Encyclopedia Genomica: UK Scientists Print the Book of Life in 130 Volumes
By Kevin Davies
December 28, 2012 | Nowadays it is cheaper to sequence the human genome than to print out a full hard copy. We know this because earlier this year, Cas Kramer and a group of scientists at the University of Leicester decided to print out a complete version of the human genome.
The genome print out spans 130 volumes, with each page printed on both sides in 4-point font, with precisely 43,000 characters per page. The X chromosome is made up of seven volumes, while the Y chromosome occupies one. The exercise cost a little less than 4,000 pounds (about $6,000).
|University of Leicester staff with the human genome
(hard copy). Cas Kramer and Ed Hollox, back row (right).
The genome encyclopedia project was born when Kramer and his colleague Ed Hollox participated in the Royal Society Summer Science Exhibition in London with an exhibit entitled “Breathless Genes.” The idea was to illustrate how six known variants in the genome could impact lung function. “We thought it would be great to show the public how big 3,000 million letters is!” says Kramer.
Kramer’s accent reveals only a faint trace of his native home in The Netherlands. As a bench scientist in the UK, he studied the biology of fungi and circadian rhythms. In 2005, caught between grants, he accepted an invitation to become a lecturer in a new CETL (Centre for Excellence in Teaching and Learning) at the University of Leicester’s Department of Genetics—dubbed GENIE (Genetics Education Networking for Innovation and Excellence).
For the London exhibit, Kramer originally asked the Wellcome Trust if his group could borrow an existing hard copy of the human genome that the charity had printed. “They said no, so we said, ‘You know what, we’re going to print it ourselves.’”
Hollox asked PhD student John Wagstaff to write a program to print out the publicly available reference genome with a pre-specified number of characters on each page and a roughly equal number of pages for each volume, as well as some navigational information at the top of each page.
The GENIE group next approached a local printer and asked if they could print out an extremely large number of PDFs. In addition, Kramer and Hollox asked to have the volumes for each chromosome bound in the same color as a standard chromosome fluorescence karyotype. That proved problematic, because the printer only had a few basic colors in stock. (The company subsequently managed to obtain the other colors for the covers.)
Says Kramer: “When they brought [the finished volumes] over to us, they said, ‘What actually did we print? It was so boring!’ After all, it was just endless letters in very small print. They didn’t really have a clue what they were printing!”
In the printed genome, all the exomes are in upper-case letters. Because the print is so small, Kramer says it is very easy to see repeat sequences. This is not a surprise, however; the department’s most famous occupant—the father of DNA fingerprinting, Sir Alec Jeffreys—had already established a precedent for that. “Alec Jeffreys tells us he used to photocopy genome sequences very small to look for repeats in that way,” says Kramer.
The 130-volume human genome is currently on display at a local museum in Leicester to coincide with an exhibit called “Inside DNA.” Kramer organized this loan arrangement even before the material was printed. A permanent home for the genome has yet to be decided, although the university’s new library building is one possibility. Kramer is considering splurging on a second printout, so one copy can be used for other public engagements.
He has already used the volumes in medical student lectures, unveiling the volumes hidden under a tablecloth like a magician, highlighting key mutations for diseases such as sickle-cell anemia and cystic fibrosis. “I’m sure all those students will never forget what a huge amount those 3,000 million letters are!” he says.
In addition to being a useful educational tool, the printed genome has other medical virtues, such as providing a decent cardio workout. “It is actually quite heavy—about 26 boxes,” says Kramer.