BGM1004/L16 Genetic Analysis of Human Disease Flashcards
What percentage of human DNA is the same across the whole species?
> 99%
Why do chromosomes become ‘mixed’?
Crossover during meiosis
What are sequence variations?
Sequences that co-segregate with variants through generations
E.g., SNO, RFLPs, microsatellites
What are variable number tandem repeats?
Repeated sequences organised at sequential (tandem) repeats
Why do variable number tandem repeats vary between individuals?
Unequal corssover, replication errors etc.
How long are simple sequence repeats and short tandem repeats?
3-7 nucleotides
How many times are SSRs and STRs repeated?
<100x
How are SSRs and STRs distributed in the genome?
Every few 1000 base pairs
What are minisatellites?
GC-rich variant repeats of 10-100 bases
Where do 90% of minisatellites occur in humans?
Sub-telomeric region of chromosomes
What method can be used to detect numbers of repeats at various loci?
PCR
What are single nucleotide polymorphisms?
Single base differences (SNPs)
How often do SNPs occur?
Every -300 nucleotides
What are changes to base sequence that change the size of the restriction fragments on a Southern Blot?
RFLPs
What are CpG islands?
Regions of DNA highly enriched in CpG sites
What region are CpG islands frequently associated with?
5’ region (promoters) of genes
How can CpG islands be identified?
When sequence is not known since sites for some restriction enzymes cluster in CpG-rich regions
Approximately what percentage of genes contain CpG islands?
70%
How were the causative mutations of Cystic Fibrosis found?
Linkage and RFLP analyses
Positional cloning
What kind of protein is encoded by the Cystic Fibrosis gene?
Chloride transporter
What kind of mutation leads to Cystic Fibrosis?
3 nucleotide deletion of Phe 508
What is the term describing a set of linked polymorphic markers?
Haplotype
What are SNP maps useful for? (2)
Locating genes that might be associated with particular phenotypes
Diagnosing potential (future) problems/phenotypes
Describe BeadChips (Illumina). (5 steps)
PCR amplification of whole genome
Fragment and hybridise to primers bound to beads on a chip
Each primer ends 1 base before the position of a known SNP
Extend the primer by 1 nucleotide
Read in scanner to identify labelled bases added
What is the GWAS approach?
Genome-Wide Association Study
How is a GWAS conducted? (4)
Collect large number of case & control samples
Put through assays for SNPs spread across genome
Analyse data for significant association of particular variants with cases
Use other SNPs in region of interest to confirm association
How can information from GWAS be used? (2)
Informs patient care/screening
Identify genes/pathways influencing particular phenotypes
Informs about human history
Where is the great majority of human DNA sequencing focused?
High income countries
