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Modeling and Estimation for Real-Time Microarrays

Vikalo, Haris and Hassibi, Babak and Hassibi, Arjang (2008) Modeling and Estimation for Real-Time Microarrays. IEEE Journal of Selected Topics in Signal Processing, 2 (3). pp. 286-296. ISSN 1932-4553. https://resolver.caltech.edu/CaltechAUTHORS:20090916-153943053

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Abstract

Microarrays are used for collecting information about a large number of different genomic particles simultaneously. Conventional fluorescent-based microarrays acquire data after the hybridization phase. During this phase, the target analytes (e.g., DNA fragments) bind to the capturing probes on the array and, by the end of it, supposedly reach a steady state. Therefore, conventional microarrays attempt to detect and quantify the targets with a single data point taken in the steady state. On the other hand, a novel technique, the so-called real-time microarray, capable of recording the kinetics of hybridization in fluorescent-based microarrays has recently been proposed. The richness of the information obtained therein promises higher signal-to-noise ratio, smaller estimation error, and broader assay detection dynamic range compared to conventional microarrays. In this paper, we study the signal processing aspects of the real-time microarray system design. In particular, we develop a probabilistic model for real-time microarrays and describe a procedure for the estimation of target amounts therein. Moreover, leveraging on system identification ideas, we propose a novel technique for the elimination of cross hybridization. These are important steps toward developing optimal detection algorithms for real-time microarrays, and to understanding their fundamental limitations.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1109/JSTSP.2008.924383DOIArticle
http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=4550568PublisherArticle
Additional Information:© 2008 IEEE. Manuscript received September 5, 2007; revised March 8, 2008. This work was supported in part by a Grubstake Award from California Institute of Technology, in part by a grant from the David and Lucille Packard Foundation, and in part by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech. The associate editor coordinating the review of this manuscript and approving it for publication was Prof. Ahmed Tewfik.
Group:Millard and Muriel Jacobs Genetics and Genomics Laboratory
Funders:
Funding AgencyGrant Number
CaltechUNSPECIFIED
David and Lucile Packard FoundationUNSPECIFIED
Millard and Muriel Jacobs Genetics and Genomics LaboratoryUNSPECIFIED
Subject Keywords:Cross hybridization; DNA microarrays; real-time; statistical modeling
Issue or Number:3
Record Number:CaltechAUTHORS:20090916-153943053
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20090916-153943053
Official Citation:Vikalo, H.; Hassibi, B.; Hassibi, A., "Modeling and Estimation for Real-Time Microarrays," Selected Topics in Signal Processing, IEEE Journal of , vol.2, no.3, pp.286-296, June 2008 URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=4550568&isnumber=4550544
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:15892
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:23 Sep 2009 19:46
Last Modified:03 Oct 2019 01:04

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