Index

Genetics for MRCOG Part 1 — Complete Deep-Dive Study Guide

Exam Weighting: High. Genetics underlies prenatal screening, congenital anomalies, hereditary cancer syndromes, and recurrent pregnancy loss. Expect 15–20% of MCQ content. Last Updated: May 2026

Table of Contents

1. Molecular Genetics Basics
2. Epigenetics
3. Chromosomes & Cytogenetics
4. Inheritance Patterns
5. Chromosomal Abnormalities
6. Prenatal Genetics & Screening
7. Haemoglobinopathies
8. Common Genetic Disorders in O&G
9. Oncogenetics
10. Population Genetics
11. Genetic Counselling

1. Molecular Genetics Basics

1.1 DNA Structure

Primary Structure: - DNA is a linear polymer composed of nucleotides. Each nucleotide consists of: - A phosphate group - A deoxyribose sugar (pentose) - A nitrogenous base — one of four: adenine (A), guanine (G), cytosine (C), thymine (T) - Nucleotides are linked by phosphodiester bonds between the 3′-hydroxyl of one sugar and the 5′-phosphate of the next → creating a sugar-phosphate backbone with a 5′→3′ directionality.

Secondary Structure — The Double Helix (Watson & Crick, 1953): - Two antiparallel polynucleotide strands wound around each other in a right-handed helix. - Antiparallel orientation: One strand runs 5′→3′, the complementary strand runs 3′→5′. This is critical for replication and transcription. - Base pairing rule: A pairs with T (2 hydrogen bonds), G pairs with C (3 hydrogen bonds → higher melting temperature). - Dimensions: - Diameter: ~2 nm - Rise per base pair: ~0.34 nm - Helical pitch (one full turn): ~3.4 nm (~10 base pairs per turn) - Major and minor grooves: The asymmetric positioning of the sugar-phosphate backbones creates a wider major groove and a narrower minor groove. Proteins (transcription factors) bind predominantly in the major groove where base-pair-specific hydrogen bond donors/acceptors are more accessible.

Tertiary Structure: - DNA is further packed into chromatin (see Section 1.4). In its most compact form, DNA is organised into chromosomes.

Clinical Correlation: | Feature | Clinical Relevance | |---------|-------------------| | GC-rich regions | Higher melting point; CpG islands regulate gene expression | | DNA damage | Repair defects → cancer (e.g., BRCA in breast/ovarian cancer) | | Antiparallel nature | Okazaki fragments on lagging strand during replication |

Memory Aid — "AT/GC": - Australian Tourists = Adenine + Thymine (2 bonds, weak) - Get Cancelled = Guanine + Cytosine (3 bonds, strong)

1.2 Genes

A gene is the fundamental physical and functional unit of heredity — a segment of DNA that encodes an RNA product (which may be translated into a polypeptide or function directly as RNA).

Gene Structure:

Gene Organization in the Human Genome: - Total genes: ~20,000–25,000 protein-coding genes - Average gene size: ~27 kb (range: <1 kb to >2 Mb) - Gene density: Varies enormously — chromosome 19 is gene-rich, chromosomes 4 and 18 are gene-poor - Non-coding DNA: >98% of the genome is non-coding — includes introns, regulatory elements, transposons, repetitive sequences, and non-coding RNA genes (microRNAs, lncRNAs, snoRNAs)

Key Terminology: - Allele: Alternative version of a gene at a given locus - Homozygous: Two identical alleles at a locus - Heterozygous: Two different alleles at a locus - Genotype: The genetic constitution of an individual - Phenotype: The observable expression of the genotype (influenced by environment and epigenetics) - Dominant: An allele that produces its phenotype even when heterozygous - Recessive: An allele that produces its phenotype only when homozygous (or hemizygous)

1.3 Chromosomes

Definition: Chromosomes are the highest-level packaging of DNA — each is a single, continuous molecule of double-stranded DNA with associated histone and non-histone proteins.

Chromosome Morphology:

Human Karyotype: - 46 chromosomes in somatic cells: 22 pairs of autosomes + 1 pair of sex chromosomes - 46,XX — female; 46,XY — male - Haploid number (n): 23 chromosomes (gametes) - Diploid number (2n): 46 chromosomes (somatic cells)

Telomere Function: - Prevent chromosome ends from being recognised as double-strand breaks (distinguish natural ends from broken DNA) - Serve as a "mitotic clock" — each cell division shortens telomeres by 50–200 bp - Telomerase (reverse transcriptase + RNA template) adds TTAGGG repeats to chromosome ends - Active in germ cells, stem cells, and most cancers - Inactive in most somatic cells → contributes to cellular senescence

1.4 Chromatin

Definition: Chromatin is the complex of DNA, histones, and non-histone proteins that packages the genome within the nucleus.

Hierarchical Packaging:

Euchromatin vs. Heterochromatin:

Constitutive vs. Facultative Heterochromatin: - Constitutive: Permanently condensed — centromeres, telomeres. Same regions in all cell types. - Facultative: Condensed only in certain cell types or developmental stages — e.g., the inactivated X chromosome.

Histone Modifications (Part of Epigenetics — see Section 2): - Acetylation of histone tails (by HATs) → neutralises positive charge → loosens DNA-histone interaction → activates transcription - Deacetylation (by HDACs) → represses transcription - Methylation of H3K4 → activation; H3K9me3, H3K27me3 → repression - Phosphorylation → involved in chromosome condensation during mitosis

1.5 DNA Replication

Fundamental Principle — Semiconservative Replication (Meselson & Stahl, 1958): - Each of the two parental strands serves as a template for a new daughter strand - Each daughter molecule contains one parental strand and one newly synthesised strand

Key Enzymes and Proteins:

The Replication Fork:

Origins of Replication: - Eukaryotic chromosomes have multiple origins (humans: ~30,000–50,000 per cell) - Origins fire throughout S phase in a regulated sequence (euchromatin early, heterochromatin late) - Licensing: Each origin is "licensed" for one round of replication per cell cycle by the pre-replication complex (ORC, Cdc6, Cdt1, MCM)

Errors and Repair: - Mutation rate: ~1 × 10⁻⁸ per base pair per generation in germline; higher in somatic cells - Repair mechanisms: - Mismatch repair (MMR): Corrects replication errors (defects → Lynch/HNPCC) - Nucleotide excision repair (NER): Repairs bulky DNA adducts (defects → xeroderma pigmentosum) - Base excision repair (BER): Repairs small base modifications - Homologous recombination (HR) & Non-homologous end joining (NHEJ): Repair double-strand breaks (BRCA1/BRCA2 → HR) - Proofreading: DNA polymerase has 3′→5′ exonuclease activity that removes misincorporated nucleotides

1.6 Transcription

Definition: The process by which RNA is synthesised from a DNA template.

RNA Polymerases in Eukaryotes:

Transcription Cycle:

1. Initiation:
2. Transcription factors (TFIIA, TFIIB, TFIID [includes TBP — TATA-binding protein], TFIIE, TFIIF, TFIIH) assemble at the promoter
3. TFIIH has helicase activity and kinase activity (phosphorylates Pol II CTD)

4. RNA Pol II begins transcription

5. Elongation:

6. Pol II moves along template strand (3′→5′), synthesising RNA 5′→3′

7. Template strand (antisense, 3′→5′) is read; coding strand (sense, 5′→3′) has the same sequence as the RNA (T substituted for U)

8. Termination:

9. Polyadenylation signal (AAUAAA) is transcribed
10. Cleavage and polyadenylation specificity factor (CPSF) cleaves the transcript ~15–30 nt downstream
11. Poly-A polymerase adds ~200 A residues
12. Remaining RNA downstream is degraded by 5′→3′ exoribonuclease (RAT1/XRN2) → "torpedo model"

Post-Transcriptional Modifications:

Alternative Splicing: - One gene can produce multiple protein isoforms by different combinations of exons - ~95% of human multi-exon genes undergo alternative splicing - Clinical relevance: Mutations affecting splice sites often cause disease (e.g., β-thalassaemia, spinal muscular atrophy)

Spliceosome: - Complex of 5 snRNPs (U1, U2, U4, U5, U6) and >150 proteins - Recognises 5′ splice site (GU), branch point (A), and 3′ splice site (AG) - Catalyses two transesterification reactions

1.7 Translation

Definition: The process by which the genetic code (mRNA sequence) directs the synthesis of a polypeptide chain.

The Genetic Code: - Codons: Triplets of nucleotides, each specifying one amino acid or a stop signal - Degeneracy: 61 sense codons for 20 amino acids + 3 stop codons (UAA, UAG, UGA) - Wobble hypothesis: The third base of the codon (3′ end) can pair non-standardly with the first base of the anticodon (5′ end) → allows one tRNA to recognise multiple codons - Start codon: AUG (methionine) - Stop codons: UAA ("ochre"), UAG ("amber"), UGA ("opal")

Key Components:

Translation Cycle:

1. Initiation:
2. eIF4E binds 5′ cap; eIF4G bridges cap and poly-A tail (circularisation)
3. 40S subunit with initiator Met-tRNA scans mRNA for AUG in Kozak consensus (GCCRCCaugG)

4. 60S subunit joins → functional 80S ribosome

5. Elongation:

6. A site (aminoacyl): incoming aminoacyl-tRNA delivered by eEF1α·GTP
7. P site (peptidyl): holds the growing polypeptide on peptidyl-tRNA
8. E site (exit): discharged tRNA leaves
9. Peptidyl transferase (RNA catalytic activity — the ribosome is a ribozyme) transfers peptide from P-site tRNA to A-site aminoacyl-tRNA

10. Translocation by eEF2·GTP moves ribosome one codon 3′ → tRNA from A→P→E

11. Termination:

12. eRF1 enters A site when stop codon is encountered
13. Polypeptide released from P-site tRNA
14. Ribosome dissociates into subunits

Post-Translational Modifications:

1.8 Mutation Types

Classification by Effect on DNA Sequence:

Trinucleotide Repeat Expansion Disorders — Key for MRCOG:

Anticipation: Earlier onset and/or increased severity in successive generations due to expansion of unstable repeats during meiosis (particularly paternal for CAG repeats, maternal for CTG repeats).

Nomenclature: - c.152C>T — nucleotide change at coding DNA position 152, C→T - p.Glu6Val (or E6V) — amino acid change at protein position 6, glutamic acid → valine - IVS4+1G>A — mutation in intron 4, +1 position of splice donor, G→A (IVS = intervening sequence)

Loss of Function vs. Gain of Function:

2. Epigenetics

2.1 Definition and Scope

Epigenetics is the study of heritable changes in gene expression that do not involve changes in the DNA sequence itself. These modifications are: - Mitotically stable (passed through cell division) - Potentially meiotically heritable (transgenerational epigenetic inheritance) - Reversible (unlike DNA sequence changes) - Tissue-specific (explains cellular differentiation despite identical genomes)

Key Players: 1. DNA methylation 2. Histone modifications 3. Non-coding RNAs (microRNAs, lncRNAs) 4. Chromatin remodelling complexes 5. Polycomb/Trithorax group proteins

2.2 DNA Methylation

Mechanism: - Addition of a methyl group (–CH₃) to the 5-carbon of cytosine residues in CpG dinucleotides - Catalysed by DNA methyltransferases (DNMTs): - DNMT3A / DNMT3B — de novo methylation (establishes patterns during embryogenesis) - DNMT1 — maintenance methylation (copies methylation pattern to daughter strand during replication) - S-adenosylmethionine (SAM) is the methyl donor

CpG Islands: - Regions with a high density of CpG dinucleotides (found in ~60% of gene promoters) - Usually unmethylated in active genes → open chromatin, permissive transcription - Methylated CpG islands → gene silencing (recruits methyl-binding proteins like MeCP2 → histone deacetylases → condensed chromatin)

CpG Methylation Pattern:

Clinical Correlations: - Rett syndrome: Mutation in MECP2 (X-linked) — methyl-binding protein — causes neurodevelopmental regression in girls - ICF syndrome: Mutation in DNMT3B — immunodeficiency, centromeric instability, facial anomalies - Cancer: Global hypomethylation + promoter-specific hypermethylation of tumour suppressor genes (e.g., BRCA1, MLH1, p16)

2.3 Histone Modifications

The Histone Code Hypothesis: Combinations of histone tail modifications act as a "code" that is read by other proteins to determine chromatin state and gene expression.

Major Modifications:

Key Complexes: - Polycomb Repressive Complex 2 (PRC2): Contains EZH2 → catalyses H3K27me3 → gene silencing (important in development, X-inactivation, stem cell maintenance) - Polycomb Repressive Complex 1 (PRC1): Catalyses H2AK119ub → chromatin compaction - Trithorax group (TrxG): Antagonise Polycomb — maintain active gene expression

Bivalent Domains: - Chromatin regions with both H3K4me3 (activating) and H3K27me3 (repressive) marks - Keep developmental genes "poised" for rapid activation or stable silencing - Resolved during differentiation — important in embryonic stem cells

2.4 Genomic Imprinting

Definition: An epigenetic phenomenon where genes are expressed in a parent-of-origin-specific manner. Some genes are expressed only from the maternal allele, others only from the paternal allele.

Mechanism: - Imprinting is established in the germline by differential DNA methylation of imprinting control regions (ICRs) - Imprints are erased in primordial germ cells and re-established according to the sex of the parent - After fertilisation, the imprint is maintained in somatic cells throughout development - Imprinted genes are often clustered in chromosomal domains controlled by single ICRs

Why Relevant to O&G: - Imprinted genes are critical for placental development and fetal growth - Paternally expressed genes tend to promote growth (fetal/placental) - Maternally expressed genes tend to restrict growth (maternal resource conservation — "parental conflict" hypothesis)

Key Imprinting Disorders — MUST KNOW for MRCOG:

Mnemonic for PWS vs AS (15q11-q13): - Prader-Willi = Paternal deletion (70%) - Angelman = Maternal deletion (70%)

Or: "If Mom's copy is gone, the child is Angelic (smiling/gentle). If Dad's copy is gone, the child is Prader-Weight gain."

Uniparental Disomy (UPD): - Both copies of a chromosome inherited from one parent, none from the other - Heterodisomy: Two different homologues from the same parent (meiosis I error) - Isodisomy: Two identical copies from the same parent (meiosis II error or post-fertilisation duplication) - Causes disease when it disrupts imprinting (e.g., UPD15 → PWS or Angelman) or when isodisomy unmasks a recessive mutation

2.5 X-Inactivation (Lyonisation)

Definition: In female mammals, one of the two X chromosomes is transcriptionally silenced in each somatic cell to achieve dosage compensation between XX females and XY males.

Key Facts: - Proposed by Mary Lyon (1961) - Occurs at the late blastocyst stage (day 5–6 in humans) — random in embryonic tissues - The inactivated X chromosome becomes a Barr body (visible in cell nuclei) - Inactivation is stable and clonal — all descendants of a cell inactivate the same X (explains "tortoiseshell" cats and mosaic expression of X-linked disorders in heterozygotes)

Mechanism:

X-Inactivation in O&G Context:

Genes that Escape X-Inactivation: - ~15% of X-linked genes escape inactivation entirely - Another ~10% escape in some females but not others (variable escape) - Located mainly in the pseudoautosomal regions (PAR1 and PAR2) at the tips of Xp and Xq, where sequence is shared with the Y chromosome - Key escape genes: SHOX (short stature homeobox), KDM6A, KDM5C, EIF2S3 (haploinsufficiency → Turner stigmata)

2.6 Epigenetics in Reproduction and Development

Key Reproductive Epigenetic Phenomena:

1. Gametic imprinting establishment:
2. Sperm: Imprints are established during spermatogenesis (protamine packaging, widespread DNA methylation)
3. Oocyte: Imprints are established post-natally during oocyte growth (gradual methylation acquisition)

4. Assisted reproductive technology (ART) concern: In vitro maturation and culture may disrupt imprinting → increased risk of Beckwith-Wiedemann and Angelman syndromes (odds ratio ~3–6 for BWS after ART)

5. Maternal-fetal interface:

6. Trophoblast has a unique epigenome (global hypomethylation, distinct histone marks)

7. Imprinted genes are highly expressed in placenta (e.g., IGF2, H19, PEG10)

8. Epigenetic clocks:

9. DNA methylation patterns change with age (Horvath clock)
10. Relevance to: oocyte ageing, recurrent miscarriage

MDC (Memory Device) — Key Imprinting Facts: - BWS (Beckwith-Wiedemann): Overgrowth → Big Womb Syndrome - SRS (Silver-Russell): Under-growth → Small Russell Syndrome - Both involve 11p15 — opposite epigenetic defects

3. Chromosomes & Cytogenetics

3.1 Karyotyping

Definition: The complete set of chromosomes of an individual, arranged systematically by size, centromere position, and banding pattern.

Indications in O&G: - Advanced maternal age (≥35 at delivery) - Abnormal prenatal screening (NT, serum markers, NIPT) - Fetal structural anomalies on ultrasound - Parental chromosome rearrangement (balanced translocation carriers) - Recurrent pregnancy loss (≥2–3 miscarriages) - Stillbirth - Suspected aneuploidy in a newborn - Sexual ambiguity / disorders of sex development - Premature ovarian insufficiency (Turner mosaic)

G-Banding (Giemsa Banding): - Method: Chromosomes are treated with trypsin (digests some chromosomal proteins) then stained with Giemsa - Pattern: Dark bands (G-dark = AT-rich, gene-poor, late-replicating) alternate with light bands (G-light = GC-rich, gene-rich, early-replicating) - Resolution: ~400–550 bands per haploid set in a standard karyotype; high-resolution (prometaphase) can yield 850+ bands - ISCN (International System for Human Cytogenomic Nomenclature): Standardised system for describing chromosome abnormalities

Numbering Conventions: - Each chromosome is numbered 1–22 in decreasing size order, plus X and Y - Chromosome 1 is the largest (~248 Mb, ~2,000 genes) - Chromosome 21 is the smallest autosome (~47 Mb, ~500 genes) - Each chromosome arm is divided into regions, bands, and sub-bands - Example: 11p15.5 → - 11 = chromosome 11 - p = short arm - 15 = region 1, band 5 - .5 = sub-band 5

3.2 Chromosome Classification by Centromere Position

Acrocentric Chromosomes — Special Features: - Carry NORs (nucleolar organising regions) on stalks (satellite stalks) of the p arms - NORs contain rRNA genes (tandem repeats of ~350 copies) - Acrocentric short arms are variable in length and can form satellites (distal p arm segments) - Robertsonian translocations occur exclusively between acrocentric chromosomes (13, 14, 15, 21, 22) through fusion at the centromere

3.3 ISCN Nomenclature — Reading Karyotypes

Basic Format: <total chromosome number>,<sex chromosomes><abnormality description>

Symbols and Abbreviations (Key Ones):

3.4 Mosaicism vs. Chimerism

Confined Placental Mosaicism (CPM): - Karyotypically abnormal cell line in the placenta but normal in the fetus - Occurs in ~1–2% of CVS samples - Can cause discordance between CVS result and fetal karyotype - Follow-up amniocentesis is recommended to confirm fetal status - Commonest: trisomy 16 → intrauterine growth restriction (IUGR)

3.5 Fluorescence In Situ Hybridisation (FISH)

Principle: Fluorescently labelled DNA probes hybridise to complementary target sequences on chromosomes — allows visualisation of specific DNA sequences in metaphase spreads or interphase nuclei.

Probe Types:

Advantages over Karyotyping: - Can analyse interphase cells (no need for cell culture, faster — 24–48 hours vs 7–14 days) - Higher resolution for microdeletions - Can detect low-level mosaicism

Limitations: - Only tests for the specific targets in the probe set - Cannot detect balanced rearrangements (without specific probes) - Will miss unexpected abnormalities

Prenatal Applications: - Rapid aneuploidy detection (RAD): FISH for chromosomes 13, 18, 21, X, Y on uncultured amniocytes or CVS — results in 24–48 hours - Interphase FISH on fetal blood or urine samples - Telomere FISH for cryptic rearrangements in couples with recurrent miscarriage or infertility

3.6 Comparative Genomic Hybridisation (CGH) and Array CGH

Principle (Classic CGH): - Test DNA (labelled green) and reference DNA (labelled red) are co-hybridised to normal metaphase chromosomes - Ratio of green:red fluorescence along each chromosome → regions of gain (green ↑) or loss (green ↓, red ↑) - Resolution: ~5–10 Mb — limited by metaphase chromosome length

Array CGH (aCGH): - Test and reference DNA are hybridised to a microarray of cloned DNA fragments (BACs, oligonucleotides) or SNP probes - Resolution: <1 kb possible (high-density arrays) — dramatically better than classic CGH - Detects copy number variants (CNVs) — gains and losses - Cannot detect: - Balanced translocations and inversions (no net gain/loss) - Point mutations - Low-level mosaicism (<10–20%)

SNP Arrays: - Also detect loss of heterozygosity (LOH) — regions of homozygosity that indicate UPD or consanguinity - More sensitive for mosaicism (can detect as low as 5–10%) - Can detect triploidy (unlike aCGH which normalises total DNA)

O&G Applications:

Important Terminology: - Variant of uncertain significance (VUS): A CNV with unclear clinical impact — challenging in prenatal counselling - Benign CNV: Normal population variation (inherited from a healthy parent) - Pathogenic CNV: Known to cause disease (usually de novo or segregating with disease)

4. Inheritance Patterns

4.1 Autosomal Dominant (AD)

Key Features: - The disorder manifests in heterozygotes (one mutant allele is sufficient) - Vertical transmission — affected individuals have an affected parent (except de novo mutations) - Each child of an affected parent has a 50% chance of inheriting the mutation - Males and females are equally affected - Male-to-male transmission occurs (unlike X-linked) - Reduced penetrance and variable expressivity are common

Key Concepts:

Must-Know AD Disorders for MRCOG:

Mnemonic for Penetrance vs Expressivity: - Penetrance = Present or absent (binary — like being Pregnant, you either are or aren't) - Expressivity = Extent or degree (range — like body weight)

4.2 Autosomal Recessive (AR)

Key Features: - Disorder manifests only in homozygotes (or compound heterozygotes — two different mutant alleles at the same locus) - Horizontal transmission — affected individuals are usually in a single sibship, not across generations - Parents are typically unaffected carriers (heterozygotes) - Each child of carrier parents has a 25% chance of being affected - Males and females are equally affected - Often associated with consanguinity (increased proportion of homozygotes for rare recessive alleles) - Carrier frequency in the general population can be high (e.g., CF 1/25 Caucasians, β-thalassaemia 1/30 Mediterranean)

Founder Effect: Certain recessive mutations are common in specific populations due to a small ancestral population.

Key AR Disorders for MRCOG:

Mnemonic for AR Inheritance counselling: - Both parents Carrier → Child 1 in 4 affected - Parents clinically normal → Consanguinity clue - Consanguinity → Common Cause of Childhood Conditions

4.3 X-Linked Recessive (XLR)

Key Features: - Disorder manifests in hemizygous males (one X copy) and homozygous females (rare) - No male-to-male transmission (father passes Y to sons, X to daughters) - All daughters of an affected male are obligate carriers - Sons of a carrier female have a 50% chance of being affected - Carrier females are usually unaffected but may have mild features (skewed X-inactivation) - Severity in females possible: 45,X (Turner), structurally abnormal X, extreme skewing

Key XLR Disorders for MRCOG:

Mnemonic — XLR Pedigree Pattern: - "No son of a king passes the crown to his son" (no male-to-male) - "Daughters carry the torch" (obligate carriers) - "Sons of carrier mothers who marry carrier daughters..." (rare affected females)

4.4 X-Linked Dominant (XLD)

Key Features: - Both males and females can be affected, but females more commonly (2:1 female:male ratio) - Male-to-male transmission is absent (father cannot pass X to son) - Affected males pass the trait to all their daughters and none of their sons - Affected females have a 50% chance of passing to each child regardless of sex - Lethal in males for many XLD conditions (males are hemizygous → more severe, often non-viable) - Females are mosaic due to X-inactivation → variable expressivity

Key XLD Disorders for MRCOG:

Clinical Tip: If a pedigree shows affected females, no male-to-male transmission, and more severely affected (or absent) males — think X-linked dominant.

4.5 Mitochondrial Inheritance

Key Features: - Maternal inheritance — mitochondria are inherited exclusively from the oocyte (sperm mitochondria are eliminated post-fertilisation by ubiquitination) - Both males and females can be affected, but only females pass the trait to their children - All children of an affected female are at risk (depending on heteroplasmy) - Heteroplasmy: Cells contain a mixture of mutant and wild-type mitochondrial DNA (mtDNA) - Threshold effect: A minimum proportion of mutant mtDNA is required for disease expression (varies by tissue — high-energy tissues have lower thresholds) - Mitotic segregation: The proportion of mutant mtDNA can shift during cell division (explains variable tissue involvement) - Tissue specificity: Tissues with high energy demand are preferentially affected (brain, muscle, heart, retina, cochlea, endocrine pancreas)

Mitochondrial DNA Features: - 16.6 kb circular genome - 37 genes: 13 protein-coding (all oxidative phosphorylation subunits), 22 tRNAs, 2 rRNAs - No introns — high gene density - Polyploidy: 2–10 mtDNA copies per mitochondria, hundreds to thousands per cell - Mutation rate: 10–20× higher than nuclear DNA (lack of histones, limited repair capacity) - No recombination — all mtDNA is maternally inherited as a single linkage unit

Key Mitochondrial Disorders — Must Know:

Prenatal Diagnosis for mtDNA Disorders: - Genetic counselling is complex due to heteroplasmy and threshold effects - Preimplantation genetic testing (PGT): Analyse blastomere/trophoblast for heteroplasmy level - Prenatal diagnosis (amniocentesis/CVS): Heteroplasmy in fetal tissues may not predict brain heteroplasmy (inter-tissue variation) - Mitochondrial replacement therapy (MRT): "Three-parent IVF" — uses donor oocyte cytoplasm with healthy mtDNA. Legal in UK under strict regulation (HFEA). Not without ethical controversy.

MDC — Who gives mitochondria? - Mitochondria = Mother's donation → Maternal inheritance

5. Chromosomal Abnormalities

5.1 Numerical Abnormalities — Aneuploidy

Definition: A deviation from the exact multiple of the haploid chromosome number. Most common chromosomal abnormality in humans — detected in ~50% of first-trimester spontaneous abortions.

Incidence: | Aneuploidy | Incidence at Birth | Main Risk Factor | |------------|-------------------|-----------------| | Trisomy 21 (Down) | 1/700 | Maternal age | | Trisomy 18 (Edwards) | 1/5,000 | Maternal age | | Trisomy 13 (Patau) | 1/15,000 | Maternal age | | 45,X (Turner) | 1/2,500 females | Not age-related (paternal error) | | 47,XXY (Klinefelter) | 1/650 males | Paternal age (mild) | | 47,XXX | 1/1,000 females | Maternal age | | 47,XYY | 1/1,000 males | Not age-related |

Maternal Age and Risk: | Maternal Age at Delivery | Risk of Down Syndrome | Total Aneuploidy Risk* | |-------------------------|----------------------|-----------------------| | 20 | 1/1,500 | 1/500 | | 25 | 1/1,350 | 1/450 | | 30 | 1/900 | 1/350 | | 35 | 1/350 | 1/200 | | 37 | 1/225 | 1/150 | | 40 | 1/100 | 1/65 | | 42 | 1/65 | 1/40 | | 45 | 1/25 | 1/15 |

*Includes trisomies 21, 18, 13, 47,XXY, 47,XXX; excludes 45,X and 47,XYY

Mechanisms of Aneuploidy:

Nondisjunction — Meiosis I vs Meiosis II: - Meiosis I error: Both homologues go to same pole → one daughter cell gets 2 copies, the other gets 0 - Meiosis II error: Sister chromatids fail to separate → one gamete has 2 identical copies of a chromosome (isodisomy), the other has 0 - Most human trisomies result from maternal meiosis I errors (especially trisomy 21, 16, 18) - The "maternal age effect" is strongest for meiosis I errors → reflects ageing of the oocyte (increased susceptibility of the meiotic spindle to breakdown, loss of cohesion between homologues over decades of dictyate arrest)

5.2 Structural Abnormalities

Types:

Reciprocal Translocations — Pedigree and Recurrence: - Balanced carrier: 45 chromosomes in 2 rearranged pieces (phenotypically normal) - At meiosis, a quadrivalent forms → 6 possible segregation patterns: - Alternate → balanced gametes (normal or carrier) - Adjacent-1 → unbalanced (duplication/deficiency) - Adjacent-2 → unbalanced - 3:1 → tertiary monosomy/trisomy - Recurrence risk depends on the specific translocation, which chromosomes are involved, and the sex of the carrier (females usually have higher risk) - Empiric risk for unbalanced offspring: ~5–30% depending on translocation

Robertsonian Translocations — Special Category: - Occur only in acrocentric chromosomes (13, 14, 15, 21, 22) - Fusion of the long arms; short arms are lost (no phenotypic effect — redundant rRNA genes on remaining acrocentrics compensate) - Commonest: t(13;14), t(14;21) - t(14;21) carrier: Female carrier → ~10% risk of Down syndrome; Male carrier → ~2% risk

Unbalanced Products of Robertsonian Carriers:

5.3 Microdeletion Syndromes

Definition: Contiguous gene deletion syndromes — loss of 0.5–5 Mb of DNA, too small to detect on standard karyotyping but detectable by FISH or array CGH.

Key Points for MRCOG: - 22q11.2 deletion is the commonest microdeletion and the commonest cause of syndromic cleft palate - Array CGH should be offered when fetal structural abnormalities (especially cardiac, cleft palate) are detected - FISH with specific probes can detect microdeletions rapidly - Most are de novo (~90%) — low recurrence risk (~1–2%) unless a parent carries a balanced rearrangement

5.4 Common Aneuploidies — Detailed Overview

Trisomy 21 (Down Syndrome) — 47,XX/XY,+21

Trisomy 18 (Edwards Syndrome) — 47,XX/XY,+18

Trisomy 13 (Patau Syndrome) — 47,XX/XY,+13

Turner Syndrome (45,X)

Klinefelter Syndrome (47,XXY)

Triple X (47,XXX) and 47,XYY

6. Prenatal Genetics & Screening

6.1 Overview of Prenatal Screening Tests

Screening vs. Diagnostic: - Screening: Offered to all pregnant women; identifies those at higher risk; non-invasive; no risk of miscarriage - Diagnostic: Offered to women with positive screen or risk factors; invasive (CVS, amnio); diagnostic accuracy >99%; carries miscarriage risk (~0.5–1%)

Screening Timeline (UK NHS):

6.2 Nuchal Translucency (NT)

Definition: The sonolucent space at the back of the fetal neck (between the soft tissue over the cervical spine and the skin) measured at 11–13+6 weeks (CRL 45–84 mm).

Normal NT: <3.5 mm (or <99th centile for CRL) — varies with gestational age (typically <2.5 mm at 11 weeks, <3.0 mm at 13+6 weeks)

Increased NT (>99th centile): - Aneuploidy: Trisomy 21 (~75% have NT >95th centile), trisomy 18, 13, Turner, triple X, triploidy - Structural anomalies: CHD (increased NT is the strongest prenatal predictor of CHD), diaphragmatic hernia, skeletal dysplasias - Genetic syndromes: Noonan syndrome (can present with increased NT/cystic hygroma), Noonan spectrum syndromes, many others - Other: Congenital infection, haematologic disorders (e.g., α-thalassaemia → hydrops)

Pathophysiology of increased NT: - Transient cardiac failure / altered haemodynamics - Lymphatic stasis / delayed jugular lymphatic sac development - Extracellular matrix composition changes (e.g., collagen deficiency in Noonan)

Management of Increased NT: 1. Offer invasive testing (CVS) for rapid aneuploidy detection 2. Offer array CGH on CVS sample 3. Offer fetal echocardiography at 18–20 weeks 4. Offer follow-up scan at 16–20 weeks for structural survey 5. If normal karyotype + normal 20-week scan → prognosis is excellent (≥95% normal outcome)

6.3 Combined Test (First-Trimester Screening)

Components:

MoM (Multiple of the Median): All values expressed as MoM to adjust for gestational age, maternal weight, smoking, ethnicity, diabetes, and other confounders.

Performance: - Detection rate: ~85–90% for T21 at a 5% false positive rate - Detection rate with NIPT as contingent test: ~99%

Patterns by Condition:

Mnemonic for Combined Test (T21): - PAPP-A goes Down - Beta-HCG goes Up - NT goes Up

6.4 Quadruple Test (Second-Trimester Screening)

Components (14–20 weeks, optimal 15–18 weeks):

Performance: - Detection rate: ~80% for T21 (lower than combined test) - Used when booking is too late for combined test (>14 weeks) - Also screen for NTD (open neural tube defect) — AFP is ↑ in NTD

Triple Test: Similar but without inhibin A (lower sensitivity missing inhibin A)

Quadruple Test Patterns:

6.5 Cell-Free Fetal DNA (NIPT/NIPD)

Principle: - During pregnancy, cell-free fetal DNA (cffDNA) circulates in maternal plasma, originating from apoptotic trophoblast cells - cffDNA represents 5–20% of total cell-free DNA in maternal plasma - cffDNA can be detected from ~5 weeks gestation, but testing is reliable from 10 weeks - cffDNA is cleared from the maternal circulation within hours of delivery (undetectable by 24–48 hours postpartum) - cffDNA fragments are shorter (~143 bp) than maternal cfDNA fragments (~165–200 bp)

Technologies:

Performance:

Note: NIPT is a screening test, not diagnostic. All positive results require confirmation by CVS or amniocentesis.

Causes of False Positive NIPT: - Confined placental mosaicism (the abnormal cell line is only in the placenta) - Maternal mosaicism (unbalanced translocation, maternal aneuploidy) - Vanishing twin (resorbed aneuploid twin cfDNA persists) - Maternal malignancy (tumour cfDNA sheds) - Technical error (low fetal fraction, sequencing artefact)

Causes of False Negative NIPT: - Low fetal fraction (<4%) — associated with obesity, early gestation, trisomy 13/18 - True fetal mosaicism (low-level mosaicism) - Technical failure (uncommon)

Fetal Fraction: Factors that decrease fetal fraction: - Maternal obesity (inverse correlation with BMI — blood volume dilution) - Early gestation (<10 weeks) - Trisomy 13/18 (smaller placenta → less cffDNA shedding) - Smoking, autoimmune disease, anticoagulation

NIPT for Sex Chromosome Aneuploidies: - Can detect 45,X, 47,XXY, 47,XXX, 47,XYY - Lower sensitivity than for T21 (especially for 45,X) - PPV lower — many false positives (especially for 45,X)

NIPT for Microdeletions: - Detection of 22q11 (DiGeorge), 1p36, 15q11 (Angelman/Prader-Willi), 5p (Cri-du-chat) - Much lower PPV (<10–30%) due to low prevalence — most screen positives are false positives - Counselling should reflect the high false positive rate

NIPT in Multiple Pregnancy: - Twin pregnancies: cffDNA is a mixture from all fetuses - If NIPT indicates aneuploidy, it cannot distinguish which twin is affected (unless using SNP-based NIPT which can count haplotypes) - Higher failure rate (lower fetal fraction per fetus) - NRBC test may be helpful: cell-free fetal DNA originates from NRBCs (nucleated red blood cells) of fetal origin

NIPD (Non-Invasive Prenatal Diagnosis): - For single-gene disorders where the paternal mutation is distinguishable from the maternal sequence - Used for: RhD genotyping (RhD-negative mother, RHD gene in fetus), sex determination (X-linked disorders), achondroplasia (de novo FGFR3 mutation) - Can be used for paternal exclusion testing (detect absence of paternal mutation in cfDNA)

6.6 Amniocentesis

Amniotic Fluid AFP (AFAFP): - Elevated in open NTD (anencephaly, open spina bifida), omphalocele, gastroschisis, fetal death, congenital nephrosis - Can be caused by fetal blood contamination - Acetylcholinesterase (AChE) gel electrophoresis: A second band confirms NTD (more specific than AFP alone)

6.7 Chorionic Villus Sampling (CVS)

CPM (Confined Placental Mosaicism): - Most common with trisomy 16 - Fetal trisomy 16 is non-viable, but if mosaic in placenta only → IUGR - Follow-up with amniocentesis to confirm fetal karyotype

Comparison — CVS vs Amniocentesis:

6.8 Preimplantation Genetic Diagnosis (PGD)

Definition: Genetic testing of embryos created by in vitro fertilisation (IVF) before transfer to the uterus — enables selection of unaffected embryos.

Indications: - PGD for monogenic disorders (PGT-M): Cystic fibrosis, Huntington, sickle cell, haemophilia, BRCA1/BRCA2, myotonic dystrophy, fragile X, spinal muscular atrophy, Tay-Sachs - PGD for chromosomal rearrangements (PGT-SR): Balanced translocation carriers → select embryos without unbalanced translocation - PGD for aneuploidy screening (PGT-A — formerly PGS): Screening embryos for chromosome number — used in advanced maternal age, recurrent IVF failure, recurrent miscarriage

Techniques:

Genetic Analysis Methods:

Karyomapping: Uses SNP genotyping across the genome to follow inheritance of parental haplotypes — a universal approach for PGT-M without needing mutation-specific primers. Requires DNA from both parents, a known affected child or carrier, and an unaffected relative.

Limitations and Ethical Issues: - Embryo wastage: Many embryos are affected or aneuploid - Mosaicism: ~4–8% of embryos are mosaic; biopsies sample 5–10 cells from one location — biological mosaicism may be missed - Mitochondrial DNA disorders: PGT for heteroplasmy levels - HLA typing: Creating "saviour siblings" — ethical controversy - Sex selection: For medical reasons only (X-linked disorders) — not for non-medical sex selection (regulated by HFEA in UK)

6.9 Screening for Haemoglobinopathies (UK Antenatal Programme)

See also [Section 7 — Haemoglobinopathies].

UK NHS Antenatal Screening Programme: - Universal screening: Offered to all pregnant women at booking (before 12 weeks) - Screening test: Full blood count (MCV, MCH) + Hb HPLC (or Hb electrophoresis + sickle cell solubility test for HbS) - Cutoffs: MCV <80 fL or MCH <27 pg → suggestive of α/β-thalassaemia trait or iron deficiency - Counselling: Women identified as carriers → partner should be tested - Prenatal diagnosis offered: If both parents are carriers of significant haemoglobinopathy (at-risk couple for HbSS, HbSC, HbSβ-thal, α-thal Bart's hydrops, β-thal major)

7. Haemoglobinopathies

7.1 Sickle Cell Disease (SCD)

Molecular Pathology: - Point mutation in HBB gene (11p15): GAG → GTG at codon 6 (c.20A>T) - Substitution of valine for glutamic acid at position 6 of β-globin (Glu6Val) - This single amino acid change creates a hydrophobic patch on the surface of deoxygenated HbS - HbS molecules polymerise → form long, rigid fibres → sickling of RBCs → haemolysis + vaso-occlusion

Haemoglobin Composition:

Clinical Features — Sickle Cell Disease:

SCD in Pregnancy — MRCOG Focus:

Neonatal Screening (UK): All newborns offered Guthrie test (heel-prick blood spot at day 5–8) — includes Hb HPLC for sickle cell disease and β-thalassaemia.

Mnemonic for Sickle Cell Mutation: - GAG → GTG (DNA level) - Glu → Val (protein level) - Glutamic acid is charged (soluble) → Valine is hydrophobic (sticky → polymerisation)

7.2 α-Thalassaemia

Genetics: - α-globin gene cluster on 16p13 - Two α-globin genes per chromosome: HBA1 and HBA2 (both identical in coding sequence) - Total: 4 α-globin genes (2 on each chromosome 16) - Disease severity is proportional to the number of functional α-globin genes

Classification:

Deletions: - α⁺-thalassaemia: Single α-gene deletion (-α) — very common in African, Mediterranean, Middle Eastern populations - α⁰-thalassaemia: Both α-genes deleted (--) — common in Southeast Asian, Chinese populations (--SEA, --FIL, --THAI deletions) - Non-deletional α-thalassaemia: Point mutations affecting α-globin expression — rarer but can cause more severe HbH disease

Hb Bart's Hydrops Fetalis (--/--): - Complete absence of α-globin chains - Fetal γ-globin forms Hb Bart's (γ₄) — tetramers of γ chains - Hb Bart's has extremely high oxygen affinity → zero oxygen delivery to tissues → severe tissue hypoxia - Ultrasound findings: Hydrops fetalis (generalised oedema), IUGR, hepatosplenomegaly, placentomegaly, polyhydramnios, cardiac failure - Maternal risks: Pre-eclampsia, antepartum haemorrhage, obstructed labour (large baby/placenta), postpartum haemorrhage - Management: Offer termination of pregnancy; if continuing pregnancy, fetal transfusion may be attempted (survival possible with intrauterine transfusion + postnatal stem cell transplant)

Prenatal Testing Strategy: - Screen with MCV (<80 fL) → if low, test for iron deficiency - If iron replete + low MCV → Hb HPLC (normal HbA₂ → likely α-thal trait) - For at-risk couples (both α⁰ carriers, especially Southeast Asian): offer DNA testing for common deletions → PND by CVS/amnio if needed

7.3 β-Thalassaemia

Genetics: - β-globin gene cluster on 11p15 - One β-globin gene per chromosome (HBB) — two copies total - Disease severity depends on the extent of β-globin reduction (β⁰ = no β-globin; β⁺ = reduced β-globin) - >200 mutations identified — most are point mutations (not deletions, unlike α-thalassaemia) - Promoter mutations → reduced transcription - Nonsense/frameshift → β⁰ - Splice-site mutations → aberrant splicing - Polyadenylation signal mutations → reduced mRNA stability

Classification:

Key Diagnostic Feature — β-Thalassaemia Trait: - ↑ HbA₂ (>3.5%) is the hallmark of β-thalassaemia trait - In α-thalassaemia trait, HbA₂ is normal or slightly reduced - Mild ↓ MCV, ↓ MCH (MCV usually 60–75 fL) - Usually asymptomatic — no treatment needed

β-Thalassaemia Major: - Presents at 6–12 months (when γ→β globin switch completes) - Features: Severe anaemia, pallor, failure to thrive, hepatosplenomegaly, frontal bossing (marrow expansion), skeletal deformities, growth retardation - Treatment: Regular blood transfusions (every 3–4 weeks) + iron chelation (deferasirox, deferoxamine, deferiprone) - Without chelation: Iron overload → cardiomyopathy, liver cirrhosis, endocrine failure (diabetes, hypogonadism, hypothyroidism) - Cure: Haematopoietic stem cell transplant (HSCT) — ideal if HLA-matched sibling (best outcomes <5 years of age) - Gene therapy: LentiGlobin (BB305) — recently approved — uses modified lentivirus to insert functional β-globin; exagamglogene autotemcel (Casgevy) — CRISPR-based editing; results promising

β-Thalassaemia in Pregnancy: - Minor: Usually well-tolerated; monitor Hb; ensure Hb >100 g/L for optimal fetal oxygenation - Major/Intermedia: Pre-conception counselling required; cardiac iron assessment (MRI T2*); avoid pregnancy if significant iron overload cardiomyopathy; risk of IUGR, pre-eclampsia, preterm birth

7.4 Haemoglobin Electrophoresis and HPLC

Methods for Haemoglobin Identification:

HPLC Patterns — Quick Reference:

Antenatal Screening Algorithm: 1. Full blood count at booking: MCV <80 fL or MCH <27 pg → proceed 2. Check ferritin / iron studies (to exclude iron deficiency anaemia) 3. Hb HPLC: - ↑ HbA₂ → β-thalassaemia trait → test partner - Normal HbA₂ → α-thalassaemia trait (if MCV low, iron replete) → α-globin deletion analysis - HbS/HbC/HbE peak → variant haemoglobin → test partner 4. If both partners are carriers of a significant haemoglobinopathy → offer prenatal diagnosis (CVS or amniocentesis) and genetic counselling

8. Common Genetic Disorders in O&G

8.1 Cystic Fibrosis (CF)

Common Mutation: - ΔF508 (c.1521_1523delCTT) — deletion of phenylalanine at codon 508 — accounts for ~70% of CF chromosomes in Northern Europeans - >2,000 CFTR mutations known — classified into 6 classes by mechanism

CFTR Mutation Classes:

Clinical Features:

CF in O&G Context:

Diagnosis: - Newborn screening: Immunoreactive trypsinogen (IRT) on Guthrie → elevated → sweat chloride test - Sweat chloride test: Gold standard; >60 mmol/L = CF; 30–59 mmol/L = borderline - Genetic sequencing: Identifies specific mutations — important for CFTR modulator eligibility

8.2 Fragile X Syndrome

Repeat Ranges:

Expansion Risk (Premutation → Full Mutation): - Maternal transmission: Expansion occurs only when passed through a female (not through a male — male premutation passes to daughters as premutation) - Risk of expansion increases with repeat size: - 55–59 repeats: ~3% risk - 60–69 repeats: ~5% risk - 70–79 repeats: ~31% risk - 80–89 repeats: ~73% risk - 90–99 repeats: ~94% risk - >100 repeats: ~100% risk

Fragile X Syndrome — Full Mutation (>200 repeats):

Premutation-Associated Conditions — MRCOG Critical:

Fragile X-Associated Primary Ovarian Insufficiency (FXPOI)

Fragile X-Associated Tremor Ataxia Syndrome (FXTAS)

• Occurs in male premutation carriers (especially >50 years old)
• Symptoms: intention tremor, ataxia, parkinsonism, cognitive decline, neuropathy
• Not seen in full mutation males (no FMR1 mRNA → no RNA toxicity)

Genetic Testing for Fragile X: - PCR (with repeat-primed PCR for large expansions) — determines exact CGG repeat number - Southern blot — detects full mutations >200 repeats + methylation status (methylated = silenced) - Indications: Family history of fragile X, intellectual disability, autism, POI <40, ataxia/tremor in male relatives

Prenatal Diagnosis: - Offered to known female premutation carriers - CVS or amniocentesis → determine fetal CGG repeat length + methylation - PGT available for IVF (identify embryos with normal repeats)

8.3 Myotonic Dystrophy

Type 1 (DM1 — Steinert Disease):

Repeat Ranges:

Clinical Features:

Congenital Myotonic Dystrophy — MRCOG Critical:

Type 2 (DM2 — Proximal Myotonic Myopathy):

8.4 Spinal Muscular Atrophy (SMA)

Genetic Mechanism: - SMN1 produces full-length SMN protein (essential) - SMN2 is a nearly identical copy gene (~99% homologous) — differs by a single base in exon 7 (C→T) → most SMN2 transcripts skip exon 7 → truncated unstable protein (only ~10–20% of SMN2 transcripts produce full-length SMN) - SMA occurs when SMN1 is deleted or mutated - Disease severity is inversely correlated with SMN2 copy number - SMN2 copies: 0–1 → severe (Type I); 2–3 → intermediate (Type II); 3–4 → mild (Type III/IV)

SMA Types:

Carrier Screening for SMA: - Carrier test: Quantitative PCR to detect SMN1 deletion (detects ~95% of carriers) - Residual risk after negative screen: ~1/1,500 (if no family history) - Recommended by ACMG for all pregnant women (or women planning pregnancy)

Treatment Advances: - Nusinersen (Spinraza): Antisense oligonucleotide — increases SMN2 exon 7 inclusion → more full-length SMN. Intrathecal administration. Dramatically improves survival and motor function - Zolgensma (onasemnogene abeparvovec): AAV9-based gene therapy — delivers functional SMN1 cDNA. Single IV dose. Best outcomes when given pre-symptomatically - Risdiplam (Evrysdi): Small molecule oral SMN2 splicing modifier

Prenatal Diagnosis: - Offer to known carrier couples or couples with an affected child - CVS or amniocentesis → SMN1 deletion analysis - PGT available

8.5 Noonan Syndrome

Key Features — "Noonan" = "NBWN" (Noonan = Neck, Brain, White (pulmonary stenosis murmur), No growth):

MRCOG Relevance: - Prenatal presentation: Increased NT/cystic hygroma (12–14 weeks) — most common genetic cause after Turner syndrome - Differential for Turner syndrome — both present with webbed neck, short stature, CHD, lymphatic dysplasia. Key differences: Noonan is AD (not 45,X), affects both sexes, normal karyotype - Prenatal diagnosis: Karyotype normal → consider Noonan if NF+CHD on ultrasound; molecular testing (gene panel for RASopathy genes) - Recurrence: If a parent has Noonan → 50% recurrence; if de novo → low (but consider gonadal mosaicism) - Pregnancy management: Echocardiography if fetal CHD; plan delivery in tertiary centre for neonatal cardiology support

RASopathies — Related Conditions: | Syndrome | Gene(s) | Distinguishing Features | |----------|---------|------------------------| | Noonan | PTPN11 (50%) | — | | Noonan with multiple lentigines (LEOPARD) | PTPN11, RAF1 | Lentigines, deafness, HCM, more severe | | Costello | HRAS | Coarse facies, papillomata, loose skin, severe feeding difficulty, HCM, malignant hyperthermia risk | | Cardiofaciocutaneous (CFC) | BRAF, MAP2K1, MAP2K2, KRAS | Coarse facies, sparse curly hair, severe ID, ichthyosis-like skin, HCM | | Neurofibromatosis-Noonan | NF1 | Mixed features of NF1 + Noonan |

8.6 Neurofibromatosis Type 1 (NF1, von Recklinghausen Disease)

Diagnostic Criteria — NIH Consensus Panel (need ≥2 of 7):

Additional Features (not in criteria but common): - Plexiform neurofibromas (10–30%) — can undergo malignant transformation to MPNST (malignant peripheral nerve sheath tumour) — lifetime risk ~8–13% - Learning difficulties (30–60%), ADHD, autism - Hypertension (renovascular → renal artery stenosis; phaeochromocytoma ~1%) - Optic gliomas (~15%) — most are benign and slow-growing - Breast cancer: NF1 mutation carriers have an ~2–3× increased risk of breast cancer <50 years (overlaps with NF1 gene's role in DNA repair)

NF1 in Pregnancy:

Prenatal Diagnosis: - PND available for known familial mutation (targeted sequencing on CVS/amnio) - PGT available for known familial mutation - Important: De novo mutations can't be predicted — no NIPT currently for de novo NF1

9. Oncogenetics

9.1 BRCA1 and BRCA2 — Hereditary Breast and Ovarian Cancer (HBOC)

Population Frequency: - General population: BRCA1 ~1/500–800; BRCA2 ~1/500–800 - Ashkenazi Jewish: Founder mutations — BRCA1 185delAG and 5382insC; BRCA2 6174delT - Combined carrier frequency: ~1/40 in Ashkenazi Jews

Management of BRCA Carriers — O&G Perspective:

Breast Cancer Risk Management:

1. Breast awareness + monthly self-exam
2. Annual breast MRI (age 25–29 → annual MRI; age 30–50 → annual mammogram + MRI; >50 → annual mammogram)
3. Risk-reducing mastectomy (RRM) — reduces breast cancer risk by >90%
4. Lifestyle modification (avoid alcohol, maintain weight; however, reducing environmental risk factors in high-penetrance carriers has limited impact)
5. Chemoprevention (tamoxifen → 50% risk reduction in BRCA2 carriers; less effective in BRCA1)

Ovarian Cancer Risk Management:

1. Risk-reducing salpingo-oophorectomy (RRSO) — gold standard
2. BRCA1: Recommend RRSO by age 35–40 (or after completion of childbearing)
3. BRCA2: Recommend RRSO by age 40–45
4. RRSO reduces ovarian cancer risk by ~80–90%
5. RRSO also reduces breast cancer risk in pre-menopausal women by ~50%
6. Salpingectomy alone (interval salpingectomy with delayed oophorectomy) is investigational
7. Annual CA125 + transvaginal ultrasound — not proven to reduce mortality (used for women who decline RRSO)
8. Oral contraceptive pill — reduces ovarian cancer risk by ~50% in BRCA carriers (but → ↑ breast cancer risk, especially in BRCA1 — use with caution; discuss)

HRT After RRSO: - If breast cancer never: low-dose combined HRT is safe for symptom management (no increase in risk in BRCA1/2 without personal breast cancer history) - If breast cancer history: avoid HRT

Pregnancy Considerations for BRCA Carriers:

PARP Inhibitor Mechanism: - Synthetic lethality: BRCA-deficient cells cannot repair double-strand breaks by homologous recombination. PARP inhibitors prevent repair of single-strand breaks → collapse of replication forks → double-strand breaks accumulate → cell death - Effective only in BRCA-deficient (or HRD — homologous recombination deficient) tumours - Niraparib also works in HRD-positive tumours regardless of BRCA mutation status (based on PRIMA trial)

Testing Criteria — NICE Guidelines (UK): Offer BRCA testing to: - Women with ovarian cancer (any type, any age — especially high-grade serous) - Women with breast cancer + family history suggestive of HBOC - Ashkenazi Jewish women with breast or ovarian cancer - Women with breast cancer <40 years - Women with triple-negative breast cancer <60 years - Male breast cancer

Parental Genetic Testing Cascade: - First, the affected family member (index / proband) is tested - If a mutation is found → predictive testing for at-risk relatives (including adult children) - Testing of minors is generally deferred until age 18 (except for childhood-onset cancers)

9.2 Lynch Syndrome (Hereditary Non-Polyposis Colorectal Cancer — HNPCC)

Cancers — MLH1/MSH2 (higher risk):

Amsterdam II Criteria (clinical diagnosis): ≥3 relatives with Lynch-associated cancers (colorectal, endometrial, small bowel, ureter, renal pelvis) where: 1. One is a first-degree relative of the other two 2. ≥2 successive generations affected 3. ≥1 cancer diagnosed before age 50 4. FAP excluded 5. Tumours verified by pathology

Revised Bethesda Guidelines (for tumour testing): Tumour should be tested for MSI if: - Colorectal cancer diagnosed <50 years - Synchronous/metachronous Lynch-associated tumour (any age) - Colorectal cancer with MSI-H histology <60 years - Colorectal cancer + ≥1 first-degree relative with Lynch-associated cancer <50 years - Colorectal cancer + ≥2 first-degree relatives with Lynch-associated cancer (any age)

Tumour Testing:

IHC Patterns:

Gynaecological Surgeon — Management of Lynch Syndrome:

Endometrial Cancer Risk Management:

1. Annual endometrial biopsy (office Pipelle) beginning at age 35 (or 5 years before earliest family diagnosis)
2. Transvaginal ultrasound (TVUS) for endometrial thickness — lower sensitivity than biopsy
3. Risk-reducing hysterectomy + BSO — typically offered at age 40–45 or after completion of childbearing
4. Reduces endometrial cancer risk by ~100% and ovarian cancer risk by ~90%
5. Also consider at time of colectomy for CRC

Ovarian Cancer Risk Management:

• RRSO is effective but Lynch ovarian cancer risk is lower than BRCA → RRSO timing can be later (age 40–50)
• Risk-reducing salpingectomy alone is under investigation

Colorectal Cancer Surveillance:

• Colonoscopy every 1–2 years starting at age 25 (or 5 years before earliest family diagnosis)
• Aspirin (600 mg daily) reduces colorectal cancer risk by ~50% in Lynch (CAPP2 trial)

MSI Testing in Endometrial Cancer: - Universal MSI/IHC testing of endometrial cancer is recommended in the UK (NICE guidelines) - Screening catch → identification of women with likely Lynch syndrome - Somatic MLH1 promoter methylation: If methylation is present, the MSI is likely sporadic — no germline testing needed

Pregnancy and Lynch Syndrome: - No direct impact on fertility - Women may elect to delay RR hysterectomy + BSO until after childbearing (individualised counselling) - PGT for Lynch — available but controversial (partial penetrance, highly treatable/chemonavigable cancers)

9.3 Other Inherited Cancer Syndromes in O&G

Mnemonic for Ovarian Cancer Hereditary Syndromes: - BRCA1/2 (most common — HBOC) - Lynch (HNPCC) - Peutz-Jeghers - Cowden - DICER1

10. Population Genetics

10.1 Hardy-Weinberg Equilibrium (HWE)

The Equation: For a diallelic locus with alleles A (frequency p) and a (frequency q), where p + q = 1:

p² + 2pq + q² = 1

Derivation: Random union of gametes → genotype frequencies are the product of allele frequencies: - P(AA) = p × p = p² - P(Aa) = p × q + q × p = 2pq - P(aa) = q × q = q²

Clinical Applications:

Assumptions of HWE (why a population might deviate):

Applications in Clinical Genetics: - Carrier frequency estimation from disease prevalence - Population screening (e.g., CF carrier frequency in different ethnic groups) - Consanguinity risk calculation — increased homozygosity for recessive alleles - Hardy-Weinberg testing in quality control for GWAS and population datasets

Example Calculation — CF Carrier Frequency: - Incidence in Caucasians: 1/2,500 live births → q² = 1/2,500 - q = √(1/2,500) = 1/50 = 0.02 - p = 1 – 0.02 = 0.98 (≈ 1) - Carrier frequency = 2pq = 2 × 0.98 × 0.02 ≈ 0.0392 ≈ 1/25

10.2 Founder Effect and Genetic Drift

Founder Effect: - A genetic bottleneck caused by a small group establishing a new population - Allele frequencies in the founder population differ from the original source population - Consequence: Certain recessive disease mutations become common in isolated populations

Clinically Important Founder Mutations:

Genetic Drift: - Random fluctuation of allele frequencies in a population due to sampling effects (especially in small populations) - Bottleneck effect: Population dramatically reduced (famine, war, epidemic) → random alleles lost/gained - Effect: ↑ random changes, ↑ fixation of alleles, ↓ heterozygosity - Clinically relevant: Explains why isolated populations have unique disease profiles

10.3 Consanguinity

Definition: A union between individuals who share a common ancestor (up to second cousins).

Types and Coefficients of Inbreeding (F):

Inbreeding Coefficient (F): The probability that an individual receives two identical-by-descent (IBD) alleles at a given autosomal locus from a common ancestor.

Effects of Consanguinity on Offspring:

Calculation — Risk of AR Disease in Consanguineous Union: - For a recessive allele with frequency q: - Random mating: risk = q² (both parents transmit the mutant allele by chance) - First-cousin mating: risk = q² + Fpq (where F = 1/16) - The consanguinity contribution is Fpq = (1/16) × p × q - For a rare disease (q is very small): q² is tiny; Fpq ≈ (1/16) × 1 × q = q/16 — this dominates - Example: q = 1/50 (carrier frequency 1/25): - Random risk = (1/50)² = 1/2,500 - First-cousin risk = 1/2,500 + (1/16 × 1 × 1/50) = 1/2,500 + 1/800 = 1/615 - Risk is ~4× higher

Practical Relevance for MRCOG: - Genetic counselling for consanguineous couples — individualised risk counselling, not presumptive guilt - Offer carrier screening for common AR disorders in their ethnic group - Offer referral to clinical genetics for detailed discussion - First-cousin marriage is not inherently wrong — but couples should be informed of the ~2× increased risk of congenital anomalies and AR disorders, and offered appropriate screening - Many communities have high rates — Muslim communities (Pakistan, Bangladesh, Middle East) — first-cousin marriage is common; consanguinity rate can exceed 30–50% - Runs of homozygosity (ROH) on SNP array — a measure of genome-wide consanguinity; >1.5% of genome in ROH suggests second-cousin or closer parental relationship

10.4 Carrier Screening — Population Perspectives

Expanded Carrier Screening (ECS): - Offers screening for hundreds of AR and X-linked conditions simultaneously - Advantages: Comprehensive, population-agnostic (aims to cover all ethnicities) - Disadvantages: Many conditions are extremely rare; VUS and carrier results for conditions with unknown severity; counselling burden - UK position: Not yet standard in NHS; some private providers offer it

11. Genetic Counselling

11.1 Indications for Genetic Counselling Referral

11.2 The Genetic Counselling Process

Core Principles:

Process — The Genetic Counselling Consultation:

1. Pre-counselling:
2. Obtain medical records, family history, previous genetic testing results

3. Identify the proband (index case in the family)

4. Information gathering:

5. Detailed pedigree (at least 3 generations) — use standardised symbols
6. Document: ages, sex, affected/unaffected, age at diagnosis, cause of death, carrier status

7. Verify diagnoses where possible (medical records, death certificates, pathology reports)

8. Risk assessment:

9. Determine the mode of inheritance
10. Calculate recurrence risk (empiric or Bayesian)

11. Discuss probability of carrier status

12. Testing options discussion:

13. Carrier testing, diagnostic testing, presymptomatic testing, prenatal testing, PGT
14. Test limitations (false negatives, VUS, reduced penetrance)

15. Turnaround time, sample requirements

16. Risk communication:

17. Use absolute risk (not just relative risk)
18. Frame risks in multiple ways (1/100 = 1% = low/medium/high)

19. Check understanding ("Can you tell me what this means for you?")

20. Decision-making support:

21. Non-directive — present options without bias
22. Address emotional, religious, cultural, and social factors

23. Offer support resources (patient support groups, counselling services)

24. Post-test counselling:

25. Disclose results in person (or by secure telemedicine — context-dependent)
26. Discuss medical management implications
27. Discuss implications for other family members (cascade testing)
28. Offer ongoing support and follow-up

11.3 Pedigree Drawing (Standard Symbols)

Pedigree Analysis — Pattern Recognition:

11.4 Recurrence Risks

**Empiric Recurrence Risks:

Bayesian Calculation — Carrier Risk Modification: - Used when a genetic test result modifies the prior risk - Formula: Posterior odds = Prior odds × Likelihood ratio - Example: A woman with a brother with Duchenne MD has the following: - Prior probability of being a carrier given family history: 50% (she's the sister of an affected male whose mother is confirmed carrier) - But she has 2 unaffected sons (she's had 2 sons without DMD) - Likelihood of having 2 unaffected sons if she is a carrier: (1/2)² = 1/4 - Likelihood of having 2 unaffected sons if she is not a carrier: 1 - Posterior odds = (1/1) × (1/4) = 1/4 → Posterior probability = (1/4) / (1 + 1/4) = 1/5 = 20%

11.5 Ethical Issues in Genetic Counselling

11.6 Key Legislation and Regulatory Bodies

Quick-Reference Tables

Table 1: Inheritance Patterns — Summary

Table 2: Prenatal Screening Markers — Quick Reference

Table 3: Common AR Disorders — Carrier Frequencies

Table 4: Repeat Expansion Disorders — Quick Reference

Table 5: Key Genes in O&G Oncology

Essential Mnemonics for MRCOG

Key Recent Exam Themes (MRCOG Part 1 — Genetics)

Based on analysis of past MRCOG Part 1 papers, the following themes are frequently tested:

1. NIPT — cffDNA origin (trophoblast), fetal fraction, false positive/negative causes, limitations for microdeletions
2. Imprinting — PWS/Angelman mechanism (15q11, parent-of-origin); BWS/SRS (11p15); UPD concept
3. Combined test biochemistry — PAPP-A ↓ + free β-hCG ↑ for T21; know the MoM patterns
4. Robertsonian translocation — acrocentric chromosomes only; t(14;21) → Down risk by parent sex
5. Consanguinity risk — AR disease risk increased by Fpq
6. Fragile X premutation — POI in female carriers, FXTAS in male carriers; CGG repeat ranges
7. Haemoglobinopathy screening — MCV <80 or MCH <27 → Hb HPLC; HbA₂ in β-thal trait
8. BRCA/ Lynch — which ovarian/endometrial/breast cancer patients should be tested; RRSO timing
9. Mosaicism — confined placental mosaicism (CVS → need follow-up amnio); Turner mosaicism
10. Mitochondrial inheritance — maternal transmission, heteroplasmy, threshold effect; MELAS, MERRF
11. Mutation types — missense (sickle cell), nonsense (CF), frameshift, splice-site; anticipation
12. DM1 congenital — maternal transmission, polyhydramnios, talipes, floppy infant
13. X-inactivation — Barr body, XIST, escape genes (SHOX), skewed X-inactivation → manifesting carriers
14. Array CGH — detects CNVs, cannot detect balanced rearrangements; VUS counselling challenge
15. Hardy-Weinberg — calculate carrier frequency from disease incidence; applications in counselling

Practice Questions

Q1: A 30-year-old woman has a brother with Duchenne muscular dystrophy. She has had two unaffected sons. What is the probability she is a carrier?

Ans: Carrier probability given family history = 1/2 (obligate carrier mother's daughter). Given she has 2 unaffected sons, Bayesian calculation: Posterior odds = (1/1) × (1/4) = 1/4 → Posterior probability = (1/4)/(1+1/4) = 1/5 = 20%.

Q2: What is the recurrence risk of Down syndrome for a 45-year-old woman?

Ans: ~1/25 (4%) for free trisomy 21 (maternal age-related). However, recurrence risk after one affected child with free T21 is ~1% at any age (if parents have normal karyotype).

Q3: A healthy 35-year-old woman has a first-trimester combined test showing NT 4.0 mm, PAPP-A 0.4 MoM, free β-hCG 2.5 MoM. What is her most likely diagnosis?

Ans: Trisomy 21 (Down syndrome) — increased NT, decreased PAPP-A, increased free β-hCG is the classic pattern.

Q4: What is the inheritance pattern of Beckwith-Wiedemann syndrome?

Ans: Complex — usually sporadic. Can be AD with imprinting defect. Most cases involve 11p15 (paternal UPD, loss of function of maternal CDKN1C, gain of methylation at ICR1). Recurrence risk is low (<1% for sporadic cases with negative family history), but up to 50% if there is a maternal translocation affecting 11p15.

Q5: A couple of Ashkenazi Jewish descent request pre-conception carrier screening. Which conditions should be offered?

Ans: Tay-Sachs (HEXA), Canavan (ASPA), Familial dysautonomia (IKBKAP), Bloom syndrome (BLM), Fanconi anaemia (FANCC), Niemann-Pick type A (SMPD1), Gaucher (GBA), Mucolipidosis IV (MCOLN1), and CF (CFTR). BRCA founder mutations also prevalent but screening for cancer predisposition has different considerations.

Q6: A woman with a child with β-thalassaemia major presents for prenatal counselling. Both parents are carriers. What is the risk of an affected child in her next pregnancy?

Ans: 25% (1 in 4) for each pregnancy — autosomal recessive, carrier parents (both β-thalassaemia trait).

Q7: What is the significance of uniparental disomy (UPD) in Prader-Willi syndrome?

Ans: Maternal UPD15 (both copies of chromosome 15 from the mother, none from the father) accounts for ~25% of PWS. The critical imprinted genes in 15q11-q13 rely on paternal expression. Conversely, paternal UPD15 causes Angelman syndrome (loss of maternal expression of UBE3A).

Q8: A woman with a balanced Robertsonian translocation t(14;21) wants to know her chance of having a child with Down syndrome.

Ans: ~10–15% for female carriers; ~2% for male carriers. The exact risk depends on the specific translocation and the sex of the carrier.

End of Genetics Study Guide for MRCOG Part 1

Total content: ≈22,000+ words covering all 11 core sections with tables, mnemonics, clinical correlations, and exam-specific preparation material.