Genomics Flashcards
The study of an entire genome or genomes
Genomics
Two major subfields of genomics:
- Functional Genomics
2. Comparative Genomics
The global analysis of the function of sequences in a genome.
- Understand genome and phenotype of an organism
- Useful when considering complex traits.
Functional genomics
Comparison of entire genomes from different species, individuals, or groups.
- Studies genetic variation, evolutionary relatedness
- Asks “what sequences are different and what are similar?”
Comparative Genomics
An example of genomics: identification of genes linked to drought tolerance in plants:
- Tomato plants grown in high vs. low water conditions
- Performed microarray to identify genes that are differentially transcribed in these conditions
An example of genomics: identification of genes that make us human:
- HAR-1= Human Accelerated Region 1
- Chicken and chimp HAR-1 nearly identical
- Chimp and human HAR-1 a lot different
- HAR-1 encodes a small noncoding RNA (fxn unknown)
- Expressed in a region of the brain that undergoes a unique deelopmental process in humans
- Other genes: FOXP2 (speech) and ASPM (brain size)
An example of genomics: identification of genes hat make certain cancers aggressive
- Sequence DNA from different breast cancers, some with good prognosis (less aggressive and easily treatable) and some from patients with poor prognosis (from highly aggressive tumors)
- Identify and compare mutations and copy number variants between the two groups
- Compare genome from your patient’s tumor to the known genomes
- Why is this beneficial?
Selected techniques used in genomics:
- Whole genome sequencing
- Bioinformatics
- Transcriptomics
- RNAseq
Combines biology and computer science.
Bioinformatics
Bioinformatics examples
- Find DNA with a sequence of interest.
- Align sequences for similarities.
- Predict structure, therefore function of RNA and protein
- Describe gene interactions (interacto maps)
- Map phylogenetic relationships
Part of the promoter region; transcription factors will bind to for transcription to proceed.
Response element
Compare the sequence of a gene product with unknown function to a similar gene product with known function.
- Analyze a region of sequence that might encode a particular protein function.
- Goal: to assign a predictive function for a gene (or a set of genes) of interest.
Sequence Similarity Searches
The study of the complete set transcripts that are produced by a genome under a specific condition.
-Uses RNAseq
Transcriptomics
Method provides the sequences of all transcripts in a sample.
-Transcriptome= all transcripts
RNAseq
Method of RNAseq
- extract RNA
- Make cDNA
- Sequence cDNA using Next Gen. sequencing technology
What can RNAseq tell you?
The relative amounts of each transcript and different splice variants.
