MULTIPLEX (+/-) STRANDED ARRAYS AND ASSAYS FOR DETECTING CHROMOSOMAL ABNORMALITIES ASSOCIATED WITH CANCER AND OTHER DISEASES
First Claim
1. A method for detecting chromosomal rearrangements, comprising receiving a DNA sample and analyzing the DNA sample via comparative genomic hybridization for chromosomal rearrangements using an array of plus (+)-stranded DNA probes and minus (−
- )-stranded DNA probes.
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Abstract
Multiplex (+/−) stranded analyses, such as array comparative genomic hybridization (aCGH), are provided for detecting chromosomal rearrangements associated with cancer and other diseases. For example, an illustrative multiplex array for CGH includes discrete plus (+) strand and minus (−) strand DNA probes, complementary to each other but separable on the CGH array. The minus (−) strand DNA probes recover diagnostic information lost to conventional microarrays, since many genes transcribe from the minus (−) strand. In an illustrative system, patient and control DNA samples are prepared for CGH by amplification and labeling using comprehensive primers that generate both plus (+) strands and minus (−) strands of DNA in the samples. The breakpoints of a translocated chromosome may be detected on a multiplex microarray by DNA probes of one polarity, while DNA copy number changes associated with the translocation region may be detected by corresponding DNA probes of the complementary polarity. Related methods for identifying translocation partner genes are also provided.
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Citations
25 Claims
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1. A method for detecting chromosomal rearrangements, comprising receiving a DNA sample and analyzing the DNA sample via comparative genomic hybridization for chromosomal rearrangements using an array of plus (+)-stranded DNA probes and minus (−
- )-stranded DNA probes.
- View Dependent Claims (2, 3, 4, 5)
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6. A method for detecting chromosomal rearrangements, comprising:
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receiving a subject DNA sample; receiving a control DNA sample; adding primers to the subject DNA sample and the control DNA sample for amplifying chromosomal regions; amplifying the subject DNA sample to produce plus (+) strands of patient DNA and minus (−
) strands of subject DNA representing the chromosomal regions, the (+) strands of subject DNA and the minus (−
) strands of subject DNA within a subject DNA product that includes amplified subject DNA and unamplified subject DNA;labeling the plus (+) strands and the minus (−
) strands of the subject DNA product with at least a first label to provide a labeled subject DNA product;amplifying the control DNA sample to produce plus (+) strands of control DNA and minus (−
) strands of control DNA representing the chromosomal regions, the (+) strands of control DNA and the minus (−
) strands of control DNA within a control DNA product that includes amplified control DNA and unamplified control DNA; andlabeling the plus (+) strands and the minus (−
) strands of the control DNA product with at least a second label to provide a labeled control DNA product. - View Dependent Claims (7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18)
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19. A method for detecting chromosomal rearrangements, comprising:
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obtaining a DNA sample; amplifying the DNA sample to produce plus (+)-stranded DNA and minus (−
)-stranded DNA representing chromosomal regions of diagnostic interest within a DNA product that includes amplified DNA and unamplified DNA;labeling the plus (+)-stranded DNA and the minus (−
)-stranded DNA with at least a first label to provide a labeled DNA product;hybridizing the labeled DNA product to an array that includes plus (+)-stranded DNA targets and complementary minus (−
)-stranded DNA targets; andanalyzing the microarray to detect a chromosomal translocation in the labeled DNA product. - View Dependent Claims (20)
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21. An array for the detection of chromosomal abnormalities comprising plus (+)-stranded DNA probes and minus (−
- )-stranded DNA probes.
- View Dependent Claims (22, 23, 24, 25)
Specification