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Flashcards in 3 - Genomics trigger Deck (30):
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exome

protein coding regions of the genome

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epigenome

modification to the genome

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examples of modifications to the genome

methylation

histone acetylation

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karyotype

chromosomal content of a cell

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transgene

cDNA coding for any gene that is introduced into a cell

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proband

the affected individual

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SNP

single nucleotide polymorphism

e.g. insertions and deletions

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example of a simple monogenic disorder

cystic fibrosis

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GWAS

genome wide association study

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examples of polygenic diseases

diabetes
Alzheimer's

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gDNA

genomic DNA
chromosomal dna

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epigenetic

changes to DNA that do not affect its base sequence –

often environmental

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linkage analysis

study aimed at establishing a linkage between genes

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define linkage

the tendency for genes to be inherited together due to location on the chromosome

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what is linkage a measure of

how resistant to recombination a genetic marker and phenotype are

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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

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how do you confirm your suspected mutant gene

transfect the gene in a wild-type transgene

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why is genetic linkage important

allows causes of rare disease to be identified

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what does GWAS look for

SNPs that are over-represented in disease patients

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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

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what does GWAS stand for

genome wide association stufy

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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

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polygenic disease

associated with the effects of multiple genes in combination with lifestyle and environmental factors
e.g. diabetes, alzheimers
not guaranteed inheritance

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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

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why is mendelian randomisation not affected by confounding variables

genotype is radnomly assigned to you at birth

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what is RNA sequencing used for

quantifying how much of each mRNA from each gene you have under different conditions

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3 steps in rna sequencing

purify mRNA
reverse transcribe
sequence the cDNA

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why is software used in RNA seq

aligns results against database of known mRNAs

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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

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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