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BF - MM2

Identifying Disease Genes

What are 3 exogenous mutagens? X-rays, uv light, O2 radicals
What is an endogenous mutation causing event? Replication errors
nDNA vs mtDNA - Which has lower mutation rate? nDNA
nDNA vs mtDNA - Which has more robust DNA repair mechanisms? nDNA
nDNA vs mtDNA - Which is susceptible to damage by reactive O2 species? mtDNA
Mutations in DNA coding can be grouped into what two classes? 1. Synonymous (silent) mutations 2. Non-synonymous mutations
What are synonymous (silent) mutations? No change in gene product (degenerate code) Common
Are synonymous (silent) mutations common/ rare? Common
What are non-synonymous mutations? Change in sequence of gene product
Are non-synonymous mutations common/ rare? Rare
What are the 4 main instabilities in the human genome? Base substitutions, insertions, deletions, chromosomal abnormalities
In base substitutions, what are transitions? Pyramidine-pyramidine or purine-purine
In base substitutions, what are transversions? Pyramidine-purine or vice versa
What are the 3 types of single base substitutions? Missense (replaced) Nonsense (replaced with stop codon) Spice (alters signal from exon-intron splicing)
What are multiple base substitutions? Gene conversion-like events
Insertions - One or more nucleotides is called what? Frameshift
Insertions - Triplet repeat expansions lead to what? Instability
Insertions - What are substantial repeat insertions called? Tandem repeats
Check you understand DNA libraries (see notes)
What are the two major methods of identifying disease genes? Position independent cloning and positional cloning
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
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
Position-independent DNA sequence knowledge - How is sequence identified? Southern blotting techniques
Position-independent DNA sequence knowledge - From the 'anticipation' in the southern blot, what can be identified? Longer/ shorter expansions
Positional cloning - What is it? Isolation of a gene by identifying its precise chromosomal location, by a combination of physical and genetic mapping
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
Linkeage analysis - What are SNPs? Single nucleotide polymorphism (unique genomic marker)
Linkeage analysis - Use of SNPSs? Find an SNP near gene of interest
Linkeage analysis - What therefore does frequency of the SNP and disease indicate? The relative proximity of the SNP to the disease causing gene
Linkeage analysis - How can the exact position of the disease causing gene then be identified? Method called 'chromosome walking'
What are cytogenetic abnormalities? e.g. Chromosomal abnormalities, seen on a karyotype, accompanying a disease e.g. DMD
DMD - Type of inheritance? X-linked recessive
DMD - familial or sporadic? 2/3 familial, 1/3 sporadic
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
Created by: benfenner1