Methods for preparing optimal combination of oligonucleotides
AssigneeSeegene, Inc.
InventorMi Hyun Jang
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Abstract
The present invention relates to optimization logic for preparing an optimal combination of oligonucleotides hybridized with a plurality of target nucleic acid sequences, in a completely different approach from conventional methods, i.e., empirical and manual methods. In addition, the optimization logic of the present invention may be used to (i) preparing an oligonucleotide combination used to detect a plurality of target nucleic acid sequences with a target coverage of interest, (ii) selecting target nucleic acid sequences to be detected by a multiplex target detection with a highest target coverage by using a limited number of oligonucleotides, and (iii) determining a conserved region in a plurality of target nucleic acid sequences.
Claims11
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
-
- :
-
-
- ∑
- p
- =
- 1
- a
-
- x
- p
- Objective
-
-
- formula
-
-
- 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;
- ∑
- s
- =
- 1
- b
-
- c
- s
- ≥
- m
- ×
- S
- Constraint
-
-
- formula
-
-
- 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;
- ∑
- p
- =
- 1
- a
-
- y
- s
- ,
- p
-
- x
- p
- ≥
- c
- s
-
-
- for
-
-
- all
-
-
- s
- Constraint
-
-
- formula
-
-
- 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.
A non-transitory computer readable storage medium containing instructions to configure a processor to perform a 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, the method comprising:
- selecting from the pool of oligonucleotides a combination of the 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:
- Min
-
- :
-
-
- ∑
- p
- =
- 1
- a
-
- x
- p
- Objective
-
-
- formula
-
-
- 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;
- ∑
- s
- =
- 1
- b
-
- c
- s
- ≥
- m
- ×
- S
- Constraint
-
-
- formula
-
-
- 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;
- ∑
- p
- =
- 1
- a
-
- y
- s
- ,
- p
-
- x
- p
- ≥
- c
- s
-
-
- for
-
-
- all
-
-
- s
- Constraint
-
-
- formula
-
-
- 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.
Dependencies are inferred from the claim text.