Identifying Disease Genes
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| What are 3 exogenous mutagens? | X-rays, uv light, O2 radicals
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| What is an endogenous mutation causing event? | Replication errors
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| nDNA vs mtDNA - Which has lower mutation rate? | nDNA
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| nDNA vs mtDNA - Which has more robust DNA repair mechanisms? | nDNA
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| nDNA vs mtDNA - Which is susceptible to damage by reactive O2 species? | mtDNA
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| Mutations in DNA coding can be grouped into what two classes? | 1. Synonymous (silent) mutations
2. Non-synonymous mutations
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| What are synonymous (silent) mutations? | No change in gene product (degenerate code)
Common
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| Are synonymous (silent) mutations common/ rare? | Common
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| What are non-synonymous mutations? | Change in sequence of gene product
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| Are non-synonymous mutations common/ rare? | Rare
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| What are the 4 main instabilities in the human genome? | Base substitutions, insertions, deletions, chromosomal abnormalities
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| In base substitutions, what are transitions? | Pyramidine-pyramidine or purine-purine
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| In base substitutions, what are transversions? | Pyramidine-purine or vice versa
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| What are the 3 types of single base substitutions? | Missense (replaced)
Nonsense (replaced with stop codon)
Spice (alters signal from exon-intron splicing)
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| What are multiple base substitutions? | Gene conversion-like events
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| Insertions - One or more nucleotides is called what? | Frameshift
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| Insertions - Triplet repeat expansions lead to what? | Instability
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| Insertions - What are substantial repeat insertions called? | Tandem repeats
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| Check you understand DNA libraries | (see notes)
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| What are the two major methods of identifying disease genes? | Position independent cloning and positional cloning
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| Functional coding - 4 main steps 1. Isolate... 2. Determine... (2) 3. Synthesize...for... 4. Screen DNA library to... | 1. Isolate protein product of a disease gene
2. Determine a.a. sequence of protein and therefore cDNA sequence
3. Synthesize oligonucleotide probes for cDNA
4. Screen cDNA library to recover sequence
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| Position-independent DNA sequence knowledge - Requires knowledge of what? e.g. | Disease pathology e.g. Disorders which show 'anticipation', such as those with trinucleotide repeat expansions
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| Position-independent DNA sequence knowledge - How is sequence identified? | Southern blotting techniques
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| Position-independent DNA sequence knowledge - From the 'anticipation' in the southern blot, what can be identified? | Longer/ shorter expansions
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| Positional cloning - What is it? | Isolation of a gene by identifying its precise chromosomal location, by a combination of physical and genetic mapping
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| Positional cloning - What are the 5 main steps? 1. Define... 2. Obtain... 3. Identify... 4. Prioritise... 5. Test candidate genes for? | 1. Define the candidate region (linkeage analysis/ chromosomal abnormalities)
2. Obtain clones of all the DNA of the region
3. Identify all the genes in the region
4. Prioritize them for mutation screening
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| Linkeage analysis - What are SNPs? | Single nucleotide polymorphism (unique genomic marker)
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| Linkeage analysis - Use of SNPSs? | Find an SNP near gene of interest
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| Linkeage analysis - What therefore does frequency of the SNP and disease indicate? | The relative proximity of the SNP to the disease causing gene
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| Linkeage analysis - How can the exact position of the disease causing gene then be identified? | Method called 'chromosome walking'
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| What are cytogenetic abnormalities? e.g. | Chromosomal abnormalities, seen on a karyotype, accompanying a disease e.g. DMD
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| DMD - Type of inheritance? | X-linked recessive
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| DMD - familial or sporadic? | 2/3 familial, 1/3 sporadic
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| What are the three steps in subtraction cloning (use example of DMD)? (3) | 1. Assume large deletion included disease causing (DMD) gene
2. Clone missing DNA from normal x chromosome
3. Fine map region to find DMD gene
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Created by:
benfenner1
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