Automated DNA sequencer valuable tool for BYU stud

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    By CHRIS ONSTOTT

    BYU research in genetics-related fields shifted gears to overdrive this year thanks to a useful but expensive piece of equipment. A new automated DNA sequencer began processing bits and pieces of long DNA chains last semester, and has cleared the way for faster and less tedious research for many professors on campus.

    The sequencer automatically determines the sequence of DNA fragments strand using florescent dies and passing the fragment in front of a laser that determines the bases that make up the chain of DNA and reports the results on a computer, according to Michael Whiting, a BYU professor of Zoology who also servers as director of the sequencing lab.

    “Before this, professors had to go though the tedious chore of manually sequencing the DNA strands using radio active chemicals that were expensive and less safe,” he said.

    Although the sequencer lab was an expensive investment for the university, costing upwards of $450,000 with the machine alone costing $130,000, the money is well spent, according to Whiting.

    “In terms of cost-per-base it’s significantly cheaper than any other sort of way to sequence DNA,” Whiting said. Manual sequencing labs cost more in chemicals and time. The idea is to have one automated central facility where people can deposit samples and retrieve sequences, instead of having different labs for every professor.

    Whiting said it costs researchers about four or five times as much for each nucleotide sequenced through manual sequencing.

    The idea of having a core laboratory is catching on nationally according to Whiting, because one automated laboratory can do the work that used to require several individually run manual laboratories. . . For instance, Harvard also uses an automated core sequencer for their studies. The sequencer is used heavily for medical research. Harvard also operates a Web site where information about the sequencer may be found. The University of Utah also runs an extensive Website said Whiting.

    Whiting said that a Website may also be in BYU’s future. With a Website our clients could submit information about the sample over the Internet, he said. We have got a $45,000 grant and part of that money will be used to hire a computer geek to set up a Website.

    “Using the automated sequencer frees up a considerable amount of time for researchers,” Whiting said.

    “In six or eight months we have generated about 3 million nucleotides of sequence,” Whiting said. The amount of time it takes to process data has sped up by about 50 to 100 times.

    Researchers can also bite off bigger chunks of DNA to process in each sample of automatically sequenced DNA, with more than 600 bases processed per sample as compared with about 350 for manually sequenced DNA.

    “The sequencer makes for not only faster research, but also better research. Automated sequencing is considerably more accurate than manual research,” said Whiting.

    The sequencer to this point is being used for fields other than those dealing with human genetics.

    “Thus far we haven’t done any human genetics,” Whiting said. It’s being used to address problems with organismal evolution and molecular evolution … It’s also being used by people who work with crops and the people in animal science for work with cattle and horses trying to improve breeds and look for genetic markers.

    Paige Humphreys, head technician for the lab said the lab has also processed DNA of rabbits, pigs, mice and many other animals. Despite all the research being done, the lab is still only being run to about 50 percent of its capacity he said.

    The automated sequencing lab is one of only two in Utah, with the other being a much larger facility at the University of Utah. According to Whiting, three times as many machines are used at the University of Utah laboratory because of work being done field of medicine, as well as outside requests for sequencing.

    Whiting said BYU is putting itself in a position to compete with the U of U for outside clients which he said will make money for BYU and help make additional improvements on the lab.

    Despite only being in existence for a few months, the laboratory, like everything else at BYU will be changing locations in September when renovations are complete for its permanent home on the sixth floor of the Widtsoe Building. The laboratory is now located in Room 123 of the Widtsoe Building.

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