Bioinformatics Flashcards
What are the 3 types of point mutations?
- Silent
- Nonsense (STOP)
- Missense
What are the two types of mis-sense mutations?
- Conservative (different amino acid with same properties)
- Non-conservative
What is sickle cell anaemia caused by?
A non-conserved missense mutation
How is bioinformatics used in genetics?
- Determining sequence of DNA
- comparing between controls and disease individuals
How does an affymetrix SNP array work?
- Probes that detect the most common allele (A) or less common (C)
- 2 red dots = hetrozygous
- 1 red 1 black = homozygous
How does an illumina SNP array work?
half sequence can bind then probe can bind
- yellow dot means heterozygous
- red dot means homozygous
What are the two methods of SNP arrays?
- Affymetrix
- Illumina
Why are SNP arrays used + list 3 restrictions of them
- GWAS (genome wide)
- Only uses 100,000-1M SNPs
- Only used with pre-existing knowledge
- Only works for common SNP (>5%)
What is a simple disease?
- Rare
- Single high impact mutation in protein coding region (e.g. cystic fibrosis)
What is a complex disease?
- Common
- # of low impact mutations in and outside protein coding regions (e.g. Asthma)
Did GWAS fail?
- It was able to identify large number of variants for complex diseases
- Could not identify high impact mutations
What is the gold standard for variant detection?
Sanger Sequencing
- Not probe-based (base-by-base interrogation of a region of interest)
- ~500 base pairs
What is WGS v.s. WES
WGS: genome sequencing
WES: exome sequencing
What do all nuclear receptors have?
A DNA binding site
What are the 4 key bioinformatics uses for DNA
- Genetics
- Methylation
- Histone modification
- Transcription factors
What are the 4 key bioinformatic uses for RNA
- Gene expression
- miRNA expression
- Alt. splicing
What is the transcriptome?
collection of all RNA molecules in a cell
DNA is the same in all cells. RNA differs from cell to cell. True or False?
True
What is used to sequence RNA ?
RNA-Seq
What happens when you do over 20 genetic tests?
100% one of the results is a false positive
What is proteomics?
A collection of all proteins in and outside of the cell
What are the 3 key uses for proteins in bioinfomatics?
- Proteomics
- Phosphorylation
- Glycosylation
What is multi-omics?
integrating one or more levels of bioinformatics e.g. phenomics, metabolomics etc
What is an expression quantitative trait loci?
- Compare genetic data w/ gene expression data
- Help identify role of variants in non-coding regions
