Flashcards in MCB Lecture 24 ENCODE Deck (21)
What does ENCODE stand for?
Encyclopaedia of DNA elements
When did ENCODE occur?
What is Celera and what effect did it have on ENCODE
This is a private company that started its own project.
This accelerated the completion of the public project ENCODE
What were the goals of ENCODE?
1. Complete sequence
2. Identify all genes
3. Physical and genetic map
4. Detailed annotation
What is important about Sanger sequencing?
This was used to carry out the ENCODE project
Describe the process of Sanger sequencing
1. Single stranded DNA, primers, DNA pol, dNTP and ddNTP are combined
2. The DNA pol elongates the complimentary DNA strand
3. Every so often, a ddNTP will be added in, and no more nucleotides may be added because there is no hydroxyl group on the 3' carbon
4. This creates DNA fragments of many different lengths
5. The fragments are run on a gel that resolves down to differences of one nucleotide
6a. Read manually 6b. Automated reading
What was the important technical advance with Sanger sequencing that allowed the ENCODE project to occur?
Describe the change in cost of Sanger sequencing over the years
Reduced in cost
Before: $1 per base
How many bases can Sanger sequencing do per run?
What are 5 new generation sequencing techniques?
Imaging detects different colours associated with the different nucleotides
Describe 454 sequencing
Fluoretic chambers containing DNA
Detect the length of nucleotides added
Describe Ion torrent sequencing
When a nucleotide is added, a proton is given off
This is detected by a very sensitive pH monitor
Describe ChIP Seq
Sonic action of the DNA to break it up
Specific proteins bound to DNA are selected out
The protein is degraded.
We now have DNA that is associated with a certain protein
Sequence this DNA
This allows us to determine activity of different bits of DNA at different points in time in different tissues
Describe RNA seq
RNAs synthesised from DNA are sequenced
This tells us about transcribed regions in different tissues at different times
When did the next generation techniques arise?
After the end of the ENCODE project, 2003
What is good about the next generation sequencing techniques
Describe 3 cases of personal genomics
23 and me
What do the cancer sequencing projects intent to do?
Sequence many cancers to identify mutations that cause cancer
Also, what sort of mutations they are, how they arose
What are some issues to do with the ENCODE project?
A raw sequence is difficult to interpret
What about function?
We don't need the entire sequence to identify disease linked mutations