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Celera History HGP
History
In 1976, the genome of the virus Bacteriophage MS2 was the first complete genome
to be determined, by Walter Fiers and his team at the University of Ghent
(Ghent, Belgium)[7][8]. The idea for the shotgun technique came from the use of
an algorithm that combined sequence information from many small fragments of DNA
to reconstruct a genome. This technique was pioneered by Frederick Sanger to
sequence the genome of the Phage Φ-X174, a tiny virus called a bacteriophage
that was the first fully sequenced genome (DNA-sequence) in 1977[9]. The
technique was called shotgun sequencing because the genome was broken into
millions of pieces as if it had been blasted with a shotgun. In order to scale
up the method, both the sequencing and genome assembly had to be automated, as
they were in the 1980s.
The modern whole genome shotgun technique came into its own with the sequencing
of the first free-living organism, the 1.8 million base pair genome of the
bacterium Haemophilus influenzae in 1995. It involved the use of automated
sequencers, longer individual sequences using approximately 500 base pairs at
that time. Paired sequences separated by a fixed distance of around 2000 base
pairs. Which were critical elements enabling the development of the first genome
assembly programs for reconstruction of this bacterial genome.
Three years later, in 1998, the announcement by the newly-formed Celera Genomics
that it would scale up the shotgun sequencing method to the human genome was
greeted with much skepticism in some circles. The success of both the public and
privately funded effort hinged upon a new, more highly automated capillary DNA
sequencing machine, called the Applied Biosystems 3700, that ran the DNA
sequences through an extremely fine capillary tube rather than a flat gel. Even
more critical was the development of a new, larger-scale genome assembly
program, which could handle the 30-50 million sequences that would be required
to sequence the entire human genome with this method. At the time, such a
program did not exist. One of the first major projects at Celera Genomics was
the development of this assembler, which was written in parallel with the
construction of a large, highly automated genome sequencing factory. The first
version of this assembler was demonstrated in 2000, when the Celera team joined
forces with Professor Gerald Rubin to sequence the fruit fly Drosophila
melanogaster using the whole-genome shotgun method. At 130 million base pairs,
it was at least 10 times larger than any genome previously assembled. One year
later, the Celera team published their assembly of the 3 billion base pair human
genome.
How it was accomplished
The Celera group used the technique denoted as the “whole-genome shotgun”
technique. The shotgun technique breaks the DNA into fragments of various sizes,
ranging from 2,000 to 300,000 base pairs in length, forming what is called a DNA
"library". Using an automated DNA sequencer the DNA is read in 800bp lengths
from both ends of each fragment. This method became a standard approach to the
sequencing and assembly of bacterial genomes beginning in 1995, when the first
bacterial genome, Haemophilus influenzae, was sequenced. Using a complex genome
assembly algorithm and a supercomputer, the pieces are combined and the genome
can be reconstructed from the millions of short, 800 base pair fragments.
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