Jiří Navrátil
Genetic determination of disease
•Heredity
•Genetic variability (mutations  polymorphism)
•Monogenic  complex diseases
History
• Johann Gregor Mendel was a meteorologist, mathematician, biologist, Augustinian friar and abbot of St. Thomas' Abbey
in Brno
He worked with seven characteristics of pea plants: plant height, pod shape and color, seed shape and color, and flower
position and color.
• Laws of Mendelian genetics
1. Law of dominance
In a heterozygote, one trait will conceal the presence of
another trait for the same characteristic. Rather than both
alleles contributing to a phenotype, the dominant allele
will be expressed exclusively
2. Law of segregation
When an organism makes gametes, each gamete
receives just one gene copy, which is selected randomly
3. Law of independent assortment
The alleles of two (or more) different genes get sorted
into gametes independently of one another → the allele a
gamete receives for one gene does not influence the
allele received for another gene.
Genetics
• Genetics – specialised field of biology focusing on variability and heritability in living
organism
• Human genetics
• study variability and heritability in human
• Clinical genetic
• study pathological states, diagnostics, genetic counselling and prevention
(family members)
• Cytogenetics
• chromosome alterations
• Molecular genetics
• study of the structure and function of isolated genes
• Population genetics
• study of variability in populations
• comparative and evolutionary genetics
• inter-species comparisons and evolution of species
Genomics
• study of the structure and function of genomes by means of genetic mapping, sequencing and functional analysis of
genes
• aims to understand entire information contained in DNA
o structural genomics = structure of genomes
• construction of detail genetic, physical and transcriptional maps of genomes with ultimate aim to
complete entire DNA sequence
• (e.g. HUGO project)
o functional genomics = function of genes and other parts of genome
• understanding of the function of genes; very often using model organisms (mouse, yeast, nematodes,
Drosophila etc.) as an alternative to higher organisms (many generations in relatively short time)
o Bioinformatics = concerned with the acquisition, storage, analysis, and dissemination of biological data,
most often DNA and amino acid sequences
• uses computer programs for a variety of applications, including determining gene and protein
functions, establishing evolutionary relationships, and predicting the three-dimensional shapes of
proteins)
Genetic Terminology
• gene, allele, genome, chromozome
• locus
• alleles
- dominant
- recessive
• homozygote
• heterozygote
• genotype
• phenotype
Chromosomal basis of heredity
• DNA and RNA
DNA: is the hereditary material in humans
and almost all other organisms containing
the instructions needed for an organism
to develop, survive and reproduce
It is made of chemical building blocks called nucleotides that are made of three parts:
1. A phosphate group
2. A sugar group
3. A nitrogen base (adenine (A), thymine (T), guanine (G) and cytosine (C))
To form a strand of DNA, nucleotides are linked into chains, with the phosphate and sugar groups alternating
• DNA double helix
RNA: molecule similar to DNA. Unlike DNA,
RNA is single-stranded
messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA)
combined form the repeating ‘backbone’ of the DNA strands
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Central dogma of molecular biology
DNA
• DNA was discovered in 1869 by Swiss researcher Friedrich Miescher, who
was originally trying to study the composition of lymphoid cells (white
blood cells). Instead, he isolated a new molecule he called nuclein (DNA
with associated proteins) from a cell nucleus
• In 1953 when James Watson and Francis Crick deduced how nucleotides
are organized within DNA.
• 1962 The Nobel Prize in Physiology or Medicine ( - Rosalind Franklin)
Gene
basic physical and functional unit of heredity
Genes are made up of DNA
Some genes act as instructions to make molecules called proteins. However, many
genes do not code for proteins
• Structural genes
• Genes for RNA
• Regulatory genes
• Exon = portion of a gene that codes for amino acids
• Intron = portion of a gene that does not code for aa
• Intronless genes - single-exon genes
• Gene family = A group of genes that are related
in structure and often in function. The genes in a gene
family are descended from an ancestral gene. For example,
the hemoglobin genes belong to one gene family that was
created by gene duplication and divergence
Gene structure
The human karyotype
• A karyotype is an individual's collection of
chromosomes → each organism has
different number and shape of
chromosomes
• mouse 40 chromosomes
• crayfish 200 chromosomes
• fruit flies 8 chromosomes
• Diploid human cells contain 46
chromosomes
• 44 autosomes
• 2 sex chromosomes, which are XX in
females and XY in males
• At mitotic metaphase, each of the 46
chromosomes consists of two identical
sister chromatids
Analysis of mitotic chromosomes
• Staining by dyes (e.g. Giemsa) leads to the characteristic band pattern
• Quinacrine – Ultraviolet irradiation causes some of the quinacrine molecules that
have inserted into the chromosome to emit energy. Parts of the chromosome
shine brightly, whereas other parts remain dark.
• This bright-dark banding pattern is highly reproducible and is also specific for each
chromosome
• The most advanced technique used by cytogeneticists today is called chromosome
painting. With this technique, colorful chromosome images are created by treating
chromosome spreads with fluorescently labeled DNA fragments that have been
isolated and characterized in the laboratory. Such a fragment may, for instance,
come from a particular gene.
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Human genome
• Human Genome Project (HUGO)
1990 - 2003
• ~3.3109 bp in haploid genome
• 99.9% identical sequence
• only ~3% coding sequences
• ~30 000 genes expressed in variable
periods of life
• ~25 000 proteins
• the rest are RNAs and others regulators
• ~75% formed by unique (nonrepetitive)
sequence, the rest are
repetitions
• function is not clear, could be structure
effects or evolutionary reserve
• types of repetitions
• tandem
• microsatellites
• minisatellites
• Alu-repetitions
• L1-repetitions
• density of genes in and between each
chromosome is quite heterogeneous
• mitochondrial DNA
• several tens of genes coding proteins
involved in mitochondrial processes
• respiratory chain
• inherited from mother!
• HapMap project 2003 – 2005
• n=269 subjects of 4 ethnicities
(Yoruba, Han, Japanese, Caucasian)
to asses character of LD and extent
of genetic variability (= 0.1%)
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Non-nuclear DNA
Mitochondrial DNA (mtDNA)
• origin: alfaproteobacteria fused by eukaryotickou buňkou
• During evolution, many mitochondrial genes were transferred to the nucleus
(proterins coded by these genes and very similar to genes coded by bacteria)
• In humans, for example, the mtDNA consists of 16,571 base pairs
• 37 distinct genes are packed into a 16- to 17-kb circle
o 2 for ribosomal RNAs
o 22 for transfer RNAs
o 13 for polypeptides involved in oxidative phosphorylationmaternální dědičnost
Circulating free DNA (cfDNA)
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Repetitive sequences
Repetitive sequences = sequences that are repeated many times over
• concentrated in centromeres, which anchor spindle fibers to chromosomes during
mitosis, and telomeres, which are special structures at the ends of
chromosomes.
• necessary to format expression of unique coding sequence files and to organise
additional functions essential for genome replication and accurate transmission
to progeny cells
• possible evolutionary reserve
• Interspersed repeats
o DNA transposomes (eg. „Sleeping Beauty“ – gene therapy)
o retrotranspozony
• LTR - Identical or nearly identical DNA sequences at opposite ends of an integrated
retrovirus or a retroviruslike element.
• Long-Interspersed Elements (LINEs)
• Short-Interspersed Elements (SINEs) – (Alu family in humans)
• Tandem repeats = za sebou jdoucí identické repetice, VNTR
o Short tandem repeat (STR) (microsatellite) - A highly polymorphic tandem repeat
of a sequence only two to five nucleotide pairs in length.
o Variable number tandem repeat (VNTR) (minisatellite) - A highly polymorphic
tandem repeat of a sequence of 10 to 80 nucleotide pairs in length.
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Repetitive sequences - clinical examples
• Huntington disease – progressive brain disorder that causes uncontrolled
movements, emotional problems, and loss of thinking ability (cognition).
• Caused by the mutation in the HTT gene. The HTT gene provides instructions for
making a protein called huntingtin. Although the function of this protein is
unclear, it appears to play an important role in nerve cells (neurons) in the
brain.
• The HTT mutation that causes Huntington disease involves a DNA segment
known as a CAG trinucleotide repeat. This segment is made up of a series of
three DNA building blocks (cytosine, adenine, and guanine) that appear multiple
times in a row. Normally, the CAG segment is repeated 10 to 35 times
within the gene. In people with Huntington disease, the CAG segment is
repeated 36 to more than 120 times. People with 36 to 39 CAG repeats may
or may not develop the signs and symptoms of Huntington disease, while
people with 40 or more repeats almost always develop the disorder.
• An increase in the size of the CAG segment leads to the production of an
abnormally long version of the huntingtin protein. The elongated protein is cut
into smaller, toxic fragments that bind together and accumulate in neurons,
disrupting the normal functions of these cells.
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Repetitive sequences - clinical examples
• Myotonic dystrophy – part of a group of inherited disorders called muscular
dystrophies. It is the most common form of muscular dystrophy that begins in
adulthood
• Myotonic dystrophy is characterized by progressive muscle wasting and
weakness. People with this disorder often have prolonged muscle contractions
(myotonia) and are not able to relax certain muscles after use. For example, a
person may have difficulty releasing their grip on a doorknob or handle. Also,
affected people may have slurred speech or temporary locking of their jaw.
• Myotonic dystrophy type 1 is caused by mutations in the DMPK gene, while type
2 results from mutations in the CNBP gene
• In each case, a segment of DNA (trinucleotide CTG on 3´) is abnormally
repeated many times, forming an unstable region in the gene
• The gene with the abnormal segment produces an unusually long messenger
RNA, which is a molecular blueprint of the gene that guides the production of
proteins. The unusually long messenger RNA forms clumps inside the cell that
interfere with the production of many other proteins.
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Telomere function
• Telomeres – distinctive structures found at
the ends of our chromosomes
• made of repetitive sequences of noncoding
DNA that protect the
chromosome from damage
• In humans the telomere sequence is
TTAGGG → repeated about 3 000 times
• Each time a cell divides, 25-200 bases
are lost from the ends of the telomeres
on each chromosome
• Hayflick limit – number of times a normal
cell population divides before entering the
senescence phase
• In humans 40 to 60 times
• Telomerase enzyme
• Embryonic stem cells
• Cancer cells
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Repetitive sequences - clinical examples
• Hutchinson-Gilford Progeria Syndrome
(HGPS) – rare premature aging disorder
caused by mutations in the gene LMNA,
which encodes the nuclear matrix protein
lamin A.
• Average telomere length in
fibroblasts from HGPS patients is
shorter than in age-matched
controls.
• How mutations in lamin A lead to
shortened telomere lengths is not
known nor is the contribution of
individual chromosome ends to the
low average length understood
• Shorter telomeres are symptom not
cause of the disease!
Gene  allele  genotype  phenotype
• gene – basic unit of heritability
• gene families
• sequence evolution similarity among genes formed e.g.
by duplication
• hemoglobin chains, immunoglobulins, some isoenzymes, …
• pseudogenes
• similar to functional genes by non-functional
• each gene occupies particular site in the
chromosome = locus (e.g. 12q21.5)
• localization of genes in the same in species but
sequence is not!
• allele – sequence variant of gene
• vast majority of genes in population has several
variants (= alleles) with variable frequency =
genetic polymorphism
• genotype – combination of alleles in a given
locus in paternal and maternal chromosomes in
diploid genome
• haplotype – linear combination of alleles in a
single ch. of homologous pair
• phenotype – expression of genotype
• trait –measurable, very often continuous variable
• QTL – quantitative trait locus (e.g. weight, height, …)
• phenotype – set of traits
• intermediate phenotype – similar to trait but not
always continuous
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How big difference in DNA amount
between banana and human?
• 50% - 60%
• Most DNA is involved in production of proteins, enzymes for
creating or breaking down sugars, for building cellular
structures and processes, etc. etc.
• Structure of the hemoglobin pigment (a protein) has a lot of
common code with the structure of the chlorophyll pigment.
• the same basic molecule structure was basically readapted
for two very different functions
• lot of DNA has no function called "junk DNA."
• It's this junk DNA that's really a tell-tale sign of common
ancestry. Why else would there be common sequences of
base-pairs in the DNA, that are present in both species, but
serves no function in either species?
• 90% identity in mammals
• 99,9% identity between peoble
Genetic variability (~0.1%)
• DNA sequence of coding as well as
non-coding regions of genome is
variable in each individual
• genetic variability = v existence
of several variants (alleles) with
various frequency for a given
gene in population
• sources:
• 1) sexual reproduction
• 2) recombination (meiotic
crossing-over)
• 3) mutations de novo
• “errors” during DNA replication
• proof-reading of DNA
polymerase is not 100%
• effect of external mutagens
• 4) effects on the population level
(evolution) – Hardy/Weinberg law
• natural selection = adaptive
(reproductive success)
• genetic (allelic) drift = random
selection of alleles (entirely from
chance)
• “founder” effect
Crossing-over and recombination
• each gamete formed receives randomly 1 ch. of the homologous pair of chromosomes
- paternal (CHp) or maternal (CHm)
• given 23 ch. pairs there is theoretically 223 possible combinations (= 8,388,608 different
gametes)
• in fact, each gamete contains a mixture of homologous CHm and CHp due to the
process during 1st meiotic division = crossing-over and recombination
• thus alleles originally coming from different grandparents can appear in one chromosome
• creates much greater number of combinations than 8 millions
• however, probability of recombination is not the same in all parts of DNA, it
depends on the distance (linkage disequilibrium / haplotype block)
• the closer the genes are, the lesser is the probability of recombination
• such length is expressed in centiMorganes (1cM = 1% probability of recombination)
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Gene environment interaction
• Gene environment interaction – an influence on the expression of a trait that results from the
interplay between genes and the environment. Some traits are strongly influenced by genes, while other
traits are strongly influenced by the environment. Most traits, however, are influenced by one or more
genes interacting in complex ways with the environment.
• Epigenetic changes
• Malignant transformacy
• Mutagens – biological physical or phenomenon that promotes errors in DNA.
26
Genetic variability
• Source of individual variability (new combinations of alleles are created):
• Segregation of alleles
• Recombination during crossing-over
• Origin of new spontaneus combinations during fertilization
• process during which the number of alleles is changes (affects quality and quantity of genes)
• mutagenesis = The process of inducing mutations
• mutation = change in the DNA at a particular locus in an organism
Types of mutations
• Induces mutations – results from the exposure of an organism to a chemical or physical
agent that causes changes in the structure of DNA or RNA
• Spontaneous mutations – mutation that occurs without a known cause (, approx. ~10-7,
repair by polymerase and p53):
• Gene mutations
• Chromosomal aberations
• Genome mutations
Mutations
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Rare mutations and polymorfism
• Rare variants (mutations) - alternative forms of a gene that are present with a
minor allele frequency (MAF) of less than 1%
• They are often cause of death or are relatively new
• Polymorphism – common mutation, these mutations are source of interindividual
variability, existence of two or more variants in a population of individuals, with at
least two of the variants having frequencies greater than 1 percent
- SNP = Single-nucleotide polymorphism → A single base pair in the DNA that varies
in a population.
- Microsatellite and Minisatellite → multiallelic
• Germinal mutation – mutation that occurs in the reproductive cells (germ-line
cells) of the body and is transmitted to progeny (often cause of abortion),
• in each cell of the offspring, have effect on evolution, success rate 1:100000
• Somatic mutation – mutation that occurs in the nonreproductive cells (somatic
cells) of the body and is not transmitted to progeny
Germinal and Somatic mutations
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Gene (variant) mutation
• Change of individual genes (alleles), typically induced
• DNA structure is altered but integrity of chromosome is intact
• In somatic cells and gametes
• Point mutation – substitution = replaces one DNA building block (nucleotide) with
another. Substitution variants can be further classified by the effect they have on the
production of protein from the altered gene
• Missense → amino acid change may alter the function of the protein
• Nonsense → shortened protein that may function improperly, be nonfunctional, or get broken down
• Deletion = changes the DNA sequence by removing at least one nucleotide in a gene.
• Insertion = changes the DNA sequence by adding one or more nucleotides to the
gene. As a result, the protein made from the gene may not function properly.
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Gene mutations - clinical examples
• Sickle cell disease (SCD) – group of inherited red
blood cell disorders that affects hemoglobin
• In people with sickle cell disease, abnormal
hemoglobin molecules - hemoglobin S - stick to
one another and form long, rod-like structures.
These structures cause red blood cells to become
stiff, assuming a sickle shape
• Caused by a mutation in the hemoglobin-Beta
gene found on chromosome 11.
• Sickle-shaped red blood cells carry oxygen much
worse. Therefore, people with sickle cell disease
have more red blood cells than ordinary people.
This gives them a big advantage over malaria,
giving them a better chance of surviving.
ancestral mutant
DNA -CTC- -CACmRNA
-GAG- -GUGAA
-glu- -val-
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Gene mutations - clinical examples
• Beta thalassemia – blood disorder that reduces the
production of hemoglobin
• Mutation in HBB gene → instructions for making
a protein called beta-globin
• The absence of beta-globin is referred to as
beta-zero (β0) thalassemia
• In people with beta thalassemia, low levels of
hemoglobin lead to a lack of oxygen in many
parts of the body.
• People with beta thalassemia are at an increased
risk of developing abnormal blood clots.
ancestral mutant
DNA -AGT- -ACTmRNA
-UCA- -UGAAA
-ser- -STOP
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Gene mutations - clinical examples
• Hemophilia A – hereditary bleeding disorder caused
by a lack of blood clotting factor VIII → without
enough factor VIII, the blood cannot clot properly to
control bleeding.
• Caused by an inherited X-linked recessive trait,
with the defective gene located on the X
chromosome.
• Insertion of 3000 bp → changes in F8 gene
• If a woman has a defective factor VIII gene, she
is considered a carrier (two copies of X
chromosome)
• Males have only one X chromosome. If the factor
VIII gene is missing on a boy's X chromosome,
he will have hemophilia
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Gene mutations - clinical examples
• Cystic fibrosis (CF) – inherited disorder that causes
severe damage to the lungs, digestive system and
other organs in the body.
• In cystic fibrosis, a defect (mutation) in a gene
— the cystic fibrosis transmembrane
conductance regulator (CFTR) gene — changes a
protein that regulates the movement of salt in
and out of cells. The result is thick, sticky mucus
in the respiratory, digestive and reproductive
systems, as well as increased salt in sweat.
• Deletion of 3 bp from position 1652 to 1655 in
exon 10 (deletion of phe in codon 508)
ancestral mutant
DNA -TAG-AAA-CCA- -TA A-CCAmRNA
-AUC-UUU-
GGU-
-AUU-GGUAA
-ile-phe-gly- -ile-gly-
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Gene mutations - clinical examples
• Duchenne Muscular Dystrophy (DMD) – is a
genetic disorder characterized by progressive muscle
degeneration and weakness.
• caused by mutations in DMD (encoding
dystrophin) that prevent the production of the
muscle isoform of dystrophin. Mutations in DMD
can also cause Becker muscular dystrophy
(BMD).
• In DMD, frameshifting mutations or nonsense
cause premature truncation of protein
translation, leading to non-functional and
unstable dystrophin
ancestral mutant
DNA -CAC-TGT -CAC-TTG-T..mRNA
-GUG-ACA- -GUG-AAC-U..AA
-val-thr- -ile-gly-
34
Chromosomal mutations – aberations
• A chromosome mutation is an unpredictable change that occurs in a
chromosome.
• Chromosome mutations can result in changes in the number of
chromosomes in a cell or changes in the structure of a
chromosome.
• Unlike a gene mutation which alters a single gene or larger segment of
DNA on a chromosome, chromosome mutations change and impact the
entire chromosome.
35
Chromosomal mutations – aberations
Structural chromosomal aberations
• Chromosome structure changes are often harmful to an individual
leading to developmental difficulties and even death. Some changes
are not as harmful and may have no significant effect on an
individual. There are several types of chromosome structure changes
that can occur.
• They can be divided into two groups: balanced (amount of genetic
materiál is same) and unbalanced (genetic material is missing or
reside).
• Deficience = external part of the chromosome is missing or has
been deleted.
• Deletion = internal part of the chromosome is missing or has been
deleted.
• Duplication = part of the chromosome has been duplicated,
resulting in extra genetic material.
• Inversion = part of the chromosome has broken off, turned by 180°
and reattached.
• Translocation = part of one chromosome is transferred to another
chromosome → new trait can be created.
• Fragmentation = disintegration into small parts.
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Chromosomal mutations – aberations
37
Chromosomal mutations - clinical examples
• Cri Du Chat (46,XX/XY, del(5)(p?) – chromosomal
deletion
• Cri du chat syndrome is a rare chromosomal disorder
caused by a deletion of genetic material on part of
chromosome 5.
• Other names for the condition are cat cry syndrome
and 5p- syndrome.
• Symptoms can vary depending on the size and area of
the deletion of chromosome 5.
• The most common symptom is a shrill, cat-like cry that
newborns make.
• There’s no cure for cri du chat. But, with prompt
diagnosis and early intervention, child may be capable
of reaching their fullest potential and leading a
meaningful life.
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Chromosomal mutations - clinical examples
• Hunter Syndrome (MPS II)– chromosomal inversion
• X-linked recessive disorder caused by the deficiency of
iduronate 2-sulfatase (IDS)
• Major rearrangements of the IDS gene.
• Manifests almost exclusively in males – also observed
in females
39
Chromosomal mutations - clinical examples
• Charcot-Marie-Tooth disease type 1 – chromosomal
duplication
• A subtype of CMT1 called CMT1A (caused by a
duplication or, less commonly, a point mutation in the
PMP22 gene on chromosome 17) accounts for around
70% to 80% of CMT1 cases, making it the most
common subtype of CMT1.
• Duplication of PMP22 leads to accumulation of the
peripheral myelin protein 22 (PMP22) protein, and point
mutations alter its distribution.
• PMP22 is vital for the normal creation and maintenance
of the myelin sheath.
• CMT1 patients usually present with typical CMT onset
within adolescence but remain ambulatory with no
reduced life expectancy
40
Chromosomal mutations – aberations
Numerical chromosomal aberrations
• Numerical chromosomal aberrations are defined as changes in the number of
chromosomes or the entire set of chromosomes
• Structure of chromosomes is intact, but there can be pathological change in number
of total genes
• Result from disturbances in the mitotic spindle apparatus during cell division. In the
process called nondisjunction, chromosomes of a given pair fail to separate in the
normal way during anaphase
• aneuploidy - numerical aberation of one or more concrete chromosome – not whole
set of chromosome! Chromosome can be
• Added - trisomy (3x – three copies of chromosome), tetrasomy (4x …),
• Lost - monosomy (1x – one copy of chromosome), nulisomy (0x …)
• polyploidy - „heritable“! condition of possessing more than two complete sets of
chromosomes.
• Polyploidy occurs in humans in the form of triploidy, with 69 chromosomes
(sometimes called 69, XXX), and tetraploidy with 92 chromosomes (sometimes called
92, XXXX)
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Chromosomal mutations - clinical examples
• Turner syndrome (45, X0) (gonosomal monosomy) –
chromosomal condition that affects development in females.
• Turner syndrome results when one normal X
chromosome is present in a female's cells and the other
sex chromosome is missing or structurally altered. The
missing genetic material affects development before
and after birth
• Females with Turner syndrome have extra folds of skin
on the neck (webbed neck), a low hairline at the back
of the neck, puffiness or swelling (lymphedema) of the
hands and feet, skeletal abnormalities, or kidney
problems. One third to one half of individuals with
Turner syndrome are born with a heart defect
• Mosaic Turner syndrome – in an affected individual, it
occurs as a random event during cell division in early
fetal development. As a result, some of an affected
person's cells have the usual two sex chromosomes,
and other cells have only one copy of the X
chromosome.
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Chromosomal mutations - clinical examples
• Patau syndrome (47, XX/XY +13) (autosomal trisomy)
– chromosomal condition associated with severe intellectual
disability and physical abnormalities in many parts of the
body.
• The cause of Patau syndrome is the presence of three
copies of chromosome 13; this is due most commonly
to nondisjunction in meiosis, occurring more frequently
in mothers of advanced age (age greater than 35).
• Individuals with trisomy 13 often have heart defects,
brain or spinal cord abnormalities, very small or poorly
developed eyes (microphthalmia), extra fingers or toes,
an opening in the lip (a cleft lip) with or without an
opening in the roof of the mouth (a cleft palate), and
weak muscle tone (hypotonia).
• In some people, only a portion of cells contains the
extra chromosome 13 (mosaic trisomy 13)
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Chromosomal mutations - clinical examples
• Edwards syndrome (47, XX/XY +18) (autosomal
trisomy) – chromosomal condition associated with
abnormalities in many parts of the body.
• The cause of Edwards syndrome is the presence of
three copies of chromosome 18; is due to
nondisjunction, mostly during meiosis II, occurring
more frequently in mothers of advanced age (age
greater than 35).
• Individuals with trisomy 18 often have slow growth
before birth (intrauterine growth retardation) and a low
birth weight. Affected individuals may have heart
defects and abnormalities of other organs that develop
before birth. Other features of trisomy 18 include a
small, abnormally shaped head; a small jaw and
mouth; and clenched fists with overlapping fingers.
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Chromosomal mutations - clinical examples
• Down syndrome (47, XX/XY +21) (autosomal trisomy)
– chromosomal condition that is associated with intellectual
disability, a characteristic facial appearance, and weak
muscle tone (hypotonia) in infancy.
• The majority of full trisomy 21 is caused by chromosomal
nondisjunction occurring during maternal meiotic division
(∼90%). Errors occur more frequently in the first maternal
meiotic division than the second (73% vs. 25%)
• Individuals with Down syndrome often have a characteristic
facial appearance that includes a flattened appearance to
the face, outside corners of the eyes that point upward
(upslanting palpebral fissures), small ears, a short neck,
and a tongue that tends to stick out of the mouth. Affected
individuals may have a variety of birth defects.
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Chromosomal mutations - clinical examples
• Klinefelter (47 XXY) (gonosomal trisomy) – the most
common chromosomal disorder in men and is associated
with hypergonadotropic hypogonadism and infertility
• Triple X syndrome (47 XXX) (gonosomal trisomy) –
characterized by the presence of an additional X
chromosome in each of a female's cells. Although females
with this condition may be taller than average, this
chromosomal change typically causes no unusual physical
features. Most females with triple X syndrome have normal
sexual development and are able to conceive children.
• 47, XYY syndrome (47 XYY) (gonosomal trisomy) –
characterized by an extra copy of the Y chromosome in
each of a male's cells. Although many males with this
condition are taller than average, the chromosomal change
sometimes causes no unusual physical features. Most males
with 47,XYY syndrome have normal production of the male
sex hormone testosterone and normal sexual development,
and they are usually able to father children.
46
Classification of genetic causes of diseases
• practically every diseases (i.e. onset,
progression and outcome) is, to some extent,
modified by genetic make-up subject;
however, under the different mode
• with except of trauma, serious intoxications and
highly virulent infections
• chromosomal aberrations - inborn but nor
inherited!
• monogenic diseases
• single critical “error” (allele) of a single gene is
almost entirely responsible for the development of
disease (phenotype)
• characteristic pedigree (segregation of phenotype
) due to the mode of inheritance (recessive x
dominant)
• complex (polygenic) diseases
• genetic dispositions + effect of non-genetic factors
• combination of several
alleles in several loci
47
Monogenic diseases
• The development of molecular-biological methods has enabled a detailed analysis of
the genetic basis of many Mendelian inherited monogenic diseases.
• In these diseases, the hereditary basis is a large factor, meaning it is present in
practically all patients and it is provably a causal factor (e.g. defects in the
dystrophin gene in muscular dystrophies), to which are added additional genetic
factors and external environmental factor. The cause of these diseases are mainly
rare alleles.
• Determined by alleles in one locus
• Characteristic way of inheritance in families
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Monogenic diseases
• Childhood diseases
• Less than 10% of them appear after puberty and only 1% appear after
reproductive age
• often significantly pathological
• In a population study of 1 million infants, the incidence of serious monogenic
diseases was estimated at 0.36%, with 6-8% of hospitalized children
considering monogenic diseases.
• so far known diseases comprised in OMIM (On-line Mendelian Inheritance in
Man) ~6000 clinically significant phenotypes
• Four basic types of inheritance:
Dominant Recessive
Autosomal Autosomal dominant Autosomal recessive
X-linked X-dominant (XD) X-recessive (XR)
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Monogenic diseases
Types of inheritance
• autosomal
• genes on both autosomes are normally active
• gonosomal (X-chromosom linked)
• men are normally hemizygote
• women have 1 X-chromosom inactivated
• (imprinting, mosaicism)
According to the expression of genotype in the phenotype
• recessive
• diseases develops only in mutated homozygote
• dominant
• disease in both heterozygote and mutated homozygote
• incomplete dominance
• gradual increase of severity of the disease in heterozygote and mutated homozygote
• co-dominant
• both normal and pathological allele expressed in phenotype
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Monogenic diseases – AD x AR
Autosomal dominant AD
• Result of both mutations transmitted
between generations and newly
arise
• Disease is manifested in every
generation - the affected individual
has a affected parents (and
grandparents), a mother or father
• Risk 0,5; if both parent are affected
then 0,75, but this is extremely rare
• familiar hypercholesterolemia
(1/500),
• myotonic dystrophy (1/1000)
• Huntington disease (1/3000)
Autosomal recessive AR
• very often enzyme defects
• affected mutated homozygote,
heterozygous parents are carriers
(asymptomatic)
• risk 0.50  0.50 = 0.25
• both genders affected equally
• frequency of carriers in population →
frequency of disease
• most common AR diseases in whites
is cystic fibrosis
• f disease 1/2000, f carriers 1/22
!!!
• consanguinity and inbreeding
significantly increase the risk
• arranged marriages
• genetically isolated populations
(e.g. Ashkenazi Jews – Tay-Sachs
disease )
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Monogenic disease - X-linked
• women 3 genotypes, men only 2
• X-linked diseases manifest in all men who have inherited the
mutation and only in homozygous women
• Hemophilia A
• Duchenne muscular dystrophy
• Wiskott-Aldrich syndrome (immunodeficiency)
• Inactivation of X-chromosome in women
• Dose compensation and expression of X-linked genes
• Lyon hypothesis ("lyonization")
• in somatic cells one X chromosome is inactivated and appears
in the interphase as a "Barr" body
• the process is random, it can involve both paternal and
maternal X.
• the result is variable expression of X-linked genes in
heterozygotes ("manifesting carrier")
• functional mosaicism
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Complex diseases
• Multifactorial, polygenic.
• Combination of both certain genes and certain environmental respectively is important.
• Unlike the genetics of Mendelian diseases, most of the general principles of multifactorial diseases are still
unclear.
• In clinical practice, the results of genetic studies that seek to reveal the genetic basis of complex diseases
often vary, from unreasonable expectations about the genes found to have a large effect to great skepticism
about the existence of genetic evidence in a population of numerous diseases (over 1%) - for example
essential hypertension in cardiology.
• if the disease has a provably familial occurrence, we must expect the genetic basis to contribute to its
manifestation, even if it is not yet well defined or we do not consider the current knowledge to be
convincing.
• Even relatively remote proximal phenotypes, such as the quality of life in patients with chronic
cardiovascular disease, have a genetic background.
• Each disease has a genetic background, the role of which in the manifestation of the disease is
different.
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Complex diseases
• diseases developing due to the ethiopathogenic “complex“ of genetic,
epigenetic and environmental factors
• phenotype does not follows Mendel rules (dominant or recessive mode of inheritance)
• “predisposing genes/alleles” increase probability to become affected,
however, do not determine unequivocally its development
• effect of non-genetic factors is a necessary modifier
• diet, physical activity, smoking, ….
• genes interact between themselves
• typical features of complex diseases
• incomplete penetrance of pathological phenotype
• some subjects inherited predisposing alelles never become ill
• existence of phenocopies
• pathological phenotype can develop in subjects not predisposed, entirely due to the non-genetic factors
• genetic heterogeneity (locus and allelic)
• manifestation (clinical) is not specific but the same syndrom can develop as a consequence of various loci (=
locus heterogeneity) in which there could be several variants (= allelic heterogeneity)
• polygenic inheritance
• predisposition to disease is significantly increased only in the presence of the set of several risk alleles
(polymorphisms), hence their high population frequency
• in isolated occurrence the effect is mild
• other modes of transmission
• mitochondrial,
• examples of complex diseases: essential
hypertension, diabetes (type 1 and 2),
dyslipidemia, obesity, allergy,
Alzheimer disease, …
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Complex diseases
• Complex diseases are characterized by:
• incomplete penetrance of the pathological phenotype
• in a certain group of people, even though they inherit an
unfavorable genotype the pathological phenotype does not develop
• existence of phenocopies
• the pathological phenotype may be present in people who are not
carriers of said genotype
• genetic heterogeneity (locus and allelic)
• the clinical picture is not specific, but it can develop due to
changes in genes located at different loci (= locus heterogeneity),
there may be several mutations or polymorphisms in individual
genes (= allelic heterogeneity)
• Polygenic inheritance
• the predisposition to develop a pathological phenotype increases
only when a certain set of alleles occur simultaneously
• high population frequency of alleles responsible for the development of
the pathological phenotype
• each individual predisposing allele does not have to be
significantly pathogenic
• interaction of other transmission mechanisms
• mitochondrial inheritance, imprinting
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Complex diseases - clinical examples
• The Thrifty Gene Hypothesis (autosomal trisomy) –
suggests that particular gene variants evolved to favor
efficient use of nutrients in the calorie-limited environment
in which humans evolved.
• Promotes obesity and type 2 diabetes in the modern,
calorie-rich environment.
• A large number of studies in animals and humans linked
poor prenatal nutrition with subsequent predisposition to
disease, including obesity later in life and in subsequent
generations.
• Despite considerable study, there are very few concrete
details on the molecular mechanisms that promote a thrifty
phenotype, although, there are some indications that leptin
resistance and epigenetic mechanisms are .involved
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Genetic studies
• The basic debate over the genetic
basis of diseases logically starts with
the strategy of selecting candidate
genes. This question is much simpler
in Mendelian diseases, where the
altered function of one gene is easier
to identify.
• Another important approach is the
selection of a statistical methodology
that evaluates the strength of the
association of genes with diseases.
There are basically two options:
linkage analysis and association
studies. In principle, both methods
can be used to detect specific genetic
regions and genes involved in disease
transmission.
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Genetic studies
Kandidátní geny
Linkage analysis
• Tests cosegregation of gene marker and disease phenotype in the family → their marker and the disease should always
occur together in a given family.
Association studies
• Genetic association studies test for a correlation between disease status and genetic variation to identify candidate genes or
genome regions that contribute to a specific disease.
• A higher frequency of a single-nucleotide polymorphism (SNP) allele or genotype in a series of individuals affected with a
disease can be interpreted as meaning that the tested variant increases the risk of a specific disease
• SNPs are the most widely tested markers in association studies, but microsatellite markers, insertion/deletions, variablenumber
tandem repeats (VNTRs), and copy-number variants (CNVs) are also used
• Case-Control Study
• The simplest study design used to test for association is the case–control study, in which a series of cases affected with
the disease of interest are collected together with a series of control individuals.
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Clinical genetic
• Deals with diagnostics, treatment and prevention of genetic diseases
• Genetic counselling
• congenital malformations - disorders of organ formation that occurred during the period of
intrauterine life, as well as functional disorders (mental retardation) and disorders at the
biochemical and molecular level (ongenital metabolic defects).
Group Cause Repr.
Primary (genetic)
Chromosomal aberation 10 %
Monogenic inheritance 20 %
Secondary (environment)
Drugs, infection, radiance 5 %
Birth wounds 12 %
After birth infrection 7 %
Unknown (multifactorial) Gene + environment 46 %
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Clinical genetics – Prenatal diagnosis
• Karyotype test - looks at the size, shape, and number of
chromosomes. Methods of sample collection:
• Amniocentesis
• Chorionic villus sampling (CVS)
• Ultrasound
• MRI
• Quantitative fluorescent PCR (QF-PCR) – or amnioPCR
is used for prenatal diagnosis of the most common
aneuploidies
• comparison of DNA markers of mother and fetus →
determination of the number of individual
chromosomes in the fetus.
• Cell-free fetal DNA (cffDNA) – cffDNA circulating in
maternal plasma has enabled development of safer, earlier
testing based on a simple maternal blood sample. A number
of clinical diagnostic tests have now been implemented,
including fetal sex determination, RHD blood group
determination and the detection or exclusion of de novo or
paternally inherited monogenic disorders
• +Preimplantation diagnostics
Thank you for your attention