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Lecture 12

Lecture 12 - Detection of Mutations and Genetic Variations

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Western University
Biology 2581B
Jim Karagiannis

LECTURE 11: DETECTION OF MUTATIONS AND GENETIC VARIATIONS Key Concepts 1. Single nucleotide polymorphisms 2. Short repeated sequences 3. Mini-satellites and fingerprinting 4. Positional cloning How do Individuals Differ within a Species? • Not all individuals within a species have identical genomes • Question: how to distinguish between genetic variations a wild type allele and a mutation? • Alocus with two or more alleles where each allele is present in more than 1% of the populations = polymorphic • Alleles of a polymorphic locus are called genetic variations rather than wild-type or mutants • Advanced sequence technologies allows sequencing of complete genomes from individuals • 2.021,206 single nucleotide sequences • 5,015 cause amino acid changes of expressed proteins • Single nucleotide substitutions in the genomic region for the cystic fibrosis gene • Most of them do not have any effect on function • Only approximately 2% of the nucleotides in this region are part of coding sequences • Not only base substitutions, over 100,000 deletion and insertion ranging from 2 to 37,896 base pairs • Overall genome length differ as much as 1% between healthy individuals Locus-Loci • Any location within the genome that has a defined chromosomal location – irrespective of function, coding or non-coding, short or long • Single base pair substitution – one gene – several genes • Allele – genetic variation at a specific locus Polymorphic Loci • Single nucleotide polymorphisms = SNPs or “snips” • Insertions and deletions = InDels or DIPs • Simple sequence repeats = SSRs • Copy number polymorphisms = CNPs • None of the above are complex variants SNPs • Are the most common genetic variation • Spontaneous – during replication • Induced – chemical mutagen • SNPs are base pair substitutions • How to detect SNPs 1. Southern blot analysis of restriction site altering SNPs 2. PCR analysis of restriction site altering SNPs Size separate restriction digested PCR fragments by gel electrophoresis 3. Using allele specific oligonucleotide hybridization Design a SNP probe to a known SNP sequence Sickle CellAnemia • Single base pair substitution resulting in a single amino acids change in the β-globin chain of haemoglobin • This promotes the aggregation of haemoglobin under low oxygen conditions which distorts red b
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