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Grant Details

Grant Number: 5R03CA165070-02 Interpret this number
Primary Investigator: Betensky, Rebecca
Organization: Harvard School Of Public Health
Project Title: Signal Processing for Accurate Detection of Copy Number Variants in Cancer
Fiscal Year: 2013


DESCRIPTION (provided by applicant): Human genomic variability occurs at different scales, from single nucleotide polymorphisms to DNA segments containing a large number of genes. Copy number variations (CNVs) represent a significant part of human genetic heterogeneity and have also been associated with a wide range of diseases and disorders. Although large CNVs may be detectable in noisy array-based data, short, localized aberrations may be undetectable due to low signal-to-noise ratio (SNR). Short CNVs may, however, play an important role in human disease, and thus highly sensitive methodologies are needed for their detection. For meaningful identification of disease CNVs, it is necessary to first estimate the locations and levels of normal allelic aberrations for baseline comparison. We have successfully developed a signal processing-based methodology for sequence denoising followed by pattern matching, to increase SNR in normal genomic data and improve CNV detection in normals. We propose to further develop this method for normals, and then to develop and extend it for application in the cancer setting, in particular, for atypical meningioma and lung squamous cell carcinoma, for highly sensitive and specific detection of cancer related CNV's. CNV detection in cancer is critical for understanding the etiology of disease and ultimately for the development of therapeutic targets, and our methodology will contribute uniquely and substantially to this goal. We will use The Cancer Genome Atlas resource of the National Cancer Institute for normal array data and for the lung cancer data.


Cognitive resilience in clinical and preclinical Alzheimer's disease: the Association of Amyloid and Tau Burden on cognitive performance.
Authors: Rentz D.M. , Mormino E.C. , Papp K.V. , Betensky R.A. , Sperling R.A. , Johnson K.A. .
Source: Brain imaging and behavior, 2017 Apr; 11(2), p. 383-390.
PMID: 27738998
Related Citations

Optimization of Signal Decomposition Matched Filtering (SDMF) for Improved Detection of Copy-Number Variations.
Authors: Stamoulis C. , Betensky R.A. .
Source: IEEE/ACM transactions on computational biology and bioinformatics, 2016 May-Jun; 13(3), p. 584-91.
PMID: 27295643
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Synergistic effect of β-amyloid and neurodegeneration on cognitive decline in clinically normal individuals.
Authors: Mormino E.C. , Betensky R.A. , Hedden T. , Schultz A.P. , Amariglio R.E. , Rentz D.M. , Johnson K.A. , Sperling R.A. .
Source: JAMA neurology, 2014 Nov; 71(11), p. 1379-85.
PMID: 25222039
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Amyloid and APOE ε4 interact to influence short-term decline in preclinical Alzheimer disease.
Authors: Mormino E.C. , Betensky R.A. , Hedden T. , Schultz A.P. , Ward A. , Huijbers W. , Rentz D.M. , Johnson K.A. , Sperling R.A. , Alzheimer's Disease Neuroimaging Initiative , et al. .
Source: Neurology, 2014-05-20; 82(20), p. 1760-7.
EPub date: 2014-04-18.
PMID: 24748674
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