genetic determination of diseases
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Heritability Genetic variability (mutations polymorphism) Monogenic complex diseases. Genetic determination of diseases. Genetics, genomics. genetics specialised field of biology focusing on variability and heritability in living organism human genetics - PowerPoint PPT PresentationTRANSCRIPT
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Genetic determination of diseasesHeritabilityGenetic variability (mutations polymorphism)Monogenic complex diseases
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Genetics, genomics genetics
– specialised field of biology focusing on variability and heritability in living organism
human genetics clinical genetics
genetics of 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
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) 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)
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Nucleoside nucleotide base DNA
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DNA replication
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Gene DNA contains defined
regions called genes – basic unit of heritability
gene = segment of DNA molecule containing the code for (m r t) RNA sequence and necessary regulatory sequences for the regulation of gene expression– promoter (5’-flanking region)
binding sites for transcription factors
– exons– introns– 3’ untranslated region (UTR)
transcription creates RNA – 1) hnRNA is complementary to
the entire gene (1. exon poly-A tail)
– 2) mRNA formed by slicing of introns from hnRNA
translation forms proteins
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RNA splicing
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Translation
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Translation – tRNA / amino acid
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Genetic code determines the
sequence of AA in protein– universal
Similar/the same principle in most living organisms
– triplet combination of 3
out 4 available nucleotides (A, C, G, T)
– degenerated 43 = 64, but only
21 AA
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Chromatin chromatide chromosome DNA is organised in
chromosomes– chromatin + chromosomal
proteins (histones) chromosome = linear sequence
of genes interspaced by non-coding regions
chromatin is in a relaxed form in the nucleus in non-dividing cells
it becomes highly organised/condensed into visible chromosomes in dividing cells– prometaphase/metaphase
structure of chromosome– centromere/telomeres– arms
long - q short – p
2 copies of a given chromosome after replication (before cytokinesis) = sister chromatides
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Human karyotype set of chromosomes characteristic for a
given eukaryote species (number and morphology) – human
somatic cells are diploid (46 chromosomes) 22 pairs of homologous autosomes 1 pair of gonosomes (44XX or 44XY)
gametes (oocyte, spermatide) 23 – haploid– mouse 40 chromosomes– crayfish 200 chromosomes– fruit flies 8 chromosomes
examination of karyotype (karyogram)– synchronising of cell division in metaphase by
colchicin – staining by dyes (e.g. Giemsa) leads to the
characteristic band pattern– standard classification by numbering according
to the size assessment and interpretation of karyogram
– manual – most often lymphocytes or fetal cells from amniotic fluid obtained by amniocentesis
photography and manual pairing– automatic (microscopy + software)
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Cell division mitosis
– 1 cycle of DNA replication followed by chromosome separation and cell division
prophasis prometaphasis metaphasis anaphasis telophasis cytokinesis
– 2 daughter cells with diploid number of chromosomes
meiosis (“to make small”)– 1 cycle of replication followed by 2 cycles
of segregation of chromosomes and cell division
1. meiotic (reduction) division – separation of homologous chromosomes
significant! – meiotic crossing-over (recombination) – none of the gametes is identical!
abnormalities of segregation – non-disjunction - e.g. polyploidy, trisomy, …
2. meiotic division – separation of sister chromatides
– humans oogonia oocyte + 3 polar bodies
very long period of completion, thus vulnerable
spermatogonia 4 sperms continually
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Mitosis - detail
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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 allele genotype phenotype gene – basic unit of heritability
– gene families sequence similarity among genes formed e.g. by
duplication during evolution 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)
– localisation 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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Human genome Human Genome Project (HUGO)
– ~3.3109 bp in haploid genome– 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 (non-repetitive) 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!
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Microsatellites
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Genetic variability 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
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Evolution – selection for continually changing environment??
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Types of DNA substitutions 1) genome
– number of chromosomes (trisomy, monosomy)
– sets of chromosomes (aneuploidy, polyploidy)
2) chromosomal (aberrations) – significant structural change of
particular chromosome duplication, deletion, insertion,
inversion, translocation, … 3) gene
– shorter (1 – thousands of bp) = the true source of population genetic variability point variants (transitions and
transversions) often bi-allelic single nucleotide
polymorphisms (SNPs) ~ 6 000 000 in human genome (HapMap project)
length variants repetitions (microsatellites! (e.g. CA12) deletions (1bp – MB) insertions + duplications inversions
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Mutation vs. polymorphism based on population frequency !!!
– mutation = minor allele population frequency (MAF) <1% – polymorphism = existence of several (at least 2) alleles for given gene with MAF 1%
sometimes are mutations vs. polymorphisms classified according to the functional impact (mutations = significantly pathogenis, polymorphisms = mild or neutral)
functional effects of substitutions – depends on the localisation in the gene!– coding regions (exons)
none (“silent”) new stop-codon and lack of protein (“nonsense”) – e.g. thalasemia, … AA exchange (“missense”) – e.g. pathological haemoglobins, … shift of the reading frame (“frameshift”) – e.g. Duchenne muscular dystrophy, Tay-Sachs, … expansion of trinucleotide repetition – e.g. Huntington disease, … deletion of protein – e.g. cystic fibrosis alternative splicing – qualitative (structure) as well as quantitative effect (affinity, activity,
stability)– non-coding regions
5’ UTR (promoters) = quantitative effect (e.g. variable transcription) introns - qualitative effect (splicing sites) or quantitative effect (binding of repressors or
enhancers)– 3’ UTR - effect on mRNA stability (“gene-dosage effect”)
pathologic consequences– gametes genetically determined (inherited) diseases– somatic cells tumors
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Missense and frameshift substitutions
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Interindividual variability physiological interindividual
variability of phenotypes/traits is a consequence of genetic variability– the more independent factors affect the
given trait the more “normal” the population distribution is
– if the effect of one factor dominates over the others or there are significant interactions the distribution becomes asymmetrical, discontinuous etc.
interindividual variability of a given trait is present in whole population incl. healthy as well as diseases subjects– disease as a “continuous function of the
trait” aetiology of diseases
– “monofactorial” incl. monogenic – “multifactorial” incl. polygenic (complex)
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Genetic determination of disease 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
– 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)– chromosomal aberrations - inborn but nor inherited!– complex (polygenic) diseases
genetic dispositions + effect of non-genetic factors combination of several
alleles in several loci what indicates that disease is, at
least partly, genetically conditioned ?? familiar aggregation
» prevalence in families of affected probands >>> prevalence in general population
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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 eho 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, imprinting (<1% of all alleles in genome)
examples of complex diseases: essential hypertension, diabetes (type 1 and 2), dyslipidemie, obesity, atopy, Alzheimer disease, …
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Genetic epidemiology there are a lot of methods available suitable
for different problems– positional mapping - linkage studies
follows the transmission of genetic marker (most often microsatellite) and phenotype (affected vs. unaffected subjects)
group of related subjects (family) trios of both parents and affected child (transmission
disequilibrium test, TDT) sibling pairs
» concordant (both affected)» discordant (1. yes, 2. no)
parametric = known/estimated model of inheritance (suitable for monogenic diseases)
non-parametric = unknown mode of inheritance (suitable for some complex diseases)
association studies compare frequencies of genetic marker(s) (most
often SNPs) between phenotypically disparate groups of unrelated subjects
case x control selection of genes is either pathogenetically based
(hypothesis-driven) or random (hypothesis-free) number of genes/alleles studied – 1 to n
whole genome association (WGA) ~ 500 000 SNPs subtypes of studies
cross-sectional retrospective prospective
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