Big Data Flashcards
Name the ‘OMICS’
- Genomics
- Transcriptomics
- Proteomics
- Metabolomics
- Epigenomics
What can microscopy data show?
- Live flourescent tagging imaging in cells
- Automated image analysis
- Fixed cell staining
What is the transcriptomics experimental strategy?
Looking at what does factor X do to Cell type Y?
- Extract mRNA and convert to cDNA
- Sequencing library is prepared
- Sequenced on a Next Generation sequencing machine
- Statistical computer comparisons (e.g comparing mRNA expression levels)
What is FoldChange?
DIfference in gene expression from tested and control groups
What is a volcano plot?
A plot used for gene expression analysis
- Plots significance on one axis and foldchange on the other which basically shows the magnitude of the difference
What is meant by a heterogenous population?
heterogeneous population consists of individual elements or units that differ from one another in various characteristics.
What does single cell RNA sequencing do?
profile the gene expression of individual cells within a heterogeneous population.
How does single cell RNA sequencing work?
- Isolation of individual cells
- Break it down e.g. dissect tissue
- Single cell suspension then occurs
- Sequencing library is then prepared
- Ran through illumina NGS machine
- Data plotted on a UMAP plot
Why is a UMAP plot good?
- Can see which genes are expressed by particular cell types
- Can see if cell type specific gene expression changes
- Can see change in cells over time
Why are Genome wide association studies perfect for big data and genomics?
- When looking at disease-related genes, there isn’t just one
- GWAS identifies SNPs found more frequently in patients than healthy individuals
- High-scoring SNPs are then associated with the disease and are implied to potentially have causative roles
How is GWAS data presented?
Manhattan plot
- Genome position on x axis as chromosome number
- Y axis shows degree of association
- Each plot is a labelled individual SNP
How would we find out what the SNP is doing to the patient?
- Combine GWAS with gene expression studies
- Identify the cell types in which the genetic variants have functional consequences and how those variants regulate gene expression
What is the 100,000 genome project?
- Patients with rare diseases and cancer can receive personalised treatment
- Provide blood sample, genome sequenced, molecular diagnosis
What is the UK biobank?
- 500,000 adults had anatomical, biochemical and physiological measurements taken
- Followed over time, which developed diseases
- Measurements used to make disease causative associations
