Genetics & Molecular Biology

01 Overview & Scope of Medical Genetics

Medical genetics is the study of heredity, genes, and genetic variation as they relate to human health and disease. It integrates molecular biology, cytogenetics, biochemical genetics, and clinical medicine to explain how genetic factors cause, predispose to, or modify the course of disease. A working knowledge of genetics is indispensable for understanding congenital anomalies, inborn errors of metabolism, cancer, pharmacologic variability, and the growing field of precision medicine.

Core Domains of Medical Genetics

02 Key Terminology & Abbreviations

Essential Genetic Quantities

03 DNA Structure, Chromatin & Chromosomes

Deoxyribonucleic acid (DNA) is the hereditary material of all cellular organisms. Its structure determines how genetic information is stored, replicated, and expressed.

DNA Double Helix

• Sugar-phosphate backbone — alternating deoxyribose sugars and phosphodiester bonds; 5′ to 3′ directionality
• Base pairing — adenine (A) pairs with thymine (T) via 2 hydrogen bonds; guanine (G) pairs with cytosine (C) via 3 hydrogen bonds
• Antiparallel strands — the two strands run in opposite directions (5′→3′ and 3′→5′)
• Major and minor grooves — transcription factors and regulatory proteins bind primarily in the major groove
• B-form DNA — the predominant right-handed helix with ~10.5 bp per turn

Nucleotide Chemistry

Chromatin Organization

Histone Modifications

Telomeres

Telomeres are repetitive TTAGGG sequences at chromosome ends that protect against degradation, end-to-end fusion, and replication-associated shortening. Telomerase (a reverse transcriptase with an RNA template component, hTERC) adds telomeric repeats and is active in germ cells, stem cells, and ~90% of cancers. Somatic cells lack significant telomerase activity, leading to progressive telomere shortening with each division (end-replication problem) and eventual replicative senescence.

04 DNA Replication

DNA replication is semiconservative (each daughter strand retains one parental strand), as demonstrated by the Meselson–Stahl experiment. Replication proceeds bidirectionally from origins of replication and requires a complex machinery of enzymes.

Replication Machinery

05 Transcription & RNA Processing

Transcription is the synthesis of RNA from a DNA template by RNA polymerase. In eukaryotes, three RNA polymerases exist, each responsible for different RNA species.

Eukaryotic RNA Polymerases

Steps of Eukaryotic Transcription

• Initiation — transcription factors (TFIID with TBP subunit) bind the TATA box (~25 bp upstream of start site) → recruit RNA Pol II → form pre-initiation complex
• Elongation — RNA Pol II synthesizes mRNA in the 5′→3′ direction, reading the template (antisense) strand 3′→5′
• Termination — polyadenylation signal (AAUAAA) triggers cleavage and release of transcript

Post-Transcriptional RNA Processing

Types of RNA

06 Translation & the Genetic Code

Translation is the process by which ribosomes decode mRNA into polypeptide chains. It occurs in the cytoplasm (free ribosomes) or on the rough endoplasmic reticulum (secreted and membrane proteins).

The Genetic Code

• Triplet — each codon consists of 3 nucleotides encoding one amino acid
• Degenerate (redundant) — most amino acids are specified by more than one codon (wobble position = 3rd base)
• Non-overlapping — codons are read sequentially without overlap
• Universal — the same code is used by virtually all organisms (minor exceptions in mitochondria)
• Unambiguous — each codon specifies only one amino acid
• Start codon — AUG (methionine); also serves as internal methionine codon
• Stop codons — UAA, UAG, UGA (“U Are Annoying, U Are Gone, U Go Away”)

Steps of Translation

Antibiotics Targeting Translation

Post-Translational Modifications

• Signal peptide cleavage — signal recognition particle (SRP) directs nascent proteins to ER
• Glycosylation — N-linked (asparagine, in ER) and O-linked (serine/threonine, in Golgi)
• Phosphorylation — by kinases on Ser, Thr, Tyr residues; key signaling mechanism
• Ubiquitination — tags proteins for proteasomal degradation
• Hydroxylation — proline and lysine hydroxylation in collagen (requires vitamin C)

Protein Trafficking Destinations

07 Regulation of Gene Expression

Gene expression is regulated at multiple levels — from chromatin remodeling to post-translational modification. Understanding these mechanisms is critical for comprehending disease pathogenesis and therapeutic targets.

Levels of Gene Regulation

Regulatory RNA Species

• miRNA — small (~22 nt) non-coding RNA; binds 3′ UTR of target mRNA → translational repression or mRNA degradation; Drosha processes in nucleus, Dicer processes in cytoplasm
• siRNA — small interfering RNA; double-stranded; induces RISC-mediated mRNA cleavage (used therapeutically, e.g., patisiran for TTR amyloidosis, inclisiran for PCSK9)
• lncRNA — long non-coding RNA (>200 nt); roles in X-inactivation (XIST RNA coats inactive X), imprinting, chromatin remodeling
• Antisense oligonucleotides (ASOs) — synthetic single-stranded nucleic acids that bind target mRNA; modulate splicing or block translation (nusinersen for SMA, mipomersen for familial hypercholesterolemia)
• Ribozymes — catalytic RNA molecules; peptidyl transferase (23S rRNA) is the classic example; self-splicing introns (Group I and II introns)

Cell Signaling Pathways Relevant to Gene Regulation

08 Types of Mutations

A mutation is any heritable change in the DNA sequence. Mutations range from single nucleotide changes to large chromosomal rearrangements and are the fundamental basis of genetic disease, evolution, and cancer.

Point Mutations (Single Nucleotide)

Missense Mutation Subtypes

• Conservative — substituted amino acid has similar properties (e.g., Asp → Glu, both acidic); often tolerated
• Non-conservative — substituted amino acid has different properties (e.g., Glu → Val in sickle cell); more likely pathogenic

Frameshift Mutations

Splice Site Mutations

Mutations at intron-exon boundaries (GT donor or AG acceptor sites) cause exon skipping, intron retention, or activation of cryptic splice sites. Many cases of β-thalassemia result from splice site mutations.

Other Mutation Types

• Trinucleotide repeat expansion — unstable repeats that grow with each generation (see Section 14)
• Loss-of-function — reduced or absent protein function; typically recessive
• Gain-of-function — new or enhanced protein activity; typically dominant
• Dominant-negative — mutant protein interferes with wild-type protein function (e.g., mutant p53, osteogenesis imperfecta type II)

Transition vs. Transversion

• Transition — purine → purine (A↔G) or pyrimidine → pyrimidine (C↔T); more common
• Transversion — purine ↔ pyrimidine; less common but more likely to be non-conservative

09 DNA Damage & Repair Mechanisms

DNA is continuously damaged by endogenous (replication errors, oxidative stress) and exogenous (UV, radiation, chemicals) agents. Multiple repair pathways exist to maintain genomic integrity, and defects in these pathways are the basis of many cancer predisposition syndromes.

DNA Repair Pathways

Common DNA Damaging Agents

Cancer-Associated DNA Repair Syndromes Summary

10 Autosomal Dominant Inheritance

Autosomal dominant (AD) disorders require only one mutant allele for phenotypic expression. Affected individuals are typically heterozygous (Aa). Each child of an affected parent has a 50% chance of inheriting the disorder.

Characteristics of AD Inheritance

• Vertical transmission (affected individuals in every generation)
• Males and females equally affected
• Male-to-male transmission possible (distinguishes from X-linked)
• Unaffected individuals do not transmit the trait
• Variable expressivity and incomplete penetrance are common
• Often involves structural proteins or regulatory proteins

High-Yield AD Disorders

Autosomal Dominant Connective Tissue Disorders Compared

11 Autosomal Recessive Inheritance

Autosomal recessive (AR) disorders require two mutant alleles (homozygous aa) for phenotypic expression. Heterozygous carriers (Aa) are typically unaffected. When two carriers mate, each child has a 25% chance of being affected, a 50% chance of being a carrier, and a 25% chance of being unaffected.

Characteristics of AR Inheritance

• Horizontal pattern (affected siblings, unaffected parents)
• Parents are typically heterozygous carriers
• Consanguinity increases risk
• Males and females equally affected
• Often involves enzyme deficiencies (inborn errors of metabolism)
• Carrier frequency can be calculated from disease prevalence using Hardy–Weinberg

High-Yield AR Disorders

Lysosomal Storage Diseases (AR)

12 X-Linked & Mitochondrial Inheritance

X-Linked Recessive (XLR)

XLR disorders predominantly affect males (hemizygous, XY) because they have only one X chromosome. Carrier females (heterozygous) are usually unaffected but may show mild manifestations due to skewed X-inactivation.

• No male-to-male transmission (father passes Y to sons)
• Affected males transmit the carrier state to all daughters
• Carrier mothers have a 50% chance of affected sons and 50% carrier daughters

High-Yield XLR Disorders

X-Linked Dominant (XLD)

Rare. Affected mothers transmit to 50% of sons and 50% of daughters. Affected fathers transmit to all daughters and no sons. Some XLD conditions are lethal in hemizygous males.

• Rett syndrome — MECP2 mutation; almost exclusively in girls (lethal in males); stereotypic hand-wringing, regression after 6–18 months
• Incontinentia pigmenti — IKBKG/NEMO; skin lesions in lines of Blaschko; lethal in males
• Alport syndrome (most common form) — COL4A5; sensorineural hearing loss, ocular abnormalities, progressive glomerulonephritis

Mitochondrial (Maternal) Inheritance

Mitochondrial DNA (mtDNA) is inherited exclusively from the mother. All children of an affected mother may be affected; an affected father cannot transmit the disease. Variable expression due to heteroplasmy (mixture of normal and mutant mitochondria).

13 Pedigree Analysis & Genetic Counseling

Pedigree analysis is the cornerstone of clinical genetics. Recognizing inheritance patterns from family histories allows proper diagnosis, risk calculation, and counseling.

Pedigree Pattern Recognition

Bayesian Analysis in Genetics

Bayesian analysis combines prior probability (based on pedigree) with conditional probability (based on additional information, such as test results or number of unaffected children) to calculate posterior probability. This is frequently tested in the context of calculating carrier risk for X-linked disorders.

Bayesian Analysis Example

A classic board scenario: A woman’s brother has hemophilia A (XLR). Her mother is an obligate carrier. She wants to know her risk of being a carrier, given that she has two unaffected sons.

Her carrier risk decreases from 1/2 to 1/5 after having two unaffected sons. Each additional unaffected son further reduces her posterior carrier probability.

14 Trinucleotide Repeat Disorders & Anticipation

Trinucleotide repeat expansions are unstable mutations in which a three-nucleotide sequence is repeated an abnormal number of times. These repeats tend to expand during meiosis, leading to anticipation — earlier onset and/or more severe disease in successive generations.

Major Trinucleotide Repeat Disorders

15 Genomic Imprinting & Uniparental Disomy

Genomic imprinting is the epigenetic silencing of one parental allele, so that only the allele from the other parent is expressed. This means loss or mutation of the active allele cannot be compensated by the silenced allele.

Imprinting Disorders

16 Mosaicism, Incomplete Penetrance & Variable Expressivity

Mosaicism

Mosaicism refers to the presence of two or more genetically distinct cell populations in a single individual, arising from a post-zygotic mutation.

• Somatic mosaicism — mutation in somatic cells; affects only tissues derived from the mutant clone; not transmitted to offspring
• Germline (gonadal) mosaicism — mutation in germ cells; phenotypically normal parent can transmit a mutation to multiple offspring; explains recurrence of “de novo” disorders in siblings (e.g., osteogenesis imperfecta)
• Confined placental mosaicism — abnormal karyotype in placenta but normal fetus; can cause false-positive CVS results

Incomplete Penetrance vs. Variable Expressivity

Other Non-Mendelian Concepts

• Locus heterogeneity — mutations in different genes produce the same phenotype (e.g., retinitis pigmentosa has >80 associated genes)
• Allelic heterogeneity — different mutations in the same gene produce the same disorder (e.g., >2,000 CFTR mutations all cause CF)
• Phenocopy — an environmentally caused phenotype that mimics a genetic disorder (e.g., thalidomide-induced phocomelia resembling Holt–Oram syndrome)
• Compound heterozygote — two different pathogenic alleles at the same locus (common in AR disorders like CF)

Multifactorial Inheritance

Multifactorial (complex) disorders result from the combined effects of multiple genes and environmental factors. They do not follow Mendelian patterns but show familial clustering.

Threshold Model

The liability threshold model explains multifactorial disorders with a discontinuous phenotype (present or absent). Individuals exceeding a threshold of combined genetic and environmental liability develop the condition.

• Risk increases with the number of affected relatives
• Risk increases with severity of the condition in the proband
• Risk is higher when the affected individual is of the less commonly affected sex (e.g., pyloric stenosis is more common in males; a female proband suggests higher genetic load, so her relatives have higher recurrence risk)

Common Multifactorial Conditions

• Neural tube defects — anencephaly, spina bifida; risk reduced by periconceptional folic acid supplementation
• Congenital heart defects — most common birth defects; VSD most frequent
• Cleft lip/palate — recurrence risk ~4% for first-degree relatives
• Type 2 diabetes mellitus — strong genetic component; HLA associations less prominent than in type 1
• Coronary artery disease — polygenic risk scores increasingly used clinically
• Pyloric stenosis — 5:1 male predominance; threshold model example

17 Chromosomal Structure & Aberrations

Chromosomal aberrations are changes in chromosome number or structure visible by cytogenetic techniques. They are a major cause of congenital anomalies, intellectual disability, and pregnancy loss.

Structural Aberrations

Microdeletion Syndromes

Meiosis and Nondisjunction

Understanding the stages of meiosis is critical for explaining how aneuploidies arise.

18 Autosomal Aneuploidies

Aneuploidy is an abnormal chromosome number that is not a multiple of the haploid set (n = 23). It most commonly results from nondisjunction during meiosis I or meiosis II. Advanced maternal age is the primary risk factor.

Major Autosomal Aneuploidies

Prenatal Screening for Aneuploidies

19 Sex Chromosome Disorders

Turner Syndrome (45,X)

The only monosomy compatible with life. Affects females. Most 45,X conceptions end in spontaneous abortion (99%); live-born incidence is ~1/2,500 female births.

• Short stature, shield chest, widely spaced nipples, webbed neck (cystic hygroma remnant)
• Primary amenorrhea, streak gonads, infertility
• Coarctation of the aorta (preductal), bicuspid aortic valve
• Horseshoe kidney, lymphedema at birth
• Normal intelligence (may have difficulties with spatial processing)
• No Barr bodies (only one X chromosome)

Klinefelter Syndrome (47,XXY)

Affects males. Incidence ~1/600 male births. Most common cause of hypogonadism and infertility in males.

• Tall stature, long extremities (eunuchoid body habitus)
• Testicular atrophy, infertility (dysgenesis of seminiferous tubules)
• Gynecomastia, decreased facial/body hair
• ↑ FSH, ↑ LH, ↑ estrogen, ↓ testosterone
• One Barr body (inactivated extra X)
• Mild intellectual disability (verbal); increased risk of breast cancer and SLE

Other Sex Chromosome Conditions

Disorders of Sexual Development (DSD)

20 Oncogenes & Tumor Suppressors

Cancer is fundamentally a genetic disease arising from accumulated mutations in genes controlling cell growth, differentiation, and death. Two major categories of cancer genes exist: oncogenes (gain-of-function, dominant) and tumor suppressors (loss-of-function, recessive at the cellular level).

Cell Cycle Review

CDK Inhibitors (Tumor Suppressors)

• p21 (CDKN1A) — induced by p53; universal CDK inhibitor; mediates G1 arrest after DNA damage
• p27 (CDKN1B) — inhibits cyclin E-CDK2; regulates G1/S; loss associated with poor cancer prognosis
• p16 (CDKN2A/INK4a) — specifically inhibits CDK4/6; frequently deleted or silenced in cancers; same locus encodes ARF (p14) which stabilizes p53

Proto-Oncogenes → Oncogenes

Proto-oncogenes are normal genes that promote cell growth. A single activating mutation converts them to oncogenes (gain-of-function, dominant). Mechanisms include point mutation, gene amplification, and chromosomal translocation.

Tumor Suppressor Genes

Tumor suppressors inhibit cell proliferation or promote apoptosis. Both alleles must be inactivated for loss of function (Knudson’s two-hit hypothesis). In hereditary cancer syndromes, one hit is inherited (germline) and the second is somatic.

High-Yield Chromosomal Translocations in Cancer

21 Hereditary Cancer Syndromes

Hereditary cancer syndromes account for 5–10% of all cancers. They result from germline mutations in tumor suppressor genes or DNA repair genes and follow an autosomal dominant inheritance pattern with incomplete penetrance.

Major Hereditary Cancer Syndromes

22 Population Genetics & Hardy–Weinberg Equilibrium

Population genetics studies allele and genotype frequencies in populations and the forces that change them over time.

Hardy–Weinberg Equilibrium

In a large, randomly mating population with no selection, mutation, migration, or genetic drift, allele and genotype frequencies remain constant across generations.

Applying Hardy–Weinberg

Board-style application: If an AR disease has a prevalence of 1/10,000, then:

• q² = 1/10,000 → q = 1/100
• p = 1 − 1/100 = 99/100 ≈ 1
• Carrier frequency (2pq) = 2 × 1 × 1/100 = 1/50

Forces That Disrupt Hardy–Weinberg Equilibrium

Heterozygote Advantage

Balanced polymorphism: heterozygous carriers of certain AR conditions have a selective advantage, maintaining the disease allele at a higher frequency than expected.

Genetic Epidemiology Measures

Consanguinity and Inbreeding

The coefficient of inbreeding (F) is the probability that an individual is homozygous at a locus due to shared ancestry of the parents.

• First cousins: F = 1/16
• Second cousins: F = 1/64
• Parent-offspring or sibling: F = 1/4

Consanguinity increases the proportion of homozygous loci, thereby increasing the risk of autosomal recessive conditions. In populations with high consanguinity rates, AR disorders are more prevalent than predicted by Hardy–Weinberg (which assumes random mating).

23 Genetic Testing & Molecular Diagnostics

Advances in molecular technology have transformed genetic diagnosis. Understanding the capabilities and limitations of each technique is essential for clinical practice and is frequently tested.

Major Genetic Testing Methods

Gel Electrophoresis & Restriction Enzymes

• Restriction endonucleases — cut DNA at specific palindromic sequences; create restriction fragment length polymorphisms (RFLPs) useful for genetic mapping
• Gel electrophoresis — separates DNA/RNA/protein fragments by size (smaller fragments migrate faster toward the anode); DNA is negatively charged (phosphate backbone)

PCR Variants

Clinical Genetic Testing Approach

• Known familial mutation → targeted PCR/Sanger sequencing
• Suspected chromosomal abnormality → karyotype (gross) or CMA (submicroscopic)
• Suspected microdeletion → FISH or CMA
• Undiagnosed genetic condition → whole exome/genome sequencing
• Prenatal aneuploidy screening → cell-free fetal DNA (NIPT), followed by amniocentesis/CVS for confirmation

24 Pharmacogenomics

Pharmacogenomics studies how genetic variation affects drug metabolism, efficacy, and toxicity. Individualizing drug therapy based on genotype is a cornerstone of precision medicine.

Cytochrome P450 Polymorphisms

Other Pharmacogenomic Associations

Phase I vs. Phase II Drug Metabolism

25 Gene Therapy & Emerging Technologies

Gene Therapy Approaches

Viral Vectors for Gene Delivery

26 Clinical Correlates Across Specialties

Genetics intersects with virtually every clinical specialty. Understanding these connections is essential for integrated clinical reasoning.

Specialty-Specific Genetic Considerations

Newborn Screening

All US states mandate newborn screening (NBS) for a core panel of conditions. Screening typically uses dried blood spot collected 24–48 hours after birth.

• Phenylketonuria (PKU) — elevated phenylalanine; dietary restriction prevents intellectual disability
• Congenital hypothyroidism — elevated TSH; early thyroxine replacement prevents cretinism
• Galactosemia — elevated galactose-1-phosphate; dietary galactose restriction
• Sickle cell disease — hemoglobin electrophoresis; penicillin prophylaxis
• Cystic fibrosis — elevated immunoreactive trypsinogen (IRT); confirmatory sweat chloride test
• Maple syrup urine disease — elevated branched-chain amino acids
• Biotinidase deficiency — enzyme assay; biotin supplementation
• CAH (21-hydroxylase deficiency) — elevated 17-hydroxyprogesterone

Prenatal Diagnostic Procedures

27 High-Yield Review & Board Pearls

Classic Associations

Ethical & Legal Issues in Genetics

Epigenetic Therapies in Cancer

• DNMT inhibitors (azacitidine, decitabine) — demethylate silenced tumor suppressor genes; used in MDS and AML
• HDAC inhibitors (vorinostat, romidepsin) — increase histone acetylation → re-express silenced genes; used in cutaneous T-cell lymphoma
• IDH inhibitors (ivosidenib, enasidenib) — block oncometabolite 2-hydroxyglutarate production; used in IDH-mutant AML
• EZH2 inhibitors (tazemetostat) — block H3K27 trimethylation; used in EZH2-mutant follicular lymphoma

Board Exam Strategies for Genetics Questions

• When given a pedigree, first determine the inheritance pattern, then calculate risk
• For enzyme deficiency questions, think autosomal recessive unless stated otherwise
• For structural protein defects, think autosomal dominant
• If a question mentions consanguinity, suspect an AR disorder
• If only males are affected across generations (through carrier mothers), think X-linked recessive
• For trinucleotide repeat questions, identify the repeat, the gene, and whether it shows anticipation through the maternal or paternal line
• For cancer genetics, know the difference between oncogenes (gain of function, one hit) and tumor suppressors (loss of function, two hits)
• For Hardy–Weinberg, start with q² = disease prevalence and solve from there