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ML Estimation of DNA Initial Copy Number in Polymerase Chain Reaction (PCR) Processes

Vikalo, H. and Hassibi, B. and Hassibi, A. (2007) ML Estimation of DNA Initial Copy Number in Polymerase Chain Reaction (PCR) Processes. In: IEEE International Conference on Acoustic, Speech and Signal Processing (ICASSP 2007), Honolulu, HA,. Vol.I. IEEE , Piscataway, NJ, I-417-I-420. ISBN 1-4244-0728-1. https://resolver.caltech.edu/CaltechAUTHORS:VIKicassp07

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Abstract

Estimation of DNA copy number in a given biological sample is an extremely important problem in genomics. This problem is especially challenging when the number of the DNA strands is minuscule, which is often the case in applications such as pathogen and genetic mutation detection. A recently developed technique, real-time polymerase chain reaction (PCR), amplifies the number of initial target molecules by replicating them through a series of thermal cycles. Ideally, the number of target molecules doubles at the end of each cycle. However, in practice, due to biochemical noise the efficiency of the PCR reaction, defined as the fraction of target molecules which are successfully copied during a cycle, is always less than 1. In this paper, we formulate the problem of joint maximum-likelihood estimation of the PCR efficiency and the initial DNA copy number. As indicated by simulation studies, the performance of the proposed estimator is superior with respect to competing statistical approaches. Moreover, we compute the Cramer-Rao lower bound on the mean-square estimation error.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
https://doi.org/10.1109/ICASSP.2007.366705DOIUNSPECIFIED
Additional Information:© Copyright 2007 IEEE. Reprinted with permission. [Posted online: 2007-06-04] This work was supported in part by the National Science Foundation under grant no. CCR-0133818, by the Office of Naval Research under grant no. N00014-02-1-0578, and by Caltech’s Lee Center for Advanced Networking.
Subject Keywords:DNA, genetics, maximum likelihood estimation, mean square error methods, molecular biophysics
Record Number:CaltechAUTHORS:VIKicassp07
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:VIKicassp07
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9072
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:25 Oct 2007
Last Modified:02 Oct 2019 23:57

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