Loyola's Genomics Facility uses next generation sequencing to study genetic make-up of organisms

Loyola University Chicago's Genomics Facility is using an advanced technology called next generation sequencing to assist a broad range of researchers studying the genetic make-up of organisms ranging from viruses to humans.

"We're forming collaborations with researchers at Loyola and other centers doing basic science research as well as studies with more immediate clinical applications," said Michael Zilliox, PhD, director of the Loyola Genomics Facility. "Lab manager Gina Kuffel and I are ready to help."

Next generation sequencing enables researchers to sequence DNA and RNA much more quickly and cheaply than an older technology called Sanger sequencing. The technology is revolutionizing genomics (the study of genes and their functions) and molecular biology.

DNA sequencing determines the precise order of four chemicals within DNA that spell out the unique genetic code of an organism. These chemicals, adenine, thymine, guanine and cytosine, can be thought of as the four letters of the DNA alphabet -- A,T, G, C.

Loyola's Genomics Facility uses a desktop next generation sequencing system called Illumina MiSeq. Next-generation sequencing produces an extraordinary amount of data. The data are sent over a 10-gigabyte connection to a high-performance computing cluster at Loyola's Stritch School of Medicine.

Dr. Zilliox said next generation technology will accelerate the trend toward personalized medicine, in which treatments are tailored to the individual characteristics of a patient. For example, sequencing the genes of a cancer patient's tumor can help physicians prescribe the drug that is most likely to work on that individual patient.

Dr. Zilliox is using next-generation sequencing to identify biomarkers that could predict whether a kidney lesion is benign or cancerous. In another project, Dr. Zilliox is looking for biomarkers that would help predict outcomes of patients with oral squamous cell carcinoma. Such biomarkers could help physicians determine how aggressively to treat a patient.

The Loyola Genomics Facility assisted a team of Loyola researchers that found that bacteria live in the bladders of healthy women, discrediting the common belief that normal urine is sterile. The Genomics Facility also is working with other teams studying mutations in bladder cancer tumors; genetic mechanisms of sickle cell disease; viruses in Lake Michigan; and many other projects.

"We offer a very flexible platform that enables us to work on many different types of experiments," Dr. Zilliox said.