Scientists Develop New Computer Program To Speed Determination Of Gene Function

June 23, 1998

DALLAS, Texas, June 23, 1998 -- A computer program recently developed at UT Southwestern Medical Center at Dallas has found the markers on all DNA sequenced so far in the international Human Genome Project, and the list is now available on the Internet.

A UT Southwestern study, which developed and validated the computer code known as POMPOUS, is described in today's issue of Proceedings of the National Academy of Sciences. Markers are small bits of deoxyribonucleic acid (DNA) that can vary among individuals but are usually inherited within related groups. Differences in markers are called polymorphisms, and they can alter how a gene affects the body. The markers are used in identifying diseases, predicting risk of disease and in forensics investigations.

"Because of all the information coming out of the genome project, there needs to be more and more effort in computational biology to extract value from the raw DNA sequences and relate it to the function of the 100,000 or so genes and all the medical implications of the variations in each gene," said senior author Dr. Harold "Skip" Garner, associate director of UT Southwestern's federally funded Genome Science and Technology Center and holder of the Philip O'Bryan Montgomery Jr., M.D., Distinguished Chair in Developmental Biology. "Our system facilitates the step between genomic sequencing and using the data to discover the impact of genes on the quality of life."

In a collaborative effort with Dr. John Minna -- director of the Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research and the W.A. "Tex" and Deborah Moncrief Jr. Center for Cancer Genetics and holder of the Max L. Thomas Distinguished Chair in Molecular Pulmonary Oncology, the Sarah M. and Charles E. Seay Distinguished Chair in Cancer Research and the Lisa K. Simmons Distinguished Chair in Comprehensive Oncology -- the researchers applied POMPOUS (polymorphic marker prediction of ubiquitous simple sequences) to a 750,000 base pair region on human chromosome 3P. Minna used this section of DNA to study small-cell lung carcinoma, one of the deadliest forms of cancer.

"We ran the code on this region, identified about 40 markers and tested them," said Garner, co-director of the Biomedical Inventions Center. "Then Dr. Minna used the markers that the computer predicted in his research. It accelerated his ability to analyze and identify the genes and the properties of the sequence region."

In the verification process the computer accurately predicted the markers 67 percent of the time. Garner said this development significantly enhances the discovery of gene function. In addition it costs only about $20 to $40 to find a marker using this method.

"Using a parallel supercomputer on loan from Hewlett-Packard, we have pre-calculated the markers in all the genes that have been sequenced thus far so we have a list of 13,000 to 14,0000 markers on our Web site; we basically are giving them away to the world," he said. "We also put a server on the Web site so that anyone can submit their own sequence, and the code will predict the marker and hand them back oligonucleotide sequences ( bits of DNA used to identify genes) pre-designed for the laboratory technician to test the sequence in the lab."

Other UT Southwestern researchers involved in the study were cell and molecular biology graduate student John Fondon; Hamon Center research assistant Gina Mele; Hamon Center postdoctoral fellow Dr. Ruth Brezinschek; a UT Southwestern Science Teachers' Access to Resources at Southwestern (STARS) researcher Donna Cummings; Eugene McDermott Center for Human Growth and Development graduate student Jonathan Wren; surgery student research assistant Ashwini Pande; McDermott Center postdoctoral fellow Dr. Kevin O'Brien; and McDermott Center senior research scientist, Kenneth Kupfer. Drs. Ming-Hui Wei and Michael Lerman of the Laboratory of Immunobiology at the National Cancer Center in Frederick, Md., were also part of the study group.

The research was supported by grants from the Whitaker Foundation, the National Cancer Institute, Specialized Program of Research Excellence (SPORE) in Lung Cancer, Texas ARP (Advanced Research Projects) and the G. Harold and Leila T. Mathers Charitable Foundation.

The list of markers is available at

UT Southwestern Medical Center

Related Cancer Articles from Brightsurf:

New blood cancer treatment works by selectively interfering with cancer cell signalling
University of Alberta scientists have identified the mechanism of action behind a new type of precision cancer drug for blood cancers that is set for human trials, according to research published in Nature Communications.

UCI researchers uncover cancer cell vulnerabilities; may lead to better cancer therapies
A new University of California, Irvine-led study reveals a protein responsible for genetic changes resulting in a variety of cancers, may also be the key to more effective, targeted cancer therapy.

Breast cancer treatment costs highest among young women with metastic cancer
In a fight for their lives, young women, age 18-44, spend double the amount of older women to survive metastatic breast cancer, according to a large statewide study by the University of North Carolina at Chapel Hill.

Cancer mortality continues steady decline, driven by progress against lung cancer
The cancer death rate declined by 29% from 1991 to 2017, including a 2.2% drop from 2016 to 2017, the largest single-year drop in cancer mortality ever reported.

Stress in cervical cancer patients associated with higher risk of cancer-specific mortality
Psychological stress was associated with a higher risk of cancer-specific mortality in women diagnosed with cervical cancer.

Cancer-sniffing dogs 97% accurate in identifying lung cancer, according to study in JAOA
The next step will be to further fractionate the samples based on chemical and physical properties, presenting them back to the dogs until the specific biomarkers for each cancer are identified.

Moffitt Cancer Center researchers identify one way T cell function may fail in cancer
Moffitt Cancer Center researchers have discovered a mechanism by which one type of immune cell, CD8+ T cells, can become dysfunctional, impeding its ability to seek and kill cancer cells.

More cancer survivors, fewer cancer specialists point to challenge in meeting care needs
An aging population, a growing number of cancer survivors, and a projected shortage of cancer care providers will result in a challenge in delivering the care for cancer survivors in the United States if systemic changes are not made.

New cancer vaccine platform a potential tool for efficacious targeted cancer therapy
Researchers at the University of Helsinki have discovered a solution in the form of a cancer vaccine platform for improving the efficacy of oncolytic viruses used in cancer treatment.

American Cancer Society outlines blueprint for cancer control in the 21st century
The American Cancer Society is outlining its vision for cancer control in the decades ahead in a series of articles that forms the basis of a national cancer control plan.

Read More: Cancer News and Cancer Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to