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Journal of Statistical Theory and Practice

, Volume 6, Issue 1, pp 220–238 | Cite as

Pooling Design and Bias Correction in DNA Library Screening

  • Takafumi Kanamori
  • Hiroaki Uehara
  • Masakazu Jimbo
Article

Abstract

We study the group test for DNA library screening based on a probabilistic approach. The group test is a method of detecting a few positive items from among a large number of items, and has a wide range of applications. In DNA library screening, a positive item corresponds to the clone having a specified DNA segment, and it is necessary to identify and isolate the positive clones for compiling the libraries. In the group test, a group of items, called a pool, is assayed in a lump in order to save the cost of testing, and positive items are detected based on the observation from each pool. It is known that the design of grouping, that is, pooling design, is important to achieve accurate detection. In the probabilistic approach, positive clones are picked up based on the posterior probability. Naive methods of computing the posterior, however, involve exponentially many sums, and thus we need a device. The loopy belief propagation (loopy BP) algorithm is one of the popular methods to obtain approximate posterior probability efficiently. There are some works investigating the relation between the accuracy of the loopy BP and the pooling design. Based on these works, we develop a pooling design with a small estimation bias of posterior probability, and we show that the balanced incomplete block design (BIBD) has nice properties for our purpose. Some numerical experiments show that bias correction under the BIBD is useful to improve the estimation accuracy.

AMS Subject Classification

62-07 90-08 

keywords

BIB design Group test Loopy belief propagation Pooling design 

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Copyright information

© Grace Scientific Publishing 2012

Authors and Affiliations

  • Takafumi Kanamori
    • 1
  • Hiroaki Uehara
    • 1
  • Masakazu Jimbo
    • 1
  1. 1.Nagoya University, FurochoChikusakuJapan

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