Genetic analysis of human disease (lecture 16) Flashcards
what is genetic analysis of of human disease?
using variations between our genomes to track genetic lesions and susceptibility alleles
consequences of crossing over in multiple generations
chromosomes become mixed due to crossing over many times
what are sequence variations?
SNPs
RFLPs
microsatelites
what are variable number tandem repeats?
repeated sequences organised as sequential (tandem) repeats
due to unequal cross over and replication errors
errors in DNA replication lead to these repeats expanding or contracting
what are short tandem repeats (STRs)?
short repeating units of 5 nucleotides or less in length
repeated less than 100x
repeat number varies between individuals
useful for genotyping and identifying individuals
what are minisatellites?
repetitive GC-rich variant repeats of 10-100 bases
what are single nucleotide polymorphisms (SNPs)?
approx. 1 every 300 nucleotides = 10M in human genome
some base changes produce/remove new sites for restriction endonucleases
the sizes of the restriction fragments seen on a genomic southern blot are changed
these changes = RFLPs (restriction fragment length polymorphisms)
how are genes identified in a DNA sequence?
by CpG islands
what are CpG islands?
regions of DNA highly enriched in CpG sites
frequently associated with 5’ region (promotors) of genes
can be identifies when the sequence is not known since sites for some restriction enzymes cluster in CpG rich regions
what is a haplotype?
a set of linked polymorphic markers
what is the international Hapmap project?
a community resource for disease gene discovery
an effort to generate comprehensive SNP maps of the human genome
many SNPs are inherited together in blocks called haplotypes
how are SNPs analysed?
BeadChips/GeneChips
what are BeadChips?
1) PCR amplification of the whole genome
2) fragment DNA into smaller pieces and hybridise to specific primers bound to beads on chips
3) each primer ends 1 base before the position of known SNP
4) extend primer by 1 nucleotide - nucleotides are labelled
5) read in scanner - identifies the base added
what is GWAS?
Genome Wide Association Study
1) collect a large number of disease and control samples
2) put though assays for SNPs spread across the genome
3) analyse data for significant association
what can the information from SNP studies be used for?
inform patient care/screening
can be used to identify genes that influence particular phenotypes
tells us about human history
insurance
