Adobe Systems Medical genetics – introduction Michael Doubek Clinical genetics (aVLKG7X1c) Adobe Systems Learning outcomes ̶Basic concepts of contemporary genetics will be presented ̶ ̶The student will learn principles of heredity ̶ ̶Diagnostics of genetic diseases will be introduced ̶ Clinical genetics (aVLKG7X1c) Adobe Systems Lecture content ̶Basic concepts of genetics ̶ ̶Genome and its analysis ̶ ̶Modes of inheritance ̶ ̶Example from practice Clinical genetics (aVLKG7X1c) Adobe Systems Why medical genetics? Genome role in diagnostics, therapy and prevention = application in medical practice It is possible to implement into practice only what I know and what I have in mind ̶ Clinical genetics (aVLKG7X1c) Adobe Systems What you should already know What is a gene genes: structural for functional RNAs - housekeeping genes - gene expression - exones, intrones, non-transcribed regions, promotors Informational macromolecules Transcription, alternative splicing, translation Chromosomes ̶ Clinical genetics (aVLKG7X1c) Adobe Systems What is a DNA? cold ethanol + salt + detergent > 1 m DNA Clinical genetics (aVLKG7X1c) Adobe Systems What is a DNA? Cavendish Laboratory and The Eagle Pub Watson + Crick + Wilkins + Franklin Image result for dna discovery cambridge Clinical genetics (aVLKG7X1c) Adobe Systems What is a DNA? Clinical genetics (aVLKG7X1c) Adobe Systems What is a DNA? Clinical genetics (aVLKG7X1c) Adobe Systems Chromosomes Clinical genetics (aVLKG7X1c) Adobe Systems Terminology Clinical genetics (aVLKG7X1c) Genetics: study of genes, genetic variation, and heredity in living organism Ø Genome: complete set of DNA within a single cell of an organism Ø Genomics: focuses on the structure, function, evolution, and mapping of genomes Adobe Systems Terminology Clinical genetics (aVLKG7X1c) Genetics Genome Genomics Genome is more than just a sum of genes Adobe Systems Terminology Clinical genetics (aVLKG7X1c) Genetics Genome Genomics - Structural (DNA, chromosomes) - Functional (RNA, gene expression) - Comparative Adobe Systems Terminology Clinical genetics (aVLKG7X1c) Genetics Genome Genomics Microbiome Ø Transcriptome Ø Epigenetics Adobe Systems Terminology Clinical genetics (aVLKG7X1c) Genetics Genome Genomics Microbiome Ø Transcriptome Ø Epigenetics Community of microorganisms inhabiting a particular environment Adobe Systems Terminology Clinical genetics (aVLKG7X1c) Genetics Genome Genomics Microbiome Ø Transcriptome Ø Epigenetics Set of all RNA molecules in one cell or a population of cells in certain time Adobe Systems Terminology Clinical genetics (aVLKG7X1c) Genetics Genome Genomics Microbiome Ø Transcriptome Ø Epigenetics Study of heritable changes in gene function that do not involve changes in the DNA sequence Adobe Systems Genome Human genome: 3.2 x 109 bp, ~ 20,000 genes karyotypes.jpg Clinical genetics (aVLKG7X1c) Adobe Systems Genome Human genome: 3.2 x 109 bp, ~ 20,000 genes karyotypes.jpg Clinical genetics (aVLKG7X1c) Genome Variability § Nucleotide polymorphism - Single Nucleotide Polymorphisms - SNP § Structural variations - Copy Number Variations – CNV - Short Tandem Repeats – STR (2-5) Adobe Systems Genome Human genome was published in 2001 Clinical genetics (aVLKG7X1c) Adobe Systems Genome Individual sequences of human genomes were published in 2007 and 2008 220px-James_D_Watson_Genome_Image 220px-Craigventer2 J. D. Watson C. Venter Clinical genetics (aVLKG7X1c) Adobe Systems Genome Individual sequences of human genomes were published in 2007 and 2008 220px-James_D_Watson_Genome_Image 220px-Craigventer2 J. D. Watson C. Venter Clinical genetics (aVLKG7X1c) Difference in 7648 amino acid substitutions Adobe Systems Genome Individual sequences of human genomes were published in 2007 and 2008 220px-James_D_Watson_Genome_Image 220px-Craigventer2 J. D. Watson C. Venter Clinical genetics (aVLKG7X1c) The 1000 genome project published in 2010 Adobe Systems Genome Clinical genetics (aVLKG7X1c) Adobe Systems Postgenomic era Genomes were described Ø Ongoing genomes annotations Clinical genetics (aVLKG7X1c) Adobe Systems Genetics today from phenotype to genotype from genotype to phenotype DNA RNA protein phenotype Clinical genetics (aVLKG7X1c) Adobe Systems Modern techniques of genome analysis Clinical genetics (aVLKG7X1c) Adobe Systems NGS flexibility Clinical genetics (aVLKG7X1c) whole genome exome targeted genes or hotspots 3 200 000 000 bp 30 x coverage 20 000 genes 100 x coverage < 100 genes ≥ 1000 x coverage Adobe Systems Modern techniques of genome analysis Clinical genetics (aVLKG7X1c) Adobe Systems Mutation vs. genome variability Clinical genetics (aVLKG7X1c) •Every 1000th base could be mutated Þ 3.2 x 106 variants •One men has approx. 0.5 x 106 variants •Exome analysis (1.5% of genome) Þ tens thousands of variants • Which of the found variants is the disease causing one? Adobe Systems Mutation vs. genome variability Clinical genetics (aVLKG7X1c) •Every 1000th base could be mutated Þ 3.2 x 106 variants •One men has approx. 0.5 x 106 variants •Exome analysis (1.5% of genome) Þ tens thousands of variants • Which of the found variants is the disease causing one? mutations x polymorphisms Adobe Systems Mutation vs. genome variability Clinical genetics (aVLKG7X1c) Mutations: spontaneous vs. induced gene vs. chromosomal Mutations: missense nonsense (terminating triplet) same sense frameshift Adobe Systems Mutation vs. genome variability Clinical genetics (aVLKG7X1c) Adobe Systems Mutation vs. genome variability Clinical genetics (aVLKG7X1c) Microsatelites (STR) Adobe Systems Mutation vs. genome variability Clinical genetics (aVLKG7X1c) Sickle-cell anemia Adobe Systems Germline vs. somatic mutations Germline mutation Somatic mutation Clinical genetics (aVLKG7X1c) Adobe Systems The role of genome in the disease onset Clinical genetics (aVLKG7X1c) Mendelian hereditary diseases 8% Ø Multifactorial 90% Ø Other 2% Adobe Systems Inheritance types Clinical genetics (aVLKG7X1c) Mendelian monogenic: one gene Þ one feature X-linked and Y-linked (sex-linked disorders) Polygenic several genes Þ one feature Mitochondrial Environmental factors Adobe Systems What is the procedure of hereditary diseases tracing? pedigree disease frequency in population Ø molecular biology methods Ø functional tests Clinical genetics (aVLKG7X1c) Adobe Systems Pedigree Clinical genetics (aVLKG7X1c) Adobe Systems Pedigree ̶ two common ancestors in previous generation: parents ̶ 4 grandparents, 8 great-grandparents ̶ the number of ancestors in generation n is 2n ̶ ̶ ̶ ̶ ̶ ̶ ̶ ̶ ̶ ̶40th generation (1000 years back): 240 = 1.09 x 1012 ̶so many people didn’t live on this planet (7.0 x 109) Clinical genetics (aVLKG7X1c) Adobe Systems Mitochondrial inheritance Clinical genetics (aVLKG7X1c) Adobe Systems Y chromosome inheritance Clinical genetics (aVLKG7X1c) Adobe Systems Autosomal dominant inheritance Clinical genetics (aVLKG7X1c) Adobe Systems Autosomal recessive inheritance Clinical genetics (aVLKG7X1c) Adobe Systems Enviromental factors Beer vepřo2 Bachovy esence a stres Clinical genetics (aVLKG7X1c) Adobe Systems Monogenic disorders Clinical genetics (aVLKG7X1c) Adobe Systems Autosomal recessive disorders hemochromatosis (1:10) Ø factor V Leiden mutation (1:20) Ø cystic fibrosis (1:25) Ø spinál muscular atrophy (1:40) Clinical genetics (aVLKG7X1c) Adobe Systems Autosomal recessive disorders Founder effect Ø Small closed populations: Ashkenazi Jews franco-Canadiens Iceland surroundings od Maracaibo lake… Ø Marriages of relatives Clinical genetics (aVLKG7X1c) Adobe Systems Consanguinity Clinical genetics (aVLKG7X1c) Homozygous mutation BLM gene c.1642C>T, p.(Gln548*) Adobe Systems Syndrome Nijmegen breakage, NBS Seemanová, 1985 Clinical genetics (aVLKG7X1c) NBN gene for nibrin in 8q21 Heterozygotes 1:130-150 Common ancestor Adobe Systems Autosomal dominant disorders Achondroplasia Huntington chorea Marfan syndrome Polycystic kidneys Neurofibromatosis Clinical genetics (aVLKG7X1c) Adobe Systems Gonosomal disordres Gonosomal dominant - vitamin D resistant rachitis Gonosomal recessive - hemofilia A, B - Duchenne muscular dystrophy Clinical genetics (aVLKG7X1c) Adobe Systems Clinical case from practice Clinical genetics (aVLKG7X1c) Adobe Systems Clinical case Clinical genetics (aVLKG7X1c) Obrázek2.png Functional analysis of ETV6 : fluorescence microscopy Adobe Systems What are the skills of clinical geneticist? Clinical genetics (aVLKG7X1c) complex examination gene/s analysis indication - exome sequencing - genome sequencing - functional tests results interpretation (from practitioners to clinical geneticists) therapeutic and preventive intervenation proposal - respecting wishes of affected individuals together with ethical aspects Adobe Systems CRISPR/Cas9 Clinical genetics (aVLKG7X1c) Adobe Systems Take home message ̶The genome is all the DNA in a cell / organism ̶Exome is DNA coding sequence ̶We have about 20,000 genes ̶Modern methods of DNA analysis make it possible to analyze whole genomes ̶Human genome variability - what causes disease? ̶Genetics skills ̶Genome editing Clinical genetics (aVLKG7X1c) Lékařská fakulta Masarykovy univerzity 2021 Adobe Systems