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A Sequence of Events Leads to Genetic Sequencer   

The school recently acquired a Genetic Sequencer, a scientific instrument that few high schools have and that opens new opportunities for Loomis Chaffee students.  

Genetic Sequencers are used to help scientists read genetic code.   

DNA sequencing, notes Science Department Head Neil Chaudhary '05, “is the way we read the language of life. We can take a sample and determine every single letter of the genetic code, and there is a lot we cannot do unless we have that code.”  

Students throughout the science curriculum at Loomis have been able to do a lot of work with DNA — except the final step. They have copied DNA, the biological process of producing two identical replicas of DNA from one original DNA molecule. They have edited DNA, a method for making specific changes to the DNA of a cell or organism. They have inserted DNA into other cells.   

“But reading the code,” Neil said, “is the thing we have not been able to do here for lack of equipment.”  

Having a Genetic Sequencer is a game-changer.   

The DNBSEQ-E25 sequencer came to the school as a part of a collaboration between Loomis and the sequencing company Complete Genomics. The company, seeking a pilot opportunity to explore the use of their machines in secondary school education, offered the machine at a fraction of what it would cost on the open market. Complete Genomics sent field engineer David Lambiase and field application scientist Devesh Patel to campus to install and validate the instrument. Mr. Patel then returned to train Neil and science teacher Amy Cornell on the use of the instrument.  

DNA sequencing is important in the scientific realm for many reasons. By enabling scientists to determine the genetic information in a DNA segment, the process can be used to figure out the function of specific genes.  

Before obtaining the machine, the Loomis Science Department had to send out DNA used in classes to a lab specializing in DNA sequencing. Samples are sent out to labs for various reasons, depending on the course, Neil explained.  

“In one lab, students extract DNA from fish used in sushi to determine whether the fish is labeled correctly or is a cheaper fish being passed off as a more expensive one,” Neil said. “In this lab, the sequences returned from the vendor are compared with known sequences in a database to determine the species. In another application, students who were working on genetically engineering E. coli needed to check that the edits they made were executed effectively. They sent the edited DNA in, and the sequences returned from the vendor were compared with the intended edits to confirm successful editing.”     

Outsourcing to a lab is not an uncommon practice for academic or industrial laboratories, but, as Neil says, the goal of the DNA work at Loomis Chaffee is to educate students, not just obtain information. “The more we can do in house, the more we can give students hands-on experiences,” he said.  

DNA sequencing machine from Complete Genomics

DNA sequencing is important in the scientific realm for many reasons. By enabling scientists to determine the genetic information in a DNA segment, the process can be used to figure out the function of specific genes.  

The idea for Loomis to get the Genetic Sequencer came from Li Ye, mother of freshman Iris Yan, who had heard about a California school’s gene sequencing program. She contacted Complete Genomics, based in San Jose, Calif. Complete Genomics’s mission statement states that one of its goal is to provide the equipment that allows for genomic sequencing to produce results in research, healthcare, and industrial applications to improve health. DNA sequencing can be used for disease diagnosis, treatment, and epidemiological studies.   

The first use of the machine was to complete a project — isolating viruses from the environment and sequencing the DNA — from Neil’s microbiology class during the fall term.  These are viruses found in soil and cannot affect human cells, Neil noted.  

Neil will provide feedback to the company on such things as ease of use, impact on and integration with the curriculum, capacity of the machine vs. the school’s needs, and any new programs that are enabled. Mr. Patel will be available to help if needed as Neil and Amy start using the instrument.  

Neil recently stood by the machine, not much bigger than a microwave, demonstrating how it is used. Due to its size, portability, low throughput, ease of use, and rapid run time, it is particularly suitable for a science classroom. Neil said he could not be more appreciative of the time that the people from Complete Genomics spent on the Island to validate the machine and to speak with students.     

Neil also emailed Li Ye after the training was done.  

“From the bottom of my heart, thank you for creating this connection between Complete Genomics and Loomis Chaffee,” Neil wrote. “This instrument has transformed what is possible in our labs, opening doors for our students to engage in authentic scientific discovery at a level that few high schools can offer. Because of your support, our students now have direct access to the cutting edge of modern science, and I am confident that these experiences will inspire the next generation of scientists and engineers.”  

   


 

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