Featured Research

from universities, journals, and other organizations

Faster tumor analysis software developed, speeds cancer discoveries

Date:
February 24, 2014
Source:
Mayo Clinic
Summary:
Researchers have fashioned a new key to unlocking the secrets of the human genome. The Binary Indexing Mapping Algorithm, version 3 (BIMA V3) is a freely available computer algorithm that identifies alterations in tumor genomes up to 20 times faster and with 25 percent greater accuracy than other popular genomic alignment programs. “BIMA allows us to evaluate tumor genomes in a fraction of the time it takes many popular technologies,” says the senior author of the paper. “We believe this tool will lead to a better understanding of tumor genomics, and ultimately better therapy for patients with cancer.”

Mayo Clinic researchers have fashioned a new key to unlocking the secrets of the human genome. The Binary Indexing Mapping Algorithm, version 3 (BIMA V3) is a freely available computer algorithm that identifies alterations in tumor genomes up to 20 times faster and with 25 percent greater accuracy than other popular genomic alignment programs. BIMA results are published this month in the journal Bioinformatics.

BIMA is a next-generation sequencing mapping and alignment algorithm, customized to process mate pair library sequencing. Mate pair sequencing is a comprehensive and cost-effective method for detecting changes throughout the entire genome.

“BIMA allows us to evaluate tumor genomes in a fraction of the time it takes many popular technologies,” says George Vasmatzis, Ph.D., a Mayo Clinic molecular biologist, director of the Biomarker Discovery Program in the Mayo Clinic Center for Individualized Medicine, and senior author of the paper. “We believe this tool will lead to a better understanding of tumor genomics, and ultimately better therapy for patients with cancer.”

In a side-by-side comparison with two popular sequencing alignment programs, BIMA outperformed the Burrows-Wheeler Aligner and Novoalign in all categories tested, according to the paper. In speed and reliability benchmarks, BIMA V3 aligned tumor sequences to reference genomes 20 times faster and with 25 percent greater accuracy than its competitors, according to the paper.

“We are able to study more cancer samples faster with this tool, and that has played a key role in our ability to discover new biomarkers in a range of diseases,” says Dr. Vasmatzis.

In the push to apply next-generation sequencing to cancer care, it will be essential to improve physicians’ understanding of the genomic alterations in individual patients’ tumors, says Vasmatzis. Earlier versions of BIMA already have led to Mayo Clinic discoveries in the genomics of T-cell lymphoma, prostate cancer and endometrial cancer. This latest version builds on earlier versions, improving speed and reliability.

Future development of BIMA includes validation for direct application in patient care.

The Biomarker Discovery Program last year described 13 molecular markers for cancer, many of them directly resulting from application of the BIMA software.


Story Source:

The above story is based on materials provided by Mayo Clinic. Note: Materials may be edited for content and length.


Journal Reference:

  1. T. M. Drucker, S. H. Johnson, S. J. Murphy, K. W. Cradic, T. M. Therneau, G. Vasmatzis. BIMA V3: an aligner customized for mate pair library sequencing. Bioinformatics, 2014; DOI: 10.1093/bioinformatics/btu078

Cite This Page:

Mayo Clinic. "Faster tumor analysis software developed, speeds cancer discoveries." ScienceDaily. ScienceDaily, 24 February 2014. <www.sciencedaily.com/releases/2014/02/140224171301.htm>.
Mayo Clinic. (2014, February 24). Faster tumor analysis software developed, speeds cancer discoveries. ScienceDaily. Retrieved July 30, 2014 from www.sciencedaily.com/releases/2014/02/140224171301.htm
Mayo Clinic. "Faster tumor analysis software developed, speeds cancer discoveries." ScienceDaily. www.sciencedaily.com/releases/2014/02/140224171301.htm (accessed July 30, 2014).

Share This




More Health & Medicine News

Wednesday, July 30, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Generics Eat Into Pfizer's Sales

Generics Eat Into Pfizer's Sales

Reuters - Business Video Online (July 29, 2014) Pfizer, the world's largest drug maker, cut full-year revenue forecasts because generics could cut into sales of its anti-arthritis drug, Celebrex. Fred Katayama reports. Video provided by Reuters
Powered by NewsLook.com
Nigeria Ups Ebola Stakes on 1st Death

Nigeria Ups Ebola Stakes on 1st Death

Reuters - Business Video Online (July 29, 2014) Nigerian authorities have shut and quarantined a Lagos hospital where a Liberian man died of the Ebola virus, the first recorded case of the highly-infectious disease in Africa's most populous economy. David Pollard reports Video provided by Reuters
Powered by NewsLook.com
Running 5 Minutes A Day Might Add Years To Your Life

Running 5 Minutes A Day Might Add Years To Your Life

Newsy (July 29, 2014) According to a new study, just five minutes of running or jogging a day could add years to your life. Video provided by Newsy
Powered by NewsLook.com
Ebola Outbreak Poses Little Threat To U.S.: CDC

Ebola Outbreak Poses Little Threat To U.S.: CDC

Newsy (July 29, 2014) The Ebola outbreak in West Africa poses little threat to Americans, according to officials with the Centers for Disease Control and Prevention. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins