia pigmenti (IKBKG), X-linked hypophosphatemic rickets (PHEX).

Mitochondrial Inheritance

Mitochondrial DNA (mtDNA) is a 16.5 kb circular molecule encoding 37 genes (13 polypeptides, 22 tRNAs, 2 rRNAs). Inheritance is strictly maternal — mitochondria in the oocyte are passed to all offspring, but an affected father cannot transmit. Heteroplasmy (mixture of normal and mutant mtDNA within a cell) explains variable expressivity and the threshold effect — disease manifests when the proportion of mutant mtDNA exceeds a tissue-specific threshold. Examples: MELAS, MERRF, Leber hereditary optic neuropathy.

Multifactorial (Complex) Inheritance

Caused by the interaction of multiple genes and environmental factors. Does not follow simple Mendelian patterns. Recurrence risks are empiric (based on population data) rather than calculated. Features: risk increases with number of affected relatives, severity of disease, and relatedness of affected individuals. Examples: neural tube defects, cleft lip/palate, congenital heart defects, type 2 diabetes, hypertension.

04 Genetic Variation & Epigenetics

Types of Genetic Variation

Epigenetics

Heritable changes in gene expression without alteration of DNA sequence. Major epigenetic mechanisms include:

DNA methylation: Addition of a methyl group to cytosine at CpG dinucleotides by DNA methyltransferases (DNMTs). Promoter methylation typically silences gene expression. Aberrant methylation is implicated in cancer (tumor suppressor silencing) and imprinting disorders.

Histone modification: Post-translational modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination) that alter chromatin structure. Histone acetylation generally opens chromatin (euchromatin, active transcription); deacetylation compacts chromatin (heterochromatin, gene silencing).

Genomic imprinting: Parent-of-origin-specific gene expression. Some genes are expressed only from the maternally inherited allele, others only from the paternally inherited allele. Mediated by differential methylation established in gametogenesis. Clinically critical examples:

• Prader-Willi syndrome: loss of paternal 15q11-13 expression (paternal deletion, maternal UPD, or imprinting center defect)
• Angelman syndrome: loss of maternal UBE3A expression at 15q11-13 (maternal deletion, paternal UPD, UBE3A mutation, or imprinting defect)
• Beckwith-Wiedemann syndrome: overgrowth disorder at 11p15.5 involving IGF2/H19

X-inactivation (Lyonization): Random inactivation of one X chromosome in each cell of 46,XX females, occurring early in embryogenesis (~day 16). Mediated by the XIST gene (X-inactivation specific transcript) on Xq13. Results in dosage compensation between males (1 active X) and females (1 active X, 1 Barr body). X-inactivation is random but fixed — all daughter cells maintain the same inactive X. Skewed X-inactivation (>80:20 ratio) can cause carrier females to manifest X-linked recessive conditions (e.g., a carrier female with hemophilia A symptoms).

05 Key Terminology & Abbreviations

06 Autosomal Trisomies (21, 18, 13)

Down Syndrome (Trisomy 21)

The most common autosomal aneuploidy compatible with long-term survival, affecting ~1 in 700 live births. Three cytogenetic types:

Clinical features: characteristic facies (upslanting palpebral fissures, epicanthal folds, flat nasal bridge, small ears, protruding tongue, Brushfield spots on iris), hypotonia, intellectual disability (mild to moderate, mean IQ ~50), single transverse palmar crease, sandal gap (wide space between 1st and 2nd toes), short stature, brachycephaly.

Complications requiring surveillance:

• Cardiac: congenital heart defects in ~40–50% — most common is endocardial cushion defect (AVSD), followed by VSD, ASD, tetralogy of Fallot
• GI: duodenal atresia ("double bubble" sign), Hirschsprung disease, celiac disease
• Hematologic: transient myeloproliferative disorder (TMD) in neonates (~10%), increased risk of ALL (10–20×) and AML (150× for AMKL)
• Endocrine: hypothyroidism (~15–20%, annual screening), type 1 diabetes
• Neurologic: early-onset Alzheimer disease (nearly universal neuropathology by age 40, clinical dementia in ~50–70% by age 60 — due to APP gene on chromosome 21)
• Cervical spine: atlantoaxial instability (~15%), requires screening before anesthesia/sports
• ENT: hearing loss (75%), obstructive sleep apnea (50–75%)
• Ophthalmologic: refractive errors, strabismus, cataracts

Edwards Syndrome (Trisomy 18)

Second most common autosomal trisomy at birth (~1 in 5,000 live births). 95% due to free trisomy 18 from maternal meiotic nondisjunction. Clinical features: severe intellectual disability, IUGR, prominent occiput, micrognathia, clenched fists with overlapping fingers (index over 3rd, 5th over 4th), rocker-bottom feet, short sternum, congenital heart defects (~90% — VSD, PDA most common), omphalocele, renal malformations. Prognosis: median survival ~5–15 days; ~5–10% survive to 1 year.

Patau Syndrome (Trisomy 13)

Third most common autosomal trisomy (~1 in 10,000–20,000 live births). Clinical features: severe intellectual disability, holoprosencephaly (failure of forebrain to divide — spectrum from alobar to lobar), midline facial defects (cleft lip/palate, cyclopia in severe cases), microphthalmia, polydactyly (postaxial), cutis aplasia (scalp defects), congenital heart defects (~80%), renal anomalies. Prognosis: median survival ~7–10 days; ~5% survive to 6 months.

07 Sex Chromosome Disorders

Turner Syndrome (45,X)

Occurs in ~1 in 2,000–2,500 live female births. Most common sex chromosome abnormality in females. ~99% of 45,X conceptions result in spontaneous abortion (most common chromosomal cause of first-trimester miscarriage). Approximately 50% have 45,X; others are mosaic (45,X/46,XX) or have structural X abnormalities (isochromosome Xq, ring X, Xp deletion).

Clinical features: short stature (mean adult height ~147 cm without treatment — related to SHOX gene haploinsufficiency on Xp), gonadal dysgenesis (streak gonads, primary amenorrhea, infertility in most), lymphedema (especially hands and feet in neonates), webbed neck (pterygium colli, from fetal cystic hygroma resolution), shield chest with widely spaced nipples, low posterior hairline, cubitus valgus. Intelligence is typically normal, though nonverbal learning disabilities and difficulties with visuospatial processing are common.

Management:

• Growth hormone: recombinant hGH starting early childhood (can add ~5–8 cm to final height)
• Estrogen replacement: start at ~11–12 years to induce puberty; followed by combined estrogen-progesterone for uterine protection
• Cardiac screening: bicuspid aortic valve (~30%), coarctation of the aorta (~10%), aortic root dilation with risk of dissection — baseline and periodic echocardiography and cardiac MRI
• Renal: horseshoe kidney (~30%), collect system anomalies — renal ultrasound at diagnosis
• Thyroid: autoimmune thyroiditis (~25–30%) — annual screening
• Hearing: sensorineural or conductive hearing loss — audiologic monitoring
• Fertility: oocyte/embryo cryopreservation in mosaic patients with residual ovarian function; donor oocyte IVF

Klinefelter Syndrome (47,XXY)

Most common sex chromosome aneuploidy in males (~1 in 600–1,000 live male births). Often underdiagnosed; only ~25% diagnosed in lifetime. Clinical features: tall stature with long legs (eunuchoid proportions), small firm testes (<4 mL), infertility (azoospermia in ~95%; some oligospermia in mosaics), gynecomastia (~40%), reduced facial/body hair, increased risk of metabolic syndrome, osteoporosis, and breast cancer (20× general male population). Intelligence is usually normal but average IQ ~10 points lower than siblings; language and learning disabilities common. Management: testosterone replacement starting at puberty; fertility options include micro-TESE with ICSI in select patients.

Other Sex Chromosome Variants

47,XYY (~1 in 1,000 males): tall stature, usually normal phenotype, normal fertility, possible learning difficulties; previously controversially associated with aggressive behavior (not supported by evidence). 47,XXX (Triple X, ~1 in 1,000 females): tall stature, usually normal phenotype and fertility, mild learning difficulties possible; most never diagnosed. 48,XXXY and 49,XXXXY: increasingly severe phenotype with additional X chromosomes (more severe intellectual disability, skeletal anomalies, hypogonadism).

08 Microdeletion & Microduplication Syndromes

Microdeletion syndromes result from submicroscopic chromosomal deletions (typically 1–5 Mb) detectable by FISH or chromosomal microarray but often below the resolution of standard G-banded karyotype (~5–10 Mb). Most occur de novo.

09 Connective Tissue Disorders (Marfan, EDS)

Marfan Syndrome

Autosomal dominant disorder of connective tissue caused by mutations in FBN1 (fibrillin-1) on chromosome 15q21.1. Prevalence ~1 in 5,000. ~25% de novo mutations. Fibrillin-1 is a major component of extracellular microfibrils; its deficiency leads to dysregulated TGF-β signaling.

Revised Ghent Nosology (2010) for diagnosis — two main criteria:

1. Aortic root dilation/dissection (Z-score ≥2, or aortic root dissection)
2. Ectopia lentis (lens subluxation, typically superotemporal)

Diagnosis requires: aortic root dilation/dissection AND ectopia lentis; OR aortic root dilation/dissection AND FBN1 mutation; OR aortic root dilation/dissection AND systemic score ≥7; OR ectopia lentis AND FBN1 mutation known to cause aortic disease. The systemic score includes: wrist AND thumb sign (3), wrist OR thumb sign (1), pectus carinatum (2), pectus excavatum or chest asymmetry (1), hindfoot deformity (2), plain flat foot (1), pneumothorax (2), dural ectasia (2), protrusio acetabuli (2), reduced upper/lower segment ratio AND increased arm span/height (1), scoliosis or thoracolumbar kyphosis (1), reduced elbow extension (1), facial features 3/5 (dolichocephaly, enophthalmos, downslanting palpebral fissures, malar hypoplasia, retrognathia) (1), skin striae (1), myopia >3 diopters (1), mitral valve prolapse (1).

Management:

• Cardiovascular: beta-blockers (atenolol) or ARBs (losartan) to slow aortic root dilation; annual echocardiography; prophylactic aortic root replacement when diameter ≥5.0 cm (or ≥4.5 cm with risk factors: family history of dissection, rapid growth >0.5 cm/year, significant AR)
• Ophthalmologic: annual slit-lamp exam; surgical lens repositioning if needed
• Musculoskeletal: scoliosis monitoring, orthotics
• Activity restrictions: avoid contact sports, isometric exercise, competitive athletics
• Pregnancy: high risk of aortic dissection (especially if root >4.0 cm); requires multidisciplinary management

Ehlers-Danlos Syndromes (EDS)

A group of heritable connective tissue disorders characterized by joint hypermobility, skin hyperextensibility, and tissue fragility. The 2017 International Classification recognizes 13 subtypes.

10 Neurocutaneous Syndromes (NF, TSC)

Neurofibromatosis Type 1 (NF1)

Autosomal dominant, caused by mutations in the NF1 gene (17q11.2) encoding neurofibromin, a RAS-GAP (tumor suppressor). Prevalence ~1 in 3,000. ~50% de novo. Complete penetrance by age 5 but highly variable expressivity.

NIH Diagnostic Criteria (revised 2021) — diagnosis requires ≥2 of:

1. ≥6 café-au-lait macules (>5 mm prepubertal, >15 mm postpubertal)
2. ≥2 neurofibromas of any type OR 1 plexiform neurofibroma
3. Axillary or inguinal freckling (Crowe sign)
4. Optic pathway glioma
5. ≥2 Lisch nodules (iris hamartomas) or ≥2 choroidal abnormalities
6. Distinctive osseous lesion (sphenoid dysplasia, tibial pseudarthrosis, long bone bowing)
7. First-degree relative with NF1 by above criteria
8. Heterozygous pathogenic NF1 variant

Complications: plexiform neurofibromas (can undergo malignant transformation to MPNST in ~8–13%), learning disabilities (~50–75%), scoliosis, hypertension (renal artery stenosis, pheochromocytoma), brain tumors. Surveillance: annual comprehensive exam, ophthalmologic screening, blood pressure monitoring, MRI as clinically indicated. Selumetinib (MEK inhibitor) approved for symptomatic, inoperable plexiform neurofibromas in children ≥2 years.

Neurofibromatosis Type 2 (NF2)

Autosomal dominant, caused by mutations in NF2 (merlin/schwannomin) on 22q12.2. Much rarer than NF1 (~1 in 25,000). Hallmark: bilateral vestibular schwannomas (presenting with hearing loss, tinnitus, balance problems, usually by age 20–30). Associated with meningiomas, ependymomas, and posterior subcapsular cataracts. Management: surgical resection, stereotactic radiosurgery, bevacizumab for progressive schwannomas; cochlear/brainstem implants for hearing.

Tuberous Sclerosis Complex (TSC)

Autosomal dominant, caused by mutations in TSC1 (hamartin, 9q34) or TSC2 (tuberin, 16p13.3). These form a complex that inhibits mTOR signaling; loss leads to uncontrolled cell growth and hamartoma formation in multiple organs. Prevalence ~1 in 6,000–10,000. ~2/3 de novo.

2021 Updated Diagnostic Criteria — Definite TSC: 2 major criteria OR 1 major + ≥2 minor OR pathogenic TSC1/TSC2 variant. Possible TSC: 1 major OR ≥2 minor.

Management: mTOR inhibitors (everolimus) for SEGA, renal angiomyolipomas, and LAM; antiepileptic medications (vigabatrin is first-line for infantile spasms in TSC); regular surveillance of brain (MRI), kidneys (MRI or ultrasound), lungs (CT for LAM in women), heart (echo), skin, eyes, and neurodevelopment.

11 Trinucleotide Repeat & Other AD Disorders

Huntington Disease

Autosomal dominant neurodegenerative disorder caused by CAG trinucleotide repeat expansion in HTT gene (4p16.3). The expanded polyglutamine tract causes toxic gain of function. Prevalence ~5–10 per 100,000 in European populations.

Clinical features: onset typically 30–50 years with progressive chorea (involuntary, irregular, non-patterned movements), psychiatric symptoms (depression, irritability, personality changes — often precede motor symptoms), and cognitive decline progressing to dementia. Juvenile form (Westphal variant) presents with rigidity, bradykinesia, and seizures rather than chorea. Anticipation is marked, especially with paternal transmission (spermatogenesis predisposes to further expansion). Death typically 15–20 years after onset.

Achondroplasia

Most common skeletal dysplasia causing dwarfism (~1 in 15,000–40,000). Autosomal dominant, caused by a gain-of-function mutation in FGFR3 (fibroblast growth factor receptor 3) on 4p16.3. ~80% are de novo mutations; virtually all caused by the same Gly380Arg variant. Advanced paternal age is a risk factor. Features: rhizomelic limb shortening, macrocephaly with frontal bossing, midface hypoplasia, trident hands, lumbar lordosis, average adult height ~131 cm (males) and ~124 cm (females). Complications: foramen magnum stenosis (infants), spinal stenosis (adults), recurrent otitis media, obstructive sleep apnea. Vosoritide (C-type natriuretic peptide analog) is FDA-approved for children ≥5 years to increase growth velocity.

Familial Hypercholesterolemia (FH)

Autosomal dominant (codominant). Mutations in LDLR (most common, ~85–90%), APOB (~5–10%), or PCSK9 (gain of function, ~1%). Heterozygous FH prevalence ~1 in 250; homozygous ~1 in 300,000. Heterozygous FH: LDL-C 190–400 mg/dL, tendon xanthomas (especially Achilles), corneal arcus, premature ASCVD (MI by age 40–50 in males). Homozygous FH: LDL-C >500 mg/dL, cutaneous xanthomas in childhood, ASCVD in childhood/adolescence, aortic valve disease. Dutch Lipid Clinic Network criteria used for clinical diagnosis. Management: high-intensity statins, ezetimibe, PCSK9 inhibitors (evolocumab, alirocumab), LDL apheresis for homozygous FH.

Myotonic Dystrophy Type 1 (DM1)

Autosomal dominant, caused by CTG trinucleotide repeat expansion in DMPK gene on 19q13.3. Most common adult muscular dystrophy (~1 in 8,000). Normal: 5–34 repeats; premutation: 35–49; mild: 50–150; classic: 100–1,000; congenital: >1,000. Clinical features: myotonia (delayed relaxation after muscle contraction), progressive muscle weakness and wasting (distal > proximal; facial, neck, and hand muscles first), cataracts (posterior subcapsular, "Christmas tree" pattern), cardiac conduction defects (first-degree AV block, bundle branch block — sudden death risk), frontal balding, testicular atrophy, insulin resistance. Congenital DM1 (maternally transmitted with massive expansions) presents with severe neonatal hypotonia, respiratory failure, and intellectual disability. Marked anticipation, especially with maternal transmission.

Hereditary Spherocytosis

Most commonly autosomal dominant (~75%). Mutations in red cell membrane/cytoskeletal proteins: ankyrin (ANK1, most common), band 3 (SLC4A1), spectrin (α or β), protein 4.2. Spherical, osmotically fragile RBCs are trapped and destroyed in the spleen. Features: hemolytic anemia (variable severity), jaundice, splenomegaly, pigmented gallstones. Diagnosis: positive osmotic fragility test or eosin-5-maleimide (EMA) binding test. Management: folate supplementation, splenectomy for severe cases (ideally after age 6, with prior vaccination against encapsulated organisms).

Polycystic Kidney Disease (ADPKD)

Autosomal dominant, caused by mutations in PKD1 (16p13.3, ~85%, more severe) or PKD2 (4q22.1, ~15%, milder course). Most common hereditary kidney disease (~1 in 400–1,000). Progressive bilateral renal cysts leading to ESRD (median age ~55 for PKD1, ~75 for PKD2). Extrarenal manifestations: hepatic cysts (~80%), intracranial aneurysms (~5–10% — screen with MRA if family history of rupture or SAH), mitral valve prolapse, diverticulosis. Tolvaptan (V2 receptor antagonist) slows cyst growth and GFR decline in rapidly progressive disease.

12 Cystic Fibrosis

Autosomal recessive disorder caused by mutations in the CFTR gene (7q31.2) encoding the cystic fibrosis transmembrane conductance regulator, a chloride/bicarbonate channel on epithelial cell surfaces. Most common life-shortening AR disorder in Caucasians (~1 in 2,500–3,500 births; carrier frequency ~1 in 25). Over 2,000 CFTR variants identified; F508del (p.Phe508del) accounts for ~70% of pathogenic alleles worldwide.

CFTR Mutation Classes

Clinical Features

• Pulmonary: thick, dehydrated airway mucus → chronic bacterial infections (Staphylococcus aureus early, Pseudomonas aeruginosa later, Burkholderia cepacia complex — poor prognosis), bronchiectasis, progressive obstructive lung disease (leading cause of death)
• GI/Pancreatic: pancreatic insufficiency (~85%, presents with steatorrhea, fat-soluble vitamin deficiency — A, D, E, K), meconium ileus (~15% of neonates — virtually pathognomonic for CF), distal intestinal obstruction syndrome (DIOS), CF-related diabetes (CFRD, ~20% of adolescents, ~50% of adults), biliary cirrhosis
• Reproductive: males — congenital bilateral absence of vas deferens (CBAVD) causing infertility (~98%); females — reduced fertility from thick cervical mucus
• Other: nasal polyps, sinusitis, digital clubbing, CF-related bone disease

Diagnosis

Newborn screening: immunoreactive trypsinogen (IRT) on dried blood spot, followed by CFTR mutation analysis and/or repeat IRT. Confirmed by sweat chloride test (gold standard): ≥60 mmol/L diagnostic, 30–59 mmol/L intermediate, ≤29 mmol/L normal. CFTR genotyping identifies specific mutations for prognostic and therapeutic purposes.

CFTR Modulator Therapy

13 Sickle Cell Disease & Hemoglobinopathies

Sickle cell disease (SCD) is caused by a missense mutation in the HBB gene (11p15.4): Glu6Val (GAG → GTG) producing hemoglobin S (HbS). Autosomal recessive. Most common monogenic disorder worldwide; carrier frequency ~8–10% in African Americans.

SCD Genotypes

Complications

• Vaso-occlusive crisis (VOC): most common reason for hospitalization; dactylitis (hand-foot syndrome) often first manifestation in infants <2 years
• Acute chest syndrome: new infiltrate + respiratory symptoms ± fever; leading cause of death in adults; triggered by infection, fat embolism from bone marrow, or hypoventilation
• Stroke: ~11% by age 20 without prevention; transcranial Doppler (TCD) screening annually ages 2–16; chronic transfusion therapy if TCD velocity ≥200 cm/s
• Splenic sequestration: acute splenic enlargement with hemoglobin drop ≥2 g/dL; can be fatal; functional asplenia by age 5 in HbSS — risk of overwhelming sepsis from encapsulated organisms
• Aplastic crisis: parvovirus B19 infection → transient red cell aplasia → acute severe anemia
• Chronic organ damage: avascular necrosis (especially femoral head), proliferative retinopathy, chronic kidney disease, pulmonary hypertension, leg ulcers, priapism, cholelithiasis

Management

Hydroxyurea: increases HbF production; reduces VOC by ~50%, reduces ACS, reduces need for transfusion; recommended for all patients ≥9 months with HbSS or HbS/β⁰-thal. L-glutamine (Endari): reduces oxidative stress in sickled RBCs; adjunctive to hydroxyurea. Crizanlizumab: anti-P-selectin antibody, reduces VOC. Voxelotor: HbS polymerization inhibitor, improves Hb. Chronic transfusion: target HbS <30% for primary/secondary stroke prevention. Hematopoietic stem cell transplant: only curative option (matched sibling donor); >90% cure rate. Gene therapy: lovotibeglogene autotemcel (Lyfgenia, lentiviral) and exagamglogene autotemcel (Casgevy, CRISPR-based — first FDA-approved CRISPR therapy) approved for severe SCD in patients ≥12 years.

14 PKU, SMA & Other AR Disorders

Phenylketonuria (PKU)

Caused by mutations in PAH (phenylalanine hydroxylase) gene on 12q23.2. Inability to convert phenylalanine (Phe) to tyrosine → Phe accumulation causes intellectual disability if untreated. Newborn screening detects elevated Phe on dried blood spot (all 50 US states since 1960s). Classification: classic PKU (Phe >1,200 μmol/L untreated), moderate PKU (600–1,200), mild PKU (360–600), mild HPA (<360, often does not require treatment). Treatment: Phe-restricted diet (lifelong), supplemented with medical formula; target blood Phe 120–360 μmol/L. Sapropterin (BH4, Kuvan): cofactor for PAH, effective in ~25–50% of patients (mostly milder forms). Pegvaliase (Palynziq): enzyme substitution for adults with uncontrolled PKU. Maternal PKU: uncontrolled maternal Phe during pregnancy causes microcephaly, congenital heart defects, and intellectual disability in the fetus (regardless of fetal genotype) — strict dietary control before and throughout pregnancy is essential.

Spinal Muscular Atrophy (SMA)

Caused by homozygous deletion or mutation of SMN1 gene on 5q13. SMN2 copy number modifies severity (more copies = milder phenotype). AR; carrier frequency ~1 in 50. Prevalence ~1 in 10,000.

Therapies: Nusinersen (Spinraza): antisense oligonucleotide that modifies SMN2 splicing to increase functional SMN protein; intrathecal injection every 4 months after loading doses. Onasemnogene abeparvovec (Zolgensma): AAV9-based gene therapy delivering functional SMN1 gene; single IV infusion; approved for age <2 years; one of the most expensive drugs ever (>$2M). Risdiplam (Evrysdi): oral SMN2 splicing modifier; approved for age ≥2 months. Pre-symptomatic treatment (identified by newborn screening) has shown the best outcomes, with many treated infants achieving near-normal motor development.

Other Key AR Disorders

Tay-Sachs disease: HEXA gene mutations → deficiency of hexosaminidase A → GM2 ganglioside accumulation in neurons. Infantile form: normal development until ~6 months, then progressive neurodegeneration, cherry-red spot on macula, seizures, macrocephaly, death by age 3–5. High carrier frequency in Ashkenazi Jewish (~1 in 30), French-Canadian, and Cajun populations. Carrier screening recommended.

Gaucher disease: GBA gene → deficiency of glucocerebrosidase → glucocerebroside accumulation in macrophages ("Gaucher cells"). Type I (non-neuronopathic, most common): hepatosplenomegaly, bone disease (Erlenmeyer flask deformity, avascular necrosis), cytopenias; does NOT affect the brain; treated with enzyme replacement therapy (imiglucerase, velaglucerase alfa) or substrate reduction therapy (eliglustat, miglustat). Type II (acute neuronopathic): severe CNS involvement, death by age 2. Type III (chronic neuronopathic): intermediate CNS involvement, variable survival. GBA heterozygous carriers have 5–8× increased risk of Parkinson disease.

Wilson disease: ATP7B gene → defective copper transport → copper accumulation in liver (hepatitis, cirrhosis), brain (movement disorders, psychiatric symptoms), and cornea (Kayser-Fleischer rings). Low serum ceruloplasmin (<20 mg/dL), elevated 24-hour urine copper (>100 μg/day), elevated hepatic copper (>250 μg/g dry weight). Treatment: chelation with D-penicillamine or trientine; zinc (blocks intestinal absorption); liver transplant for fulminant hepatic failure.

Hereditary hemochromatosis: HFE gene; C282Y homozygosity accounts for ~80–90% of cases in European populations. Iron overload → liver cirrhosis (increased HCC risk), diabetes ("bronze diabetes"), cardiomyopathy, arthropathy (2nd and 3rd MCP joints), hypogonadism, skin hyperpigmentation. Low penetrance (~10–25% of C282Y homozygotes develop clinical disease, higher in males). Diagnosis: elevated transferrin saturation (>45%), elevated ferritin; HFE genotyping. Treatment: phlebotomy (target ferritin 50–100 μg/L).

15 Duchenne & Becker Muscular Dystrophy

X-linked recessive disorders caused by mutations in the DMD gene (Xp21.2), the largest known human gene (2.4 Mb, 79 exons), encoding dystrophin, a critical structural protein linking the cytoskeleton to the extracellular matrix in muscle fibers.

Duchenne Muscular Dystrophy (DMD)

Incidence ~1 in 3,500–5,000 live male births. Caused by out-of-frame mutations (usually large deletions) that abolish dystrophin production. Clinical features: normal early development; progressive proximal muscle weakness beginning age 2–5; Gowers sign (using hands to "walk up" the legs when rising from floor); calf pseudohypertrophy (replacement of muscle with fat/fibrotic tissue); loss of ambulation by age 12; cardiomyopathy (dilated); respiratory failure; death in 20s–30s without ventilatory support. CK massively elevated (10,000–50,000+ U/L). Diagnosis confirmed by genetic testing (multiplex ligation-dependent probe amplification — MLPA, or sequencing).

Becker Muscular Dystrophy (BMD)

Caused by in-frame mutations that produce a partially functional (truncated or partially functional) dystrophin protein. Later onset (typically age 5–15), slower progression, ambulation often maintained into 20s–40s, cardiomyopathy can be the predominant feature. CK elevated but typically lower than DMD.

Management:

• Corticosteroids: deflazacort or prednisone (standard of care) — prolongs ambulation by ~2–3 years, delays scoliosis and cardiomyopathy
• Cardiac: ACE inhibitors or ARBs starting at diagnosis or by age 10 (before cardiomyopathy onset); beta-blockers if LV dysfunction develops
• Respiratory: regular PFTs; nocturnal non-invasive ventilation when FVC <50% predicted
• Exon-skipping therapies: antisense oligonucleotides that restore the reading frame for specific deletions — eteplirsen (exon 51, ~13% of patients), golodirsen and viltolarsen (exon 53, ~8%), casimersen (exon 45, ~8%); approved under accelerated approval, modest dystrophin restoration
• Gene therapy: delandistrogene moxeparvovec (Elevidys, AAV-based micro-dystrophin); approved for ages 4–5 years

16 Hemophilia, G6PD & Other X-Linked Disorders

Hemophilia A & B

X-linked recessive bleeding disorders. Hemophilia A: deficiency of factor VIII (F8 gene, Xq28); ~1 in 5,000 males; ~50% due to intron 22 inversion. Hemophilia B (Christmas disease): deficiency of factor IX (F9 gene, Xq27.1); ~1 in 25,000 males.

Management: factor replacement (recombinant preferred); prophylaxis for severe disease (regular infusions to maintain trough >1%). Extended half-life factor products reduce infusion frequency. Emicizumab (Hemlibra): bispecific antibody bridging FIXa and FX (mimics FVIII function); subcutaneous, every 1–4 weeks; revolutionary for hemophilia A prophylaxis, including patients with inhibitors. Fitusiran: anti-antithrombin siRNA for hemophilia A or B. Gene therapy: valoctocogene roxaparvovec (Roctavian, AAV5-FVIII) for hemophilia A; etranacogene dezaparvovec (Hemgenix, AAV5-FIX Padua) for hemophilia B.

G6PD Deficiency

X-linked recessive. Most common enzymopathy worldwide (~400 million affected). Glucose-6-phosphate dehydrogenase is essential for generating NADPH via the pentose phosphate pathway, which protects red cells from oxidative damage. Carrier advantage: partial protection against Plasmodium falciparum malaria.

Triggers of hemolytic crisis: infections (most common trigger), fava beans (favism), medications (primaquine, dapsone, sulfonamides, nitrofurantoin, rasburicase, methylene blue). Hemolysis pattern: acute intravascular hemolysis 24–72 hours after exposure; Heinz bodies (denatured Hb inclusions) and bite cells on peripheral smear; self-limited as older, more vulnerable RBCs are destroyed and replaced by younger cells with higher G6PD activity. G6PD assay may be falsely normal during acute hemolysis (test after recovery). Management: avoid triggers; supportive care; transfusion if severe anemia.

Fabry Disease

X-linked (affects males severely; carrier females can have mild-moderate disease due to skewed X-inactivation). GLA gene → deficiency of α-galactosidase A → accumulation of globotriaosylceramide (Gb3) in vascular endothelium, kidneys, heart, and nervous system. Classic presentation in males: acroparesthesias (burning pain in hands/feet, childhood onset), angiokeratomas (skin), corneal verticillata (whorl-like opacities), hypohidrosis, progressive renal failure, cardiomyopathy (LVH), stroke. Treatment: enzyme replacement therapy (agalsidase alfa or beta) or oral chaperone therapy (migalastat for amenable GLA mutations).

Hunter Syndrome (MPS II)

X-linked recessive. IDS gene → deficiency of iduronate-2-sulfatase → accumulation of heparan sulfate and dermatan sulfate. Features: coarse facies, hepatosplenomegaly, dysostosis multiplex, joint stiffness, cardiac valve disease, hearing loss. Neuronopathic (severe) form: progressive intellectual disability, death in teens. Non-neuronopathic (attenuated) form: normal intelligence, survival to adulthood. Treatment: enzyme replacement (idursulfase); HSCT considered for severe form if diagnosed early.

Lesch-Nyhan Syndrome

X-linked recessive. HPRT1 gene → deficiency of hypoxanthine-guanine phosphoribosyltransferase → massive overproduction of uric acid. Features: hyperuricemia/gout, nephrolithiasis, intellectual disability, and characteristic self-injurious behavior (lip and finger biting, head banging). Treatment: allopurinol for hyperuricemia (does not affect neurologic features); behavioral interventions.

17 Fragile X & Trinucleotide X-Linked Disorders

Fragile X Syndrome

Most common inherited cause of intellectual disability and most common monogenic cause of autism spectrum disorder. Caused by CGG trinucleotide repeat expansion in the 5′ UTR of the FMR1 gene (Xq27.3), leading to promoter hypermethylation and gene silencing (→ absence of FMRP, a protein essential for synaptic plasticity).

Rett Syndrome

X-linked dominant disorder caused by mutations in MECP2 (Xq28). Almost exclusively affects females (~1 in 10,000–15,000 female births); usually lethal in males. ~99% de novo. Clinical course: apparently normal development until 6–18 months → developmental regression (loss of purposeful hand use, loss of spoken language) → characteristic stereotypic hand movements (wringing, clapping, mouthing) → acquired microcephaly, seizures (~80%), scoliosis, autonomic dysfunction (breathing irregularities, cardiac QT prolongation), gait apraxia. Classified by classic Rett (4 stages) and atypical variants. Management is supportive; trofinetide (Daybue) is the first FDA-approved treatment for Rett syndrome.

18 Mitochondrial Disorders

Mitochondrial disorders can be caused by mutations in mitochondrial DNA (mtDNA) or nuclear DNA genes encoding mitochondrial proteins. mtDNA-encoded disorders follow maternal inheritance (mother transmits to all children; father cannot transmit). The clinical phenotype depends on the mutation, the proportion of mutant mtDNA (heteroplasmy), and the energy demands of affected tissues (brain, muscle, heart, and retina are most vulnerable).

Key Mitochondrial Disorders

Diagnostic approach: elevated lactate (blood and/or CSF), elevated lactate:pyruvate ratio (>20), brain MRI (stroke-like lesions, basal ganglia abnormalities in Leigh syndrome), muscle biopsy (ragged red fibers with modified Gomori trichrome, COX-negative fibers), mtDNA testing (blood or muscle). Genetic confirmation through mtDNA sequencing or targeted testing.

Treatment: largely supportive. Coenzyme Q10 (ubiquinone), riboflavin, L-carnitine, and alpha-lipoic acid are commonly used though evidence is limited. Idebenone has shown benefit for LHON vision recovery. Avoidance of mitochondrial toxins (valproate, aminoglycosides, statins at high doses). Cardiac pacing for conduction defects. Seizure management (avoid valproate in POLG mutations). Genetic counseling is complex due to heteroplasmy and the bottleneck effect in maternal transmission.

19 Amino Acid & Organic Acid Disorders

Amino Acid Disorders

Organic Acidemias

20 Urea Cycle Defects

The urea cycle converts toxic ammonia (from protein catabolism) to urea for renal excretion. Six enzymes are involved; deficiency of any leads to hyperammonemia. Overall incidence ~1 in 30,000. OTC deficiency (ornithine transcarbamylase, X-linked) is the most common (~1 in 14,000); all others are autosomal recessive.

Urea Cycle Enzymes & Disorders

Clinical Presentation

Neonatal severe form (usually complete enzyme deficiency): presents within 24–72 hours of life with poor feeding, lethargy progressing to coma, tachypnea (respiratory alkalosis from central hyperventilation), seizures, and cerebral edema. Ammonia levels often >1,000 μmol/L (normal <50). Without treatment, rapid progression to brain damage and death.

Late-onset/partial deficiency: triggered by catabolic stress (intercurrent illness, high protein intake, postpartum state, valproate use). Presents with episodic vomiting, confusion, ataxia, psychiatric symptoms, and headaches. May be misdiagnosed as Reye syndrome, psychiatric illness, or cyclic vomiting.

Long-term management: protein-restricted diet with essential amino acid supplementation, oral nitrogen scavengers (sodium phenylbutyrate or glycerol phenylbutyrate), arginine or citrulline supplementation, sick-day protocols (increase calories, reduce protein, have emergency letter). Liver transplant is curative for severe defects (corrects the enzymatic deficiency in the liver but does not reverse existing brain injury).

21 Fatty Acid Oxidation Disorders

Mitochondrial fatty acid oxidation (FAO) provides energy during fasting and prolonged exercise by converting fatty acids to acetyl-CoA for ketone body production. FAO disorders present with hypoketotic hypoglycemia (the hallmark — inability to generate ketones during fasting), hepatopathy, cardiomyopathy, and/or rhabdomyolysis.

General management principles: avoid prolonged fasting (maximum safe fasting time age-dependent: neonates 3–4 hours, infants 6–8 hours, children 10–12 hours); frequent meals; uncooked cornstarch at bedtime for sustained glucose release; low-fat diet (long-chain FAO disorders) with MCT oil supplementation (bypasses long-chain pathway); IV D10 during illness/surgery; carnitine supplementation (for MCADD, controversial for long-chain defects). Emergency protocol for acute decompensation: IV D10 at high rate to suppress lipolysis.

22 Lysosomal Storage Diseases

Lysosomes are membrane-bound organelles containing acid hydrolases that degrade macromolecules. Deficiency of specific lysosomal enzymes leads to substrate accumulation and progressive cellular dysfunction. Most are autosomal recessive (exceptions: Fabry and Hunter — X-linked). Collectively affect ~1 in 5,000–8,000 births.

Mucopolysaccharidoses (MPS)

Other Key Lysosomal Storage Diseases

23 Glycogen Storage Diseases

Glycogen storage diseases (GSD) result from defects in glycogen synthesis, degradation, or regulation. Most are autosomal recessive. Classification is by the affected enzyme.

24 Peroxisomal Disorders & Newborn Screening

Peroxisomal Disorders

Peroxisomes are organelles involved in very long-chain fatty acid (VLCFA) β-oxidation, bile acid synthesis, plasmalogen biosynthesis, and reactive oxygen species metabolism.

Zellweger spectrum disorders (ZSD): peroxisome biogenesis disorders caused by mutations in PEX genes. Three phenotypes of decreasing severity along a spectrum:

• Zellweger syndrome (most severe): neonatal hypotonia, characteristic facies (high forehead, flat supraorbital ridges, wide fontanelles), seizures, hepatomegaly, renal cysts, stippled epiphyses (chondrodysplasia punctata), absent peroxisomes on liver biopsy; death in first year
• Neonatal adrenoleukodystrophy (intermediate): similar but milder features, survival into childhood
• Infantile Refsum disease (mildest): sensorineural hearing loss, retinitis pigmentosa, intellectual disability; survival to adulthood possible

X-linked adrenoleukodystrophy (X-ALD): ABCD1 gene; VLCFA accumulation. Three main phenotypes: childhood cerebral ALD (inflammatory demyelination, rapid neurologic decline, adrenal insufficiency; HSCT can halt disease if done early), adrenomyeloneuropathy (adult males, slowly progressive spasticity and neuropathy), and isolated Addison disease. Diagnosis: elevated plasma VLCFA (C26:0, C26:0/C22:0 ratio). Added to the Recommended Uniform Screening Panel (RUSP) for newborn screening.

Newborn Screening

Universal newborn screening (NBS) in the US uses dried blood spots collected at 24–48 hours of life. The Recommended Uniform Screening Panel (RUSP) contains 37 core conditions and 26 secondary conditions (as of 2024). The backbone technology is tandem mass spectrometry (MS/MS), which can simultaneously measure acylcarnitines (for fatty acid oxidation and organic acid disorders) and amino acids from a single dried blood spot.

Principles of screening: NBS is a screening test, not a diagnostic test — all positive results require confirmatory testing. Sensitivity is prioritized over specificity (false positives are acceptable; false negatives are not). Second screens (repeat at ~2 weeks) performed in some states. Point-of-care screening includes pulse oximetry for critical congenital heart disease and hearing screening (otoacoustic emissions or auditory brainstem response).

25 Hereditary Breast & Ovarian Cancer

BRCA1 (17q21) and BRCA2 (13q13) encode proteins essential for homologous recombination DNA repair. Autosomal dominant with high penetrance. BRCA1: lifetime breast cancer risk ~55–72%, ovarian cancer ~39–44%. BRCA2: lifetime breast cancer risk ~45–69%, ovarian cancer ~11–17%. BRCA2 also increases risk of male breast cancer, pancreatic cancer, and prostate cancer. Founder mutations are common in Ashkenazi Jewish populations (BRCA1 185delAG, BRCA1 5382insC, BRCA2 6174delT; combined carrier frequency ~1 in 40).

NCCN Management Guidelines (High-Risk Screening & Prevention)

Therapeutic implications: BRCA-mutated cancers are sensitive to platinum chemotherapy and PARP inhibitors (olaparib, rucaparib, niraparib, talazoparib) via synthetic lethality (HR-deficient cells cannot repair PARP-inhibitor-induced DNA damage).

Other high-risk genes for breast cancer: PALB2 (partner and localizer of BRCA2; lifetime breast cancer risk ~33–58%), TP53 (Li-Fraumeni), PTEN (Cowden syndrome), CDH1 (hereditary diffuse gastric cancer + lobular breast cancer), STK11 (Peutz-Jeghers), ATM and CHEK2 (moderate-risk genes, ~2× relative risk).

26 Lynch Syndrome & GI Cancer Genetics

Lynch Syndrome (Hereditary Nonpolyposis Colorectal Cancer — HNPCC)

Autosomal dominant; caused by germline mutations in DNA mismatch repair (MMR) genes: MLH1 (most common), MSH2, MSH6, PMS2, or EPCAM (deletions silencing MSH2). Most common hereditary colorectal cancer syndrome (~3–5% of all CRC). Lifetime CRC risk: ~40–80% (MLH1/MSH2), ~10–22% (MSH6), ~15–20% (PMS2). Also increases risk of endometrial cancer (~25–60%), ovarian (~4–24%), gastric, urinary tract, small bowel, hepatobiliary, and sebaceous neoplasms.

Diagnostic Criteria

Revised Bethesda Guidelines (for selecting tumors for MSI/IHC testing): CRC diagnosed <50; synchronous/metachronous Lynch-associated tumors; CRC with MSI-H histology <60; CRC with ≥1 first-degree relative with Lynch tumor <50; CRC with ≥2 first/second-degree relatives with Lynch tumor at any age.

Universal tumor screening (now recommended): all CRCs tested by immunohistochemistry (IHC) for MLH1, MSH2, MSH6, PMS2 protein expression AND/OR microsatellite instability (MSI) testing. Loss of MLH1/PMS2 → test for MLH1 promoter methylation and BRAF V600E (if both positive, likely sporadic; if negative, germline MLH1 testing). Loss of MSH2/MSH6 or MSH6 alone or PMS2 alone → proceed directly to germline testing.

Lynch Syndrome Surveillance

• Colonoscopy: every 1–2 years starting age 20–25 (or 2–5 years before youngest CRC in family)
• Endometrial cancer: education about symptoms; consider endometrial sampling annually starting age 30–35; discuss risk-reducing hysterectomy + BSO after childbearing (especially MLH1/MSH2)
• Aspirin: 600 mg daily shown to reduce CRC incidence (CAPP2 trial); optimal dose under study (ongoing CAPP3 trial at 100 mg, 300 mg, 600 mg)
• Immunotherapy: MSI-H/dMMR tumors respond dramatically to immune checkpoint inhibitors (pembrolizumab approved first-line for MSI-H CRC; dostarlimab for dMMR rectal cancer — 100% complete clinical response in initial trial)

Familial Adenomatous Polyposis (FAP)

Autosomal dominant; APC gene (5q21). Classic FAP: >100 colorectal adenomatous polyps by teens–20s; ~100% CRC risk by age 40 without colectomy. Attenuated FAP: 10–100 polyps, later onset, lower (but still elevated) CRC risk. Gardner syndrome: FAP + desmoid tumors, osteomas (mandible, skull), epidermoid cysts, dental anomalies. Turcot syndrome: FAP + CNS tumors (medulloblastoma in APC-related Turcot; glioblastoma in Lynch-related Turcot). Management: prophylactic total colectomy (proctocolectomy with IPAA) typically in late teens to 20s; upper GI surveillance (periampullary adenomas → duodenal cancer risk).

Hereditary Diffuse Gastric Cancer

Autosomal dominant; CDH1 gene (E-cadherin). Lifetime gastric cancer risk ~70% (diffuse/signet ring type); lobular breast cancer risk in women ~40–50%. Screening endoscopy has poor sensitivity for diffuse gastric cancer (tumor grows beneath mucosa). IGCLC guidelines recommend prophylactic total gastrectomy at age 20–30 for confirmed pathogenic variant carriers.

27 MEN Syndromes, VHL & Other Cancer Predisposition

Multiple Endocrine Neoplasia (MEN) Syndromes

RET testing and prophylactic thyroidectomy: MEN2B (highest risk) — thyroidectomy within first 6 months of life; MEN2A high risk (C634R) — by age 5; MEN2A moderate risk — may delay if calcitonin normal, but usually by teens. Annual screening for pheochromocytoma (plasma/urine metanephrines) and hyperparathyroidism (calcium, PTH) starting in childhood.

Von Hippel-Lindau Disease (VHL)

Autosomal dominant; VHL gene (3p25.3), a tumor suppressor involved in HIF (hypoxia-inducible factor) degradation. Loss of VHL → constitutive HIF activation → VEGF overproduction → highly vascular tumors. Components: CNS hemangioblastomas (cerebellum > spinal cord > brainstem, ~60–80%), retinal hemangioblastomas (~60%), clear cell renal cell carcinoma (~40%, bilateral/multifocal, leading cause of death), pheochromocytoma (~10–20%), pancreatic neuroendocrine tumors (~15%), endolymphatic sac tumors (hearing loss), pancreatic cysts, epididymal cystadenomas. Surveillance: annual ophthalmologic exam, annual plasma metanephrines, abdominal MRI/ultrasound, brain/spine MRI every 2 years — all starting in childhood/adolescence. Nephron-sparing surgery for renal tumors (to preserve renal function given multifocality). Belzutifan (HIF-2α inhibitor) approved for VHL-associated RCC, hemangioblastomas, and pNET.

Li-Fraumeni Syndrome

Autosomal dominant; TP53 germline mutation. p53 is the "guardian of the genome" — master regulator of DNA repair, cell cycle arrest, and apoptosis. Extremely high cancer risk: ~50% by age 30, >90% lifetime. Core tumors (SBLA): Sarcomas, Breast cancer (premenopausal), Leukemia/lymphoma, Adrenal cortical carcinoma (childhood), brain tumors (especially choroid plexus carcinoma). Also: lung, GI, thyroid, gonadal, many others. Surveillance: annual whole-body MRI, brain MRI, breast MRI, colonoscopy, dermatologic exam, and others (Toronto protocol). Avoid radiation exposure when possible (increased susceptibility to radiation-induced malignancy).

Retinoblastoma

Caused by loss of function of RB1 (13q14), the prototypical tumor suppressor gene. Knudson two-hit hypothesis: bilateral/hereditary retinoblastoma requires one germline mutation ("first hit," present in all cells) + one somatic mutation ("second hit," loss of remaining allele in retinal cell); sporadic retinoblastoma requires two somatic mutations in the same cell (hence unilateral and later onset). Hereditary form (~40%): bilateral, multifocal, mean age 12 months; also predisposes to osteosarcoma, soft tissue sarcomas, melanoma, and other cancers in adulthood. Sporadic form (~60%): unilateral, unifocal, mean age 24 months. Management: enucleation, chemotherapy, focal therapies (laser, cryotherapy); genetic counseling for all families.

28 Tumor Suppressor Genes vs Oncogenes

Understanding the two major classes of cancer genes is fundamental to cancer genetics.

29 Carrier Screening & Prenatal Screening

Carrier Screening

ACOG recommends offering carrier screening to all pregnant individuals (or those planning pregnancy). Two approaches:

• Ethnicity-based screening (traditional): targeted to high-prevalence conditions in specific populations — CF (all), SCD/hemoglobinopathies (African, Mediterranean, SE Asian), Tay-Sachs (Ashkenazi Jewish, French-Canadian, Cajun), β-thalassemia (Mediterranean, SE Asian, African), Canavan disease and familial dysautonomia (Ashkenazi Jewish)
• Expanded carrier screening (ECS) (increasingly standard): pan-ethnic panels testing 100–400+ conditions simultaneously using NGS; identifies carriers of conditions that ethnicity-based screening would miss; ACOG supports offering ECS to all patients regardless of ethnicity

Prenatal Screening for Aneuploidy

Serum marker patterns (useful for boards):

30 Prenatal Diagnostic Testing & PGT

Invasive Prenatal Diagnostic Tests

Preimplantation Genetic Testing (PGT)

Performed during in vitro fertilization (IVF) by biopsy of trophectoderm cells from day 5–7 blastocysts. Three types:

• PGT-M (monogenic/single-gene disorders): tests for a specific known familial mutation (e.g., CF, SCD, Huntington disease). Requires prior probe development from family samples
• PGT-A (aneuploidy): screens for whole-chromosome gains/losses. Used to improve IVF success rates by selecting euploid embryos, particularly in advanced maternal age, recurrent miscarriage, or recurrent implantation failure. Controversial — not universally recommended
• PGT-SR (structural rearrangements): for carriers of balanced translocations or inversions who are at risk of producing unbalanced embryos

31 Teratology & Genetic Counseling

Teratology

A teratogen is any agent that causes structural or functional abnormalities in the developing embryo/fetus. The effect depends on: timing of exposure (critical period), dose, genetic susceptibility, and the specific agent.

Critical periods: weeks 3–8 of gestation (embryonic period) is the time of greatest susceptibility to major structural malformations (organogenesis). Before week 3 — "all-or-none" effect (either embryo dies or survives without defect). After week 8 (fetal period) — exposure mainly causes functional defects and growth restriction rather than major structural anomalies, though some organs (e.g., brain, genitalia) continue to be vulnerable.

Key Teratogens

TORCH Infections

Genetic Counseling Principles

Genetic counseling is the process of helping individuals and families understand and adapt to the medical, psychological, and familial implications of genetic contributions to disease (NSGC definition). Core principles include:

• Non-directive approach: providing information and support without making recommendations for reproductive decisions; respecting patient autonomy
• Risk assessment: calculation of recurrence risks based on inheritance pattern, family history, Bayesian analysis, and genetic test results
• Informed consent: thorough discussion of benefits, risks, limitations, and possible outcomes of genetic testing before testing is performed
• Psychosocial support: addressing grief, guilt, anxiety, and family dynamics related to genetic diagnoses
• Privacy and confidentiality: GINA (Genetic Information Nondiscrimination Act) protects against discrimination by health insurers and employers based on genetic information; does NOT cover life, disability, or long-term care insurance

32 Cytogenetic & Molecular Cytogenetic Testing

Conventional Karyotype (G-banding)

Gold standard cytogenetic test. Cells are cultured (from blood, amniotic fluid, or tissue), arrested in metaphase with colchicine, stained with Giemsa to produce characteristic banding patterns. Resolution: ~5–10 Mb (can detect deletions, duplications, and rearrangements only if they are large enough to alter the banding pattern). Detects: numerical abnormalities (aneuploidies, polyploidy), large structural rearrangements (translocations, inversions, large deletions/duplications, ring chromosomes, isochromosomes). Turnaround time: 7–14 days (requires cell culture). Limitations: cannot detect submicroscopic CNVs (<5 Mb), balanced rearrangements may appear normal, point mutations are invisible.

Fluorescence in situ Hybridization (FISH)

Uses fluorescently labeled DNA probes that hybridize to specific chromosome regions. Can be performed on metaphase or interphase cells (no culture needed for interphase FISH — results in 24–48 hours). Resolution: ~100 kb–1 Mb depending on probe size.

Chromosomal Microarray (CMA)

Now recommended as a first-tier test (over karyotype) for patients with intellectual disability, developmental delay, autism spectrum disorder, and multiple congenital anomalies (ACMG 2010 guideline). Resolution: ~50–100 kb (50–100× higher than karyotype). Two main platforms:

Diagnostic yield of CMA: ~15–20% in developmental delay/ID (compared with ~3% for karyotype). However, CMA cannot detect balanced rearrangements (reciprocal translocations, inversions) or low-level mosaicism (<20%). Variants of uncertain significance (VOUS/VUS) are found in ~5–10% of cases — parental testing and database searches help reclassify over time.

33 Molecular Genetic Testing (Sequencing)

Sanger Sequencing

The original DNA sequencing method (chain termination). Reads one gene (or one exon) at a time. Resolution: single nucleotide. Used for: confirmatory testing, targeted testing of known familial variants, sequencing of small genes, and validation of NGS findings. Limitations: labor-intensive and expensive for multi-gene analysis; cannot detect large deletions/duplications (use MLPA for those).

Next-Generation Sequencing (NGS) Panels

Massively parallel sequencing of many genes simultaneously. Gene panels are curated lists of genes associated with a specific phenotype (e.g., cardiomyopathy panel: 50–100+ genes; hereditary cancer panel: 50–80+ genes; epilepsy panel: 200+ genes; RASopathy panel). Advantages: faster and cheaper per gene than Sanger; high depth of coverage (>100×). Limitations: limited to selected genes; may miss genes not on the panel; VUS are common.

Whole Exome Sequencing (WES)

Sequences all ~22,000 protein-coding genes (the exome — ~1.5% of the genome, but contains ~85% of known disease-causing mutations). Diagnostic yield: ~25–40% for undiagnosed genetic conditions (higher in consanguineous families, ~50–60%). Trio analysis (proband + both parents) greatly improves interpretation by identifying de novo mutations and defining phase (cis/trans). Increasingly used as a first-line test for undiagnosed suspected genetic conditions after negative CMA and targeted testing.

Whole Genome Sequencing (WGS)

Sequences the entire genome, including non-coding regions. Advantages over WES: detects structural variants, intronic variants affecting splicing, mitochondrial DNA mutations, and provides uniform coverage. Diagnostic yield: ~5–10% higher than WES in some studies. Limitations: enormous data volume, many VUS, higher cost, longer analysis time, incidental findings in non-coding regions.

RNA Sequencing (RNA-seq)

Complements DNA sequencing by analyzing gene expression, alternative splicing, and fusion transcripts. Particularly useful for detecting splicing abnormalities caused by intronic or synonymous variants that are difficult to interpret from DNA sequence alone. Emerging as a tool for resolving VUS and increasing diagnostic yield in patients negative by WES.

Other Specialized Tests

• Methylation analysis: detects epigenetic changes; essential for diagnosing Prader-Willi/Angelman syndromes, Beckwith-Wiedemann, and imprinting disorders; Southern blot or methylation-specific PCR/MLPA
• Trinucleotide repeat testing: PCR-based or Southern blot for specific repeat expansions (Fragile X CGG, Huntington CAG, myotonic dystrophy CTG, Friedreich ataxia GAA, SCA CAG); standard sequencing cannot reliably size large expansions
• MLPA (multiplex ligation-dependent probe amplification): detects deletions/duplications of individual exons; essential for DMD/BMD, SMA (SMN1 copy number), and other conditions where intragenic deletions/duplications are common

34 Pharmacogenomics

Pharmacogenomics studies how genetic variation affects drug response, including efficacy and toxicity. Implementation of pharmacogenomic testing can optimize drug selection and dosing, reduce adverse drug reactions, and improve clinical outcomes. The Clinical Pharmacogenetics Implementation Consortium (CPIC) provides evidence-based guidelines.

35 ACMG Variant Classification & Pedigree Symbols

ACMG/AMP Variant Classification (2015 Standards and Guidelines)

The American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) established a five-tier classification system for sequence variants, using defined criteria with weighted evidence categories.

Standard Pedigree Symbols

Pedigree construction follows standardized nomenclature recommended by the National Society of Genetic Counselors (NSGC) and the Pedigree Standardization Work Group.

36 Genetic Testing Algorithm by Clinical Scenario

37 Medications in Genetics

Enzyme Replacement Therapy (ERT)

Substrate Reduction Therapy (SRT)

Gene Therapies (Approved)

Molecular Modulators & Targeted Therapies

38 Abbreviations Master List & Reference Tables

Abbreviations

Inheritance Pattern Quick Reference

Common Trinucleotide Repeat Disorders