Non-in situ hybridization method for detecting chromosomal abnormalities
First Claim
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1. A method for detecting a target nucleic acid in a test sample, said method comprising:
- forming on a solid support a complex comprising the target nucleic acid, a first nucleic acid probe hybridizing to a first segment of the target nucleic acid, said first nucleic acid probe labeled with a detectable label, and a second nucleic acid probe hybridizing to a second segment of the target nucleic acid, said second nucleic acid probe anchored to the solid support, and detecting said complex by detecting incorporated detectable label, wherein at least one of said first and second nucleic probe is at least 50 nucleotides in length.
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Abstract
The present invention provides methods of detecting chromosomal or genetic abnormalities associated with various diseases or with predisposition to various diseases. In particular, the present invention provides advanced methods of performing DNA hybridization, capture, and detection on solid support. Invention methods are useful for the detection, diagnosis, predicting response to therapy, detecting minimal residual disease, prognosis, or monitoring of disease treatment or progression of particular disease conditions such as cell proliferative disorders
52 Citations
50 Claims
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1. A method for detecting a target nucleic acid in a test sample, said method comprising:
forming on a solid support a complex comprising the target nucleic acid, a first nucleic acid probe hybridizing to a first segment of the target nucleic acid, said first nucleic acid probe labeled with a detectable label, and a second nucleic acid probe hybridizing to a second segment of the target nucleic acid, said second nucleic acid probe anchored to the solid support, and detecting said complex by detecting incorporated detectable label, wherein at least one of said first and second nucleic probe is at least 50 nucleotides in length. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A method for detecting the presence or absence of a genetic abnormality in a target nucleic acid in a test sample, said method comprising:
forming on a solid support a complex comprising the target nucleic acid, a first nucleic acid probe hybridizing to a first segment of the target nucleic acid, said first nucleic acid probe labeled with a detectable label, and a second nucleic acid probe hybridizing to a second segment of the target nucleic acid, said second nucleic acid probe anchored to the solid support, and detecting said complex by detecting incorporated detectable label, wherein hybridization of both the first and second probes to the same target nucleic acid indicates detection of genetic abnormality in the target nucleic acid, while hybridization of only one of said probes to the same target nucleic acid indicates the absence of a genetic abnormality in the target nucleic acid. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
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23. A method for analyzing nucleic acid from a sample of an individual to determine if the individual has a duplication or deletion associated with a particular chromosomal segment or gene, comprising,
a) forming on a solid support a complex comprising the nucleic acid associated with the particular chromosomal segment or gene which is obtained from the sample, a first nucleic acid probe hybridizing to a first segment of the nucleic acid associated with the particular chromosomal segment or gene, said first nucleic acid probe labeled with a detectable label, and a second nucleic acid probe hybridizing to a second segment of the nucleic acid associated with the particular chromosomal segment or gene, wherein said second nucleic acid probe is anchored to the solid support, and b) measuring a test value representing the amount of complex formed with nucleic acid associated with the particular chromosomal segment or gene by detecting the amount of detectable label incorporated into the complex, and c) comparing the amount measured in step b) to a control value obtained for another particular chromosomal segment or gene, wherein an increase in the test value compared to the control value is indicative of a duplication and a decrease in the test value compared to the control value is indicative of a deletion.
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33. A method for detecting a chromosomal translocation of a target nucleic acid in a test sample, said method comprising,
forming on a solid support a complex comprising the target nucleic acid, a first nucleic acid probe hybridizing to a region of a first chromosome of the translocation, said first nucleic acid probe labeled with a detectable label, and a second nucleic acid probe hybridizing to a region of a second chromosome of the translocation, wherein said second nucleic acid probe is anchored to the solid support, and detecting the complex by detecting detectable label incorporated into the complex, wherein said detecting indicates the presence of the chromosomal translocation.
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39. A method of determining diagnosis, predicting response to therapy, detecting minimal residual disease or prognosis of a disease in an individual, said method comprising,
a) forming on a solid support a complex comprising the target nucleic acid from a test sample of the individual, a first nucleic acid probe hybridizing to a first segment of the target nucleic acid, said first nucleic acid probe labeled with a detectable label, and a second nucleic acid probe hybridizing to a second segment of the target nucleic acid, wherein said second nucleic acid probe is anchored to the solid support, b) measuring the amount of complex formed by detecting the amount of detectable label incorporated into the complex; - and
c) comparing the amount of complex formed using target nucleic acid from the test sample to the amount of complex formed using target nucleic acid from a reference sample, wherein a difference in amount of complex formed from the test sample as compared to the reference sample is diagnostic, predicts response to therapy, detects minimal residual disease or is prognostic for said disease. - View Dependent Claims (40)
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43. A method of monitoring progression of a disease, said method comprising, obtaining a first sample containing a target nucleic acid from an individual having a disease,
a) forming on a first solid support a first complex comprising a target nucleic acid from said first sample, a second nucleic acid probe hybridizing to a first segment of said target nucleic acid, said first nucleic acid probe labeled with a detectable label, and a second nucleic acid probe hybridizing to a second segment of said target nucleic acid, wherein said second nucleic acid probe is anchored to the first support, and detecting said first complex by measuring the amount of detectable label incorporated into said complex, b) obtaining a second sample containing a target nucleic acid from said individual having a disease, wherein said second sample is obtained after the first sample; -
c) forming on a second solid support a second complex comprising a target nucleic acid from said second sample, a first nucleic acid probe hybridizing to a first segment of said target nucleic acid, said first nucleic acid probe labeled with a detectable label, and a second nucleic acid probe hybridizing to a second segment of said target nucleic acid, wherein said second nucleic acid probe is anchored to the second support, and detecting said complex by measuring the amount of detectable label incorporated into said complex, d) comparing the amount of said first complex formed from the first sample to the amount of second complex formed from the second sample, wherein a difference in the amount of first complex and second complex is related to the progression of the disease. - View Dependent Claims (44, 45, 46)
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47. A method of measuring the tumor burden in an individual suspected of having cancer, said method comprising,
a) forming on a solid support a first complex comprising a first target nucleic acid from a body fluid test sample, a first nucleic acid probe hybridizing to a first segment of said first target nucleic acid, said first nucleic acid probe labeled with a detectable label, and a second nucleic acid probe hybridizing to a second segment of said first target nucleic acid, wherein said second nucleic is anchored to the solid support, and detecting said first complex, b) comparing the amount measured in step a) to a reference value or set of reference values that relate the amount in step a) to tumor burden.
Specification