Introduction to Genomic Medicine Exeter Expert Series: Cardiology

Transcription

1 Introduction to Genomic Medicine Exeter Expert Series: Cardiology 2-3 November, 2017 Session I. Introductory concepts of genomics: gene, genome and variants Presented by Júlia Baptista PhD Clinical Scientist and Honorary Lecturer Developed with Sawsan Khuri PhD 1

2 Genetics and genomics is the study of DNA 2

3 Central dogma of biology Replication DNA Transcription Translation RNA Proteins 3

4 DNA DNA = deoxyribonucleic acid Stable double-stranded polymer of nucleotides: Deoxyribose sugar, Phosphate, Base (A, T, C & G) nucleotide end end 4

5 DNA Bases Purines (2 rings): Adenine & Guanine Pyrimidines (1 ring): Thymine & Cytosine 5

6 DNA Base-pairs (bp) Complementary base-pairing A with T (two hydrogen bonds) G and C (three hydrogen bonds) 6

7 DNA Sequence

8 DNA Structure Two antiparallel strands Either or both may code for genes 8

9 Nucleosomes 9

10 LMNA gene (dilated cardiomyopathy) Chromosomes BRCA1 gene (Breast Cancer) Chromosomes are made DNA and proteins called histones. Located in the nucleus of cells Each contains genes in a linear order. Human body cells contain 46 chromosomes in 23 pairs Chromosome pairs 1 22 are called autosomes. The 23rd pair are called sex chromosomes: XX is female, XY is male. HNF4A gene (MODY) 10

11 DNA Function Long-term storage of genetic code Human diploid genome ~6 billion base pairs! ~1-2% protein coding in ~23,000 genes 11

12 structure Genes Coding region and non-coding: transcribed into mrna Exons (protein-coding) and introns ( spacers ) Regulators (cis or trans): involved in transcription Promoters, silencers, enhancers and insulators 3 Silencer downstream TSS 5 UTR Exon 1 Exon 2 Exon 3 3 UTR Coding region of gene upstream Insulator Enhancer 5 12

13 How is a gene converted into a protein? DNA in nucleus - permanent central record of data mobile transfer of selected data messenger RNA decoding of data by assembly machine the ribosome components amino acids functional units proteins 13

14 Gene to protein 14

15 So few genes, so many proteins Genome Transcriptome Proteome 15

16 RNA = ribonucleic acid RNA Unstable single-stranded polymer of nucleotides: Ribose sugar, Phosphate, Base (A, U, C & G) nucleotide OH OH OH 16

17 RNA Functions Many different types with different functions Messenger RNA (mrna): coding intermediary between DNA and proteins Non-coding RNA (ncrna): various roles Protein synthesis: ribosomal (rrna), transfer RNA (trna) Gene Regulation: microrna (mirna), small interfering or silencing RNA (sirna), long non-coding RNA (lncrna) Catalysis: Ribozymes 17

18 Proteins Long sequence of amino acids 20 different R groups Amino acid Peptide bond 18

19 Amino acids All have 3- and 1-letter abbreviations Side-chains have different sizes and properties Non-polar, hydrophobic (G, A, V, L, I, M) Aromatic (F, Y, W) Polar, hydrophilic, uncharged (S, T, C, P, N, Q) Charged Positive/Basic (K, R, H) Negative/Acidic (D, E) 19

20 Protein Function Antibody (bind to foreign particles) Enzyme (catalyse biochemical reactions) Messenger (between and within cells) Structural component (maintain cell/tissue shape) Transport/storage (bind, carry or channel things)

21 Triplet code Three DNA base-pair (triplet or codon) encodes each amino acid Code is degenerate, i.e. has in-built redundancy 21

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23 Changes to Coding Sequence Single base changes Synonymous ( silent ): change in DNA sequence, no change to protein Non-synonymous: change in DNA sequence changes protein sequence Missense: change of amino acid Nonsense*: premature stop codon or splice variant Insertions/deletions In-frame: insertion/deletion 3x base pairs Frameshift*: truncating *RNA may be eliminated by nonsense-mediated decay (NMD) 23

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25 Causes of variation Exogenous factors (chemical agents, UV radiation) Endogenous factors Replication slippage/slipped strand mis-pairing Recombination (large scale variants) Segregation (Aneuploidies) 25

26 Somatic and germline variation Variants that are present in the germ cells (cells that give rise to the gametes) can be passed onto the next generation when that cell participates in fertilization. These variants are important in evolution. Variants that arise in a cell lineage other than the germline are somatic. These are postzygotic events and cannot be inherited. Somatic changes are mosaic. 26

27 Human Genome Variation Society International body for defining gene variation nomenclature under the umbrella of the Human Genome Organization (HUGO) and the International Federation of Human Genetics Societies (IFHGS). HGVS aim: standardisation of nomenclature across all genes Designed to be: stable meaningful memorable Unequivocal 27

28 Nomenclature CFTR NM_ Wild type: p.548 Leu 549 Ser 550 Gly 551 Gly 552 Gln 553 Arg 554 Ala CTG AGT GGA GGT CAA CGA GCA Mutant: p.548 Leu 549 Ser 550 Gly 551 Asp 552 Gln 553 Arg 554 Ala CTG AGT GGA GA T CAA CGA GCA CFTR NM_ : c.1652g>a, p.(gly551asp)

29 The Human Genome Project

30 ENCODE: identify all functional elements in the human genome from the ENCODE project

31 Mapping genomic variation Retired in 2016 Completed in 2015 UK now on 100,000 Genomes Project African, Japan, Singapore, India... genome projects currently ongoing

32 Interpreting variants in the clinic ~ 3-4 million variants per genome Mostly common variants not connected with a disease phenotype Variants that cause rare genetic disorders tend to be rare. Important evidence: Population data Disease databases De novo data Segregation Functional data Computational predictions 32

33 Summary DNA is a long polymer made of individual nucleotides DNA contains genes that encode proteins through transcription and translation A genome is the total DNA of an organism. Genomic Medicine is the use of genomic information and its emerging technologies for disease diagnosis, prognosis, and intervention. 33

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