Identification of rearrangements in nucleic acid molecules

A trimolecular sandwich comprising:

• a substrate;
• a first nucleic acid comprising the sequence of all or a portion of a first chromosome, wherein said first nucleic acid is attached to said substrate;
• a test nucleic acid, wherein a first portion of said test nucleic acid is hybridized to all or a portion of said first nucleic acid;
• and
• a second nucleic acid, wherein all or a portion of the second nucleic acid is hybridized to a second portion of the test nucleic acid, and wherein the second nucleic acid comprises the sequence of all or a portion of a second chromosome.

A method for identifying a test nucleic acid comprising a chromosomal rearrangement, the method comprising:

• providing a test nucleic acid as a template for nucleic acid synthesis;
• contacting said test nucleic acid with each of (i) a population of first primers, wherein substantially all of said first primers are detectably labeled with a first label and wherein said population of first primers is randomly generated, and wherein each of said first primers hybridizes to a portion of a first chromosome and (ii) a population of second primers, wherein substantially all of said second primers are detectably labeled with a second label and wherein said population of second primers is randomly generated, and wherein each of said second primers hybridizes to a portion of a second chromosome, and further wherein said second label is distinct from said first label;
• synthesizing a nucleic acid complementary to said test nucleic acid, wherein said test nucleic acid serves as a template for nucleic acid synthesis and one of said first primers and one of said second primers prime synthesis of the synthesized nucleic acid;
• and
• detecting a synthesized nucleic acid comprising each of said first and said second labels as an indication that the test nucleic acid comprises a chromosomal rearrangement.

A method for identifying a chromosomal rearrangement in a test nucleic acid, the method comprising:

• providing a substrate having attached thereto a first nucleic acid comprising the sequence of a first portion of a chromosome;
• contacting said substrate with a test nucleic acid under conditions that permit a first portion of the test nucleic acid to hybridize to all or a portion of said first nucleic acid;
• contacting the test nucleic with a second nucleic acid under conditions that permit hybridization of all or a portion of the second nucleic acid to a second portion of the test nucleic acid, wherein the second nucleic acid comprises the sequence of a second portion of said chromosome;
• and
• detecting hybridization of said test nucleic acid to each of said first nucleic acid and said second nucleic acid as an indication that the test nucleic acid comprises a chromosomal rearrangement.

A method for comparing a test nucleic acid with a reference nucleic acid, the method comprising:

• providing a substrate having attached thereto a first nucleic acid comprising the sequence of a first portion of a first chromosome;
• contacting said substrate with a test nucleic acid under conditions that permit a first portion of the test nucleic acid to hybridize to all or a portion of said first nucleic acid;
• contacting the test nucleic with a second nucleic acid under conditions that permit hybridization of all or a portion of the second nucleic acid to a second portion of the test nucleic acid, wherein the second nucleic acid comprises the sequence of (i) a second portion of said chromosome or (ii) a portion of a second chromosome;
• detecting hybridization of said test nucleic acid to each of said first nucleic acid and said second nucleic acid;
• and
• comparing the ability of said test nucleic acid to hybridize to each of said first nucleic acid and said second nucleic acid with the ability of said reference nucleic acid to hybridize to each of said first nucleic acid and said second nucleic acid.