Cytogenetics and Patterns of Inheritance Study Guide to Patterns of Inheritance

Fundamentals of Cytogenetics

• Definition of Cytogenetics: The study of intact chromosomes, which consist of double-stranded DNA (dsDNA) complexed with histone and non-histone proteins.

• Human Chromosome Complement:

  • Total of 46 chromosomes (23 pairs).

  • 22 pairs are homologous autosomes.

  • 1 pair is composed of sex chromosomes ($XX$ or $XY$).

• Genetic Organization: Genes are encoded within the DNA and are arrayed along the length of each chromosome.

• Karyotype: A visual representation of the chromosomes within a cell, used to identify numerical and structural abnormalities.

Categories of Genetic Disorders

• Monogenic Disorders: Single-gene disorders that follow Mendelian inheritance patterns. They generally have large effects, occur mostly in the pediatric age range, and are highly penetrant but uncommon.

• Chromosomal Disorders: Structural or numerical aberrations in chromosomes. These are highly penetrant but uncommon; many such pregnancies do not continue to term.

• Polygenic (Multifactorial) Disorders: Complex multigenic disorders that involve the cumulative effect of multiple polymorphisms and environmental factors.

Numerical Chromosomal Abnormalities

• Euploidy: Chromosome numbers that are exact multiples of the haploid set.

  • Normal state is diploid ($2N$).

  • Abnormal states include triploid ($3N$; 69 chromosomes) and tetraploid ($4N$).

• Aneuploidy: The gain or loss of a few specific chromosomes, often resulting in physical or mental maldevelopment.

  • Nondisjunction: The failure of a chromosome pair to disjoin properly during one of the two meiotic divisions.

    • Meiosis I Error: Gametes contain both members of a chromosome pair or lack the chromosome entirely.

    • Meiosis II Error: Gametes contain two copies of one parental chromosome (and none of the other) or lack the chromosome entirely.

• Common Aneusomies:

  • Autosomal Trisomies (Compatible with life):

    • Trisomy 13 (Patau Syndrome).

    • Trisomy 18 (Edwards Syndrome).

    • Trisomy 21 (Down Syndrome).

  • Trisomy 16: The most common autosomal trisomy found in spontaneous abortions; it is not reported in live births.

  • Sex Chromosome Monosomy: $45,X$ (Turner Syndrome) is the only viable monosomy.

Uniparental Disomy (UPD)

• Definition: A condition where both copies of a specific chromosome are inherited from a single parent.

• Types of UPD:

  • Heterodisomy: Two different chromosomes are inherited from the same parent. This often results from the reduction of a trisomy to a disomy (trisomy rescue).

  • Isodisomy: Two copies of the exact same chromosome from one parent. This often results from monosomy rescue involving the duplication of a single existing chromosome.

• Clinical Relevance: UPD is associated with Prader-Willi and Angelman syndromes and plays a role in the Knudson 2-Hit Hypothesis for cancer development (where UPD leads to a "copy neutral LOH" or loss of heterozygosity).

Structural Chromosomal Abnormalities

• Mechanisms: Rearrangements resulting from chromosome breakage followed by abnormal reconstitution. To be stable through mitosis and meiosis, a rearranged chromosome must possess one centromere and two telomeres.

• Classification:

  • Balanced: The chromosome set contains a normal complement of material despite the rearrangement.

  • Unbalanced: There is additional (duplex/insertion) or missing (deletion) chromosomal material.

• Specific Structural Changes:

  • Deletion: Loss of a segment (terminal or interstitial), often generating an acentric fragment.

  • Duplication: Extra copies of a segment due to unequal crossing over.

  • Inversion: A segment is reversed end-to-end.

  • Isochromosome: A chromosome that has lost one of its arms and replaced it with an exact copy of the other arm (e.g., an isochromosome for the long arm).

  • Ring Chromosome: Formed when a chromosome loses its ends and the remaining arms fuse into a circle.

  • Translocations:

    • Reciprocal Translocation: Exchange of segments between two non-homologous chromosomes. Usually harmless but can cause germ line issues in offspring.

    • Robertsonian Translocation: Fusion of the long arms of two acrocentric chromosomes (e.g., chromosomes 14 and 21) at the centromere, with the loss of the short arms (nubbins). Carriers are usually normal, but offspring may have trisomy 21 or 13.

Cytogenetic Nomenclature and Clinical Practice

• ISCN 2020 System: Chromosome descriptions consist of three parts: total number of chromosomes, sex chromosome complement, and any abnormalities.

  • Example constitutional: $45,X$.

  • Example with gain: $47,XX,+13$.

  • Mosaicism Syntax: Different cell lines are separated by a slash with the cell count in brackets, e.g., $45,X[15]/47,XXX[3]/46,XX[12]$.

• Cell Types for Analysis:

  • Peripheral blood mononuclear cells.

  • Skin biopsy (fibroblasts).

  • Transformed (immortal) lymphocytes.

  • Bone marrow (characteristically short chromosomes).

  • Fetal cells via amniocentesis or chorionic villus sampling (CVS).

• Indications for Analysis: Early growth/development problems, stillbirth, fertility issues, family history, neoplasia, and advanced maternal age.

Mendelian Inheritance Patterns

• Gene Variants: The American College of Medical Genetics and Genomics (ACMG) recommends replacing "mutation" with "variant," classified into five tiers: Pathogenic, Likely Pathogenic, Uncertain Significance (VUS), Likely Benign, and Benign.

• Zygosity Definitions:

  • Heterozygous: Two different alleles ($Aa$).

  • Homozygous: Two identical alleles ($AA$ or $aa$).

  • Compound Heterozygote: Two different heterozygous pathogenic variants in the same gene.

  • Hemizygous: A male with an abnormal allele on his single $X$ chromosome.

• Autosomal Dominant (AD):

  • 50% risk of inheritance if one parent is $Hh$ and the other is $hh$.

  • Features: Variable age of onset, incomplete penetrance (not all with the mutation show the phenotype), and variable expressivity (different degrees of severity).

  • Blau Syndrome: Resulting from $NOD2$ gene mutations causing an overactive protein and abnormal inflammatory reactions.

• Autosomal Recessive (AR):

  • 25% risk for affected offspring if both parents are carriers ($Cc \times Cc$).

  • Carrier risk for unaffected siblings is 50% ($1/2$).

  • Often associated with consanguinity (union between second cousins or closer).

• X-Linked Recessive (XLR):

  • Carrier female mating ($Dd \times D-$): 50% of sons affected, 50% of daughters are carriers.

  • Affected male mating ($d- \times DD$): All daughters are carriers; no sons are affected.

  • Lyonization: Random and permanent X-inactivation in females creating a mosaic; skewed inactivation can lead to manifesting female carriers.

• X-Linked Dominant (XLD):

  • Affected males pass the trait to all daughters and no sons.

  • Affected females pass the trait to 50% of offspring regardless of sex.

  • Often lethal in males (e.g., Rett Syndrome, caused by $MECP2$ gene mutations on the $X$ chromosome).

Non-Classical and Mitochondrial Inheritance

• Mitochondrial DNA (mtDNA): Circular dsDNA within the mitochondrial matrix encoding 37 genes (13 OXPHOS polypeptides, 22 tRNAs, 2 rRNAs).

  • Maternal Inheritance: Only the mother transmits mitochondria to children.

  • Heteroplasmy: A mixture of wild-type and mutant mtDNA within a cell.

  • Replicative Segregation: Random distribution of mitochondria to daughter cells during division.

  • Threshold Effect: Disease occurs only when the proportion of mutated mtDNA exceeds a certain level.

  • Disorders: Myoclonic epilepsy with ragged red fibers (MERFF), Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), and Leber's Hereditary Optic Neuropathy (LHON).

• Trinucleotide Repeat Disorders: Caused by unstable expansions of repetitive DNA sequences.

  • Anticipation: Successive generations show earlier onset and increased severity.

  • Premutation: An unaffected person has a repeat count at the upper limit of normal that can expand in the next generation.

Epigenetics and Genomic Imprinting

• Epigenetics: Changes that turn genes "on" or "off" without altering the DNA sequence, often via DNA methylation (silencing) or demethylation (activating).

• Genomic Imprinting: Epigenetic silencing of an allele based on the parent of origin, occurring during gametogenesis.

• Prader-Willi (PWS) vs. Angelman (AS) Syndromes:

  • Both involve the $15q11-q13$ region.

  • PWS: Loss of the paternal contribution (usually via deletion or maternal UPD). Associated with the $SNRPN$ gene; symptoms include hyperphagia (extreme hunger), obesity, and motor delays.

  • AS: Loss of the maternal contribution (usually via deletion, paternal UPD, or $UBE3A$ point mutation). Symptoms include seizures, jerky gait ("happy puppets"), and developmental disabilities.

Advanced Genetic Concepts

• Dominant Negative Variant: A mutation where the product of the mutant allele interferes with the function of the wild-type allele (e.g., Type II Osteogenesis Imperfecta).

• Mosaicism: Presence of two or more cell populations with different genotypes in one individual.

  • Somatic Mosaicism: Postzygotic mutation affecting body cells; often results in milder phenotypes.

  • Gonadal Mosaicism: Mutation exists only in germ cells; the parent is phenotypically normal but can pass the trait to multiple offspring.

• Chimera: An individual derived from two different zygotes.

• Co-dominance: Both alleles are equally expressed (e.g., ABO blood groups and $\alpha_1$-antitrypsin).

Multifactorial and Population Genetics

• Multifactorial Traits:

  • Quantitative Traits: Follow a normal distribution in a population (e.g., height, blood pressure).

  • Threshold Traits: Qualitative (yes/no) traits depending on a liability threshold (e.g., cleft lip, pyloric stenosis).

• Heritability ($H$): Estimate of genetic contribution to a trait ($H=0$ is entirely environmental; $H=1$ is entirely genetic).

• Recurrence Risk (RR): The probability that a disease will occur in relatives. Factors increasing RR include high heritability, being a first-degree relative, multiple affected family members, higher severity of the disorder, and consanguinity.

• Hardy-Weinberg Equilibrium: Describes a state where allele and genotype frequencies remain constant over generations in a large, random-mating population.

  • Assumptions: No mutations, large population size, isolation (no migration), equal survival and reproduction, and random mating.