Patent ID: 11961590
Assignee: SEEGENE, INC.
Field: Biotechnology (Chemistry)
Classification: CPC C  G | IPC C  G

Claim 0:
1. A computer-implemented method for preparing a combination of oligonucleotides used to detect a plurality of target nucleic acid sequences with a target coverage of interest from a pool of oligonucleotides, comprising:
(a) preparing the plurality of target nucleic acid sequences;
(b) preparing the pool of oligonucleotides to be hybridized with the plurality of target nucleic acid sequences;
(c) selecting from the pool of oligonucleotides a combination of a minimum number of oligonucleotides with the target coverage of interest for the plurality of target nucleic acid sequences; wherein the selection of the combination of the minimum number of oligonucleotides is performed to achieve the following objective formula 1 together with satisfying the following constraint formulas 1 and 2, or the constraint formula 2; and,
(d) preparing the combination of the minimum number of oligonucleotides selected in step (c); and, Min
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        Objective
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        formula
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        1
      
    
  

wherein Min: represents minimization, xp is a binary variable consisting of a non-selection value (Xnon-sel) and a selection value (xsel) for whether or not an oligonucleotide p is selected, and p is a serial number of the oligonucleotide p ranging from 1 to a;, ∑
            
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        formula
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        1
      
    
  

wherein cs is a binary variable consisting of a non-coverage value (cnon-cov) and a coverage value (ccov) for whether or not a target nucleic acid sequence s is covered, m is a target coverage of interest with a value of 0<m<1, S is the total number of the plurality of target nucleic acid sequences, and s is a serial number of a target nucleic acid sequence s ranging from 1 to b;, ∑
            
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        Constraint
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        formula
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        2
      
    
  

wherein ys,p is a binary constant consisting of a non-coverage value (ynon-cov) and a coverage value (ycov) representing whether or not a target nucleic acid sequence s is covered by an oligonucleotide p; xp is a binary variable for whether or not an oligonucleotide p is selected; cs is a binary variable for whether or not a target nucleic acid sequence s is covered in which cs is a coverage value (ccov) when the target coverage of interest is 100% and cs is a non-coverage value (cnon-cov) and a coverage value (ccov) when the target coverage of interest is less than 100%; and for all s represents application to all of target nucleic acid sequences s.