DNA polymorphisms

DNA polymorphisms - BIOC2603 Principles of Molecular...

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BIOC2603 Principles of Molecular Genetics DNA polymorphisms Brian Wong [email protected]
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Genetic variations in human • Compare genomic DNA of any two individuals: 99.9% identical (approximately 1 difference per 1 kb) • Size of human genome is 3 x 10 9 bp so 0.1% difference corresponds to about 3 x 10 6 bp difference • These genetic differences result in individual differences in disease susceptibility, responses to drug, etc • Finding genetic variations associated with a disease phenotype can help to locate genes responsible for the disease and these variations can also be used for diagnostic purposes • Genetic variations can also be used for personal identification and kinship testing
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CYP1A2 in liver is responsible for metabolizing caffeine. People with a certain polymorphism in this gene result in a slow metabolizer phenotype and are more likely to suffer heart attack. Those with a fast metabolizer polymorphism have a lower risk. Genetic variations resulting in individual differences Cornelis MC et al (2006) JAMA 295:1135–1141
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From: Griffiths AJF et al (1999) Modern genetics analysis. Freeman. Discontinuous and continuous variations Caused by variations in a single gene Caused by variations in many genes, and interactions between genes and the environment.
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Polymorphisms • Locus: a defined position in the genome, can be a gene, a stretch of DNA, a restriction enzyme recognition site, or a single nucleotide • Alleles: alternative forms of the same gene/locus, caused by mutations • Mutation: a change in the gene sequence. Occurs at a low frequency in a population. • A locus is polymorphic if the least frequent allele occurs at 1% or greater in a population
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Polymorphisms • Phenotypes: color, morphology, etc • Protein polymorphism (allozymes) – Differences in size and charge because of amino acid substitutions – Identified using native gel electrophoresis Other hemoglobin variants Other hemoglobin variants From: Griffiths AJF et al (1999) Modern genetics analysis. Freeman.
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Polymorphisms • DNA polymorphisms – Single-nucleotide polymorphism (SNP) – Variable number of tandem repeats (VNTR) polymorphism: • Minisatellite polymorphism: total size 0.5 - 30kb. The unit size of the repeats is variable (15-100bp) but most share a common core sequence (GGGCAGGANG). Minisatellites are also found near telomeres (10-15kb of TTAGGG repeats). • Microsatellite polymorphism: the unit size of the repeats is short (e.g. 1 to 6 bp). Also known as short tandem repeats polymorphism or simple sequence repeat polymorphism. – Both SNP and VNTR polymorphism can give rise to restriction fragment length polymorphism (RFLP)
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• Variations in the size of DNA fragments produced after restriction enzyme digestion. Due to: – Single nucleotide polymorphism: single base change abolishes or creates a restriction enzyme recognition site – VNTR: a region containing variable number of tandem repeats flanked by two restriction enzyme recognition sites.
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DNA polymorphisms - BIOC2603 Principles of Molecular...

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