Methods for detecting gene dysregulations
AssigneeQuest Diagnostics Investments Incorporated
InventorsHeather R. Sanders, Maher Albitar, Aurelia Meloni-Ehrig
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Abstract
Described herein are methods, compositions and kits directed to the detection of gene dysregulations such as those arising from gene fusions and/or chromosomal abnormalities, e.g. translocations, insertions, inversions and deletions. Samples containing dysregulated gene(s) of interest may show independent expression patterns for the 5′ and 3′ regions of the gene. The methods, compositions and kits are useful for detecting mutations that cause the differential expression of a 5′ portion of a target gene relative to the 3′ region of the target gene.
Claims45
A method for detecting a dysregulation in a target gene comprising:
- (a) amplifying a 5′ region of the target gene transcript, if present, in a nucleic acid sample with one or more 5′ target primer pairs which are complementary to the 5′ region of the target gene;
- (b) amplifying a 3′ region of the target gene transcript, if present, in the biological sample with one or more 3′ target primer pairs which are complementary to the 3′ region of the target gene;
- and
- (c) detecting the amounts of amplification product produced by the one or more 5′ target primer pairs and the one or more 3′ target primer pairs;
- (d) comparing the relative expression of the 5′ region to the 3′ region of the target gene in the nucleic acid sample to the relative expression of the 5′ region to the 3′ region of the target gene in a reference sample, and
- (e) identifying the nucleic acid sample as having a gene dysregulation when the amounts of amplification products produced by steps (a) and (b) indicates that the target gene is dysregulated.
A method for detecting the presence or absence of a target gene dysregulation in a test sample, comprising:
- (a) measuring the amount of transcription of a 5′ region of the target gene and a 3′ region of the target gene in the test sample and in a reference sample;
- and
- (h) calculating an IDE Score which compares the relative expression of the 5′ region to the 3′ region of the target gene
- (c) comparing the IDE Score in the test sample to a pre-determined cutoff value,
- (d) identifying the test sample as having a target gene dysregulation when the IDE Score in the test sample is significantly different than the cutoff value and the difference indicates the presence of a target gene dysregulation.
A method for diagnosing cancer or a susceptibility to cancer in a subject, comprising:
- (a) amplifying a 5′ region of the target gene transcript, if present, in a nucleic acid sample with one or more 5′ target primer pairs which are complementary to the 5′ region of the target gene;
- (b) amplifying a 3′ region of the target gene transcript, if present, in the biological sample with one or more 3′ target primer pairs which are complementary to the 3′ region of the target gene;
- and
- (c) detecting the amounts of amplification product produced by the one or more 5′ target primer pairs and the one or more 3′ target primer pairs;
- (d) comparing the relative expression of the 5′ region to the 3′ region of the target gene in the nucleic acid sample to the relative expression of the 5′ region to the 3′ region of the target gene in a reference sample, and
- (e) diagnosing the subject as having cancer or a susceptibility to cancer when the comparison of step (d) indicates that the target gene is dysregulated.
Dependencies are inferred from the claim text.