METHODS FOR MONITORING THE EXPRESSION OF ALTERNATIVELY SPLICED GENES
First Claim
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1. A method for determining the sequence of a variant splicing product of an initial mRNA transcript composed of exons and introns, the method comprising:
- employing different types of positive probes that hybridize with, and produce signals corresponding to, subsequences of the initial mRNA transcript in a sample solution;
employing at least one type of negative control probe corresponding to each type of positive probe to produce negative-control-probe signals;
detecting signals produced from positive probes in order to determine subsequences of the initial mRNA transcript present in a sample solution and construct an initial sequence of the variant splicing product; and
detecting signals produced from the negative control probes to resolve ambiguities in the initial sequence of the variant splicing product.
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Abstract
Methods, probe arrays and computer software products are provided for determining the arrangement of sequence elements. In one embodiment, methods for making and using exon chips are provided. The exon chips may be used to identify and quantify splice variants.
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Citations
9 Claims
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1. A method for determining the sequence of a variant splicing product of an initial mRNA transcript composed of exons and introns, the method comprising:
- employing different types of positive probes that hybridize with, and produce signals corresponding to, subsequences of the initial mRNA transcript in a sample solution;
employing at least one type of negative control probe corresponding to each type of positive probe to produce negative-control-probe signals;
detecting signals produced from positive probes in order to determine subsequences of the initial mRNA transcript present in a sample solution and construct an initial sequence of the variant splicing product; and
detecting signals produced from the negative control probes to resolve ambiguities in the initial sequence of the variant splicing product. - View Dependent Claims (2, 3, 4, 5)
- employing different types of positive probes that hybridize with, and produce signals corresponding to, subsequences of the initial mRNA transcript in a sample solution;
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6. Computer instructions that implement the method for determining the sequence of a variant splicing product of an initial mRNA transcript composed of exons and introns encoded in a computer readable data-storage medium.
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7. A microarray manufactured for use in identifying variant splicing products of an initial mRNA transcript, the microarray comprising:
- a substrate; and
an active surface of the substrate onto which features containing probe molecules are deposited, the probe molecules including;
positive probes complementary to expected subsequences of variant splicing products of the initial mRNA transcript; and
two or more different types of negative control probes. - View Dependent Claims (8, 9)
- a substrate; and
Specification