We study non-adaptive pooling strategies for detection of rare faulty items. Given a binary sparse N dimensional signal x, how to construct a sparse binary M × N pooling matrix F such that the signal can be reconstructed from the smallest possible number M of measurements y = Fx? We show that a very small number of measurements is possible for random spatially coupled design of pools F. Our design might find application in genetic screening or compressed genotyping. We show that our results are robust with respect to the uncertainty in the matrix F when some elements are mistaken.
The reconstruction algorithm that is most commonly used in compressed sensing and that has been also discussed several times for reconstruction in group testing and pooling experiments @cite_4 @cite_17 @cite_7 is based on a linear relaxation of the problem to real signal components @math . One then minimizes the @math -norm of the signal under the constraints @math . This is a convex problem that can be solved efficiently using linear programing. In what follows we will use the @math reconstruction as a reference benchmark to demonstrate the improvement that can be achieved using our pooling design and the belief propagation based reconstruction.
@cite_4 @cite_7 @cite_17
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Traditionally, group testing is a design problem. The goal is to design an optimally efficient set of tests of items such that the test results contain enough information to determine a small subset of items of interest. It has its roots in the statistics community and was originally designed for the selective service during World War II to remove men with syphilis from the draft. It appears in many forms, including coin-weighing problems, experimental designs, and public health. We are interested in both the design of tests and the design of an efficient algorithm that works with the tests to determine the group of interest because many of the same techniques that are useful for designing tests are also used to solve algorithmic problems in compressive sensing, as well as to analyze and recover statistical quantities from streaming data. This article is an expository article, with the purpose of examining the relationship between group testing and compressive sensing, along with their applications and connections to sparse function learning. Identification of rare variants by resequencing is important both for detecting novel variations and for screening individuals for known disease alleles. New technologies enable low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. We propose a novel pooling design that enables the recovery of novel or known rare alleles and their carriers in groups of individuals. The method is based on a Compressed Sensing (CS) approach, which is general, simple and efficient. CS allows the use of generic algorithmic tools for simultaneous identification of multiple variants and their carriers. We model the experimental procedure and show via computer simulations that it enables the recovery of rare alleles and their carriers in larger groups than were possible before. Our approach can also be combined with barcoding techniques to provide a feasible solution based on current resequencing costs. For example, when targeting a small enough genomic region (∼100 bp) and using only ∼10 sequencing lanes and ∼10 distinct barcodes per lane, one recovers the identity of 4 rare allele carriers out of a population of over 4000 individuals. We demonstrate the performance of our approach over several publicly available experimental data sets. Detection of rare variants by resequencing is important for the identification of individuals carrying disease variants. Rapid sequencing by new technologies enables low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. In order to improve cost trade-offs, it has recently been suggested to apply pooling designs which enable the detection of carriers of rare alleles in groups of individuals. However, this was shown to hold only for a relatively low number of individuals in a pool, and requires the design of pooling schemes for particular cases. We propose a novel pooling design, based on a compressed sensing approach, which is both general, simple and efficient. We model the experimental procedure and show via computer simulations that it enables the recovery of rare allele carriers out of larger groups than were possible before, especially in situations where high coverage is obtained for each individual. Our approach can also be combined with barcoding techniques to enhance performance and provide a feasible solution based on current resequencing costs. For example, when targeting a small enough genomic region ( 100 base-pairs) and using only 10 sequencing lanes and 10 distinct barcodes, one can recover the identity of 4 rare allele carriers out of a population of over 4000 individuals.