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Journal of Computer and System Sciences 70 (2005) 399417 www.elsevier.com/locate/jcss
 

Summary: Journal of Computer and System Sciences 70 (2005) 399417
www.elsevier.com/locate/jcss
Designing optimally multiplexed SNP genotyping assays
Yonatan Aumanna
, Efrat Manisterskia
, Zohar Yakhinib
aDepartment of Computer Science, Bar Ilan University, Ramat Gan, Israel
bAgilent Laboratories and Department of Computer Science, The Technion, Haifa, Israel
Received 20 August 2003; received in revised form 22 June 2004
Available online 1 February 2005
Abstract
WeconsiderthetaskofSNP(SingleNucleotidePolymorphism)genotyping.Inmanystudies,genotypingofalarge
number of SNPs must be performed. Multiple SNPs can be genotyped together in the same assay (a process called
multiplexed genotyping) provided they adhere to some constraints.We address the optimization problem of designing
assays that maximize the number of genotyped SNPs, subject to the multiplexing constraints. We focus on the SNP
genotyping method based on primer extension and mass-spectrometry (PEA/MS). We translate the optimization
problem to a graph coloring problem, and provide essentially optimal heuristics for solving the corresponding
coloring problem. In addition, we consider a method that enables a dramatic increase in the multiplexing rate by
modifying primer masses. In this case, the multiplexing design problem can be modelled as a matching problem
in hypergraphs. We analyze both theoretical and practical aspects of the problem, providing hardness results and

  

Source: Aumann, Yonatan - Computer Science Department, Bar Ilan University

 

Collections: Computer Technologies and Information Sciences