Genetic variation.pdf

Genetic variation, Health and Disease Dr Talat Nasim [email protected] 1  Objectives What is genetic variation, and how does it arise What is the scale of human genetic variation Why do we need genetic variation? Understand functional genetic...

Genetic variation, Health and Disease Dr Talat Nasim [email protected] 1  Objectives What is genetic variation, and how does it arise What is the scale of human genetic variation Why do we need genetic variation? Understand functional genetic variation and protein polymorphism Understand how genetic variations can lead to diseases Study some genetic variations identified in Pulmonary Arterial Hypertension As usual some application exercises. 2  References Much of the information was based on Genetics & genomics in medicine by Strachan, Goodship and Chinnery Garland Science publication The Molecular Biology of the Cell. Bruce Alberts, James Watson, Dennis Bray and Julian Lewis. First published in 1983. 3 Mutations versus Genetic Variation Mutations represent changes in the base sequence that typically occur very much less than in 1% of the population. Genetic variation occurs at >1%, and presumably arose from a mutation that was positively selected during evolution. This DNA variation is described as DNA polymorphism. Some rare variants can occur at less than 1% but are distinct from mutations 4 Is there any correct statement in the following sentences? A. Mutation changes the DNA sequence whereas genetic variation changes the RNA sequence. B. Both genetic variation and mutation change DNA and protein sequences. C. Both genetic variation and mutation are harmful and may cause disease. D. There is basically no difference between mutation and genetic variation. 5  How do mutations arise 1. Strand breakage - and several nucleotides may be lost before end- joining (an error prone process) 2. Base loss – glycosidic bond is broken or enzymatically cleaved 3. Base change – guanine is oxidised to 8-oxoguanine and then base- pairs with adenine, cytosine loses an amine group to become uracil and base-pairs with adenine. Thymidine glycol just blocks replication. Polyaromatic carbons found in cigarette tar cause bulky DNA adducts 4. DNA crosslinking – UV light cause cyclobutane dimers, and anticancer agent cis-platinum causes adjacent guanines to cross link 5. DNA replication error –some errors not corrected 6 What happens when DNA repair mechanisms fail Lead to genetic damage that isn’t repaired or repaired inaccurately (change in DNA sequence. Health consequences are: 1. Cancer susceptibility 2. Progeria (accelerated ageing) 3. Neurological defects 4. Immunodeficiency 7  Mutations A mutation is a hereditable change in: DNA sequence Chromosome number, form or structure Changes in DNA sequence most commonly arise due to errors in DNA replication Mutation rate The rate of mutation is very important, too low and organisms cannot adapt, too high and information cannot be retained 9  Mutation rates Per base per generation Transcription in vitro 10-5 DNA replication in vitro 10-9 Prokaryotic genome 10-3 Eukaryotic genome 0.1-10 Human genome 2.5−8 Mitochondrial genome 3-5 highest! 10 Genetic variation - cause All genetic changes originally arise as a consequence of mutation Recombination (crossover events in meiosis) has a huge impact on variation 11 Types of mutations Point Mutations Insertions and Deletions (indels) Changes to a single nucleotide (substitution) Few nucleotides or several kb Missense and nonsense mutations Insertions and deletions Chomosomal Mutations Polyploidy - Multiple sets of chr. Aneuploidy (abnormal number) -Extra or missing chr. Chromosome rearrangements - Parts moved to other chr. gamete fertilisation meiosis 12 (Deletion or insertion of a single base) Missense mutations - type A change in the nucleotide sequence that results in a change to the amino acid sequence Includes point mutations and frameshifts May or may not have an effect on protein function! Loss of function! e.g. PAH, many mutations in the gene cause the disease Gain of function! - dwarfism e.g. Achondroplasia, usually always His > - pro caused by the same mutation in amino acid change Can interfere with any aspect of a 13 = missense mutation function Nonsense Mutations - type A change in the nucleotide sequence that results in a premature stop codon Caused by point mutations and frameshifts Usually results in a non- functional protein PAH, mutations in the BMPR2 gene Duchenne muscular dystrophy often arises due to mutations that introduce a premature stop codon in the dystrophin gene 14 Insertions/deletions (Indels) - type Removal of one to several million nucleotides 5-10-% of all mutants 50% of all Duchenne Muscular Dystrophy cases (nonsense) Small ones often cause frame shifts resulting in missense/ nonsense Majority of α-Thalassemias (haploinsufficient) Associated with melanoma 15 (haploinsufficient) Electropherogram 16  Activity: Identify mutations Smad1 (p.V3A) Smad4 (p.N13S) Smad8 (p.K43E) Smad4 (c.1448-6T>C) Asn Val Thr Ser Ser Asn Asp Ala Val Lys Lys Leu G A A T G T G A C A A G T TT A A G TA A T G A T G C C T G A G T G A A G A A G T TA A C T T TT C T G T TA G G T C T a Asn Ala Thr Ser Ser Ser Asp Ala Val Glu Lys Leu note G A ATG T G A C A A G T T T A A G TA A T G A T G C C T G A G T G A A G A A G T T A A C T T T T C T G T T A G G T C T Nasim et al., 2011 Hum Mut  20/03/2017 Genetics and Health 18 Pulmonary Arterial Hypertension  BMPR-II functional domains 1 150 205 500 1038 LB TM LR KD CD G182D M186V R899X Q42R R899P G47N A313P N903S Q82H C347Y C348R T102A D485G S107P K512T N519K C60Y S532X C117Y C118Y E503D What are the effects of these mutations? Expanding trinucleotide repeats - type Simple tandem repeats (same bits of sequence repeated lots of times, one after the other) throughout the human genome: - CGG, CAG, CTG However during replication these can increase in copy number Around 17 diseases are known to be caused by expanding trinucleotide repeats, these include: Huntington’s Disease Fragile X syndrome Kennedy Disease Myotonic Dystrophy 21 CAG repeats in Huntington’s Disease A genetic disease – involuntary muscle CAG repeats encode a poly- movements and dementia glutamine region in a number of proteins In the IT15 gene encoding the Huntingtin protein, the region consists of 6-35 repeats Josh Cook, 22, from Huddersfield, diagnosed with 36 repeats or above causes a Huntington's disease, which will see him neurodegenerative disease - slowly lose control of his body. Huntington’s Disease “What ethical justification can be found for informing a person that he or Huntington’s Disease raises a she will later develop a lethal disease 22 number of ethical issues for which no therapy is available?” around genetic screening  Transposons - type Sequences of DNA that can move around the genome! Often regularly repeated throughout the genome and act as recombination hotspots Retrotransposons Analogous to a ‘copy and paste’ system Exhibit an intermediate RNA stage, prior to insertion into the genome DNA transposons Simply ‘cut and paste’ the transposable element (TE) Alu repeats (short interspersed elements, SINEs) The most abundant mobile element in the human genome LDL receptor has a large number of Alu repeats, which may be responsible for the 23 large number of pathogenic deletions in this 45 kb gene LDL receptor removes ‘bad’ cholesterol from the body (FH, atherosclerosis)  Selective pressure Case: Malaria Selective pressure for erythrocytes with sickle cell haemoglobin (Hb S) mutation – cause sickle cell anaemia but provide protection against malaria! Children Hb A Hb A Hb S Hb A Hb S Hb S Normal haemoglobin - susceptible to death from malaria Sickle cell trait - one gene for haemoglobin A and one gene for haemoglobin S - greater chance of surviving malaria (do not suffer adverse consequences from the Hb S gene) 25 Sickle cell disease - susceptible to death - complications of sickle cell disease Shows heterozygote advantage  Haploinsufficiency We all have two copies of a gene (one from mum, one from dad) Diploid - 2n, 2 sets of chromosomes 23 + 23 chromsomes = 46 chromomes in a human Gametes = 23 chromosomes Haploinsufficiency is when one copy is deleted, or inactivated by a mutation, so you only have one copy functioning! Haploinsuffiency means one functional gene on it’s own is not enough Loss of function mutants tend to be recessive for two reasons: Feedback loops upregulate the production of the normal gene in heterozygotes 50% of the gene product is sufficient In some situations a dosage effect may be seen: Gene product is part of a quantitative signalling system Gene products compete to determine a metabolic or developmental switch Gene products combine in a fixed stoichiometry e.g. 26 Need both α and β globins to combine to make haemoglobin in Thalassemia (anaemia) If α-globin chain affected by mutation – α-thalassemia (same with β)  Human Genetic Variation Single nucleotide changes represent 75% of genetic variation. Differences between parental genomes occur every 1000bp, but mostly are in non-coding regions! 25% of changes represent structural changes mainly in copy number variation Genetic changes can increase our risk of/susceptibility to disease, these can range from: 1, Rare high risk variant and high penetrance 2, Rare low penetrance mutation/variation and moderate risk 3, Common low risk and low penetrance variant 27 Penetrance = how frequently the disease is manifested Functional Genetic Variation and Protein Polymorphism Only 1.2% of our DNA encodes for proteins Most mutations have little effect as they are either silent mutations (don’t change the encoded amino acid) or are in regulatory regions with no discernable effect Some mutations are harmful and if reduce reproductive success will be gradually eliminated. Some mutations are beneficial and become prevalent by positive selection. 28  Summary and take home points ✓ A large amount of genetic variation exists ✓ Mutation is the ultimate source of all genetic variation, however… ✓ Recombination is also a driving force behind evolution and variability ✓ Selection acts on genetic changes positively or negatively ✓ Different types of mutation exist ✓ Chromosomal and structural aberrations ✓ Tend to either affect protein sequence (missense/nonsense) or not (silent) ✓ There is a spectrum of disease susceptibility variants ✓ Tri-nucleotide repeats 29 ✓ Transposable elements  References ✓ T. Ogo, H.M. Chowdhury, R. Randall, L. Long, J. Yang, R. Schumerly, N.W. Morrell, R.C. Trembath and M.T. Nasim*. American Journal of Respiratory Cell and Molecular Biology 48(6):733-41, 2013. ✓ M.T. Nasim*, T. Ogo, H.M. Chowdhury, L. Zhao, C.N. Chen, C. Rhodes, and R.C. Trembath. Human Mol Genetics (21):2548-58, 2012. ✓ M T. Nasim, T. Ogo, M. Ahmed, R. Randall, H.M. Chowdhury, K. Snape, T. Bradshaw, F. Soubrier, I. Jackson, M. Humbert, N. Morrell, R. C. Trembath and R. Machado. Human Mutation 12:1385-89, 2011. ✓ M.T. Nasim*, A.G. Ghouri, B.P. Patel, V. James, N. Rudarakanchana, N. Morrell and R.C. Trembath. Hum Mol Genet (11):1683-94, 2008. ✓ * Corresponding author 30