SciTech

Professors aim to unleash full potential of DNA sequencing

Carnegie Mellon professor of biology Robert Murphy has been developing a software tool that will help doctors better understand their patients’ DNA and improve disease diagonoses. (credit: Daniel Tkacik/SciTech Editor) Carnegie Mellon professor of biology Robert Murphy has been developing a software tool that will help doctors better understand their patients’ DNA and improve disease diagonoses. (credit: Daniel Tkacik/SciTech Editor)

When scientists revealed the structure of a DNA molecule in 1953, many people took this discovery to mean that the “secret of life” had been found. However, almost 60 years later, diseases still go undiagnosed while patients suffer. Many scientists believe that having a complete understanding of DNA will help doctors diagnose their patients more swiftly and accurately. That belief is no exception at Carnegie Mellon, as researchers are developing software aimed to help doctors finally make sense of patients’ DNA.

Robert Murphy, professor of biology and director of the Lane Center for Computational Biology, is heading a project that aims to create a “doctor in a box” software that combines computer science and biology to assist doctors. Murphy said that this type of research has been ongoing at Carnegie Mellon for many years, but the Personal Genome Sequencer, a machine that can swiftly decipher the code of a DNA molecule, has elevated the need for bringing this research into practical applications.

The entire DNA molecule in a human cell is made up of thousands of smaller segments called genes. These genes are made up of building blocks called nuclueotide bases, and it is the specific sequence of these bases that scientists refer to as the DNA sequence.

The combination of genes in a people’s DNA determines their particular traits, such as their hair color or what they are allergic to. If scientists can sequence or determine the specific genes in someone’s DNA, it may be possible to determine what diseases the person has.

The huge rise in DNA research over the past 30 years has helped scientists make conclusions about which genes represent which diseases. The problem, however, is that there is a multitude of information in one strand of DNA. As a result, it is practically impossible for a doctor to reach a conclusion by simply knowing a DNA sequence.

In the past, sequencing DNA was a drawn out and expensive process, making it a hassle for doctors and researchers. Jonathan Rothberg, a Carnegie Mellon alumnus and founder of the biotechnology company ION Torrent, recognizes and attempts to solve this problem.

Over the past decade, Rothberg and his company have developed a faster and cheaper method of DNA sequencing that uses small differences in the structure of DNA molecules to determine the genetic code. Their finished product, known as the Personal Genome Sequencer, was released last year at a price of $50,000.

With the ability to swiftly sequence an individual’s DNA in two hours, Murphy and his team are working with Rothberg to develop a software that can take the DNA code determined by the Personal Genome Sequencer and make conclusions about a patient’s DNA.

The project commenced less than five months ago, but Murphy is excited that he and his team “have had a lot of great discussions and the project is quickly taking shape.” He said that the software should be ready for use in the next six to 12 months.

Looking into the future, Murphy remains optimistic. “In five years, this type of software will be able to be applied to clinical practice,” he said.

One of the most important aspects of the software is the idea of endless learning. “You don’t train a system and then release it, but rather the system is continuously learning from whatever data is available,” Murphy said. In other words, the software continues to make new associations between genes and diseases from the analyzed DNA.

According to the National Human Genome Research Institute website, the price of personal DNA sequencing has plunged from $3 billion dollars to $50,000 per person with the Personal Genome Sequencer, but this price is still too high for DNA seqencing to have an impact on medicine.

The ultimate goal Murphy and Rothberg share is to make sequencing and analyzing an individual’s DNA for less than $1,000, an affordable price for clinicians.