Methods for monitoring the expression of alternatively spliced genes

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.

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.