3 - Genomics trigger Flashcards
exome
protein coding regions of the genome
epigenome
modification to the genome
examples of modifications to the genome
methylation
histone acetylation
karyotype
chromosomal content of a cell
transgene
cDNA coding for any gene that is introduced into a cell
proband
the affected individual
SNP
single nucleotide polymorphism
e.g. insertions and deletions
example of a simple monogenic disorder
cystic fibrosis
GWAS
genome wide association study
examples of polygenic diseases
diabetes
Alzheimer’s
gDNA
genomic DNA
chromosomal dna
epigenetic
changes to DNA that do not affect its base sequence –
often environmental
linkage analysis
study aimed at establishing a linkage between genes
define linkage
the tendency for genes to be inherited together due to location on the chromosome
what is linkage a measure of
how resistant to recombination a genetic marker and phenotype are
how do you test for linkagee
focus on very small chromosomal region
carry out lab studies to see if gene function is affected
think about gene therapy
how do you confirm your suspected mutant gene
transfect the gene in a wild-type transgene
why is genetic linkage important
allows causes of rare disease to be identified
what does GWAS look for
SNPs that are over-represented in disease patients
what is GWAS
observational study of a genome-wide set of variants in an indivudal to see if any genetic variation is associated with a trait
what does GWAS stand for
genome wide association stufy
steps involved in gwas
2 groups - diseased and healthy
sequence genomes to look for common SNPs
do allele frequencies differ between groups?
create odds ratio
if significantly different from 1 then SNP associated with disease
polygenic disease
associated with the effects of multiple genes in combination with lifestyle and environmental factors
e.g. diabetes, alzheimers
not guaranteed inheritance
mendelian randomisation
a method where people are grouped by their genetic variation of a known function
used to study cause and effect of exposure on disease
why is mendelian randomisation not affected by confounding variables
genotype is radnomly assigned to you at birth
what is RNA sequencing used for
quantifying how much of each mRNA from each gene you have under different conditions
3 steps in rna sequencing
purify mRNA
reverse transcribe
sequence the cDNA
why is software used in RNA seq
aligns results against database of known mRNAs
how would you quantify changes in gene expression under hypoxia and normoxia conditions
RNA sequencing
make a list of genes upregulated in hypoxia compared to normoxia
describe the graph made by RNA seq
no of mRNA copies on y-axis
different genes expression on x-axis
bar chart
2 different bars for each type of mRNA refer to the 2 different conditions e.g hypoxia/normoxia
