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Basics of human genetics

Last updated: April 13, 2021

Summarytoggle arrow icon

Human genetics is the study of the human genome and the transmission of genes from one generation to the next. The human genome consists of 23 pairs of chromosomes (22 pairs of homologous chromosomes and one pair of sex chromosomes). All homologous chromosome pairs contain two variant forms of the same gene, called “alleles,” which are passed down from parent to offspring. Genetic disorders result from new or inherited gene mutations. Epigenetic regulation of gene expression encompasses mechanisms that allow regulating the expression of the genes without modification of the DNA sequence. Hereditary disorders are passed down from parent to offspring via different patterns of inheritance, including autosomal dominant, autosomal recessive, X-linked, and mitochondrial inheritance.

For an overview of DNA and RNA structure, see “Nucleotides, DNA, and RNA.”

Genes

  • Gene: a DNA segment with a nucleotide sequence encoding an RNA product that is either directly functional or encodes a protein
  • Locus: location of a gene or a particular DNA sequence (e.g., promoter) on a chromosome
  • Allele: one of the variant forms a gene can have in a population (from a particular locus)
    • Wild-type allele: the allele that encodes for the most common phenotype in a population
    • Mutant allele: any allele that does not code for the most common phenotype in a population
  • Multiple alleles: the occurrence of more than two different alleles in a population (e.g., the ABO blood group system) [1]
  • Allele frequency: the prevalence of a particular allele at a genetic locus within a population
  • Genetic polymorphism: a gene with more than one allele occupying the same locus of that gene [2]

Chromosomes

The mitotic spindle attaches to the kinetochores, not the centromeres.

Genotype and phenotype

Compared to dominant alleles, that have the same phenotypical expression regardless of the zygosity, codominant alleles express two completely different phenotypes in homozygous and heterozygous individuals.

Genetic penetrance and expressivity

Types of genetic penetrance and expressivity
Definition Example
Penetrance
  • -
Complete penetrance
Incomplete penetrance
  • Phenotypical expression of a particular gene or genomic region is not observed in all individuals
Variable expressivity
  • The variable phenotypic expression of a given genotype, which implies that a genetic disorder can manifest with different signs, symptoms, and degrees of severity in different individuals
Pleiotropy
  • A phenomenon in which one gene influences the development of multiple phenotypical traits
Compound heterozygosity
Anticipation (genetics)
  • A phenomenon in which disease onset occurs earlier and/or the disease manifestation is more severe in offspring than in parents.
Allelic heterogeneity
  • A phenomenon in which different mutations of the same allele result in the same phenotype
Locus heterogeneity
Linkage disequilibrium
  • The property of particular alleles at two linked loci to be expressed more or less often than would be expected in the general population
  • May vary in different populations
  • May occur in settings where allelic loci are within close proximity to each other on a chromosome, therefore decreasing the probability of DNA recombination
  • individuals from the population who are not blood-related (i.e., in which a random association of the alleles would be expected).

Overview

Mutations according to the affected cell population

Terminology of chromosomal abnormalities

Most common terms of chromosomal abnormalities
Abbreviation Term Example Interpretation
del Deletion 46,XY, del(p5) Deletion of the short arm of chromosome 5 in a male individual (e.g., cri-du-chat syndrome)
dup Duplication 46,XX, dup(q3) Duplication of the long arm of chromosome 3 in a female individual
inv Inversion 46,XY, inv(3)(p23q27) Pericentric inversion of the chromosome 3 segment with breakpoints at position 23 on the short arm and 27 on the long arm in a male individual
t Translocation 46,XY, t(14;18)(q32;q21) Translocation between position 32 on chromosome 14 and position 21 on chromosome 18 in a male individual (e.g., follicular lymphoma)
rob Robertsonian translocation 46,XX, rob(14;21) Chromosomal translocation with fusion of the long arms of the acrocentric chromosomes 14 and 21 in a female individual. The short arms of the two chromosomes involved are lost.
/ Mosaicism 45,X/46, XX Presence of a normal cell population and one with X monosomy in a female individual (e.g., Turner syndrome)

Chromosomal aberrations

Introduction

Subtypes of chromosomal aberrations

Types of chromosomal translocations

All translocations are classified as structural chromosomal aberrations.

Other chromosomal aberrations

Uniparental disomy cannot be detected via karyotyping because the number of chromosomes is normal and there is no loss of genetic material.

HeterodIsomy: meiosis I error; IsodIsomy: meiosis II error

12–345: the chromosomes most frequently involved in Robertsonian translocations are chromosomes 21, 22, 13, 14, and 15.

Gene mutations

Types of gene mutations

  • Point mutation: alteration of a single DNA base pair
    • Genetic transition: the replacement of one purine with another purine (e.g., G to A), or the replacement of a pyrimidine with another pyrimidine (e.g., T to C)
    • Genetic transversion: the replacement of a purine with a pyrimidine (e.g., A to C, A to T, G to C, G to T) and vice versa
  • Deletion: loss of one or more base pairs
  • Insertion: addition of one or more base pairs
  • Substitution: one or more base pairs are replaced by different base pairs
  • Trinucleotide repeat expansion
    • Increased repetition of base triplets that leads to faulty protein synthesis or folding
    • Characterized by genetic anticipation
Trinucleotide repeat expansion diseases
Mode of inheritance Affected gene Chromosome Trinucleotide repeat Typical features
Huntington disease Autosomal dominant HTT 4 CAG Chorea, akinesia, cognitive decline, behavioral changes
Fragile X syndrome X-linked dominant FMR1 X CGG Large protruding chin, large genitalia (testes), hypermobile joints, mitral valve prolapse
Myotonic dystrophy Autosomal dominant DMPK 19 CTG Cataracts, premature hair loss in men, myotonia, arrhythmia, gonadal atrophy (men), ovarian insufficiency (women)
Friedreich ataxia Autosomal recessive FXN 9 GAA Ataxic gait, dysarthria, kyphoscoliosis, hypertrophic cardiomyopathy

Friedrich gave the fragile hunter my tonic: Friedreich ataxia, fragile X syndrome, Huntington disease, and myotonic dystrophy are examples of trinucleotide expansion disorders.
In Huntington disease, a CAG trinucleotide repeat leads to Chorea, Akinesia, and Grotesque behavior.
In fragile X syndrome, a CGG trinucleotide repeat leads to an X-tra large Chin and Giant Genitalia.
In myotonic dystrophy, a CTG trinucleotide repeat leads to Cataracts, Thinning hair (premature hair loss), and Gonadal atrophy.
In Friedreich ataxia, a GAA trinucleotide expansion leads to an ataxic GAAit.

Classification of gene mutations

Grade of mutational severity in ascending order: silent < missense < nonsense < frameshift

Compared to missense or silent mutations, nonsense and frameshift mutations lead to fundamental structural changes of the coded proteins. Consequently, these mutations result in more severe disease manifestations.

STOP the NONSENSE: NONSENSE mutations create early STOP codons in the RNA.

Examples of genetic disorders by chromosome

Overview

Main mechanisms of epigenetic regulation

DNA methylation [7]

Epigenetic regulation mechanisms: Acetylation Activates DNA; Methylation Mutes DNA.

Histone modification [13][14]

Regulatory RNA [15]

Examples of processes regulated by epigenetic mechanisms

X inactivation (lyonization)

Genomic imprinting [18]

Overview

  • Definition: the study of inherited traits or disorders and their phenotypic variability over several generations in a group of blood-related individuals by way of a pedigree chart, which depicts that group's genetic history in a family tree
  • Elements
    • Circles: female individuals
    • Squares: male individuals
    • Lines between circles and squares: familial relationship
    • Roman numerals: generations
    • Arabic numbers: children of a generation in order of birth
    • Affected family members and carriers (i.e., heterozygous individuals who have the allele but are not phenotypically affected) are represented by shaded symbols.

A basic methodological approach to pedigree analysis

  • Question 1: Does every affected family member have an affected parent?
    • Yes: dominant inheritance of the trait
    • No: recessive inheritance of the trait
  • Question 2: Are the majority of affected family members male?
    • Yes: most likely X-linked recessive inheritance
    • No: Proceed to the following questions and subsequent answers.
      • Question 2a: Do all affected male family members have an affected mother?
      • Question 2b: Do all affected male family members have unaffected sons?
      • Question 2c: Do all affected male family members have affected daughters?
        • If Questions 2a, 2b, and 2c have all been answered in the affirmative, the disease most likely follows an X-linked dominant pattern of inheritance.
        • If Question 1 has been answered in the affirmative and either Question 2a, 2b, or 2c have been answered in the negative, the disorder is most likely autosomal dominant.
        • If Question 2 and Questions 2a, 2b, and 2c have all been answered in the negative, the disorder is most likely autosomal recessive.

Overview

Examples of AD inheritance patterns

AD inheritance pattern in homozygous parents
Homozygous parent (affected)
N N
Homozygous parent (unaffected) n Nn (affected) Nn (affected)
n Nn (affected) Nn (affected)
AD inheritance pattern in heterozygous and homozygous parent
Heterozygous parent (affected)
N n
Homozygous parent (unaffected) n Nn (affected) nn (unaffected)
n Nn (affected) nn (unaffected)
AD inheritance pattern in heterozygous parents
Heterozygous parent (affected)
N n
Heterozygous parent (affected) N NN (affected) Nn (affected)
n Nn (affected) nn (unaffected)

An autosomal dominant disease with complete penetrance will always manifest with clinical features in every generation.

Examples of AD disorders

Overview

Examples of AR inheritance patterns

  • Homozygous parents: no children will be affected, but all will be carriers
AR inheritance pattern in homozygous parents
Homozygous parent (unaffected)
N N
Homozygous parent (affected) n Nn (carrier) Nn (carrier)
n Nn (carrier) Nn (carrier)
  • One heterozygous and one homozygous parent: All children inherit the allele that causes the trait or disorder, but only 50% will express the trait while other 50% will be carriers.
AR inheritance pattern in heterozygous and homozygous parent
Heterozygous mother (carrier)
N n
Homozygous father (affected) n Nn (carrier) nn (affected)
n Nn (carrier) nn (affected)
  • Heterozygous parents
    • Half of the children will be carriers, 25% will express the trait, and 25% will not express the trait.
    • Healthy individuals with an affected sibling (nn) have a two-thirds-probability of being a carrier (Nn, Nn, or NN).
AR inheritance pattern in heterozygous parents
Heterozygous parent (carrier)
N n
Heterozygous parent (carrier) N NN (unaffected) Nn (carrier)
n Nn (carrier) nn (affected)

Examples of AR disorders

Overview

  • Definition: a mode of inheritance that requires two copies of an allele on the X chromosome, one from the mother and one from the father, for the phenotypical expression of a trait or disorder in offspring
  • X-linked recessive (XR) inheritance leads to the expression of the phenotype in all male children who inherit the mutated allele.
  • Female individuals are more frequently carriers (unaffected) of X-linked inherited disorders than male individuals.
  • Individuals with Turner syndrome only have one X chromosome and are, therefore, more susceptible to X-linked recessive disorders
  • Male-to-male inheritance is impossible.
  • Male individuals tend to develop a more severe form of the XR disease.
  • This type of inheritance frequently skips generations.

Examples of XR inheritance patterns

XR inheritance pattern in heterozygous (carrier) mother and hemizygous (unaffected) father
Heterozygous mother (carrier)
x X
Hemizygous father (unaffected) X Xx (daughter, carrier) XX (daughter, unaffected)
Y xY (son, affected) XY (son, unaffected)
XR inheritance pattern in heterozygous (carrier) mother and hemizygous (affected) father
Hemizygous father (affected)
x Y

Heterozygous mother (carrier)

X Xx (daughter, carrier) XY (son, unaffected)
x xx (daughter, affected) xY (son, affected)
XR inheritance pattern in homozygous (unaffected) mother and hemizygous (affected) father
Hemizygous father (affected)
x Y
Homozygous mother (unaffected) X Xx (daughter, carrier) XY (son, unaffected)
X Xx (daughter, carrier) XY (son, unaffected)
  • Homozygous (affected) mother and hemizygous (affected) father: If both parents have the trait/disease then all children will invariably be affected.
XR inheritance pattern in homozygous (affected) mother and hemizygous (affected) father
Hemizygous father (affected)
x Y
Homozygous mother (affected) x xx (daughter, affected) xY (son, affected)
x xx (daughter, affected) xY (son, affected)

Examples of XR disorders

Overview

  • Definition: a mode of inheritance that only requires one copy of a mutated allele on the X chromosome, from either the mother or father, for the phenotypical expression of the trait or disorder in offspring
  • In X-linked dominant (XD) inheritance, male and female individuals have an equal probability of inheriting the trait or disorder.
  • Because female individuals have two X chromosomes, the inheritance of an X-linked dominant disorder typically manifests in a less severe form than in male individuals.

Examples of XD inheritance patterns

XD inheritance pattern in heterozygous mother and hemizygous (unaffected) father
Heterozygous mother (affected)
X x
Hemizygous father (unaffected) x Xx (daughter, affected) xx (daughter, unaffected)
Y XY (son, affected) xY (son, unaffected)
  • Homozygous mother and hemizygous (unaffected) father: All the children will inherit the trait/disease.
XD inheritance pattern in homozygous mother and hemizygous (unaffected) father
Homozygous mother (affected)
X X
Hemizygous father (unaffected) x Xx (daughter, affected) Xx (daughter, affected)
Y XY (son, affected) XY (son, affected)
XD inheritance pattern in heterozygous mother and hemizygous (affected) father
Hemizygous father (affected)
X Y
Heterozygous mother
(affected)
X XX (daughter, affected) XY (son, affected)
x Xx (daughter, affected) xY (son, unaffected)
  • Homozygous (unaffected) mother and hemizygous (affected) father
    • All daughters will be affected.
    • Sons are invariably unaffected.
XD inheritance pattern in homozygous (unaffected) mother and hemizygous (affected) father
Hemizygous father (affected)
X Y
Homozygous mother (unaffected) x Xx (daughter, affected) xY (son, unaffected)
x Xx (daughter, affected) xY (son, unaffected)

Examples of XD disorders

Mitochondrial inheritance

Polygenic inheritance

Heterozygote frequency

  • Definition
    • The proportion of heterozygote carriers of an allele that causes a trait/disorder in the population
    • Used to estimate a child's risk of a recessive inherited disorder if the genotype of the parents is unknown
  • Equation: The heterozygote frequency is calculated by using the Hardy-Weinberg law, a principle that states that genetic variation in a population remains constant under a set of idealized assumptions (including random mating and no migration, mutation, or selection).
    • Hardy-Weinberg equilibrium: (p+q)2 = p2 + 2pq + q2 = 1 (100%).
    • The Hardy-Weinberg law is based on the biostatistically ideal assumptions that:
      • There is no natural selection of alleles in the population.
      • No mutations occur in the allele under investigation.
      • There is random mating inside the population.
      • The population is large enough to rule out the effects of genetic drift.
      • There is no migration both outside and inside the population.
  • Example: cystic fibrosis with an incidence of ∼ 1:2,500
    • Calculate 2pq: 2pq = 2×1×1/50 = 1/25 (4%) heterozygote frequency
    • Calculate p: If (p + q)2 = 1 then p + q = 1 and p = 1 – q = 1 – 1/50 = 0.98 (98%) ≈ 1
    • Calculate q: If q2 = 1/2,500 then q = 1/50 = 0.02 (2%)
    • Since cystic fibrosis is a recessive disorder, only homozygote carriers develop the disease. The incidence corresponds to the homozygote frequency q2.
A (p) a (q)
A (p) AA (p2) Aa (pq)
a (q) Aa (pq) aa (q2)

Multifactorial inheritance disorders (MID)

  • Definition: disorders that result from a combination of mutations in multiple genes and environmental factors (e.g., type 2 diabetes mellitus, cleft palate, neural tube defects, schizophrenia, coronary artery disease)
  • Features
    • Commonly manifest with the Carter effect [20]
      • Individuals of the less commonly affected sex are more likely to pass on the disorder to their children if they develop the disease.
      • It is hypothesized the group less commonly affected possesses a higher number of susceptibility genes and the trait/disorder will, therefore, manifest less frequently, requiring more genetic loci to be affected.
      • However, the numerical increase in susceptibility genes leads to an increased probability of passing on mutated alleles to offspring.
    • Population groups with a certain heritage are more commonly affected compared to the population at large (e.g., Hispanic, Ashkenazi Jewish, West African).
    • One gender is more frequently affected.
    • Isolated occurrence is possible, but familial clustering is frequent.
  • Index case: the first person of a family to develop the trait/disorder in question
  • Threshold effect: Effect observed in some MIDs, in which the disorder only develops when genetic predispositions and external factors combine to reach a certain threshold value.
  • Gene-environment interaction: genetic predisposition affects susceptibility to the effects of environmental factors (e.g., individuals with a family history of type II diabetes may never develop the disease if they maintain a healthy lifestyle).
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