Human Genome Project – Method (1)

“The pursuit of a single gene is an arduous task… like looking at the Earth from outer space, focusing first on Lake Michigan, then finding Chicago on the shore, narrowing the view down to one neighborhood, finding a specific house, spotting a person sitting in the back yard, and then examining the hairs on the back of her hand.” John Daley, Biologist, Whitehead Institute, US

‘Sequencing the human genome depended on many technological improvements in the production and analysis of sequence data. Key innovations were developed both within and outside the Human Genome Project. Laboratory innovations included four-colour fluorescence-based sequence detection, improved fluorescent dyes, dye-labelled terminators, polymerases specifically designed for sequencing, cycle sequencing and capillary gel electrophoresis. These studies contributed to substantial improvements in the automation, quality and throughput of collecting raw DNA sequence.’ Human Genome Project, Nature

SEQUENCING

Celera Sequencing - 60 million overlapping fragments, each 2,000 to 10,000 bases long,
Human Genome Project Sequencing - 22,000 fragments, each 100,000 to 300,000 bases long
Time to assemble 12,000 bases – 1980: more than a year; 1997 - 20 minutes; 2000 - one minute.
Figs, BBC Science Online

12 000 letters of DNA decoded by the Human Genome Project every second – 20 years previously, it had taken one year.

‘The Sanger Institute has more than 1500 devices installed on its network: more than 250 PCs and some Macintosh systems and a total of more than 700 64-bit Alpha processors. The Sanger Institute main sequence storage has more than 22 Terabytes (22,000 gigabytes) capacity. The system that serves sequence searches (the BLAST farm) has more than 400 nodes.’ Wellcome Trust Sanger Institute, UK, where one third of Human Genome was sequenced

‘The method used for much of the genome is ‘shotgun sequencing’ which, in essence, involves breaking the genome up into conveniently sized chunks. The total size of the human genome is estimated to be about 3 billion base pairs, arrayed in 23 chromosomes. The chromosomes themselves are 50-250 million bases (megabases) long, too large to be sequenced directly (automated machines sequence fragments of between 400 and 700 bases), so the Human Genome Project fragments them into chunks of about 150 kilobases. Each of these large clones is then ‘shotgunned’ - broken into pieces of perhaps 1500 base pairs, either by enzymes or by physical shearing - and the fragments are sequenced separately. Shotgunning the original large clone randomly several times ensures that some of the fragments will overlap; computers then analyse the sequences of these small fragments, looking for end sequences that overlap - indicating neighbouring fragments - and assembling the original sequence of the clone… The alternative approach, ‘whole-genome shotgun sequencing’, was first used in 1982 by the inventor of shotgun sequencing, Fred Sanger, while working on phages (viruses of bacteria). In this technique, which has been used by the commercial company Celera Genomics, the whole genome is broken into small fragments that can be sequenced then reassembled. Although this approach can be highly automated and efficient - and has been very successful for the sequencing of the genomes of microorganisms and the fruitfly Drosophila - reassembling the fragments from the human genome is far more difficult and requires powerful computers.’ Wellcome Trust


Human Genome Project – Method (1)

It began, turning blind earth -
unknown geography, contours,

continents; panning sea - mining
air; hunting nuggets with needles,

teaspoons, in sluggish light,
glow-worms in dense night.

Then forks, ladles, spades;
buckets, diggers, trawlers -

storm lamps, growing brighter -
eagle eye transplanted to mole;

octopus arms to singing whale -
spotlight burning to lighthouse,

starlight seeding sun,
supernova, sunspots -

until bright nuggets strung;
sparkling, twitching beads

on silver strings -
life’s memorials

to the living and dead;
senseless knowledge

of order, space, materials -
chemical wire pulling pearls.

Spirit-pattern, matter unrealised,
insubstantial chimera of being -

spinning intricacy from simplicity -
uncovered, now revealed, displayed,

like a body put to bed in pure acid -
only known to us as mind translates

Sun to smiles - snowflakes and stars
rendered into their shining skeletons.