Using the Results of Genetics Studies Flashcards
What is the purpose of GWAS?
Identify loci in the genome associated with a phenotype/disease
What is the purpose of RNA-Seq?
Isolating RNA from a tissue or cell type and use the method to generate a snapshot of the transcriptome
What are some difficulties using GWAS?
→ Large GWAS for complex diseases detect many loci
Prioritisation- which ones do you look at?
→ 90% of GWAS SNPs are in non-coding regions of the genome
Causal variant? Causal genes?
→ What is the mechanism of action explaining the association?
Tissue/cell type?
Molecular mechanism?
What is required for RNA-Seq data?
→ Need to set significance threshold
→ P-value- low p-value so its not due to chance
→ Fold change
Normally 1.5 to 2 fold in expression
What is fold change in RNA-Seq?
the degree by which the expression of a gene has changed.
What are other applications of RNAseq?
→ Cell populations response to treatments
→ How gene expression changes through development or under disease conditions
→ Single cell transcriptome analysis
What are the difficulties using RNAseq?
→ Many expression changes likely to be found
→ Identification of differential expression does not provide biological reasoning
Compare GWAS and RNAseq
GWAS
→ Identifies associations across whole genome
→ Large number of loci
→ Doesn’t identify causal variants or genes
→ Doesn’t identify cell type/tissue/developmental stage
RNA Sequencing
→ Transcriptome of single cell/tissue type
→ Large number of differentially expressed genes
→ Misses changes in other cell types or stages of development
→ Doesn’t identify reason for differential gene expression
How are osetocytes found in mature bone?
→ Embedded in lacunae in mature bone
→ Connected via processes through canalicular channels
→ Form a mechanosensory network throughout bone
What is involved in pathway analysis?
→Generate a gene set, and compare to database
→Gene ontology (GO) and Kyoto Encyclopedia of Genes
→ Allows you to identify new biology by determining the type of genes with association/differential expression
What is required of using gene ontology for pathway analysis?
Must have been previously annotated
What are the difficulties linking loci to gene?
→Linkage Disequilibrium makes it difficult to distinguish causal variant
→90% of GWAS SNPs are in non-coding regions- so causal variants is unlikely to effect any protein sequence
→May act at a distance from effected gene(s)
→Need to determine relevant cells/tissues
What is linkage disequilibrium?
The nonrandom association of alleles of different loci
What is fine mapping?
→ High resolution study of loci attempting to pinpoint individual variants directly effecting trait
→ Statistical and probabilistic methods or comparison to a SNP correlation reference panel
How can you assign causal genes?
→ Closest gene to any fine mapping causal SNP
→ If the gene body overlapped with any of the causal SNP
→ If SNP directly caused coding change in the gene
What is ATACseq?
Method for determining chromatin accessibility across the genome
What is Hi-C?
Chromosome conformation capture technique to analyze spatial genome organization
How to progress from GWAS to biological reasoning?
→ Fine mapping to attempt to define causal variants at loci
→ Analysis of causal SNP location to predict causal gene
→ Cell type SNP enrichment analysis to determine relevant cell types
What are the three ways to combine genotype and expression data?
→ eQTL
→ Colocalisation analysis
→ TWAS
What is eQTL?
A locus that explains a fraction of the genetic variance of a gene expression phenotype
How do you generate eQTL?
→ Combine gene expression data from RNA-Seq and SNP genotyping data of the same individuals
→ Test SNPs local to each gene for association between SNP genotype and gene expression
What is colocalisation analysis?
Used to test whether two independent association signals at a locus are consistent with having a shared casual variant
How is colocalisation analysis carried out?
→ Identify the eQTL and GWAS loci that has an overlapping position
→ Compare the results of GWAS fine mapping and eQTL
How do you interpret colocalization graphs?
→ If signals from eQTL and GWAS colocalise then association peaks appear similar indicating their due to single causal variant
→ If not then two peaks, and signals are different indicating linkage disequilibrium
