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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.”
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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 post is reprinted from 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

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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 September 5, 2015 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 September 5, 2015).

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