Clinical Genetics Concepts

Clinical
Genetics 2016 Andrea Sól Kristjánsdóttir
C ONCEPTS

#1. Gene, Exon, Intron, Promoter, Splicing:
Gene:
• It’s the basic unit of inheritance. It consists of a sequence of DNA that
encodes a specific protein (or a nontranslated RNA: tRNA, rRNA or snRNA)
• A gene is a functional unit of DNA
• It’s a determinant or co-‐determinant of a character that is inherited
according to the Mendel´s rules:
§ Genes come in pairs and are inherited as distinct units, one from each
parent.
• The physical location of a gene on a chromosome is the locus
• Variation or mutation in the DNA sequence of a gene produces a new allele
at that specific locus.
• Many genes have multiple alleles
• Polymorphism: when a specific site on a chromosome has multiple alleles in
the population – dæmi: throughout human history there have been many
mutations in the beta-‐globin gene, each mutation creating a new allele in the
population, the beta-‐globin is therefore polymorphic. Some alleles cause no
clinical disease but others, like the sickle cell allele, are associated with
significant disease.

Exon:
• It’s the coding segment of the gene, that will code for proteins
• They will unite to form the mature mRNA, used for translation

Introns:
• It’s the noncoding segment of the gene that is transcriped in the nucleus but
spliced out before the mature mRNA is formed

Promoter:
• It’s a region on the DNA sequence of the gene located upstream at the 5’ end
of the transcription initiation site.
• They define where transcription of a gene will begin
• Transcription factors (RNA polymerase II) will recognize the promoter region
and bind to it – and they will separate the DNA strand so it can be read and
the transcription can begin. The template strand is read in the 3´to
5´direction as the RNA product (the primary transcript) is synthesized in the
5’ to 3’ direction. Both exons and introns are transcripted. The RNA
polymerase II ends the transcription when it reaches a terminal signal or the
therminal region of the DNA.

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Clinical Genetics 2016 Andrea Sól Kristjánsdóttir
Splicing:
The primary transcript must
undergo extensive
posttranscriptional processing
inside the nucleus to form the
mature mRNA:
• 7-‐methylguanosine cap is
added at the 5´end while
the RNA molecule is still
being synthesized. It serves
as s ribosome binding site
and helps to protect the
mRNA chain from
degradation.
• Poly-‐A tail is attached to
the 3´end to protect
against rapid degradation
and aids in the transport to
the cytoplasm.
• Introns are removed by splicosomes in the process of splicing. The hnRNA is
cut at splice sites at the 5´(donor) and 3´(acceptor) ends of the intron.
• The exons are joined together to assemble the coding region of the mature
mRNA.
• The mature mRNA molecule is transported to the cytoplasm where its
translated to form a protein.

#2. Genotype, phenotype, haplotype:
Genotype:
It’s the specific DNA sequence at a locus. In
diploid somatic cells a genotype can be:
• Homozygous: the individual has the
same allele on both homologous
chromosomes at that locus
• Heterozygous: the individual has
different alleles there – so here,
the dominant trait will be
expressed.

Phenotype:
It’s the expression of the genotype in
terms of observable characteristics.

Haplotype:
It’s the combination of alleles at
different loci on the same chromosome
that is inherited together as a single
unit.
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#3. Multifactorial inheritance, complex trait, linkage:

Multifactorial inheritance:
Most common diseases are caused by multiple genes and influenced by
environmental factors. The genetic and environmental factors involved are referred
to as risk factors and the summation of these in an individual represents that
person´s liability for the disease. So many factors are involved in causing a birth
defect, where a combination of genes from both parents play a role.

Complex trait:
Human genetic traits can be monogenic or complex. Monogenic traits are influenced
by variation within a single gene and are recognized by their classic patterns of
inheritance within families. Complex traits don’t follow strict Mendelian patterns of
interactions – they are believed to result from variation within multiple genes and
interact with behavioral and environmental factors. Dæmi: cystic fibrosis and
Huntingtons are monogenic but Alzheimers and diabetes are complex traits.

Linkage:
It’s the tendency of alleles that are close together on a chromosome to be inherited
together during the meiosis phase of sexual reproduction.

Linked genes sit close together on a chromosome, making them likely to be inherited
together. Genes on separate chromosomes are never linked. But not all genes on a
chromosome are linked. Genes that are farther away from each other are more likely
to be separated during a process of homologous recombination.

Extra info about genes and alleles:
• Chromosome is a single piece
of DNA
• Genes are segments of DNA
arranged along a chromosome
• A single chromosome can have
hundreds or thousands of
genes
• Homologous chromosomes
have the same genes arranged
in the same order, but they
have slightly different DNA
sequence
• Different versions of the same
gene are called alleles
• Alleles are important because
they account for the difference
in inherited characteristics
from one individual to another.
Dæmi: gene that codes for eye color and the different alleles will code for
different color

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#4. Wild type, mutation, dominant, recessive, X-‐linked inheritance:

Wild type:
It’s the most common genotype and its based upon a quantitative representation or
estimation of the normal or standard in a population. Since the expression of those
genes produce a set of observable characteristics (phenotype) – the wild type is the
most common phenotype in nature or in a natural breeding population. One of the
first descriptions of a wild type gene was made when studying the Drosophilia fruit
fly. The geneticist noted a white-‐eyed fly in an isolated breeding population of red-‐
eyed Drosophilia flies. Because the majority of the flies had red eyes, the geneticist
considered the white-‐eyed fly a mutant and termend the gene for red eyes the wild-‐
type gene.

Mutation:
Its any permanent, heritable change in the DNA base sequence that can be reflected
by changes in the base sequence of mRNA and sometimes by changes in the amino
acid sequence of a protein. This can cause genetic diseases. A very common type of
mutation is a single base alteration or point mutation:
• Transition: point mutation that replaces a purine-‐pyrimidine base pair with a
different purine-‐pyrimidine base pair. Dæmi: A-‐T base pair becomes G-‐C base
pair.
• Transversion: point mutation that replaces a purine-‐pyrimidine base pair
with a pyrimidine-‐purine base pair. Dæmi: A-‐T base pair becomes T-‐A or C-‐G
base pair.

Mutations are often classified
according to the effect they have on
the structure of the gene´s protein
product.

When mutations occur in cells giving
rise to gametes, the mutation can be
transmitted to future generations.

Mutations that cause a missing
protein product or decreased activity
of the protein are termed loss of
function – those that produce a
protein product with a new function
or increased activity = gain of function

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Dominant inheritance:
A genetic trait is considered dominant if its expressed in a person who has only one
copy of that gene. Skipped generations are relatively unusual.
• Autosomal dominant: the mutated gene is a dominant gene located on one
of the nonsex chromosomes, or autosomes. You need only one mutated gene
to be affected – so when reproducing, there are 50% chances of having an
affected child with one mutated gene. Its relatively rare in populations so the
typical mating pattern is a heterozygous affected individual mating with a
homozygous normal individual. If both parents would be heterozygous the
recurrence risk would be 75%. Dæmi: Huntingtons disease.
• X-‐linked dominant: it depends on if the mother or the father is affected, how
it affects the children. If the mother has it, its 50% chances for both girls and
boys to get the disease but if the father has it, the boys cannot be affect but
there are 100% chance that the girls get affected. Dæmi: fragile X-‐syndrome.

Recessive inheritance:
A condition that appears only in individuals who have received two copies of a
mutant gene, one copy from each parent.
• Autosomal recessive: the offspring must inherit one copy of the disease-‐
causing allele from each parent. Males and females are affected in roughly
equal frequencies – or 25%. Dæmi: sickle cell anemia and cystic fibrosis.
• X-‐linked recessive: these disorders are seen much more commonly in males
than females since males require only one copy of the mutation to express
the disease but females require two copies. X-‐linked inheritence is never
seen in male-‐to-‐male transmission. Skipped generations are commonly seen
because an affected male can transmit the disease-‐causing mutation to a
heterozygous daughter, who is unaffected but who can transmit the disease-‐
causing allele to her sons. Dæmi: Duchenne muscular dystrophy and red-‐
green color blindness.
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X-‐linked inheritance:
• X inactivation: since the Y chromosome carries only about 30 protein-‐coding
genes and the X chromosome carries hundres of protein-‐coding genes, a
mechanism must exist to equalize the amount of protein encoded by X
chromosomes in males and females – this is called X inactivation. It occurs in
the blastocyst (around 100 cells) during the development of female embryos.
When its inactivated, its DNA is not transcriped into mRNA and the
chromosome is visualized under the microscope as a highly condensed Barr
body in the nuclei of interphase cells. Its random if the X chromosome that’s
inactivated is inherited from the mother or the father. Its also fixed, so the
same X chromosome is inactivated in all descendants of the cell.

#5. Candidate gene, founder effect, genetic heterogeneity, co-‐segregation:
Candidate gene:
Its any gene thought likely to cause a disease. It may be a candidate because its
located in a particular chromosome region suspected of being involved in the
disease or its protein product may suggest that it could be the disease gene in
question. There are many different ways of identifying a disease gene, but all paths
converge on a candidate gene. In one way or another, a candidate gene is identified,
the researcher then tests the hypothesis that this is the disease gene.

Founder effect:
Its when a new mutation is introduced into a population and the person that is
carrying the mutation is one of the early founders of the community. As the
community rapidly expands through generations, the frequency of the mutations
can be affected by for example natural selection or genetic drift. This is the reason
why some autosomal recessive conditions often show very uneven ethnic
distribution, being common in one population and rare in others. Dæmi: maple syrup
urine disease occurs in 1/176 live births in Mennonite community in Pennsylvania
but 1/180.000 live births at other places in the USA.

Genetic heterogeneity:
• Allelic heterogeneity: different mutations in the disease-‐causing locus may
cause more or less severe expressions. Dæmi: missense mutation in the
factor 8 gene tends to produce less severe hemophilia than nonsense
mutation. It usually results in phenotypic variations between families but not
within a single family. Its rare to see genetic disorders in which there is no
allelic heterogeneity.
• Locus heterogeneity: its when the same disease phenotype can be caused by
mutations in different loci.
• Internet: it refers to the presence of a variety of genetic defects which cause
the same disease, often due to mutations at different loci on the same gene.
A common finding in many human diseases like cystic fibrosis and polycystic
kidney disease.

Co-‐segregation: the tendency for closely linked genes and genetic markers to
segregate/be inherited together.
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#6. Familiar anticipation, penetrance, expressivity:

Familiar anticipation:
It’s a pattern of inheritance in which individuals in the most recent generations of a
pedigree develop a disease at an earlier age or with greater severity than do those in
earlier generations. This can be attributed to the gradual expansion of a
trinucleotide repeat polymorphisms within or near a coding gene. Dæmi: Huntington
disease – the condition results from a gain-‐of-‐function mutation on chromosome 4
and is an example of trinucleotide repeat expansion disorder. Normal huntingin
genes have fewer than 27 CAG repeats and the number is stable from generation to
generation. In families who eventually present with Huntington disease,
premutation of 27-‐35 repeats are seen, although these individuals don’t have the
disease. Then some of these individuals, usually males, may transmit an expanded
number of repeats to their offspring. Individuals with more than 39 repeats are then
seen and these individuals will develop symptoms. The age of onset is correlated
with the number of repeats – so the more the repeats, the younger the age of onset.

Penetrance:
It’s the measurement of the proportion of individuals in a population who carry a
disease-‐causing allele and express the disease phenotype. A disease-‐causing
mutation is said to have incomplete penetrance when some individuals who have
the disease genotype (for example one copy of the mutation for an AD disease or
two copies for an AR disease) do not display the disease phenotype.
• Incomplete penetrance: retinoblastoma is an AD condition where 10% of
individuals who inherit the mutation, don’t develop the disease. So the
penetrance of retinoblastoma is 90%.
• Complete penetrance: fragile X syndrome in males – its an X-‐linked dominant
trait that has 100% penetrance in males but only 60% penetrance in females.

Expressivity:
It measures the extent to which a given genotype is expressed at the phenotypic
level. Different degrees of expression in different individuals may be due to variation
in the allelic constitution of the rest of the genome or to environmental factors.

#7. Homozygous, allele, microsatellite, locus:
• Homozygous: alleles at a locus are the same
• Allele: different forms of gene
• Locus: location of a gene on a chromosome
• Microsatellite: also known as short tandem repeats are di-‐, tri-‐ and tetra-‐
nucleotide repeats dispersed throughtout the DNA, usually (but not always)
in noncoding regions. Microsatellite instability: TGTGTG may occur at a -Lynch syndrome
particular locus. If the cells lack mismatch repair, the replicated DNA will vary -HNPCC
in the number of repeats at that locus, for example: TGTGTGTGTG or TGTG.
This variation is microsatellite instability.

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#8. Phenocopy, epistasis, Hardy-‐Weinberg equilibrium:

Phenocopy:
It’s a condition that is induced by environmental factors but closely resembles a
phenotype usually produced by a specific genotype. The trait is not inherited or
transmitted to offspring. Dæmi: in a family being studied to map a gene causing
deafness, one family member might be deaf because of head trauma or meningitis
rather than having inherited the family mutation – so he´s affected despite not have
the disease genotype.

Epistasis:
It’s a certain relationship between genes, where allele of one gene hides or masks
the visible output, or phenotype, of another gene. Its different from dominant and
recessive, which are terms that apply to different alleles of the same gene.

Hardy-‐Weinberg equilibrium:
If a population is large and if individuals mate at random with respect to their
genotypes at a locus, the population should be in Hardy-‐Weinberg equilibrium. This
means that there is a constant and predictable relationship between genotype
frequencies and allele frequencies. This relationship, expressed in the Hardy-‐
Weinberg equation, allows one to estimate genotype frequencies of one knowns
allele frequencies and vice versa. Dæmi: young women knows that she is a carrier of
PKU and wants to know the chances of her marrying a man with the disease-‐
producing allele and what would be the chances of them having a child with PKU –
so from known genetical number, we could calculate the chances for both.

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#9. SNP, nonsense-‐mediated mRNA decay:

SNP (single nucleotide polymorphism):
They are single nucleotide
substitutions of one base for
another. Not all single-‐nucleotide
changes are SNPs – to be classified
as a SNP, two or more versions of a
sequence must each be present in at
least 1% of the general population.
About 1 in every 300 nucleotide
base pairs are SNP = 10 million SNPs
within the 3 billion-‐nucleotide human
genome. This should not be confused
with a point mutation, which is also a
single-‐nucleotide difference in a DNA
sequence. To be classified as a SNP,
the change must be present in at least
1% of the general population and no
known disease-‐causing mutation is that common. Also, most
disease-‐causing mutations occur within a gene´s coding or
regulatory regions and affect the function of the protein
encoded by the gene. Unlike mutations, SNPs are not always
located within genes and they do not always affect the way a
protein functions. SNPs differs you from the rest of the world
and is the reason why for example, you respond differently do
a drug than the next person or why you have a curly hair but
not the next person. But for most of the times, SNPs don’t
show any observable difference between people.

Nonsense-‐mediated mRNA decay:
Out of 64 codons in the genetic code, 3 of them are stop
codons – so its quite common for a nucleotide substitution to
convert the codon for an internal amino acid of a protein into
a stop codon. When ribosomes encounter a stop codon they
dissociate from the mRNA and the polypeptide is released. Cells have a mechanism
called “nonsense-‐mediated decay” that detect mRNAs that contain premature
termination codons and degrades them. If these abberant mRNA transcripts were
translated, they would result in deleterious gain-‐of-‐function or dominant negative
activity of the resulting proteins.

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#10. Codon, FISH, CGH, chorion biopsy:

Codon:
Its nucleotide triplets – and each amino acid is specified by one or more codons in
the DNA.
• Each codon consists of 3 bases. There are 64 codons and they are all written
in the 5´to 3´direction
• 61 condons code for amino acids – the other 3 (UAA, UGA, UAG) are stop
codons (or nonsense codons) that terminate translation.
• There is one starting codon (AUG) that codes for methionine. Protein
synthesis begins with methionine in eukaryotes but formyl-‐methionine in
prokaryotes.
• Each codon specifies no more than one amino acid
• All amino acids except for methionine
and tryptophan have more than one
codon.
• During translation, each tRNA has an
anticodon sequence that allows it to
pair with the codon for its cognate
amino acid in the mRNA.
• The anticodon sequence in tRNA is
antiparallel and complementary to the codon translated in mRNA.

FISH (fluorescence in situ hybridization):
First we make the hybridization probe, which is a fragment of DNA (or RNA), which is
labeled with a florescent molecule. We isolate a chromosome-‐specific DNA segment
with a fluorscent tag. Than we denature the probe so we only have a single strand
segment labeled with fluorscence tags. Now we distract the chromosomes from the
patients and denature them as well. Then we mix this all together and the probes
will bind to the complementary strands and lid up under the fluorescence micrscope.
Since the probe will hybridize only with a complementary DNA sequence, the probe
will mark the presence of the chromosome segment begin tested. Dæmi: a probe
specific for chromosome 21 will hybridize in three places in the cellls of a trisomy 21
patient, providing a diagnosis of Down syndrome. An advantage of FISH is that
chromosomes do not have to be in the metaphase stage for accurate diagnosis. Even
though interphase and prophase chromosomes cannot be clearly visualized
themselves, the number of hybridization signlas can still be counted accurately.
• In metaphase the chromosomes are condensed (but more condensed in
anaphase) and aligned at in the middle of the cell at the metaphase plate.

CGH (comparative genomic hybridization):
This technique compares 2 genomic DNA samples from two sources that are most
often closely related because its suspected that they contain difference in terms of
either gains or looses of either whole chromosomes or subchromosomal regions.
This technique was originally developed for the evaluation of the difference between
the chromosomal complements of solid tumor and normal tissue.

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We isolate the DNA from the two sources and label them with fluorophores of
different colour – then we denature them so they become single stranded and then
hybridize them in 1:1 ratio. Using a fluorescence microscope and computer software,
the different coloured fluorescent signals are then compared along the length of
each chromosome for identification of chromosomal difference between the two
sources.
• Higher intensity of the test sample colour indicates the gain of material of
that region in the corresponding source sample.
• Higher intensity of the reference sample colour indicates the loss of material
in the test sample in that specific region.
• A neutral colour (yellow if the probes are green and red) indicates no
difference between the two samples at that location.

CGH is only able to detect unbalanced chromosomal abnormalities. This is because
balanced chromosomal abnormalities like inversion or ring chromosomes do not
affect the copy number, which is what is detected by CGH technologies – it detects
deletions and duplications.

Chorion biopsy: Chorionic villus sampling (CVS)
Technique performed at 10-‐12 weeks of gestation that involves the removal of a
small sample of chorionic villus material either transcervically or transabdominally.
The villi are of fetal origin and thus provide a large sample of acetively dividing fetal
cells for diagnosis. This technique has the advantage of providing a diagnosis earlier
in the pregnancy. Disadvantages are a higher fetal mortality rate than with
amniocentesis and a small possibility of diagnostic error because of placental
mosaicism (multiple cell types in the villi).

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#3. Multifactorial inheritance, complex trait, linkage:

#4. Wild type, mutation, dominant, recessive, X-‐linked inheritance:

#6. Familiar anticipation, penetrance, expressivity:

#8. Phenocopy, epistasis, Hardy-‐Weinberg equilibrium:

#9. SNP, nonsense-‐mediated mRNA decay:

#10. Codon, FISH, CGH, chorion biopsy:

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Clinical Genetics Concepts

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Clinical

Genetics 2016 Andrea Sól Kristjánsdóttir

#3. Multifactorial inheritance, complex trait, linkage:

#4. Wild type, mutation, dominant, recessive, X-­‐linked inheritance:

#6. Familiar anticipation, penetrance, expressivity:

#8. Phenocopy, epistasis, Hardy-­‐Weinberg equilibrium:

#9. SNP, nonsense-­‐mediated mRNA decay:

#10. Codon, FISH, CGH, chorion biopsy:

S-ar putea să vă placă și

#4. Wild type, mutation, dominant, recessive, X-‐linked inheritance:

#8. Phenocopy, epistasis, Hardy-‐Weinberg equilibrium:

#9. SNP, nonsense-‐mediated mRNA decay: