Nucleic acid detection combining amplification with fragmentation
First Claim
1. A method for detecting the presence or absence of a target nucleic acid by testing a sample containing unamplified nucleic acids that potentially contains the target nucleic acid in the presence of non-target nucleic acid, said method comprising:
- a) fragmenting the unamplified nucleic acids under conditions such that the non-target nucleic acid is preferentially fragmented relative to the target nucleic acid, wherein the target nucleic acid and the non-target nucleic acid are at least 50% identical at aligned nucleotide positions and the non-target nucleic acid comprises at least one fragmentation site not present in the target nucleic acid;
b) combining the unamplified nucleic acids of step a) with a polymerase chain reaction (PCR) mixture comprising a pair of primers specific for the target nucleic acid, wherein one primer of the pair spans or overlaps the at least one fragmentation site present in the non-target nucleotide sequence but absent from the target nucleotide sequence, and wherein fragmentation of the non-target nucleotide sequence in part a) prevents hybridization of said primer to the non-target nucleic acid;
c) amplifying the target nucleic acid from the unamplified nucleic acids combined with the PCR mixture in step b); and
d) detecting presence or absence of an amplification product from step c), which indicates the presence or absence of the target nucleic acid in the sample, wherein the non-target nucleic acid comprises a wild-type nucleotide sequence and the target nucleic acid comprises a mutant version of the wild-type nucleotide sequence, and wherein step a) is performed prior to step b).
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Abstract
Provided herein are methods and compositions for detection of a nucleic acid target in a sample. The methods and compositions use primer directed amplification in conjunction with nucleic acid fragmentation. The methods have high sensitivity even in the presence of a large amount of non-target nucleic acid. Also provided are oligonucleotides and kits useful in the method. Exemplary nucleic acid targets are those with mutant gene sequence such as mutant sequence of the EGFR, APC, TMPRSS2, ERG and ETV1 genes.
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Citations
35 Claims
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1. A method for detecting the presence or absence of a target nucleic acid by testing a sample containing unamplified nucleic acids that potentially contains the target nucleic acid in the presence of non-target nucleic acid, said method comprising:
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a) fragmenting the unamplified nucleic acids under conditions such that the non-target nucleic acid is preferentially fragmented relative to the target nucleic acid, wherein the target nucleic acid and the non-target nucleic acid are at least 50% identical at aligned nucleotide positions and the non-target nucleic acid comprises at least one fragmentation site not present in the target nucleic acid; b) combining the unamplified nucleic acids of step a) with a polymerase chain reaction (PCR) mixture comprising a pair of primers specific for the target nucleic acid, wherein one primer of the pair spans or overlaps the at least one fragmentation site present in the non-target nucleotide sequence but absent from the target nucleotide sequence, and wherein fragmentation of the non-target nucleotide sequence in part a) prevents hybridization of said primer to the non-target nucleic acid; c) amplifying the target nucleic acid from the unamplified nucleic acids combined with the PCR mixture in step b); and d) detecting presence or absence of an amplification product from step c), which indicates the presence or absence of the target nucleic acid in the sample, wherein the non-target nucleic acid comprises a wild-type nucleotide sequence and the target nucleic acid comprises a mutant version of the wild-type nucleotide sequence, and wherein step a) is performed prior to step b). - 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, 28, 29, 30, 31, 32, 33, 34)
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35. A method for detecting the presence or absence of a target nucleotide sequence in a sample potentially comprising both target and non-target nucleotide sequences, wherein the non-target nucleotide sequence comprises a wild-type nucleotide sequence, and the target nucleic acid comprises a mutant version of the wild-type nucleotide sequence lacking at least one fragmentation site present in the wild-type nucleotide sequence, and wherein the sample comprises only unamplified nucleic acids, comprising:
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a) fragmenting the nucleic acids in the sample under conditions such that fragmentation occurs at the at least one fragmentation site present in the non-target nucleotide sequence but absent from the target nucleotide sequence; b) subsequent to step a), combining the product of a) with a polymerase chain reaction (PCR) mixture comprising a pair of primers specific for the target nucleotide sequence, wherein one primer spans or overlaps the at least one fragmentation site present in the non-target nucleotide sequence but absent from the target nucleotide sequence, and wherein fragmentation of the non-target nucleotide sequence in part a) prevents hybridization of said one primer to the non-target nucleotide sequence; c) subsequent to step b), performing an amplification reaction on the PCR mixture of b); and d) detecting presence or absence of an amplification product in c), wherein the presence of an amplification product in d) indicates the presence of the target nucleotide sequence in the sample.
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Specification