Application of signal processing techniques for estimating regions of copy number variations in human meningioma DNA

Catherine Stamoulis, Rebecca Betensky, Gayatry Mohapatra, David N. Louis

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We applied mode-decomposition and matched-filtering, both signal processing techniques used to increase the signal-to-noise ratio (SNR), to array CGH data of human meningioma DNA, in order to extract genomic regions of copy-number changes potentially associated with tumor progression. DNA segments from different chromosomes were decomposed into a small number of dominant components (modes), and low-amplitude modes were eliminated. The SNR of the entire segment was increased and it was possible to identify local changes in the data spatial structure, previously indistinguishable due to noise. We applied matched-filtering to the mode-reduced signals, using a normal DNA sequences (averaged over 50 healthy donors) as the template. The residual signals from this process were analyzed to identify disease-related copy number changes. We were able to identify distinct local changes at different chromosomes in patients with recurrent versus primary meningiomas.

Original languageEnglish (US)
Title of host publicationProceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Subtitle of host publicationEngineering the Future of Biomedicine, EMBC 2009
PublisherIEEE Computer Society
Pages6973-6976
Number of pages4
ISBN (Print)9781424432967
DOIs
StatePublished - Jan 1 2009
Event31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009 - Minneapolis, MN, United States
Duration: Sep 2 2009Sep 6 2009

Other

Other31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009
CountryUnited States
CityMinneapolis, MN
Period9/2/099/6/09

Fingerprint

Signal-To-Noise Ratio
Meningioma
Chromosomes
Signal to noise ratio
Signal processing
DNA
DNA sequences
Noise
Tumors
Tissue Donors
Decomposition
Neoplasms

ASJC Scopus subject areas

  • Cell Biology
  • Developmental Biology
  • Biomedical Engineering
  • Medicine(all)

Cite this

Stamoulis, C., Betensky, R., Mohapatra, G., & Louis, D. N. (2009). Application of signal processing techniques for estimating regions of copy number variations in human meningioma DNA. In Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009 (pp. 6973-6976). [5333851] IEEE Computer Society. https://doi.org/10.1109/IEMBS.2009.5333851

Application of signal processing techniques for estimating regions of copy number variations in human meningioma DNA. / Stamoulis, Catherine; Betensky, Rebecca; Mohapatra, Gayatry; Louis, David N.

Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009. IEEE Computer Society, 2009. p. 6973-6976 5333851.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Stamoulis, C, Betensky, R, Mohapatra, G & Louis, DN 2009, Application of signal processing techniques for estimating regions of copy number variations in human meningioma DNA. in Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009., 5333851, IEEE Computer Society, pp. 6973-6976, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, Minneapolis, MN, United States, 9/2/09. https://doi.org/10.1109/IEMBS.2009.5333851
Stamoulis C, Betensky R, Mohapatra G, Louis DN. Application of signal processing techniques for estimating regions of copy number variations in human meningioma DNA. In Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009. IEEE Computer Society. 2009. p. 6973-6976. 5333851 https://doi.org/10.1109/IEMBS.2009.5333851
Stamoulis, Catherine ; Betensky, Rebecca ; Mohapatra, Gayatry ; Louis, David N. / Application of signal processing techniques for estimating regions of copy number variations in human meningioma DNA. Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009. IEEE Computer Society, 2009. pp. 6973-6976
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