The human genome project Flashcards
Estimated length of time of HGP?
3 billion dollars, 15 years
Length of the human genome?
3 billion base pairs
What was the main strategy for the HGP?
Clone large pieces with known order and sequence them independently
What was the size of the digested DNA fragments used in the HGP?
~300KB
First challenge of the HGP?
Finding genetic markers so they could know roughly where in the genome a fragment was from
What is a genetic marker?
A DNA sequence with a known physical location on a chromosome
How is the locaiton of a genetic marker known?
Either absolutely, or relative to another marker (e.g. 200KB down from marker X is marker Y)
What is a RFLP?
Restriction Fragment Length Polymorphism
How do fragments run further on a gel?
If they are smaller
How were genetic maps built?
Using restriction enzymes that could/could not cut sequences (depending on mutations) to make tagged fragments that were smaller/larger
Fragments were then run on a gel
Aims of the first years of the HGP?
Building more genetic markers
What is radiation hybrid mapping?
Fragmented human chromosome using ionising radiation
Hybridized them into rodent cells
Tested for co-occurence of certain known sequences
If the sequences occur close together in a chromosome, they would be in the same hybrid chromosome v often
What is hierarchical sequencing?
Fragmented the genome a lot, and looked for overlaps in the fragments to put them in an order
What is coverage in genome sequencing?
The amount of reads that you have of a certain sequence in all of the total fragments
i.e. if a specific sequence of DNA appeared in 5 fragments, the coverage is 5
How is genome assembly influenced by coverage?
The higher the coverage, the better the assembly
What is a 1x coverage?
Only have a one read of each base pair in the genome
Difference between hierarchical sequencing and shotgun sequencing?
Hierarchical breaks the genome into larger chunks, and then breaks those chunks into smaller fragments and uses coverage to order them while shotgun just does the whole genome into fragments
What does shotgun sequencing provide you?
A draft genome
Why was the first draft of the HGP a draft?
It contained 150,000 gaps of unknown size
How did they get gaps in the HGP?
When two different fragments on the same chromosome had nothing that overlapped them both
Which bits of the chromosome did the HGP not try to sequence?
Centromeres and telomeres
How many coding genes were discovered in the first draft of the HGP?
30,000-35,000
What was published in 2003?
“Complete human gome”
Characteristics of 2003 complete human genome?
400 gaps
24,000 coding genes
92% of genome coverage
No centromere or telomere
