Medical Genetics

Comprehensive study resource covering molecular genetics, chromosomal abnormalities, Mendelian inheritance, population genetics, genetic testing, cancer genetics, pharmacogenetics, developmental genetics, biochemical genetics, epigenetics, and precision medicine. Every concept, every pathway, every syndrome you need to know.

1. Molecular Genetics

DNA/RNA Structure Central Dogma Replication Transcription Translation Gene Regulation CRISPR

DNA and RNA Structure
  • DNA: Double helix (B-form).
  • Nucleotides: phosphate + deoxyribose + nitrogenous base (purines: adenine, guanine; pyrimidines: cytosine, thymine). Base pairing: A=T (2 H-bonds), G≡C (3 H-bonds).
  • Antiparallel strands (5' -> 3' and 3' -> 5').
  • Major and minor grooves for protein binding.
  • Chromatin: DNA wrapped around histones (H2A, H2B, H3, H4) forming nucleosomes, 30nm fiber, loops, and chromosomes. RNA: Single-stranded, ribose instead of deoxyribose, uracil instead of thymine.
  • Types: mRNA (messenger, protein-coding), rRNA (ribosomal, structural/catalytic), tRNA (transfer, amino acid delivery), snRNA (splicing), miRNA/siRNA (gene silencing), lncRNA (regulatory). Telomeres: TTAGGG repeats at chromosome ends.
  • Telomerase (reverse transcriptase + RNA template) maintains telomeres in stem cells/germ cells.
  • Shortening linked to aging and cellular senescence.
Central Dogma: Replication
  • Semiconservative replication (Meselson-Stahl).
  • Origins of replication: Multiple origins (eukaryotes), ORC complex.
  • Replication forks bidirectionally. Enzymes: DNA helicase (MCM complex) unwinds DNA, SSB proteins stabilize single strands, topoisomerase (Topo I/II) relieves supercoiling.
  • Primase synthesizes RNA primers.
  • DNA polymerase α (primer extension), δ (leading), ε (lagging) in eukaryotes.
  • DNA polymerase III (prokaryotes). 5' -> 3' polymerase activity, 3' -> 5' exonuclease (proofreading).
  • Leading strand (continuous), lagging strand (Okazaki fragments).
  • RNase H removes RNA primers, DNA ligase seals nicks. Telomerase: Adds TTAGGG repeats to 3' end of lagging strand.
  • Active in germ cells, stem cells, cancer cells. Cell cycle: G1 (growth), S (DNA synthesis), G2 (growth/preparation), M (mitosis: prophase, metaphase, anaphase, telophase). Checkpoints: G1/S (Rb/p53), G2/M (cyclin B/CDK1), M (spindle checkpoint).
Central Dogma: Transcription
  • RNA Polymerases: RNA Pol I (rRNA), RNA Pol II (mRNA, snRNA, miRNA, lncRNA), RNA Pol III (tRNA, 5S rRNA, U6 snRNA). Promoters: Core promoter (TATA box at -30, initiator element, downstream promoter element).
  • Proximal promoter elements (CAAT box, GC box).
  • Enhancers (distal, tissue-specific, orientation-independent).
  • Silencers, insulators/boundary elements.
  • Transcription factors: Basal (TFIIA, TFIIB, TFIID/TBP, TFIIE, TFIIF, TFIIH).
  • Mediator complex bridges activators to Pol II. Steps: Initiation (closed complex, open complex, promoter clearance), elongation (Pol II CTD phosphorylated by TFIIH/CDK7, elongation factors P-TEFb, DSIF, NELF), termination (polyadenylation signal AAUAAA, CPSF/CstF cleavage, Rat1/Xrn2 torpedo model).
  • Pre-mRNA processing: 5' capping (7-methylguanosine, protects from exonucleases, enhances translation), splicing (spliceosome: U1, U2, U4/U6, U5 snRNPs, branch point A, 5' splice site GU, 3' splice site AG, lariat intermediate, alternative splicing), 3' polyadenylation (poly-A polymerase adds ~200 As, enhances stability/export). RNA editing: Deamination of A to I (ADAR), C to U (APOBEC).
Central Dogma: Translation
  • Ribosome: Eukaryotic 80S (40S small + 60S large).
  • Prokaryotic 70S (30S + 50S). tRNA: Cloverleaf structure, anticodon loop, acceptor stem (3' CCA + amino acid).
  • Aminoacyl-tRNA synthetases charge tRNA (one per amino acid, ATP-dependent).
  • Wobble hypothesis: 3rd base flexibility allows 61 codons to be read by ~45 tRNAs.
  • Genetic code: 61 sense codons (20 amino acids + start AUG/methionine), 3 stop codons (UAA, UAG, UGA).
  • Degenerate, universal (exceptions: mitochondria).
  • Initiation: eIF4E binds 5' cap, eIF4G/eIF4A, scanning to AUG (Kozak sequence ACCAUGG). eIF2-GTP-Met-tRNAi ternary complex. 60S joins, eIFs released.
  • Elongation: eEF1A delivers aminoacyl-tRNA, peptidyl transferase (28S rRNA, ribozyme) forms peptide bond. eEF2 translocates ribosome.
  • Termination: eRF1 recognizes stop codons, eRF3 GTPase, polypeptide released. Ribosome recycling. Post-translational: Folding (chaperones Hsp70, Hsp90), glycosylation (ER/Golgi), phosphorylation, ubiquitination (proteasome), signal sequences (SRP, ER targeting), cleavage (proteases).
Gene Regulation and Epigenetics
  • Transcriptional regulation: Promoters, enhancers (looping via Mediator/cohesin), silencers, insulators (CTCF).
  • Chromatin states: euchromatin (active, open) vs heterochromatin (inactive, condensed, constitutive H3K9me3/H4K20me3, facultative).
  • Histone modifications: Acetylation (HATs: active; HDACs: repressive).
  • Methylation (H3K4me3 = active promoters; H3K9me3 = heterochromatin; H3K27me3 = Polycomb repression; H3K36me3 = transcriptional elongation).
  • Phosphorylation, ubiquitination, SUMOylation.
  • Histone code hypothesis. DNA methylation: CpG islands (promoters, mostly unmethylated in active genes).
  • DNMT3A/3B (de novo), DNMT1 (maintenance).
  • Methylation = transcriptional silencing.
  • Imprinted genes X-inactivation, retrotransposon silencing.
  • Chromatin remodeling: SWI/SNF (BAF complex, mobilizes nucleosomes, ATP-dependent), ISWI, CHD, INO80.
  • Mutations in BAF subunits (SMARCB1, ARID1A, SMARCA4) in cancers.
  • Non-coding RNAs: miRNA (22nt, Dicer processing, RISC complex, binds 3'UTR, translational repression/mRNA decay). siRNA (exogenous/viral, perfectly complementary, RNAi pathway). lncRNA (XIST, HOTAIR, MALAT1, NEAT1, dosage compensation, scaffold, guide, decoy). piRNA (germline, transposon silencing). CRISPR-Cas9: Adaptive bacterial immune system.
  • Cas9 endonuclease + guide RNA (crRNA + tracrRNA). DSB at target site: NHEJ (indels, gene disruption) or HDR (with donor template, precise editing).
  • Applications: gene knockout, knock-in, activation (CRISPRa), repression (CRISPRi), base editing (deaminase), prime editing (reverse transcriptase), epigenetic editing.
  • Clinical trials for sickle cell (exa-cel/Casgevy), T-cell engineering (CAR-T), DMD, LCA10.
High-Yield Pearls
  • DNA 5' -> 3' synthesis always. Leading = continuous. Lagging = Okazaki fragments + ligase.
  • RNA Pol II transcribes mRNA. TATA box at -30, bound by TBP (TFIID). Transcript = sense strand.
  • AUG = start (methionine). UAA/UAG/UGA = stop. Wobble at 3rd base of codon (5' end of anticodon).
  • miRNAs bind 3'UTR of mRNA -> translational repression or degradation. siRNAs perfectly complementary -> cleavage.
  • CRISPR-Cas9: NHEJ disrupts gene, HDR repairs with template. Base editing: no DSB needed.
  • Telomerase: RNA template + reverse transcriptase (TERT). Active in cancer -> target.
Red Flags
  • Mutations in splice donor (GT) or acceptor (AG) -> exon skipping, intron retention -> disease (e.g., beta-thalassemia, familial dysautonomia).
  • Expanded trinucleotide repeats in non-coding regions (FMR1 CGG, DMPK CTG, FXN GAA) -> loss of function via methylation or transcription interference.
  • DNMT3A mutations -> clonal hematopoiesis (TET2, ASXL1) -> increased risk of myeloid malignancies.
  • Off-target CRISPR editing -> unintended mutations. Use high-fidelity Cas9 variants, careful guide design.
  • RNA Pol II CTD phosphorylation by CDK9 (P-TEFb) is target of anticancer drug flavopiridol.

2. Chromosomal Abnormalities

Aneuploidy Sex Chromosomes Microdeletions Fragile X Imprinting

Numerical Abnormalities: Aneuploidy
  • Caused by meiotic nondisjunction (increases with maternal age).
  • Most aneuploidies are lethal except for specific trisomies and sex chromosome abnormalities.
  • Trisomy 21 (Down syndrome): 1:700 live births.
  • Features: intellectual disability, brachycephaly, flat facies, epicanthal folds, Brushfield spots, single palmar crease, sandal gap, duodenal atresia, AVSD/VSD, Hirschsprung disease, increased AML/ALL risk (20x), early Alzheimer disease (APP gene on chr21). 95% full trisomy (meiosis I nondisjunction), 4% Robertsonian translocation t(14;21), 1% mosaic.
  • Recurrence risk: 1% for full trisomy, 10-15% for maternal t(14;21) carrier, Trisomy 18 (Edwards): 1:5000.
  • Rocker-bottom feet clenched hands with overlapping fingers (2 -> 3, 5 -> 4), low-set ears, micrognathia, prominent occiput, VSD, horseshoe kidney. 90% die by 1yr.
  • Trisomy 13 (Patau): 1:15000.
  • Cleft lip/palate polydactyly, holoprosencephaly, microphthalmia/coloboma, scalp defects (cutis aplasia), VSD/PDA, cystic kidneys. 95% die by 1yr.
  • Triploidy: 69 chromosomes.
  • Partial molar pregnancy (69,XXY from dispermy).
  • Severe IUGR syndactyly, molar placenta. Lethal.
Sex Chromosome Aneuploidies
  • Turner syndrome (45,X): Only viable monosomy. 1:2500 females.
  • Features: short stature, webbed neck, low posterior hairline, shield chest, widely spaced nipples, cubitus valgus, lymphedema (hands/feet), coarctation of aorta, bicuspid aortic valve, horseshoe kidney, streak gonads (gonadal dysgenesis -> primary amenorrhea, infertility, absent puberty).
  • Intelligence normal but nonverbal learning deficits.
  • Mosaic forms (45,X/46,XX) can be milder.
  • Treatment: GH for height, estrogen replacement for puberty, monitor for aortic dilation.
  • Klinefelter syndrome (47,XXY): 1:600 males.
  • Tall stature gynecomastia, small firm testes, eunuchoid habitus, infertility (azoospermia), low testosterone, increased risk of breast cancer, osteoporosis, varicose veins, learning disabilities (verbal IQ 47,XYY: 1:1000 males.
  • Tall stature normal fertility, normal intelligence, slightly increased risk of behavioral/learning difficulties (ADD, autism). 47,XXX (Triple X): 1:1000 females.
  • Tall stature normal phenotype, normal fertility, slightly increased risk of learning disabilities. Most undiagnosed.
Microdeletion Syndromes
  • 22q11. 2 deletion (DiGeorge/Velocardiofacial): Most common microdeletion (1:4000).
  • Conotruncal heart defects (tetralogy of Fallot, truncus arteriosus, interrupted aortic arch type B), hypocalcemia (parathyroid aplasia), T-cell deficiency (thymic aplasia, recurrent infections, autoimmune disease), cleft palate/speech delay, dysmorphic facies (narrow palpebral fissures, tubular nose), learning disabilities, psychiatric disorders (schizophrenia risk 25x).
  • TBX1 gene is critical.
  • Williams syndrome (7q11. 23 deletion): Elfin facies (periorbital fullness, stellate iris, full lips), supravalvular aortic stenosis (ELN gene), hypercalcemia (infancy), cocktail party personality (friendly, loquacious), intellectual disability, musculoskeletal issues, growth retardation.
  • Prader-Willi (15q11-q13 paternal deletion): Infantile hypotonia/poor feeding, then hyperphagia/obesity (hypothalamic dysfunction), small hands/feet, almond-shaped eyes, intellectual disability, obsessive-compulsive behaviors, growth hormone deficiency.
  • Angelman (15q11-q13 maternal deletion): Happy puppet: severe intellectual disability, jerky ataxic gait, frequent laughter/smiling, seizures, microcephaly, absent speech.
  • UBE3A gene (expressed only from maternal allele in brain).
  • Cri-du-chat (5p deletion): Cat-like cry (laryngeal malformation), microcephaly, hypertelorism, intellectual disability, round face.
  • Miller-Dieker (17p13. 3 deletion, LIS1): Lissencephaly (smooth brain), severe intellectual disability, seizures, dysmorphic facies.
  • Smith-Magenis (17p11. 2 deletion): Self-injurious behaviors, sleep disturbance, hoarse voice, intellectual disability, brachycephaly.
  • Wolf-Hirschhorn (4p16. 3 deletion): Greek warrior helmet facies (prominent glabella, hypertelorism), microcephaly, seizures, severe ID, cleft lip/palate.
  • NF1 microdeletion (17q11. 2): More severe neurofibromatosis type 1 with increased tumor burden, dysmorphic features, intellectual disability.
Fragile X Syndrome
  • FMR1 gene CGG trinucleotide repeat expansion on X chromosome.
  • Most common inherited cause of intellectual disability.
  • Prevalence: 1:4000 males, 1:8000 females.
  • Full mutation ( > 200 CGG repeats): Methylation of FMR1 promoter -> transcriptional silencing -> loss of FMRP (RNA-binding protein regulating translation at synapses).
  • Premutation (55-200 repeats): Unstable, can expand to full mutation in offspring (anticipation, maternal transmission only).
  • Premutation carriers at risk for: fragile X-associated tremor/ataxia syndrome (FXTAS, > 50y males, intention tremor, ataxia, cognitive decline) and fragile X-associated primary ovarian insufficiency (FXPOI, 20% of carriers).
  • Clinical features (full mutation males): Long narrow face, prominent forehead, large everted ears, macroorchidism (post-pubertal), hyperextensible joints, mitral valve prolapse, intellectual disability (moderate-severe), autism spectrum disorder (30-50%), seizures (20%), ADHD, social anxiety, hand flapping, gaze aversion.
  • Females with full mutation: milder phenotype (skewed X-inactivation). Diagnosis: FMR1 CGG repeat analysis (PCR + Southern blot).
  • Treatment: Symptomatic (behavioral therapy, psychostimulants, SSRIs, targeted therapies: mGluR5 antagonists, GABA agonists in trials).
High-Yield Pearls
  • Down syndrome: 95% full trisomy (maternal meiosis I), 4% translocation t(14;21), 1% mosaic. Recurrence risk varies.
  • Turner: 45,X. Only viable monosomy. Gonadal dysgenesis. Coarctation, webbed neck, lymphedema, short stature.
  • DiGeorge (22q11.2): CATCH-22 (Cardiac, Abnormal facies, Thymic aplasia, Cleft palate, Hypocalcemia). TBX1.
  • Prader-Willi = paternal deletion of 15q11-q13. Angelman = maternal deletion of same region. UBE3A imprinted in brain.
  • Fragile X: CGG > 200 = full mutation. Premutation (55-200) -> FXTAS, FXPOI. Anticipation via maternal transmission.
Red Flags
  • Robertsonian translocation carrier t(14;21): 10-15% risk of Down syndrome if mother carries, < 1% if father.
  • Turner Y chromosome material: gonadoblastoma risk -> gonadectomy. Check FISH for Y sequences.
  • Klinefelter: increased breast cancer risk. Gynecomastia + hypogonadism + azoospermia = karyotype.
  • DiGeorge + seizure: hypocalcemia from parathyroid aplasia. Check calcium, treat with calcitriol.
  • Fragile X premutation + tremor/ataxia in elderly male relative -> cascade testing important.
  • Microarray (CMA) is first-line test for unexplained DD/ID, autism, multiple congenital anomalies.

3. Mendelian Inheritance

AD AR X-Linked Mitochondrial Anticipation Imprinting Consanguinity Mosaicism

Autosomal Dominant (AD)
  • Only one mutant allele needed for disease expression.
  • Vertically transmitted affects both sexes equally, male-to-male transmission possible.
  • Heterozygotes affected (often more severe in homozygotes, usually embryonic lethal).
  • Key features: Multiple generations affected, ~50% risk to offspring, variable expressivity, incomplete penetrance (some individuals with genotype do not manifest disease), de novo mutations common (e. g. , NF1 ~50% de novo, achondroplasia ~80% from advanced paternal age). Haploinsufficiency: One functional copy insufficient for normal function (e. g. , TBX1 in DiGeorge, ELN in Williams). Dominant negative: Mutant protein interferes with wild-type protein function (e. g. , COL1A1/2 in OI, FBN1 in Marfan). Gain-of-function: Mutant protein acquires novel toxic activity (e. g. , FGFR3 in achondroplasia, HTT in Huntington, KRAS in Noonan). Examples: Huntington disease, Marfan, NF1/2, Familial hypercholesterolemia (LDLR), ADPKD (PKD1/2), HHT (ENG), Ehlers-Danlos vascular (COL3A1), OI, Achondroplasia, Myotonic dystrophy, VHL, MEN1/2, TSC1/2, BRCA1/2, Lynch, FAP (APC).
Autosomal Recessive (AR)
  • Two mutant alleles required.
  • Both sexes equally affected.
  • Often seen in consanguineous families.
  • Heterozygous carriers are asymptomatic.
  • More severe than AD (loss-of-function of critical enzymes).
  • Key features: Usually one generation affected (siblings), horizontal pattern. 25% risk to offspring of carrier parents, 50% carriers, 25% unaffected.
  • Carrier frequency increased in certain populations (founder effect). Examples: CF (CFTR), Sickle cell (HBB), PKU (PAH), Tay-Sachs (HEXA), Gaucher (GBA), Niemann-Pick (SMPD1), GSD I (G6PC), Wilson (ATP7B), Hemochromatosis (HFE), Alpha-1 antitrypsin (SERPINA1), Friedreich ataxia (FXN), SMA (SMN1), Albinism (TYR, OCA2), Usher syndrome, Bardet-Biedl, Primary ciliary dyskinesia. Consanguinity: Increased coefficient of inbreeding (F).
  • First cousin marriage (F=1/16): 4-6% risk of recessive disorder vs 2-3% background.
  • Coefficient of relationship: first cousins share 1/8 of genes.
  • Compound heterozygote: Two different mutant alleles at same locus (e. g. , CF, hemochromatosis).
  • Locus heterogeneity: Mutations in different genes cause same phenotype (e. g. , OI: COL1A1/COL1A2; hearing loss: many genes).
X-Linked Recessive and Dominant
  • X-Linked Recessive: Affected males (hemizygous), carrier females (usually asymptomatic).
  • No male-to-male transmission.
  • All daughters of affected male are obligate carriers. 50% of sons of carrier female affected. Examples: Duchenne and Becker MD (DMD), Hemophilia A (F8) and B (F9), G6PD deficiency, Fabry (GLA), Hunter/MPS II (IDS), Lesch-Nyhan (HPRT1), Color blindness, X-linked agammaglobulinemia (BTK), Wiskott-Aldrich (WAS), X-ALD (ABCD1). Duchenne MD: DMD (dystrophin), frameshift deletion/nonsense, absent protein.
  • Becker: in-frame deletion, reduced.
  • Onset 3-5y Gowers sign, pseudohypertrophy of calves, waddling gait, cardiomyopathy, wheel chair by 12, death 20s (respiratory/cardiac).
  • Creatine kinase markedly elevated.
  • Hemophilia A: F8 intron 22 inversion common.
  • Severity correlates with factor level. X-Linked Dominant: Both sexes affected, more severe/fatal in males (often male lethal).
  • All daughters of affected male affected, no sons affected. Examples: Rett syndrome (MECP2, predominantly females due to male lethality), Incontinentia pigmenti (IKBKG/NEMO, male lethal), Vitamin D-resistant rickets/hypophosphatemic rickets (PHEX), Goltz syndrome (PORCN, male lethal), Alport syndrome (COL4A5, also AD/AR forms).
  • X-inactivation (Lyonization): Random inactivation of one X in each cell in early development.
  • Carrier females may have mild expression of X-linked recessive disorders (skewed inactivation).
  • Mosaic expression (e. g. , Rett, Fabry carriers with symptoms).
Mitochondrial Inheritance
  • Maternal transmission only. mtDNA: 16. 5kb circular, 37 genes (13 proteins, 22 tRNAs, 2 rRNAs).
  • High mutation rate (lack of histones, limited repair).
  • Heteroplasmy: variable proportion of mutant mtDNA within cells.
  • Threshold effect: clinical expression when mutant proportion exceeds tissue-specific threshold.
  • Mitotic segregation. Examples: LHON (ND1/4/6, sudden vision loss, young men), MELAS (MT-TL1, encephalopathy, lactic acidosis, stroke-like episodes), MERRF (MT-TK, myoclonic epilepsy, ragged red fibers), Kearns-Sayre (deletions, progressive external ophthalmoplegia, heart block, ataxia), Leigh syndrome (complex I/IV genes, subacute necrotizing encephalomyelopathy), Pearson syndrome (mtDNA deletion, sideroblastic anemia + pancreatic insufficiency), NARP (MT-ATP6, neuropathy, ataxia, retinitis pigmentosa). Diagnosis: Muscle biopsy (ragged red fibers, COX-deficient fibers), mtDNA sequencing.
  • Recurrence risk: ~100% if mother has mutation (but variable heteroplasmy, uncertain phenotype).
  • No transmission from affected male.
Anticipation and Triplet Repeat Disorders
  • Anticipation: Earlier onset/increased severity in successive generations due to unstable trinucleotide repeat expansions.
  • Polyglutamine (CAG) disorders: CAG repeat in coding region -> expanded polyglutamine tract -> protein aggregation, toxic gain-of-function.
  • Anticipation more pronounced with paternal transmission. Examples: Huntington disease (HTT, 4p16. 3, normal 40, CAG), SBMA/Kennedy disease (AR), SCAs 1/2/3/6/7/17, DRPLA.
  • Non-coding repeat expansions: Fragile X (FMR1 CGG 5'UTR, > 200 full, methylation silencing).
  • Myotonic dystrophy type 1 (DMPK CTG 3'UTR, 50-4000, RNA toxicity, MBNL splicing dysregulation).
  • Friedreich ataxia (FXN GAA intron 1, 70-1700, transcriptional silencing, frataxin deficiency).
  • DM2 (CNBP CCTG intron 1, 75-11000, milder, proximal weakness).
  • C9orf72 (GGGGCC intron 1, 30-2000, ALS + FTD, both gain + loss of function). Parental bias: HD and SCA: paternal -> larger expansions.
  • DM1 and Fragile X: maternal -> larger expansions.
  • FRDA: paternal contractions, maternal expansions.
Genomic Imprinting and UPD
  • Imprinting: Epigenetic phenomenon where genes are expressed only from one parental allele.
  • Imprinting control regions (ICRs) differentially methylated.
  • Prader-Willi (PWS): 15q11-q13, loss of paternally expressed genes (SNRPN, NDN, MKRN3, MAGEL2). 70% de novo paternal deletion, 25% maternal UPD, Angelman (AS): Same region, loss of maternally expressed UBE3A. 70% de novo maternal deletion, 2-5% paternal UPD, 3-5% imprinting defect, 10% UBE3A mutation.
  • Beckwith-Wiedemann (BWS): 11p15. 5, overgrowth, macrosomia, omphalocele, macroglossia, hemihypertrophy, embryonal tumors (Wilms, hepatoblastoma).
  • ICR1 (IGF2/H19) hypermethylation, ICR2 (KCNQ1OT1/CDKN1C) hypomethylation.
  • Russell-Silver (SRS): 11p15. 5 hypomethylation (50%) or maternal UPD 7 (10%).
  • IUGR, triangular face, body asymmetry.
  • TNDM: 6q24, paternal UPD or duplication. UPD testing: SNP microarray or methylation-specific MLPA.
  • Recurrence risk low for UPD but may recur with certain translocations.
Gonadal Mosaicism and Non-Traditional Inheritance
  • Gonadal mosaicism: Mutation present in some germ cells but not detectable in blood.
  • Important for recurrence risk when disease appears de novo. Example: DMD, OI, tuberous sclerosis, NF1.
  • Recurrence risk for sibs: up to 10-15% for certain disorders even if parents unaffected.
  • Empiric risk: ~1-2% for gonadal mosaicism after de novo AD mutation.
  • Multifactorial inheritance: Genetic (polygenic) + environmental.
  • Examples: NTD, cleft lip/palate, CHD, hypertension, diabetes, autism.
  • Recurrence risk: 2-5% for first-degree relatives (higher if severe, multiple affected, same sex for sex-limited traits).
  • Threshold model: continuous liability distribution with threshold for disease expression. Somatic mosaicism: Post-zygotic mutation in subset of cells. Examples: McCune-Albright (GNAS, polyostotic fibrous dysplasia, cafe-au-lait, endocrine overactivity), Sturge-Weber (GNAQ, port-wine stain), Proteus (AKT1), CLOVES (PIK3CA), segmental NF1. Heteroplasmy: Mitochondrial mosaicism.
High-Yield Pearls
  • AD: vertical, 50% risk, incomplete penetrance, variable expressivity, de novo (advanced paternal age).
  • AR: horizontal (sibs), 25% risk, consanguinity risk, carrier frequency 2pq. Founder effects common.
  • X-linked recessive: no male-to-male. Carrier females. DMD: frameshift = severe, in-frame = milder.
  • Mitochondrial: maternal only. Heteroplasmy, threshold effect. LHON, MELAS, MERRF, Kearns-Sayre.
  • Anticipation: HD (CAG, paternal), DM1 (CTG, maternal), Fragile X (CGG, maternal).
  • Gonadal mosaicism: recurrence for sibs of de novo AD up to ~10%. Counsel carefully.
Red Flags
  • De novo AD + negative family history: gonadal mosaicism possible -> recurrence risk ~1-5% for sibs (not 0%).
  • Presymptomatic testing for HD: requires extensive counseling, psychological support, consider suicide risk.
  • Consanguinity: increased risk AR disorders and multifactorial conditions. Coefficient of inbreeding F.
  • Mitochondrial disease: avoid valproate (hepatotoxicity in POLG). Supportive care only.
  • Imprinting disorders: UPD recurrence low, but consider translocation if UPD from meiosis I error.

4. Population Genetics

Hardy-Weinberg Carrier Frequency Selection Drift Founder Effect GWAS Heritability

Hardy-Weinberg Equilibrium
  • Principles: Allele and genotype frequencies remain constant across generations in the absence of evolutionary forces.
  • Equations: p + q = 1 (allele frequencies). p^2 + 2pq + q^2 = 1 (genotype frequencies). p = frequency of dominant/normal allele (A), q = frequency of recessive/mutant allele (a). Assumptions: Random mating, no mutation, no selection, no migration, infinite population size, discrete generations, equal allele frequencies in sexes.
  • Deviations indicate evolutionary forces.
  • Carrier frequency calculation (AR disease): Incidence = q^2.
  • For 1/10,000: q^2 = 0. 0001, q = 0. 01, p = 0. 99, carrier frequency 2pq = 0. 0198 (~1/50).
  • For 1/40,000: q = 0. 005, p = 0. 995, carrier ~1/100. X-linked recessive: Disease frequency in males = q.
  • Carrier frequency in females = 2pq.
  • Incidence in females = q^2 (rare).
  • Multiple alleles: (p + q + r)^2 = 1 (ABO, HLA). Testing for HWE: Chi-square test comparing observed vs expected genotype counts.
  • Deviation may indicate genotyping error, population stratification, or selection.
Selection and Fitness
  • Fitness (w): Relative reproductive success.
  • Selection coefficient (s = 1 - w).
  • Against recessive homozygotes: q decreases slowly (most deleterious alleles hidden in heterozygotes).
  • For rare recessive lethal (q is small, e. g. , 0. 01), selection is ineffective.
  • Against dominant alleles: Strong selection (all carriers affected).
  • Most AD diseases persist due to de novo mutations (achondroplasia s ~0. 8).
  • Heterozygote advantage: Heterozygote has higher fitness than either homozygote.
  • Classic: sickle cell trait (HbAS) confers malaria resistance (w ~1. 2-1. 3 in endemic regions).
  • Balanced polymorphism maintains high HbS frequency (up to 20% in parts of Africa). Other: G6PD deficiency, thalassemias, CFTR (possible typhoid resistance), CCR5-Delta32 (HIV resistance).
  • Frequency-dependent selection: Rare alleles have advantage (MHC diversity).
  • Mutation-selection balance: For AR: q = sqrt (μ/s). For AD: q = μ/s.
  • Used to estimate mutation rates for lethal disorders.
Genetic Drift and Founder Effect
  • Genetic drift: Random fluctuations in allele frequencies in small populations.
  • Leads to fixation or loss. Founder effect: Small number of founders establish new population, specific alleles become enriched.
  • Ashkenazi Jewish founder mutations: Tay-Sachs (HEXA 1278insTATC, 1:25 carrier), Gaucher (GBA N370S, 1:15), Canavan (ASPA E285A, 1:40), familial dysautonomia (IKBKAP, 1:30), Bloom (BLM, 1:100), Niemann-Pick A (SMPD1, 1:90), Fanconi C (FANCC, 1:100), Factor XI (F11, 1:10). Finnish: Congenital nephrotic (NPHS1), aspartylglucosaminuria (AGA), diastrophic dysplasia (SLC26A2).
  • French Canadian: Tay-Sachs, CF (444delA), LPL deficiency, OPMD (PABPN1). Amish/Mennonite: MSUD (BCKDHA), Glutaric acidemia I (GCDH), Ellis-van Creveld (EVC/EVC2), cartilage-hair hypoplasia (RMRP). Bottleneck: Drastic population reduction -> loss of diversity.
  • Out-of-Africa bottleneck -> lower diversity in non-Africans.
  • Effective population size (Ne): Size of ideal population with same drift rate, usually much smaller than census size.
GWAS and Linkage Disequilibrium
  • Linkage disequilibrium (LD): Non-random association of alleles at different loci.
  • D' and r^2 measures.
  • LD blocks separated by recombination hotspots. GWAS: Tests millions of common SNPs (MAF > 5%) for association with traits/diseases.
  • Case-control or quantitative trait.
  • Uses imputation (1000 Genomes, TOPMed).
  • Population structure correction (PCA, mixed models).
  • Multiple testing correction (p Findings: Most variants have small effect sizes (OR 1. 1-1. 5).
  • Explain small fraction of heritability (missing heritability).
  • Over 5000 GWAS loci identified. Post-GWAS: Fine-mapping (credible sets), functional annotation (eQTL, pQTL, splicing QTL), colocalization, Mendelian randomization.
  • Polygenic risk scores (PRS): Weighted sum of risk alleles across many SNPs.
  • Methods: LDpred, PRS-CS, Bayesian regression.
  • Used for risk stratification (CAD, breast cancer, T2D).
  • Clinical utility still limited. Heritability: Proportion of phenotypic variance due to genetics.
  • Broad-sense (H^2, all genetic) vs narrow-sense (h^2, additive).
  • Twin studies (MZ vs DZ), family studies, SNP-based heritability (GREML, LDSC). h^2 height ~0. 8, BMI ~0. 4-0. 7, schizophrenia ~0. 8, autism ~0. 8, breast cancer ~0. 3.
  • Missing heritability: Gap between GWAS and family-based heritability.
  • Sources: rare variants, structural variants, epistasis, GxE, epigenetic effects.
High-Yield Pearls
  • HWE: p^2 + 2pq + q^2 = 1. Carrier frequency = 2pq ~ 2q when p ~ 1. AR incidence = q^2.
  • Founder effect: high frequency of specific mutation in isolated population. Tay-Sachs in AJ, OCA2 in Hopi.
  • Heterozygote advantage: HbAS -> malaria resistance. Sickle allele high in malarial regions.
  • GWAS: p < 5 x 10^{-8}, small effect sizes, replication needed. Population structure = confounder.
  • PRS: aggregate small effects. Improving but clinical utility limited for most. Emerging in breast cancer screening.
  • Twin studies: MZ share 100% genes, DZ ~50%. Heritability = 2 x (rMZ - rDZ).
Red Flags
  • Population stratification in GWAS can cause spurious associations. Use PCA or mixed models to correct.
  • PRS not transferable across populations. Need diverse GWAS.
  • Consanguinity increases homozygosity genome-wide -> multiple recessive disease risk.
  • Founder effect + drift -> some deleterious alleles can reach high frequency by chance.
  • Selection coefficient estimation requires large samples and accurate fitness measurements.

5. Genetic Testing

Karyotype FISH CMA Sanger NGS WES/WGS Variant Interpretation Prenatal Newborn Screening

Cytogenetic Testing
  • Karyotype (G-banding): Gold standard for chromosome abnormalities.
  • Requires metaphase cells.
  • Resolution: 400-550 bands, detects abnormalities > 5-10 Mb.
  • Indications: suspected aneuploidy, structural rearrangements, hematologic malignancies, reproductive genetics. FISH: Targeted DNA probes, metaphase or interphase.
  • Resolution: specific locus.
  • Uses: rapid aneuploidy detection (chr13/18/21/X/Y), microdeletion syndromes (DiGeorge, Williams, Cri-du-chat), HER2 amplification, BCR-ABL fusion, MLL rearrangements.
  • Chromosomal microarray (CMA): First-line for unexplained DD/ID, autism, MCA.
  • Detects CNVs at 50-100 kb resolution.
  • Array CGH (comparative genomic hybridization) or SNP array (detects UPD, consanguinity, mosaicism).
  • Diagnostic yield ~15-20% in DD/ID (vs ~3% karyotype).
  • Limitations: balanced rearrangements, low-level mosaicism, point mutations.
  • ACMG/ISCA guidelines: report CNVs > 400-500 kb, evaluate for known syndromes.
Molecular Testing: Sequencing
  • Sanger sequencing: Gold standard for single-gene testing.
  • Dideoxy chain termination.
  • Read length ~700-900bp.
  • Used for confirmation of NGS variants, single-gene disorders (CFTR, FBN1, BRCA1/2 germline).
  • Next-generation sequencing (NGS): Massively parallel. Platforms: Illumina (sequencing by synthesis, short reads 150-300bp), Ion Torrent (semiconductor), PacBio HiFi (long reads 10-25kb), Oxford Nanopore (very long reads).
  • Targeted gene panels: 5-500 genes, high depth (100-1000x), fewer VUS.
  • Applications: hereditary cancer, cardiomyopathy, epilepsy, hearing loss, RASopathy panels.
  • Whole exome sequencing (WES): Captures all coding exons (~1% genome, ~20,000 genes). ~60-80x depth.
  • Diagnostic yield ~25-40% in selected cases (DD/ID, MCA, neurological).
  • Trio WES improves yield.
  • Whole genome sequencing (WGS): Covers coding + non-coding.
  • Higher cost more incidental findings.
  • Emerging as first-line.
  • Long-read sequencing: Solves SVs, repeats, phasing, segmental duplications.
  • Used for repeat expansions (Fragile X, HD, DM1, C9orf72), HLA typing. RNA sequencing: Detects aberrant splicing, allelic imbalance, fusions, expression outliers.
  • Adds 10-15% diagnostic yield when added to WES/WGS.
Variant Interpretation: ACMG/AMP
  • ACMG/AMP 2015: Five tiers: Pathogenic (P), Likely Pathogenic (LP), VUS, Likely Benign (LB), Benign (B).
  • Pathogenic evidence: PVS1 (null variant in LOF gene - nonsense, frameshift, canonical splice, initiation codon).
  • PS1 (same amino acid change as known P).
  • PS2 (de novo confirmed).
  • PS3 (functional assay damaging).
  • PS4 (prevalence in affected increased).
  • PM1 (hotspot/functional domain).
  • PM2 (absent in gnomAD).
  • PM3 (in trans with P for recessive).
  • PM4 (protein length change).
  • PM5 (novel missense at same codon).
  • PP1 (cosegregation).
  • PP2 (missense in gene with few benign).
  • PP3 (computational tools predict damaging).
  • PP4 (highly specific phenotype).
  • Benign evidence: BA1 (MAF > 5%).
  • BS1 (MAF > expected).
  • BS2 (observed in healthy adult).
  • BS3 (functional benign). BP1-7 (various). Combination rules: P: 1 PVS1 + > =1 PS/PM/PP, or > =2 PS, or 1 PS + > =3 PM, or 1 PS + 2 PM + > =2 PP, or > =3 PM + > =2 PP. VUS: Insufficient/conflicting evidence.
  • Up to 30% of WES findings.
  • May be reclassified.
  • Recontact policy critical. Splice prediction: SpliceAI (deep learning), MaxEntScan.
  • Population databases: gnomAD (~76k genomes, ~126k exomes).
  • ClinVar, LOVD, HGMD, ClinGen.
  • ClinGen gene-disease validity: Definitive, strong, moderate, limited, disputed, refuted.
Prenatal Genetics and Newborn Screening
  • NIPT: Cell-free fetal DNA from maternal blood, > 10 weeks.
  • Detection > 99% T21, ~97% T18, ~92% T13.
  • Also sex aneuploidies, selected microdeletions (22q11. 2, 1p36, Angelman, Prader-Willi, Cri-du-chat).
  • Screening test only - confirm with CVS/amnio.
  • CVS: 10+0 to 13+6 weeks.
  • Transcervical or transabdominal.
  • Miscarriage risk ~0. 2%.
  • Confined placental mosaicism risk ~1%.
  • Amniocentesis: 15+0 to 20+6 weeks.
  • Miscarriage risk ~0. 1-0. 2%.
  • Preferred after 15 weeks. PGT: IVF embryo biopsy day 5/6 (trophectoderm).
  • PGT-M (monogenic), PGT-A (aneuploidy), PGT-SR (structural).
  • Requires probe development for PGT-M. Carrier screening: ACOG recommends CF (pan-ethnic), SMA (pan-ethnic), hemoglobinopathies (ethnic), fragile X (if FH).
  • Expanded carrier screening (274+ genes). AJ panel: Tay-Sachs, Canavan, familial dysautonomia, Bloom, Fanconi C, Niemann-Pick A, mucolipidosis IV.
  • Newborn screening (NBS): Dried blood spot 24-48h.
  • RUSP: 35+ core conditions (PKU, MSUD, MCAD, GA1, CH, CAH, SCD, CF, hearing loss, critical CHD). Tandem MS.
  • Molecular confirmatory testing (CFTR, ACADM).
  • DTC testing: 23andMe FDA-authorized for limited BRCA1/2 AJ variants, MUTYH, CF, Bloom, G6PD, Factor XI, HH.
  • Clinical confirmation required. Not medical grade.
Family Pedigree and Bayesian Risk
  • Pedigree symbols: Square (male), circle (female), filled (affected), diagonal (deceased), arrow (proband).
  • Consanguinity: double line.
  • Bayesian calculation: Prior x conditional = joint, then normalize.
  • Refines risk with incomplete penetrance or test results. Example: BRCA1/2, unaffected 45yo woman, affected mother/sister (known familial mutation).
  • Prior: 50% inherited mutation (AD).
  • Conditional: unaffected at 45.
  • BRCA1 penetrance by 45 ~45%.
  • Conditional no phenotype given mutation = 0. 55.
  • Conditional no phenotype without mutation = ~1.
  • Joint mutation = 0. 5 x 0. 55 = 0. 275.
  • Joint no mutation = 0. 5 x 1 = 0. 5.
  • Posterior = 0. 275/(0. 275+0. 5) = 0. 355 (35. 5%).
  • Counselling framework: Pre-test: purpose, outcomes (positive/negative/VUS/incidental), family implications, GINA.
  • Post-test: results, medical management, family communication, psychological support, reproductive options.
High-Yield Pearls
  • CMA: first-line for DD/ID, autism, MCA. Yield 15-20% vs karyotype ~3%. Detects CNVs > 50kb.
  • NIPT: screening (not diagnostic) for T21/18/13, sex aneuploidies. PPV varies by age. Confirm with CVS/amnio.
  • ACMG/AMP: 5 tiers (P, LP, VUS, LB, B). PVS1 + PS1 = P. VUS ~30% of WES findings.
  • Bayesian: prior x conditional = joint, normalize. Critical for incomplete penetrance, negative tests.
  • Newborn screening: MS/MS for metabolic disorders. CF, SCD, CH, PKU, CAH, MCAD.
  • PGT-M requires family-specific probe development. PGT-A reduces miscarriage, improves IVF success.
Red Flags
  • Incidental findings (ACMG v3.0, 81 medically actionable genes): discuss pre-test opt-out options.
  • VUS reclassification: up to 20% may upgrade to P/LP over time. Recontact policy varies. Counsel upfront.
  • Maternal cell contamination in CVS/amnio: requires maternal comparison. Can cause false negative.
  • Confined placental mosaicism in CVS: 1% discrepancy with fetus. Recommend amniocentesis confirmation.
  • DTC raw data: not clinical grade. False positives, incomplete coverage. Confirm in CLIA lab before acting.

6. Cancer Genetics

Oncogenes TSGs DNA Repair Hereditary Syndromes Precision Oncology

Oncogenes, Tumor Suppressors and Two-Hit Hypothesis
  • Oncogenes: Gain-of-function, dominant.
  • Normal proto-oncogenes regulate cell growth/survival.
  • Activated by mutation, amplification, translocation, fusion. Examples: RAS (KRAS/NRAS/HRAS, ~30% of cancers, G12C/D/V, GTPase locked active).
  • MYC (amplified in many cancers).
  • EGFR (TKI-sensitive L858R/exon19 del, resistant T790M/C797S).
  • HER2 (amplified breast/gastric).
  • BRAF V600E (melanoma/colon/thyroid).
  • BCR-ABL (t(9;22) CML).
  • ALK fusions (EML4-ALK NSCLC).
  • NTRK fusions (tumor-agnostic).
  • IDH1/2 (glioma/AML).
  • Tumor suppressor genes (TSGs): Loss-of-function, recessive.
  • Knudson two-hit: both alleles inactivated.
  • First hit germline (hereditary) or somatic. Second hit: LOH, deletion, mutation, promoter hypermethylation. Gatekeeper TSGs: Directly regulate growth (RB1, APC, PTEN, NF1). Caretaker TSGs: Maintain genome stability (BRCA1/2, MSH2/MLH1, ATM, BLM, WRN). Examples: TP53 (Li-Fraumeni, most mutated gene in cancer).
  • RB1 (retinoblastoma, cell cycle).
  • APC (FAP, WNT pathway).
  • BRCA1/2 (HBOC, HR repair). VHL (HIF, RCC).
  • PTEN (Cowden, PI3K/AKT).
  • NF1 (RAS-GAP, neurofibromas).
  • CDKN2A/p16 (melanoma/pancreas).
  • Synthetic lethality: PARP inhibition in BRCA-deficient tumors (SSB repair impaired -> DSB, HR deficient -> cell death).
DNA Repair Pathways and Hereditary Syndromes
  • MMR (Mismatch Repair): Corrects replication errors.
  • MLH1/MSH2/MSH6/PMS2.
  • Defect -> MSI-H, hypermutation. Lynch syndrome: MMR germline mutations.
  • Colon 50-80% (right-sided, synchronous), endometrial 40-60%, ovarian 10-15%, also gastric, small bowel, ureter, biliary, pancreas, brain (Turcot), sebaceous (Muir-Torre).
  • Amsterdam II criteria, Bethesda guidelines.
  • IHC for MMR loss, MSI testing.
  • Aspirin reduces CRC (CAPP2).
  • NER (Nucleotide Excision Repair): Repairs bulky DNA adducts, UV dimers. XP proteins.
  • Defect -> xeroderma pigmentosum (1000x skin cancer, neurologic).
  • Cockayne syndrome (photosensitivity, growth failure, no increased cancer).
  • Trichothiodystrophy (brittle hair, ichthyosis).
  • HR (Homologous Recombination): Error-free DSB repair.
  • BRCA1/2, PALB2, RAD51, ATM, ATR, NBS1, MRE11. HBOC: BRCA1 (45-65% breast, 15-40% ovarian, triple-negative).
  • BRCA2 (45-55% breast, 10-20% ovarian, male breast ~7%).
  • PALB2 (~30% breast).
  • RRSO by 35-40, risk-reducing mastectomy, enhanced screening (MRI + mammo). PARP inhibitors.
  • Platinum sensitivity. Li-Fraumeni: TP53.
  • Sarcomas, breast brain, adrenocortical, leukemia, early onset, multiple primaries. Avoid radiation. FAP: APC.
  • Hundreds of polyps by teens, 100% colon cancer by 40.
  • Gardner (osteomas/desmoids/CHRPE). Turcot (brain). Cowden: PTEN.
  • Hamartomas, high breast/thyroid/endometrial, macrocephaly, trichilemmomas. Peutz-Jeghers: STK11/LKB1.
  • Hamartomatous polyps mucocutaneous pigmentation, high GI/breast/ovary/pancreas/cervix. NF1: Neurofibromas, cafe-au-lait, optic gliomas, MPNST, pheochromocytoma. NF2: Schwannomas, meningiomas, ependymomas. TSC1/2: Hamartomas in brain/lung/kidney/skin, SEGA, AML, LAM, epilepsy. VHL: Hemangioblastoma, RCC, pheochromocytoma, PNET. MEN1/2: Parathyroid/pituitary/pancreas (MEN1).
  • MTC/pheochromocytoma/hyperparathyroidism (MEN2, RET). RB1: Retinoblastoma, trilateral. WT1: Wilms tumor. Gorlin/BCNS: PTCH1.
  • Basal cell carcinomas, jaw keratocysts, skeletal.
Somatic Tumor Genomics and Precision Oncology
  • Driver vs passenger: Driver confers selective advantage.
  • Most tumors have 2-10 drivers. TMB: Somatic mutations/Mb.
  • High TMB ( > 10 mut/Mb) -> immunotherapy response.
  • Pembrolizumab approved tumor-agnostic for TMB-H.
  • Mutational signatures (COSMIC): SBS1 (deamination), SBS2/13 (APOBEC), SBS4 (tobacco), SBS7 (UV), SBS10 (POLE), SBS15/20 (MMR deficiency), SBS3 (HRD/BRCA). Chromothripsis: Catastrophic shattering of chromosomes.
  • Common in osteosarcoma. Kataegis: Localized hypermutation (APOBEC).
  • Tumor heterogeneity: Intratumoral, branched evolution, subclonal drivers.
  • Liquid biopsy: ctDNA for early detection, MRD, monitoring, resistance mutations.
  • Guardant360 CDx FoundationOne Liquid CDx.
  • Tumor-agnostic approvals: Pembrolizumab (MSI-H, TMB-H).
  • Larotrectinib/entrectinib (NTRK fusions). Dostarlimab (dMMR).
  • Selpercatinib (RET). Immunogenomics: Neoantigens, TILs, PD-L1, interferon gamma signature.
  • Whole genome doubling: Common (30-50%), prognostic and therapeutic implications.
High-Yield Pearls
  • Knudson two-hit: RB1 paradigm. Hereditary = bilateral, earlier onset. LOH = second hit.
  • Lynch: MSI-H, IHC loss MLH1/MSH2/MSH6/PMS2. Right colon, endometrial. Aspirin reduces CRC.
  • BRCA1/2: HBOC, PARP inhibitors, platinum. BRCA1 = triple-negative. BRCA2 = male breast.
  • TMB-H = immunotherapy. > 10 mut/Mb. POLE = ultra-hypermutated, good prognosis.
  • PARP inhibitors: synthetic lethality with BRCA/HRD. Beyond BRCA: PALB2, RAD51C/D.
  • Tumor-agnostic: MSI-H, NTRK fusions, TMB-H (pembrolizumab). RET (selpercatinib). NTRK (larotrectinib).
Red Flags
  • Triple-negative breast cancer < 60: BRCA1/2 testing. Also < 46y any breast, bilateral/male, ovarian, FH.
  • Lynch: universal tumor screening (IHC/MSI) on all newly diagnosed CRC/endometrial.
  • Li-Fraumeni: avoid radiation. Consider total body MRI surveillance.
  • VHL: annual abdominal MRI, ophthalmology, audiology, BP, metanephrines.
  • ctDNA resistance (EGFR T790M, KRAS G12C resistance): repeat biopsy or liquid biopsy.

7. Pharmacogenetics

CYP450 TPMT DPYD UGT1A1 HLA Warfarin Targeted Therapy

Cytochrome P450 Variants
  • CYP2D6: Highly polymorphic, > 100 star alleles.
  • Metabolizes ~25% of drugs (codeine, tramadol, tamoxifen, TCAs, SSRIs, beta-blockers, antipsychotics). Phenotypes: PM (~7-10% Europeans, ~2% Asians), IM, NM, UM (~1-2% Europeans, up to 30% Ethiopian/Saudi). Codeine: Prodrug activated by CYP2D6 to morphine.
  • UM -> respiratory depression.
  • FDA black box: contraindicated children Tamoxifen: Requires CYP2D6 for endoxifen.
  • PM -> reduced efficacy -> higher recurrence. TCAs: PM -> toxicity (QT prolongation).
  • UM -> no efficacy. CYP2C19: Clopidogrel (prodrug).
  • PM (~2-5% Europeans, ~15% Asians) -> reduced activation -> stent thrombosis/MI. FDA black box.
  • Alternative: prasugrel/ticagrelor. PPIs: PM -> higher efficacy.
  • Citalopram/escitalopram: PM -> QT risk (max 20mg). CYP2C9: Warfarin (S-warfarin).
  • PM (*2/*3) -> reduced clearance, bleeding risk.
  • Reduced starting dose. CYP3A4/5: Most abundant CYP.
  • Tacrolimus dosing based on CYP3A5 (expressor vs non-expressor). CYP2B6: Efavirenz PM -> CNS toxicity. CYP4F2: Warfarin, V433M increases dose requirement.
TPMT, DPYD, UGT1A1, G6PD
  • TPMT: Thiopurine metabolism (azathioprine, 6-MP, thioguanine).
  • PM (1: 300, TPMT*2/*3A/*3B/*3C) -> severe myelosuppression.
  • Heterozygotes (10%) -> dose reduce 30-50%. Pre-test standard. NUDT15: Additional risk in Asians (p.
  • Arg139Cys, ~10-15%). DPYD: Rate-limiting enzyme for 5-FU catabolism.
  • Reduced function (*2A, c. 2846A > T, c. 1679T > G, HapB3) -> severe toxicity (mucositis, diarrhea, neutropenia, HFS, death). 3-5% population carriers.
  • Dose reduce 50% for heterozygotes, avoid for homozygotes.
  • Pre-treatment uracil screening. UGT1A1: Glucuronidates bilirubin and drugs.
  • UGT1A1*28 (Gilbert, ~10% homozygotes). Irinotecan: SN-38 active metabolite. *28 -> increased SN-38 -> severe diarrhea/neutropenia.
  • FDA label: reduce dose. G6PD: X-linked, protects RBCs from oxidative stress. Class I-V.
  • African variant G6PD A- (~10-15% AA men, Class III).
  • Triggers: dapsone, primaquine, sulfonamides, nitrofurantoin, rasburicase, fava beans, infections.
  • Hemolysis, jaundice, dark urine.
  • Screen before primaquine. ALDH2: Asian variant (*2, ~40% East Asians) -> flushing, nausea, increased esophageal cancer risk.
HLA-Associated Hypersensitivity
  • HLA-B*5701: Abacavir hypersensitivity (fever, rash, GI/respiratory, hypotension, death on rechallenge).
  • Mandatory screening.
  • Positive = never use.
  • Prevalence: 5-8% Europeans, ~1% African, HLA-B*1502: Carbamazepine SJS/TEN in Asians.
  • Screen in at-risk (Han Chinese, Thai, Malay, Indonesian, Filipino, Vietnamese).
  • Avoid carbamazepine (also oxcarbazepine, phenytoin, lamotrigine; cross-reactivity). HLA-B*5801: Allopurinol SJS/TEN in Han Chinese, African American, European.
  • Screen high-risk.
  • Alternative: febuxostat. HLA-A*3101: Carbamazepine hypersensitivity (MPE, DRESS, SJS/TEN) in Europeans/Japanese. Mechanism: Abacavir binds HLA-B*57:01 F pocket, alters peptide repertoire, triggers CD8+ T-cell response. Not dose-dependent. CPIC levels: Mandatory (abacavir), strong (carbamazepine), moderate (allopurinol).
  • One-time test integration into EHR.
Warfarin Dosing and Drug Transporters
  • Warfarin: S-warfarin (active) by CYP2C9. Inhibits VKORC1.
  • CYP2C9 reduced (*2/*3): 25-75% lower dose.
  • VKORC1 (-1639G > A): AA -> ~50% lower dose. GG ~2x dose.
  • Frequency: ~40% East Asian, ~15% European, ~5% African.
  • CYP4F2 V433M: ~10% higher dose. Algorithm (IWPC): Includes CYP2C9, VKORC1, age, height, weight, race, inducers, amiodarone.
  • FDA PGx dosing tables. SLCO1B1 (OATP1B1): Hepatic statin uptake. *5 (c. 521T > C) -> increased simvastatin -> myopathy (OR 4. 5 heterozygote, 17 homozygote).
  • CPIC: avoid simvastatin 80mg in heterozygotes.
  • Atorvastatin/rosuvastatin also affected. ABCB1 (P-gp): Digoxin, tacrolimus, cyclosporine. C3435T variant.
  • Clinical utility limited. CFTR modulators: Precision therapy for CF. Ivacaftor (G551D).
  • Lumacaftor/ivacaftor (F508del).
  • Elexacaftor/tezacaftor/ivacaftor/Trikafta (F508del, ~90% of CF).
Targeted Therapy in Cancer
  • EGFR: NSCLC L858R/ex19del -> osimertinib (first-line).
  • T790M -> osimertinib.
  • C797S -> pan-resistance. BRAF V600E: Melanoma, NSCLC, CRC, thyroid, HCL.
  • Dabrafenib + trametinib (first-line).
  • Encorafenib + binimetinib. BCR-ABL: CML, ALL.
  • Imatinib (first-line).
  • Dasatinib, nilotinib, bosutinib, ponatinib.
  • T315I: ponatinib/asciminib. HER2: Breast, gastric.
  • Trastuzumab, pertuzumab T-DM1, T-DXd, lapatinib, neratinib, tucatinib. ALK: NSCLC (~5%).
  • Crizotinib, alectinib brigatinib, ceritinib, lorlatinib. NTRK: Tumor-agnostic.
  • Larotrectinib, entrectinib (high CNS). IDH1/2: AML, glioma, cholangiocarcinoma.
  • Ivosidenib, enasidenib vorasidenib (glioma). RET: NSCLC, medullary thyroid.
  • Selpercatinib, pralsetinib. METex14: NSCLC.
  • Capmatinib, tepotinib. FGFR: Bladder (FGFR3), cholangiocarcinoma (FGFR2).
  • Erdafitinib, pemigatinib, infigratinib. HRD: PARPi (olaparib, niraparib, rucaparib, talazoparib).
  • BRCA+ breast/ovarian/pancreas/prostate. Immune checkpoint: PD-L1, MSI-H, TMB-H.
  • Pembrolizumab, nivolumab, atezolizumab, durvalumab, ipilimumab. Gene fusions: BCR-ABL, EML4-ALK, TMPRSS2-ERG (prostate), EWSR1-FLI1 (Ewing), SS18-SSX (synovial), FUS-DDIT3 (myxoid liposarcoma), PAX3/7-FOXO1 (alveolar RMS).
  • RNA-seq for detection.
High-Yield Pearls
  • CYP2D6 UM: codeine -> respiratory depression (FDA black box). PM: tamoxifen -> reduced efficacy.
  • TPMT/NUDT15: thiopurine toxicity. Pre-test required. PM: 90% dose reduction or avoid.
  • DPYD: 5-FU/capecitabine toxicity. 3-5% carriers. Dose reduce 50% if heterozygous.
  • UGT1A1*28: irinotecan toxicity. Gilbert syndrome. Reduce dose.
  • HLA-B*5701: abacavir HSR. Mandatory. HLA-B*1502: carbamazepine SJS.
  • Warfarin: CYP2C9 + VKORC1 + CYP4F2. IWPC algorithm. SLCO1B1: simvastatin myopathy.
Red Flags
  • G6PD: acute hemolysis triggered by oxidant drugs (dapsone, primaquine, sulfonamides, nitrofurantoin). Screen before primaquine.
  • HLA-B*5801 + allopurinol: SJS/TEN. Screen Han Chinese, African American.
  • EGFR T790M resistance to 1st/2nd-gen TKIs. Switch to osimertinib. C797S = pan-resistance.
  • BCR-ABL T315I: resistant to imatinib/dasatinib/nilotinib. Use ponatinib/asciminib.
  • CPIC guidelines for gene-drug pairs. Pre-emptive PGx panel reduces adverse events.

8. Developmental Genetics

Morphogenesis NTD Facial Clefts CHD RASopathies Skeletal Teratogens TORCH

Morphogenesis and Neural Crest
  • Key periods: Embryonic (3-8 weeks): organogenesis, most sensitive to teratogens.
  • Fetal (9 weeks-term): growth/maturation. Neural crest: Multipotent cells from neural tube.
  • Derivatives: peripheral NS, melanocytes, adrenal medulla, craniofacial mesenchyme, cardiac outflow tract, parafollicular C-cells, Schwann cells.
  • Gene regulatory networks: HOX (anterior-posterior patterning, clustered 4 groups A-D, collinear).
  • PAX (CNS, eye, kidney).
  • SOX (sex determination, neural, chondrogenesis).
  • SHH (ventral neural tube, limb, craniofacial).
  • WNT (β-catenin canonical, planar cell polarity).
  • FGF (patterning, limb, craniofacial).
  • TGF-β/BMP (DV patterning, bone, left-right via NODAL).
  • NOTCH (lateral inhibition, neurogenesis, somitogenesis).
  • Left-right asymmetry: NODAL/LEFTY/PITX2.
  • Defects -> situs inversus, heterotaxy (Ivemark).
  • Kartagener (primary ciliary dyskinesia, DNAI1/DNAH5, 50% situs inversus). Somite formation: Segmentation clock (NOTCH/WNT/FGF).
  • Sclerotome (vertebrae), dermomyotome (muscle/dermis).
  • Defects -> Klippel-Feil, spondylocostal dysostosis.
Neural Tube Defects and Folate
  • Neurulation: Primary (days 18-26, brain/spinal cord to S2).
  • Secondary (days 26-28, sacral cord).
  • NTDs from failed closure. Types: Anencephaly (anterior neuropore, lethal).
  • Spina bifida: myelomeningocele (cord + meninges), meningocele (meninges only), occulta (bony defect, asymptomatic).
  • Encephalocele (skull protrusion). Etiology: Multifactorial.
  • MTHFR C677T folate deficiency, valproate (10x), carbamazepine, methotrexate. Prevention: Folic acid 0. 4-0. 8mg daily all women.
  • High-risk: 4-5mg daily, 3mo preconception. Screening: MSAFP 15-20wk (elevated 2. 5x open NTDs). US anatomy scan.
  • Amniotic AFP + AChE.
  • Recurrence: 2-5% after one affected.
  • Treatment: Surgical closure 24-48h, VP shunt, multidisciplinary.
  • Fetal surgery (MOMS trial: prenatal closure reduces shunting, improves motor).
  • Syndromic NTDs: Meckel-Gruber (encephalocele, polydactyly, renal cysts, lethal), Walker-Warburg (cobblestone lissencephaly), Jarcho-Levin (spondylocostal).
Craniofacial Anomalies and Skeletal Dysplasias
  • Cleft lip/palate: Multifactorial 1:1000.
  • Fusion failure 4-7wk (CL) / 8-12wk (CP). Recurrence ~4%. Syndromic: Van der Woude (IRF6, lower lip pits, AD, most common syndromic CL/P).
  • Pierre Robin (micrognathia + glossoptosis + CP, can be isolated or Stickler/22q11. 2).
  • Treacher Collins (TCOF1, malar hypoplasia, micrognathia, coloboma, hearing loss). Craniosynostosis: Sagittal (scaphocephaly), coronal (brachycephaly, FGFR).
  • Apert (FGFR2, coronal + syndactyly).
  • Crouzon (FGFR2/3, exophthalmos, no hands).
  • Pfeiffer (FGFR1/2, broad thumbs).
  • Muenke (FGFR3 P250R, hearing loss).
  • Saethre-Chotzen (TWIST1, asymmetric). Achondroplasia: FGFR3 G380R, AD, mostly de novo (advanced paternal age).
  • Rhizomelia, macrocephaly foramen magnum stenosis, spinal stenosis.
  • Vosoritide. OI: COL1A1/A2 (AD, 90%).
  • Blue sclerae hearing loss, dentinogenesis imperfecta, fractures.
  • Type I (mild) to II (lethal). Bisphosphonates. Marfan: FBN1 (AD, ~25% de novo).
  • Ectopia lentis (upward), aortic root aneurysm, arachnodactyly, pectus, scoliosis, dural ectasia. Ghent criteria.
  • Losartan/BB, elective root replacement ( > 50mm). Ehlers-Danlos: Classical (COL5A1/A2, hyperextensible skin, atrophic scars).
  • Hypermobility (hEDS, unknown).
  • Vascular (COL3A1, arterial/bowel/uterine rupture, early death, avoid elective surgery). Stickler: COL2A1 (AD).
  • Pierre Robin myopia/retinal detachment, hearing loss, midface hypoplasia. Loeys-Dietz: TGFBR1/2.
  • Aggressive aortic aneurysm, arterial tortuosity, hypertelorism, bifid uvula.
CHD and RASopathies
  • CHD: ~1% of births. Recurrence 2-5%. Genetic: Trisomy 21 (AVSD), 18 (VSD), 13 (VSD/PDA), Turner (coarctation/bicuspid). TBX5 (Holt-Oram: ASD + thumb anomalies).
  • NKX2-5 (ASD, AV block). GATA4 (ASD/VSD).
  • NOTCH1 (bicuspid AV, LVOT, aortic aneurysm). CHD7 (CHARGE).
  • RASopathies (Noonan syndrome): PTPN11 (50%, SHP2 GOF).
  • SOS1, RAF1 RIT1, KRAS, NRAS, BRAF, MAP2K1/2.
  • Features: webbed neck, pectus, PS (most common CHD), HCM, cryptorchidism, bleeding, mild ID, short stature, lymphatic. AD. LEOPARD: PTPN11/RAF1, lentigines, deafness, HCM. CFC: BRAF, severe ID, ectodermal, HCM. Costello: HRAS G12S, coarse, severe ID, HCM, cancer (rhabdomyosarcoma/bladder). CHARGE: CHD7 (AD, 65% de novo).
  • Coloboma, Heart (conotruncal), Choanal atresia, Retarded growth, Genital hypoplasia, Ear anomalies. VACTERL: Vertebral, Anorectal, Cardiac (VSD), TE fistula, Renal, Limb (radial). At least 3.
Teratogens and TORCH
  • Alcohol/FAS: Leading preventable ID.
  • Microcephaly, short palpebral fissures, smooth philtrum, thin vermillion, ID, CHD. No safe level. Isotretinoin: Highest risk.
  • CNS (hydrocephalus), craniofacial (microtia/anotia), CHD (conotruncal), thymic aplasia. iPledge.
  • Valproate: 10-15% malformations (NTD ~10%, hypospadias, cleft palate, CHD).
  • Neurodevelopmental: reduced IQ, autism 3-5x. Avoid in pregnancy. Warfarin: Embryopathy (nasal hypoplasia, stippled epiphyses). Avoid (use LMWH).
  • ACEi/ARB: 2nd/3rd trimester: fetal renal failure, oligohydramnios, pulmonary hypoplasia, skull defects. Fetotoxic. Maternal PKU: Uncontrolled Phe -> microcephaly, ID, CHD, IUGR.
  • Preconception diet (Phe 120-360).
  • Maternal diabetes: Sacral agenesis (200x), NTD, CHD, macrosomia. Lithium: Ebstein anomaly (1:1000 vs 1:20000). Antiepileptics: Phenytoin (fetal hydantoin: IUGR, microcephaly, ID, cleft palate).
  • Carbamazepine (spina bifida ~1%).
  • Topiramate (cleft lip ~2%). TORCH: Toxoplasma (hydrocephalus, chorioretinitis, intracranial calcifications).
  • Rubella (deafness, cataracts, PDA, IUGR).
  • CMV (most common congenital infection, hearing loss, microcephaly, periventricular calcifications, ID).
  • HSV (vesicular, encephalitis, disseminated).
  • Syphilis (snuffles, saddle nose, Hutchinson teeth, saber shins).
  • Zika (microcephaly, brain calcifications).
  • Parvovirus B19 (hydrops fetalis).
  • Radiation: > 0. 1 Gy: microcephaly, ID, IUGR. Methotrexate: Aminopterin syndrome (cranial dysostosis, limb defects, ID).
High-Yield Pearls
  • NTD: MSAFP screening 15-20wk. Folic acid 0.4mg preconception, 4-5mg high risk. Valproate = 10x NTD.
  • FAS: no safe alcohol. Microcephaly, smooth philtrum, thin vermillion, ID. Leading preventable ID.
  • RASopathies: Noonan (PTPN11, PS, HCM), CFC (BRAF, severe), Costello (HRAS, cancer risk).
  • Marfan: FBN1, ectopia lentis (upward), aortic root aneurysm, arachnodactyly, dural ectasia.
  • Achondroplasia: FGFR3 G380R, advanced paternal age, macrocephaly, rhizomelia, foramen magnum stenosis.
  • Isotretinoin: microtia, CNS, CHD, thymic aplasia. Highly teratogenic. iPledge.
Red Flags
  • Valproate: avoid in pregnancy. High risk NTD and neurodevelopmental impairment.
  • Maternal PKU: uncontrolled Phe -> fetal damage. Preconception diet required.
  • Vascular EDS (COL3A1): arterial rupture. Avoid elective surgery.
  • CHARGE: CHD7. Coloboma, choanal atresia, CHD, ear anomalies, genital hypoplasia, growth/ID.
  • TORCH: CMG most common congenital infection. Sensorineural HL can be late-onset.
  • Maternal diabetes teratogenicity: sacral agenesis most specific. Strict glycemic control.

9. Biochemical Genetics

PKU MSUD UCD GSD Lysosomal Storage Wilson CF Hemochromatosis

Aminoacidopathies and Organic Acidemias
  • PKU: PAH (AR).
  • Phe hydroxylase deficiency -> Phe accumulation.
  • Types: classic, mild, HPA.
  • BH4 cofactor defects. NBS.
  • Clinical: progressive ID (if untreated), microcephaly, seizures, eczema, fair skin, musty odor.
  • Treatment: Phe-restricted diet, Phe-free formula, sapropterin (BH4-responsive ~30%), pegvaliase (PEG-PAL).
  • Maternal PKU: strict preconception diet (Phe 120-360). MSUD: BCKDHA/B (AR).
  • Branched-chain ketoacid dehydrogenase deficiency.
  • Elevated Leu/Ile/Val. MSUD odor.
  • Encephalopathy, cerebral edema. Treatment: BCAA-free formula, thiamine (mild), dialysis (acute), liver transplant. Homocystinuria: CBS (AR). Elevated Met + Hcy.
  • Ectopia lentis (downward/inward), marfanoid, ID, thromboembolism, osteoporosis. Treatment: B6 (50% responsive), betaine, B12/folate, low-Met diet. MMA: MUT/MMAA/BB/CHC/D (AR). Elevated C3.
  • Metabolic acidosis hyperammonemia, encephalopathy, neutropenia, CKD, basal ganglia damage.
  • Treatment: protein restriction, carnitine, B12 (responsive forms), N-carbamylglutamate. Propionic acidemia: PCCA/PCCB (AR). Similar. Tyrosinemia I: FAH (AR).
  • Succinylacetone (pathognomonic).
  • Hepatic failure Fanconi, porphyria-like crisis, HCC.
  • Treatment: nitisinone (NTBC), Tyr-restricted diet, liver transplant.
Urea Cycle Disorders
  • Enzyme defects in ammonia to urea conversion. OTC deficiency: X-linked, most common.
  • Variable in carrier females.
  • CPS1, ASS (citrullinemia), ASL (argininosuccinic aciduria), ARG1 (arginase, milder, spastic diplegia): AR. Clinical: Hyperammonemia (neonatal or later): vomiting, lethargy, encephalopathy, cerebral edema, coma, death.
  • Respiratory alkalosis. Diagnosis: Plasma NH3 (profound > 200-1000+), amino acids (glutamine/alanine elevated, specific pattern), urine orotic acid (high in OTC, low in CPS).
  • Treatment: Acute: stop protein, IV glucose + lipids, Na benzoate/Na phenylacetate IV, arginine (except ARG1), carbamylglutamate (NAGS), hemodialysis.
  • Chronic: protein restriction, NH3 scavengers (Na phenylbutyrate/glycerol phenylbutyrate), arginine/citrulline, essential AA, liver transplant.
Glycogen Storage Diseases
  • GSD I (von Gierke): G6PC (AR). G6Pase deficiency.
  • Severe fasting hypoglycemia, lactic acidosis, hyperuricemia, hyperlipidemia, hepatomegaly, growth failure, bleeding, gout, renal disease, hepatic adenomas (HCC risk).
  • Treatment: raw cornstarch q3-4h, allopurinol. GSD II (Pompe): GAA (AR).
  • Acid alpha-glucosidase deficiency.
  • Infantile: hypotonia, cardiomegaly, macroglossia, death GSD III (Cori): AGL (AR). Debranching enzyme.
  • Milder than I, myopathy, cardiomyopathy. GSD V (McArdle): PYGM (AR).
  • Muscle phosphorylase.
  • Exercise intolerance myoglobinuria, second wind. GSD VI (Hers): PYGL (AR).
  • Mild hypoglycemia hepatomegaly. GSD VII (Tarui): PFKM (AR).
  • No second wind, hemolytic anemia. GSD IX: PHKA2 (mild, ketotic hypoglycemia, improves with age). GSD IV: GBE1 (branching, severe, hepatic failure).
Lysosomal Storage Disorders
  • Gaucher: GBA (AR).
  • Glucocerebrosidase deficiency -> glucocerebroside in macrophages (Gaucher cells).
  • Type 1 (AJ, 1: 15 carrier): hepatosplenomegaly, bone pain/crisis, thrombocytopenia.
  • Type 2 (infantile, neurologic, death Tay-Sachs: HEXA (AR).
  • Hex A deficiency -> GM2 ganglioside.
  • Cherry-red spot neurodegeneration, blindness, seizures, death Sandhoff: HEXB (AR). Both Hex A+B. Niemann-Pick A/B: SMPD1 (AR).
  • Sphingomyelinase deficiency.
  • Type A: infantile, cherry-red spot (50%), neurodegeneration, death NPC: NPC1/2 (AR).
  • Cholesterol trafficking.
  • Vertical supranuclear gaze palsy, ataxia, dystonia, dementia, cataplexy, hepatosplenomegaly. Miglustat. Fabry: GLA (X-linked).
  • Alpha-Gal A deficiency -> Gb3.
  • Classic male: acroparesthesias, angiokeratomas, cornea verticillata, hypohidrosis, renal failure, HCM, stroke. Females variable.
  • Treatment: ERT (agalsidase alfa/beta), migalastat (chaperone for amenable missense). Hurler (MPS I): IDUA (AR).
  • Alpha-L-iduronidase deficiency.
  • Coarse facies corneal clouding, dysostosis multiplex, ID, hepatosplenomegaly, cardiac valves, gibbus.
  • ERT (laronidase), HSCT ( Hunter (MPS II): IDS (X-linked).
  • Iduronate sulfatase.
  • No corneal clouding. ERT (idursulfase).
  • Metachromatic leukodystrophy: ARSA (AR).
  • Neurologic, ataxia, spasticity, neuropathy.
  • ERT intrathecal HSCT. Krabbe: GALC (AR).
  • Infantile: irritability, hypertonia, opsithotonos, decline.
  • HSCT before symptoms.
Peroxisomal, Wilson, Alpha-1, Hemochromatosis, CF
  • Zellweger: PEX genes (AR).
  • Peroxisome biogenesis.
  • Hypotonia, seizures dysmorphic (high forehead), hepatomegaly, renal cysts, chondrodysplasia punctata, elevated VLCFA. Death X-ALD: ABCD1 (X). VLCFA accumulation.
  • Childhood cerebral ALD (rapid demyelination, vision loss, behavioral, adrenal insufficiency).
  • Adrenomyeloneuropathy (adult, spastic paraparesis). NBS available.
  • Treatment: HSCT early, gene therapy (eli-cel/Skysona).
  • Lorenzo oil not effective for cerebral. Wilson: ATP7B (AR).
  • Copper accumulation.
  • Hepatic (hepatitis, cirrhosis, fulminant + Coombs-negative hemolysis), neurologic (tremor, dysarthria, dystonia), Kayser-Fleischer rings (copper in Descemet membrane, pathognomonic).
  • Diagnosis: low ceruloplasmin, elevated 24h urinary Cu, K-F rings on slit lamp, liver Cu quantitation.
  • Treatment: chelation (penicillamine, trientine), zinc (maintenance), liver transplant.
  • Alpha-1 antitrypsin deficiency: SERPINA1 (AR).
  • PI*ZZ (Glu342Lys, misfolding, liver accumulation, ~1:2000).
  • Emphysema (panacinar, lower lobe, early onset), cirrhosis, hepatoma, panniculitis. Diagnosis: AAT level, isoelectric focusing (phenotype).
  • Treatment: augmentation therapy (IV AAT), liver transplant, LTOT. Hemochromatosis: HFE (AR).
  • C282Y/C282Y (most common), C282Y/H63D (compound).
  • Iron overload -> cirrhosis, DM, bronze skin, hypogonadism, cardiomyopathy, arthritis, HCC.
  • Diagnosis: ferritin, TSAT, HFE genotyping.
  • Treatment: phlebotomy to ferritin 50-100. Cystic fibrosis: CFTR (AR).
  • F508del most common (70% in Europeans).
  • Defective Cl- channel.
  • Meconium ileus pancreatic insufficiency (fat malabsorption, CF-related DM), recurrent respiratory infections (bronchiectasis, Pseudomonas, ABPA), male infertility (CBAVD), sinusitis, nasal polyps, hepatobiliary disease.
  • Sweat Cl- > 60 mmol/L (diagnostic). NBS (IRT/DNA).
  • CFTR modulator therapy: ivacaftor (G551D), tezacaftor/ivacaftor, lumacaftor/ivacaftor (F508del), elexacaftor/tezacaftor/ivacaftor/Trikafta (F508del, most effective, ~90% of CF).
  • Gene therapy in trials. Carrier screening: ACOG pan-ethnic.
High-Yield Pearls
  • PKU: NBS, Phe-restricted diet, maternal PKU embryopathy preventable. Sapropterin, pegvaliase.
  • UCD: hyperammonemia + respiratory alkalosis. OTC deficiency X-linked. Na benzoate/phenylacetate, dialysis.
  • Gaucher: AJ founder, ERT/SRT. Types: 1 (non-neuro), 2 (infantile lethal), 3 (chronic neuro).
  • Fabry: X-linked. Acroparesthesias, angiokeratomas, cornea verticillata, renal/cardiac/stroke. ERT/migalastat.
  • CF: F508del most common. Sweat test. CFTR modulators (Trikafta for 90%). Carrier screening.
  • Wilson: Kayser-Fleischer rings, low ceruloplasmin, penicillamine, zinc. Fulminant + hemolysis.
Red Flags
  • MMA/PA: metabolic crisis in neonate. Acute management: protein off, high-calorie, carnitine, N-carbamylglutamate, dialysis.
  • OTC deficiency in heterozygote females: can present postpartum with hyperammonemia -> encephalopathy.
  • Pompe infantile: cardiomegaly on CXR, GAA activity, ERT urgently. NBS for early diagnosis.
  • X-ALD: newborn screening available. Early HSCT for cerebral form. Addison disease screening.
  • Hemochromatosis: phlebotomy to ferritin 50-100. Screen first-degree relatives. HCC risk even after iron depletion if cirrhosis.

10. Epigenetics

DNA Methylation Histone Modifications Imprinting X-Inactivation RNA Genetics Environmental Epigenetics

DNA Methylation and Histone Modifications
  • DNA methylation: Addition of methyl group to cytosine in CpG dinucleotides.
  • CpG islands (promoters, mostly unmethylated in active genes).
  • CpG shores (regions near islands, tissue-specific methylation).
  • DNMT3A/3B (de novo methylation, establishes patterns in development).
  • DNMT1 (maintenance methylation, copies patterns after replication).
  • TET1/2/3 (demethylation, oxidized 5mC to 5hmC/5fC/5caC).
  • Methylation at promoters -> transcriptional silencing (recruit MeCP2, MBD proteins, HDACs).
  • Global hypomethylation in cancer (genome instability).
  • Histone modifications: Histone code: HATs (acetylation, active, H3K9ac, H3K27ac).
  • HDACs (deacetylation, repressive).
  • H3K4me3 (active promoters, Set1/MLL).
  • H3K9me3 (heterochromatin, SUV39H).
  • H3K27me3 (Polycomb repression, EZH2/PRC2).
  • H3K36me3 (elongation, SETD2).
  • H3K79me2 (active, DOT1L).
  • H4K20me3 (heterochromatin).
  • Crosstalk: DNA methylation and H3K9me3 reinforce heterochromatin.
  • PRC2 (H3K27me3) and DNMTs cooperate.
  • Chromatin remodeling complexes: SWI/SNF (BAF, ATP-dependent nucleosome mobilization).
  • Mutations in SMARCB1 (rhabdoid tumors), ARID1A (ovarian clear cell), SMARCA4 (lung). ISWI, CHD, INO80.
Genomic Imprinting and X-Inactivation
  • Imprinting: ~150 imprinted genes expressed from only one parental allele.
  • ICRs (imprinting control centers) are differentially methylated regions (DMRs).
  • Established in germline, maintained after fertilization, erased in primordial germ cells.
  • Prader-Willi: 15q11-q13 paternal deficiency (SNRPN, NDN, MAGEL2, MKRN3). Maternal UPD 15.
  • Angelman: 15q11-q13 maternal UBE3A loss. Paternal UPD 15.
  • Beckwith-Wiedemann: 11p15. 5.
  • ICR1 hypermethylation (IGF2 biallelic, H19 silenced).
  • ICR2 hypomethylation (KCNQ1OT1 active, CDKN1C silenced).
  • Overgrowth, omphalocele macroglossia, Wilms tumor.
  • Russell-Silver: 11p15. 5 ICR1 hypomethylation (IGF2 silenced, H19 active).
  • Maternal UPD 7 (10%).
  • IUGR, triangular face, asymmetry.
  • Transient neonatal diabetes (TNDM): 6q24 paternal UPD.
  • X-inactivation (Lyon hypothesis): Early embryonic random inactivation of one X.
  • XIST lncRNA (X inactive specific transcript) coats X chromosome, recruits PRC2 (H3K27me3).
  • TSIX antisense regulates XIST.
  • Escape from X-inactivation: ~15% of X-linked genes (some biallelic expression, variable).
  • Skewed X-inactivation: non-random distribution.
  • Can occur by chance, selection, or mutation.
  • XIST mechanism: lncRNA, silences X in cis.
  • H3K27me3, macroH2A DNA methylation, late replication.
  • X-linked disease in females: Skewed inactivation can cause expression (Rett, Fabry, DMD carriers with symptoms).
RNA Genetics: miRNA, siRNA, lncRNA
  • miRNA biogenesis: RNA Pol II transcribes pri-miRNA (hairpin).
  • Drosha/DGCR8 (Microprocessor) cleaves to pre-miRNA (~70nt).
  • Exportin-5 exports to cytoplasm.
  • Dicer cleaves to ~22nt duplex.
  • RISC loading (Ago2).
  • Guide strand binds target mRNA 3'UTR (seed region, 2-7nt).
  • Translational repression and/or mRNA decay. Functions: Development, differentiation, apoptosis, metabolism, cancer (tumor suppressor miR-15/16, oncomiR miR-21). Therapeutic: Anti-miR (antagomirs), miRNA mimics. siRNA: Exogenous (viral, experimental) or endogenous (from long dsRNA).
  • Perfect complementarity Ago2 cleaves target mRNA. RNAi pathway.
  • Therapeutic: Patisiran (TTR amyloidosis, siRNA), inclisiran (PCSK9, siRNA). lncRNA: > 200nt.
  • XIST (X-inactivation).
  • HOTAIR (HOX, PRC2 recruitment, cancer).
  • MALAT1 (nuclear, splicing, metastasis).
  • NEAT1 (nuclear paraspeckles).
  • H19 (imprinted, oncofetal).
  • FMR4 (CGG repeat lncRNA in Fragile X). piRNA: 24-32nt, Piwi proteins, transposon silencing in germline.
  • Circular RNA (circRNA): Back-splicing, miRNA sponges, regulation. Epitranscriptomics: RNA modifications: N6-methyladenosine (m6A), 5-methylcytosine (m5C), pseudouridine.
  • Writers (METTL3/METTL14), erasers (FTO, ALKBH5), readers (YTHDF1-3).
  • Roles in RNA stability, splicing, translation, cancer.
Epigenetic Disorders: Rett, ICF, ATR-X, Rubinstein-Taybi, Sotos
  • Rett syndrome: MECP2 (X-linked dominant, male lethal).
  • MeCP2 binds methylated DNA, recruits HDACs, represses transcription.
  • Clinical: normal development 6-18mo, then regression, loss of speech/hand use, stereotypical hand wringing, ataxia, seizures, microcephaly, breathing abnormalities (hyperventilation, apnea).
  • MECP2 duplication syndrome (males): severe ID, hypotonia, spasticity, seizures, recurrent infections.
  • ICF syndrome (Immunodeficiency, Centromeric instability, Facial anomalies): DNMT3B (AR).
  • Hypomethylation of pericentromeric repeats.
  • Combined immunodeficiency facial dysmorphism, intellectual disability. ATR-X syndrome: ATRX (X-linked).
  • Alpha-thalassemia + mental retardation, X-linked.
  • Facial dysmorphism microcephaly, genital abnormalities, hemoglobin H inclusions.
  • ATRX protein is chromatin remodeler, deposits H3. 3 at telomeres and pericentromeric repeats.
  • Rubinstein-Taybi syndrome: CREBBP (RTS1, ~50%) or EP300 (RTS2, ~3%) (AD). HAT activity.
  • Broad thumbs/great toes, arched eyebrows, low-set ears, beaked nose, severe ID, growth retardation, keloids, increased cancer risk.
  • Sotos syndrome (cerebral gigantism): NSD1 (AD, 90% de novo).
  • Histone methyltransferase.
  • Overgrowth, macrocephaly advanced bone age, coarse facies (downslanting palpebral fissures, pointed chin, frontal bossing), ID, seizures, scoliosis. Weaver syndrome: EZH2 (AD).
  • Overgrowth, macrocephaly intellectual disability, camptodactyly. Epigenetic clock: DNA methylation age (Horvath clock, 353 CpGs).
  • Predicts chronological age, age acceleration.
  • Accelerated aging in obesity, HIV, Down syndrome, Werner.
  • Slower in centenarians.
  • Cancer cells: hypomethylated globally + hypermethylated at tumor suppressor promoters.
Environmental Epigenetics
  • Developmental origins of health and disease (DOHaD): Early life environment programs adult disease risk via epigenetic changes.
  • Dutch Hunger Winter (1944-45): Prenatal exposure to famine -> reduced birth weight, increased obesity, T2D, CVD, schizophrenia in adulthood.
  • Associated with altered DNA methylation at imprinted genes (IGF2) and metabolic genes (POMC, INS, LPL).
  • Maternal diet and supplements: Methyl donors (folate, B12, choline, methionine) influence epigenome.
  • Folic acid reduces NTDs partly via methylation.
  • Endocrine disruptors: BPA, phthalates, DES -> altered methylation, metabolic effects, transgenerational inheritance in animal models. Tobacco smoke: In utero -> altered methylation at AHRR, CYP1A1, GFI1.
  • Persistent into adulthood.
  • Nutrition and aging: Caloric restriction extends lifespan in many organisms, alters epigenetic patterns.
  • Resveratrol (SIRT1 activator, HDAC).
  • Exercise and epigenetics: Acute exercise alters methylation in muscle (metabolic genes).
  • Regular exercise changes global methylation patterns.
  • Stress and epigenetics: Early life stress -> methylation changes in NR3C1 (glucocorticoid receptor), FKBP5, SLC6A4 (serotonin transporter).
  • HPA axis programming.
  • Transgenerational epigenetic inheritance: Epigenetic marks passed to offspring.
  • Controversial in humans.
  • Clear in plants, C. elegans, mice (e. g. , agouti viable yellow allele, axin fused).
  • Possible examples: �verkalix (Swedish) studies linking grandparental nutrition to grandchild mortality.
High-Yield Pearls
  • DNA methylation: CpG islands, DNMT3A/3B (de novo), DNMT1 (maintenance). TET oxidizes 5mC to 5hmC.
  • Histone marks: H3K4me3 (active promoters), H3K27me3 (Polycomb), H3K9me3 (heterochromatin), H3K36me3 (elongation).
  • Imprinting: PWS (paternal), AS (maternal, UBE3A). BWS (11p15 ICR1 hyper, ICR2 hypo). SRS (11p15 hypo).
  • X-inactivation: XIST lncRNA coats X, PRC2 deposits H3K27me3. ~15% of X genes escape.
  • Rett: MECP2 (XLD). Regression 6-18mo, hand wringing, seizures, microcephaly, breathing abnormalities.
  • Epigenetic clock: Horvath 353 CpGs, DNA methylation age. Accelerated in obesity, HIV, Down syndrome.
Red Flags
  • Rett: MECP2 testing indicated in girls with regression, hand stereotypies, seizures, microcephaly.
  • BWS: 11p15 methylation testing. Cancer surveillance (AFP q3mo < 4yr, renal US). Hemihypertrophy risk.
  • Rubinstein-Taybi: CREBBP/EP300. Annual cardiac echo, renal US, cancer screening.
  • EZH2 (Weaver): overgrowth + ID + macrocephaly. Sotos (NSD1): advanced bone age, coarse facies, overgrowth.
  • DNMT3A mutations: clonal hematopoiesis, AML risk. TET2: same.
  • Environmental epigenetics: DOHaD paradigm. Early life nutrition, stress, toxins -> adult disease risk.

11. Precision Medicine

Newborn Screening Carrier Screening Cancer Screening NIPT PRS Gene Therapy Genetic Counseling

Population Screening and Implementation
  • Newborn screening (NBS): RUSP: 35+ core conditions.
  • Dried blood spot 24-48h.
  • MS/MS for metabolic.
  • Pulse ox for critical CHD. Hearing screen.
  • CF, SCD CH, CAH, PKU, MCAD, GA1, VLCAD.
  • Molecular second-tier for CFTR, ACADM. Carrier screening: ACOG pan-ethnic: CF, SMA, hemoglobinopathies. Ethnic-based: AJ (Tay-Sachs, Canavan, familial dysautonomia, Bloom, Fanconi C, Niemann-Pick A, mucolipidosis IV).
  • Expanded carrier screening (274-600+ genes): higher detection rate, more VUS, counseling implications.
  • Preconception ideal. Cascade screening: When a pathogenic variant identified in proband, offer testing to at-risk relatives (first-degree -> second-degree).
  • Critical for Lynch, HBOC, FH, hemochromatosis.
  • Increased detection rate, cost-effective.
  • NIPT in population screening: Cell-free DNA for trisomies 21/18/13. NGS-based.
  • Implementation in public health settings (UK, Belgium, Netherlands).
  • PPV varies: > 90% for T21, ~60-80% for T18/13, lower for sex aneuploidies.
  • Polygenic risk scores (PRS): Aggregating thousands of small-effect variants.
  • Clinical utility emerging: breast cancer (combined with mammography risk stratification), CAD (reclassify intermediate risk), T2D.
  • Implementation challenges: population transferability (Euro-centric bias), clinical actionability, education of providers/patients, regulation.
  • Precision medicine and EHR: Integration of genomic data (PGx, carrier, diagnostic) into electronic health records.
  • Clinical decision support (CDS) alerts for PGx (CPIC guidelines).
  • Pre-emptive PGx panel (e. g. , rightPGx, PG4KDS) before prescribing.
  • CPIC guidelines: 100+ gene-drug pairs with dosing recommendations.
  • Level A (CPIC, DPWG): strong recommendation.
  • Implementation in health systems: pilot studies, pharmacist-led, EHR alerts.
Liquid Biopsy and ctDNA
  • ctDNA: Cell-free tumor DNA in blood.
  • Shed from apoptotic/necrotic tumor cells.
  • Half-life ~30-120min.
  • Detection methods: digital PCR (ddPCR, BEAMing for known mutations), NGS (targeted panels, WES, WGS for comprehensive profiling). Applications: Molecular profiling when tissue inadequate (Guardant360, FoundationOne Liquid).
  • MRD detection (signatera, bespoke panels).
  • Treatment response monitoring (ctDNA levels correlate with tumor burden).
  • Resistance mutation detection (EGFR T790M, KRAS G12C resistance).
  • Early cancer detection (multi-cancer early detection MCED: Galleri, CancerSEEK).
  • Multi-cancer early detection: Methylation-based (cfDNA fragmentomics, methylation patterns tissue-specific).
  • Galleri (targeted methylation, ~50 cancers, tissue of origin ~90% accuracy).
  • Sensitivity stage-dependent (I ~20-40%, IV ~90%). Specificity > 99%.
  • Implementation considerations: false positives, overdiagnosis, cost, follow-up protocols.
  • MRD in solid tumors: ctDNA after curative intent treatment.
  • Positive MRD predicts recurrence (months to years before imaging).
  • Lead time: 3-12mo for most cancers.
  • Clinical trials: ctDNA-guided adjuvant therapy (DYNAMIC, CIRCULATE).
  • Liquid biopsy challenges: Low ctDNA fraction (early stage, brain tumors), clonal hematopoiesis of indeterminate potential (CHIP), standardization, reimbursement.
Gene Therapy and Genome Editing
  • Gene therapy approaches: Gene addition (AAV, lentivirus), gene editing (CRISPR, base editing, prime editing), gene silencing (ASO, siRNA), gene replacement (large genes, dual AAV). AAV vectors: AAV2, AAV8, AAV9.
  • Serotypes determine tropism. Capsid engineering.
  • Low immunogenicity (but pre-existing antibodies).
  • Non-integrating (episomal).
  • Limitations: packaging capacity ~4. 7kb, dilution in dividing cells.
  • Approved AAV therapies: Luxturna (AAV2, RPE65, inherited retinal dystrophy).
  • Zolgensma (AAV9, SMN1, SMA Lentiviral vectors: Integrating (risk of insertional mutagenesis). Ex vivo: CAR-T cells (tisagenlecleucel, axicabtagene ciloleucel, brexucabtagene, lisocabtagene).
  • Anti-CD19 for B-ALL/DLBCL, BCMA for multiple myeloma.
  • Gene corrected HSCs: betibeglogene autotemcel (Zynteglo, beta-thalassemia), exagamglogene autotemcel (Casgevy/exa-cel, sickle cell). CRISPR therapies: Casgevy (exa-cel): ex vivo CRISPR-Cas9 edited CD34+ HSCs (BCL11A enhancer, reactivates fetal Hb).
  • Approved for sickle cell disease and beta-thalassemia. In vivo editing: LCA10 (EDIT-101, CRISPR, CEP290, trial).
  • Transthyretin amyloidosis (NTLA-2001, in vivo CRISPR with LNP, liver editing). Base editing: Adenine base editor (ABE, A > G).
  • Cytosine base editor (CBE, C > T). No DSB needed.
  • BEAM-101 for sickle cell.
  • Prime editing: Cas9 nickase + reverse transcriptase + pegRNA.
  • Precise edits (all 12 possible base substitutions, small indels).
  • Larger edits possible (twin prime).
  • ASO/siRNA therapies: Nusinersen (Spinraza, SMA, ASO).
  • Tofersen (QALSODY, SOD1 ALS).
  • Patisiran (Onpattro, TTR amyloidosis, siRNA).
  • Inclisiran (Leqvio, PCSK9, siRNA). Germline editing: Controversial and ethically fraught.
  • International moratorium. 2018 He Jiankui case (CCR5-edited twins Lulu and Nana) condemned.
  • Somatic vs germline: Somatic: acceptable (consent required, non-heritable).
  • Germline: not currently acceptable (off-target, ethics, heritable changes).
  • Genetic counselling: Non-directive, respect patient autonomy, informed consent, psychological support, family communication, cascade testing, reproductive options (prenatal, PGD, adoption, donor gametes).
  • GINA (2008): prohibits genetic discrimination in health insurance and employment (does not cover life/disability/LTC insurance).
  • State-level variations. Ethical issues: VUS, incidental findings, recontact, privacy, data sharing, equity, justice, access, cost.
  • Duty to warn relatives varies by jurisdiction.
High-Yield Pearls
  • NBS: RUSP 35+ conditions. Dried blood spot 24-48h. MS/MS, pulse ox, hearing. CF, SCD, CH, PKU, CAH.
  • Cascade screening: test at-risk relatives after proband. Lynch, HBOC, FH, HH.
  • PRS: emerging for breast cancer (combined with mammo), CAD reclassification.
  • Liquid biopsy: ctDNA for MRD, resistance, early detection (Galleri). Challenges: CHIP, low shedding.
  • Gene therapy: AAV (Luxturna, Zolgensma), lentiviral (CAR-T, Casgevy/exa-cel SCD). CRISPR editing.
  • Genetic counseling: non-directive, GINA, informed consent, cascade testing, VUS communication.
Red Flags
  • GINA does not cover life, disability, or long-term care insurance. State laws vary.
  • Germline editing: current international consensus against. Ethical, safety, and regulatory concerns.
  • CHIP mutations in liquid biopsy: can cause false positive for ctDNA. Paired WBC sequencing required.
  • PRS transferability: Euro-centric bias. Diverse GWAS needed for equitable implementation.
  • AAV gene therapy: pre-existing antibodies may exclude patients. Limited by capsid packaging capacity.
  • VUS reclassification: need recontact mechanisms. Counsel upfront about uncertainty.

12. Cheatsheets and Summary Tables

Inheritance Patterns Chromosomal Syndromes Microdeletions Triplet Repeats Newborn Screening ACMG Classification

Inheritance Pattern Quick Reference
  • AD: Vertical, 50% risk, M-to-M, variable expressivity, incomplete penetrance, de novo, advanced paternal age
  • AR: Horizontal (sibs), 25% risk, consanguinity, carrier frequency, founder effects
  • X-linked recessive: Affected males, carrier females, no M-to-M, 50% sons, all daughters carriers
  • X-linked dominant: Both sexes, male lethal (Rett, IP), all daughters affected male
  • Mitochondrial: Maternal only, heteroplasmy, threshold, LHON/MELAS/MERRF
  • Multifactorial: Polygenic + environment, 2-5% recurrence, threshold model
Chromosomal Syndromes Summary
  • T21 (Down): 1:700, flat facies, single palmar crease, AVSD, ALL risk, early Alzheimer
  • T18 (Edwards): 1:5000, rocker-bottom feet, clenched hands, low-set ears, VSD, 90% die <1yr
  • T13 (Patau): 1:15000, cleft lip/palate, polydactyly, holoprosencephaly, scalp defects
  • Turner (45,X): 1:2500, webbed neck, coarctation, lymphedema, short stature, streak gonads
  • Klinefelter (47,XXY): 1:600, tall, gynecomastia, small testes, azoospermia, testosterone
Microdeletion Syndromes
  • 22q11.2 (DiGeorge): CATCH-22, conotruncal heart, T-cell deficiency, hypocalcemia, TBX1
  • 7q11.23 (Williams): Elfin facies, SVAS (ELN), hypercalcemia, cocktail personality, ID
  • 15q11-13 paternal (PWS): Infantile hypotonia, hyperphagia/obesity, small hands, GH deficiency
  • 15q11-13 maternal (AS): Happy puppet, ataxia, seizures, absent speech, UBE3A
  • 5p (Cri-du-chat): Cat-like cry, microcephaly, hypertelorism, ID
  • 17p13.3 (Miller-Dieker): Lissencephaly, LIS1, severe ID, seizures
Triplet Repeat Disorders
  • Huntington (CAG): HTT, >40, AD, paternal anticipation, chorea, dementia
  • DM1 (CTG): DMPK, >50, AD, maternal anticipation, myotonia, cataracts
  • Fragile X (CGG): FMR1, >200, X-linked, maternal, ID, large ears, macroorchidism
  • Friedreich (GAA): FXN, 70-1700, AR, ataxia, cardiomyopathy, diabetes
  • C9orf72 (GGGGCC): ALS+FTD, AD/penetrance, TDP-43 pathology
Newborn Screening Conditions (RUSP)
  • Metabolic (MS/MS): PKU, MSUD, MCAD, GA1, VLCAD, MMA, PA, tyrosinemia
  • Endocrine: Congenital hypothyroidism, congenital adrenal hyperplasia (21-OHase)
  • Hemoglobinopathies: Sickle cell disease, thalassemias
  • Other: CF (IRT/DNA), SMA (SMN1), SCID (TREC), hearing loss, critical CHD (pulse ox)
  • Timing: Dried blood spot 24-48h. Urgent results for metabolic: call immediately
ACMG/AMP Variant Classification
  • Pathogenic: PVS1 (null) + PS1 or >=2 PS, or 1 PS + >=3 PM, or >=3 PM + >=2 PP
  • PVS1: Nonsense, frameshift, splice site, initiation codon, deletion in LOF gene
  • PM2: Absent in gnomAD. PM3: in trans with P for recessive
  • BA1/BS1: MAF >5% (benign) or >expected. BS2: healthy adult
  • VUS: Insufficient evidence. May reclassify. Recontact policy critical
Founder Mutations by Population
  • Ashkenazi Jewish: Tay-Sachs (1:25), Gaucher (1:15), Canavan (1:40), FD (1:30), Bloom (1:100)
  • Finnish: Congenital nephrotic, aspartylglucosaminuria, diastrophic dysplasia
  • French Canadian: Tay-Sachs, CF 444delA, LPL deficiency, OPMD
  • Amish/Mennonite: MSUD, glutaric acidemia I, Ellis-van Creveld
  • East Asian: ALDH2*2 (~40%), CYP2C19 PM (~15%)
Hardy-Weinberg Calculations
  • Equations: p + q = 1. p2 + 2pq + q2 = 1
  • AR incidence = q2: 1/10,000 => q = 0.01, carrier ~ 1/50
  • X-linked: Male incidence = q. Female carriers = 2pq
  • Consanguinity F: First cousin F=1/16, risk AR ~4-6%
Prenatal Testing Timeline
  • NIPT: >10 weeks, cfDNA, screening T21/18/13/sex, PPV varies
  • CVS: 10+0 to 13+6 weeks, miscarriage ~0.2%, CPM risk ~1%
  • Amniocentesis: 15+0 to 20+6 weeks, miscarriage ~0.1-0.2%
  • PGT-M: Embryo biopsy day 5/6, monogenic, probe development required
  • MSAFP: 15-20 weeks, NTD screening, elevated 2.5x in open NTDs
Teratogens Quick Reference
  • Alcohol (FAS): Microcephaly, smooth philtrum, thin vermillion, ID. No safe level
  • Isotretinoin: Microtia/anotia, CNS, CHD, thymic aplasia. iPledge
  • Valproate: NTD 10x, hypospadias, cleft palate, CHD, autism 3-5x
  • Warfarin: Nasal hypoplasia, stippled epiphyses. Avoid, use LMWH
  • ACEi/ARB: Fetal renal failure, oligohydramnios, pulmonary hypoplasia
  • Maternal PKU: Uncontrolled Phe => microcephaly, ID, CHD
Genetic Testing Methodology Comparison
MethodResolutionDetectsMissesBest Use
Karyotype5-10 MbAneuploidy, balanced rearrangementsSmall CNVs, point mutationsPrenatal, hematologic, POC
FISH<100 kbTargeted microdeletion, fusionUnselected scanningRapid aneuploidy, HER2, BCR-ABL
CMA (aCGH/SNP)50-100 kbCNVs, UPD, mosaicismBalanced rearrangements, point mutationsFirst-line for DD/ID/autism/MCA
Sanger seq1 bpPoint mutations, small indelsLarge rearrangements, CNVsSingle-gene confirmation
NGS Panel1 bp (high depth)Point mutations, indels in targetsNon-targeted regionsHereditary cancer, cardiomyopathy
WES1 bp (exome)~85% known disease variantsNon-coding, SVs, repeatsUndiagnosed genetic disorders
WGS1 bp (genome)Coding + non-coding, SVs, repeatsComplex SVs, centromeresEmerging first-line, research

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13. Treatment Tables and Clinical Protocols

Metabolic Crisis ERT/LSD CFTR Modulators Cancer Screening PGx Dosing Recurrence Risk

Acute Metabolic Crisis Management
  • General: Stop protein, high-calorie IV dextrose (10-15% at 1. 5x maintenance) + IV lipids.
  • Correct acid-base/electrolytes.
  • Hyperammonemia (UCD): Na benzoate + Na phenylacetate (Ammonul).
  • IV arginine HCl (except arginase deficiency).
  • Carbamylglutamate for NAGS.
  • Hemodialysis if NH3 >500. MSUD crisis: High dextrose + lipids.
  • Hemodialysis for rapid Leu reduction.
  • Thiamine for responsive. MMA/PA crisis: Carnitine IV.
  • Hydroxocobalamin for MMA. Metronidazole.
  • N-carbamylglutamate. GSD I hypoglycemia: D10 IV bolus, then D10 maintenance.
  • Uncooked cornstarch 1-2 g/kg q3-4h. Tyrosinemia I: Nitisinone (NTBC) 1 mg/kg/day BID.
  • Tyr-restricted diet. Pompe infantile: ERT (alglucosidase/avalglucosidase) ASAP. X-ALD cerebral: HSCT if early (Loes Wilson fulminant: Liver transplant evaluation. Trientine + zinc.
  • Plasma exchange for hemolysis.
ERT/SRT Summary for Lysosomal Storage Disorders
  • Gaucher: Imiglucerase/velaglucerase/taliglucerase (IV q2wk).
  • Eliglustat (oral SRT, CYP2D6).
  • Miglustat (oral SRT, GI side effects). Fabry: Agalsidase alfa/beta (IV q2wk).
  • Migalastat (oral chaperone, amenable mutations). Pompe: Alglucosidase alfa/avalglucosidase alfa (IV q2wk). MPS I (Hurler): Laronidase (IV qwk).
  • HSCT MPS II (Hunter): Idursulfase (IV qwk). MPS VI: Galsulfase (IV qwk). NPC: Miglustat (reduces neurological progression).
  • Niemann-Pick B: Olipudro alfa (ERT). MLD: Metazel (intrathecal ERT). Krabbe: HSCT presymptomatic. Premedicate: Antihistamines, acetaminophen, steroids for infusion reactions.
CFTR Modulator Therapy
  • Ivacaftor (Kalydeco): G551D gating mutation, potentiator, 150mg q12h.
  • Lumacaftor/ivacaftor (Orkambi): F508del homozygotes, corrector + potentiator.
  • Tezacaftor/ivacaftor (Symdeko): F508del + residual function.
  • Elexacaftor/tezacaftor/ivacaftor (Trikafta): F508del (any genotype with one F508del, ~90% of CF).
  • FEV1 +10-14% exacerbations down 63%, sweat Cl- normalized.
  • Morning: 2 tabs (elexacaftor 100mg + tezacaftor 50mg + ivacaftor 75mg).
  • Evening: ivacaftor 150mg. Monitor LFTs q3mo.
  • CYP3A4 interactions.
Hereditary Cancer Screening (NCCN Guidelines)
  • BRCA1/2 (HBOC): Breast self-awareness 18+, clinical breast exam q6-12mo 25+, annual mammo + breast MRI 30+, consider RRM.
  • RRSO by 35-40 (BRCA1) or 40-45 (BRCA2).
  • Pancreatic screening if FH.
  • Prostate PSA 40+ (BRCA2). Lynch: Colonoscopy q1-2y starting 20-25.
  • Annual endometrial biopsy + TVUS.
  • EGD q2-4y starting 30-35. Aspirin 325mg. FAP: Colonoscopy q1y starting 10-15.
  • Colectomy when numerous adenomas. EGD starting 20-25.
  • Thyroid US. Li-Fraumeni: Annual whole-body MRI, breast MRI 20+, colonoscopy q2-5y 25+. Avoid radiation. VHL: Abdominal MRI q1-2y. Ophthalmology q1y. Metanephrines q1y. CNS MRI q2-3y. MEN2: Prophylactic thyroidectomy (RET codon).
  • Calcitonin, metanephrines, Ca/PTH screening.
PGx Dosing Algorithms Quick Reference
  • Codeine (CYP2D6): UM => contraindicated. NM => normal.
  • PM => alternative (morphine). Tamoxifen (CYP2D6): PM => consider AI if postmenopausal.
  • Clopidogrel (CYP2C19): PM => prasugrel/ticagrelor.
  • Warfarin (CYP2C9 + VKORC1): IWPC algorithm.
  • CYP2C9 *2/*3 reduce dose 25-75%.
  • VKORC1 AA => ~3mg/d, GG => ~5-7mg/d.
  • Simvastatin (SLCO1B1): CC normal. CT lower dose.
  • TT avoid simvastatin.
  • Thiopurines (TPMT + NUDT15): IM 30-50% dose.
  • PM 90% reduction or avoid. 5-FU/Capecitabine (DPYD): IM 50% dose reduction. PM avoid.
  • Irinotecan (UGT1A1): *28/*28 reduce dose ~30%.
  • Abacavir (HLA-B*5701): Positive: contraindicated.
  • Carbamazepine (HLA-B*1502): Positive (Asian): avoid.
  • Allopurinol (HLA-B*5801): Positive: avoid, febuxostat alternative.
Recurrence Risk Calculations
  • AR (carrier parents): 25% affected, 50% carrier, 25% unaffected.
  • AD (affected parent): 50% affected.
  • XLR (carrier mother): 50% sons affected, 50% daughters carriers.
  • XLD (affected father): 100% daughters affected, 0% sons.
  • Mitochondrial (affected mother): ~100% at risk (variable heteroplasmy). De novo AD: Recurrence to sibs ~1-2% (gonadal mosaicism). Multifactorial: One affected first-degree: 2-5%. Bayesian: Prior x Conditional = Joint.
  • Posterior = Joint / Sum(Joint).
Key Drug Interactions and Safety
  • Azoles + CYP3A4 substrates (tacrolimus, sirolimus, statins): increase levels, dose reduce.
  • Rifampin: potent CYP3A4 inducer => decreases levels of OCPs, immunosuppressants, warfarin.
  • Migalastat: requires amenable GLA mutation (GAL4 assay). Do not combine with ERT.
  • Trientine + iron: separate by 2h. Penicillamine: monitor proteinuria, myelosuppression.
  • ERT infusions: premedicate for infusion reactions (antihistamines, acetaminophen, steroids).
  • CFTR modulators (ivacaftor): CYP3A4 substrate. Reduce dose with strong CYP3A4 inhibitors.

14. Study Tips and Exam Preparation

Board Review High-Yield Topics Clinical Reasoning Key Studies

How to Use This Guide
  • Medical genetics is increasingly critical for USMLE, MBBS, and internal medicine boards.
  • Master these core topics in order: (1) Pedigree analysis - the single most important skill to determine inheritance pattern. (2) Chromosomal abnormalities - trisomies, microdeletions, sex chromosome disorders. (3) Mendelian inheritance - AD/AR/X-linked/mitochondrial patterns, anticipation, imprinting, recurrence risk calculations. (4) Population genetics - Hardy-Weinberg carrier frequency, founder effects, GWAS interpretation. (5) Genetic testing - when to order karyotype vs CMA vs NGS vs WES, variant interpretation (ACMG/AMP). (6) Cancer genetics - hereditary syndromes, oncogenes, tumor suppressors, PARP inhibitors. (7) Pharmacogenetics - CYP450, TPMT, DPYD, HLA, warfarin dosing, targeted therapy. (8) Biochemical genetics - PKU, MSUD, UCD, GSD, LSD, Wilson, CF.
  • Use the cheat cards and summary tables for rapid recall before exams.
Top High-Yield Concepts
Pedigree Patterns

AD (vertical, M-to-M), AR (horizontal, consanguinity), XLR (no M-to-M), XLD (male lethal), mitochondrial (maternal).

Trisomy Quick Facts

T21 (AVSD, ALL), T18 (rocker-bottom, clenched hands), T13 (holoprosencephaly, polydactyly). All increase with maternal age.

Microdeletions

22q11.2 (DiGeorge), 7q11.23 (Williams), 15q11-13 (PWS/AS), 5p (Cri-du-chat), 17p13.3 (Miller-Dieker).

Triplet Repeats

HD (CAG, AD, paternal), DM1 (CTG, AD, maternal), Fragile X (CGG, X-linked), FRDA (GAA, AR), C9orf72 (GGGGCC, ALS/FTD).

Cancer Syndromes

BRCA (HBOC, PARPi), Lynch (MSI-H, CRC/endometrial), FAP (APC, 100% CRC), Li-Fraumeni (TP53, multiple primaries).

PGx Must-Knows

CYP2D6 (codeine UM). TPMT (thiopurine). DPYD (5-FU). HLA-B*5701 (abacavir). HLA-B*1502 (carbamazepine SJS).

LSD Summary

Gaucher (glucocerebroside, AJ, ERT/SRT). Tay-Sachs (GM2, cherry-red spot). Fabry (Gb3, X-linked, acroparesthesias).

NBS Core

PKU, MSUD, MCAD, GA1, CF, SCD, CH, CAH, SMA, SCID. MS/MS. Pulse ox for critical CHD.

ACMG Variants

P/LP/VUS/LB/B. PVS1 (null), PS1 (same AA), PM2 (gnomAD absent), BA1 (MAF >5%). VUS may reclassify.

HWE Formulas

p+q=1. p2+2pq+q2=1. AR incidence=q2. Carrier=2pq. Selection Δq = -(sq2(1-q))/(1-sq2).

Teratogens

Alcohol (FAS), isotretinoin (microtia/CNS), valproate (NTD), warfarin (nasal hypoplasia), ACEi (renal), Li (Ebstein).

Key Milestones

MOMS (fetal NTD repair), CAPP2 (aspirin Lynch), SOLSTICE (Trikafta), EMBARK (elevidys DMD), Casgevy (exa-cel SCD).

Clinical Reasoning Frameworks
  • Dysmorphic child evaluation: 3-generation pedigree, teratogen history, growth parameters, dysmorphology exam, developmental assessment.
  • Karyotype + CMA first-line.
  • Targeted panel/WES if CMA negative.
  • Cancer genetic testing criteria: NCCN guidelines: age Neurodevelopmental delay: CMA first-line. Fragile X (boys).
  • Metabolic if episodic regression.
  • WES/WGS if CMA/FX negative. Brain MRI, EEG.
  • Prenatal testing: NIPT screening -> CVS/amnio for confirmation.
  • Nuchal translucency 11-13wk. Anatomy US 18-20wk.
  • Recurrence risk counseling: Establish diagnosis.
  • Mode of inheritance. Gonadal mosaicism. Penetrance.
  • Bayesian refinement.
  • Reproductive options (prenatal, PGD, donor gametes).
Final Words

Medical genetics is the foundational science of precision medicine. Master the patterns, the rules, and the exceptions. Pedigrees are a universal language - learn to read them fluently. ACMG variant classification is the standard for genomic medicine. Understand the principles; the specific genes and syndromes will follow with practice. This guide covers the entire scope of clinical genetics for medical students, residents, and board review. Updated 2026.