System and method for high resolution analysis of nucleic acids to detect sequence variations
First Claim
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1. A method for nucleic acid sequence amplification, comprising:
- identifying a target nucleic acid sequence from one or more segments of DNA, said target nucleic acid sequence having primers with melting temperatures that are within at least 15°
C. of the melting temperature of the target nucleic acid sequence;
obtaining a pair of oligonucleotide primers with an annealing curve (TA) that overlaps with a denaturation curve (TD) of the target nucleic acid sequence, in such a manner as to minimize the temperature range between the higher of the melting temperature of a pair of oligonucleotide primers and the melting temperature of the target nucleic acid sequence, wherein the temperature range does not exceed 15°
C.; and
amplifying the target nucleic acid sequence by thermocycling the target nucleic acid sequence and the pair of oligonucleotide primers within a 15°
C. temperature range,wherein thermocycling comprises;
i. denaturing the target nucleic acid sequence; and
ii. annealing of the pair of oligonucleotide primers; and
iii. extension of the target nucleic acid sequence by the pair of oligonucleotide primers,wherein an upper thermal cycle temperature in the thermocycling is selected to minimize non target denaturation and maximize target denaturation.
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Abstract
Provided herein are methods for assaying a biological sample for microorganisms having drug resistant and/or drug sensitive phenotypes, wherein the methods are capable of detecting resistant and sensitive phenotypes associated with known and/or unknown mutations. In some aspects, methods are provided for detecting drug resistant Myobacterium tuberculosis (MTb), including multi-drug resistant MTb, wherein drug resistance is associated with one or more novel mutations. Also provided are systems, kits, and compositions related to such methods.
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Citations
43 Claims
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1. A method for nucleic acid sequence amplification, comprising:
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identifying a target nucleic acid sequence from one or more segments of DNA, said target nucleic acid sequence having primers with melting temperatures that are within at least 15°
C. of the melting temperature of the target nucleic acid sequence;obtaining a pair of oligonucleotide primers with an annealing curve (TA) that overlaps with a denaturation curve (TD) of the target nucleic acid sequence, in such a manner as to minimize the temperature range between the higher of the melting temperature of a pair of oligonucleotide primers and the melting temperature of the target nucleic acid sequence, wherein the temperature range does not exceed 15°
C.; andamplifying the target nucleic acid sequence by thermocycling the target nucleic acid sequence and the pair of oligonucleotide primers within a 15°
C. temperature range,wherein thermocycling comprises; i. denaturing the target nucleic acid sequence; and ii. annealing of the pair of oligonucleotide primers; and iii. extension of the target nucleic acid sequence by the pair of oligonucleotide primers, wherein an upper thermal cycle temperature in the thermocycling is selected to minimize non target denaturation and maximize target denaturation. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 41)
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28. A method for rapid amplification of a target nucleic acid sequence, comprising:
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identifying a target nucleic acid sequence from one or more segments of DNA; determining the melting temperature of the target nucleic acid sequence via an iterative process comprising amplifying the target nucleic acid sequence and then determining the melting temperature of the target nucleic acid sequence via melting curve analysis; and generating a pair of oligonucleotide primers having an annealing curve (TA) that overlaps with a denaturation curve (TD) of the target nucleic acid sequence, in such a manner as to minimize the temperature range between the melting temperatures (Tm) of the pair of oligonucleotide primers and the melting temperature (Tm) of the target nucleic acid sequences; and amplifying the target nucleic acid sequence by thermocycling the target nucleic acid sequence and the pair of oligonucleotide primers within a 15°
C. temperature range,wherein thermocycling comprises; i. denaturing the target nucleic acid sequence; and ii. annealing of the pair of oligonucleotide primers; and iii. extension of the target nucleic acid sequence by the pair of oligonucleotide primers. - View Dependent Claims (29, 30, 31, 32, 33, 34, 35, 36, 42)
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37. A dynamic flux method of nucleic acid sequence amplification, comprising:
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a. combining a pair of forward and reverse oligonucleotide primers with a target nucleic acid sequence to be amplified; and b. amplifying the target nucleic acid sequence by thermocycling the pair of forward and reverse oligonucleotide primers and the target nucleic acid sequence within a 15°
C. temperature range that is defined by the area contained within the overlap of an annealing curve (TA) of the pair of oligonucleotide primers and the denaturation curve (TD) of the target nucleic acid sequence,wherein each forward and reverse oligonucleotide primer has a melting temperature (Tm) within 15°
C. of the Tm of the target nucleic acid sequence, andwherein thermocycling comprises; i. denaturing the target nucleic acid sequence; and ii. annealing of the forward and reverse oligonucleotide primers; and iii. extension of the target nucleic acid sequence by the forward and reverse oligonucleotide primers. - View Dependent Claims (38, 39, 40, 43)
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Specification