Early leukemia diagnostics using microsphere arrays

A method for diagnosing cancer by detecting a chromosome translocation pattern, the method comprising:

• (a) amplifying a target nucleic acid from a biological sample;
• (b) hybridizing a first oligonucleotide specific for a first region of the translocation to the amplified target under conditions in which the first oligonucleotide specifically hybridizes to the first region of the translocation,
• wherein the first oligonucleotide comprises a first capture tag;
• (c) hybridizing a second oligonucleotide specific for a second region of the translocation to the amplified target under conditions in which the second oligonucleotide specifically hybridizes to the second region of the translocation,
• wherein the second oligonucleotide comprises second a capture tag;
• (d) hybridizing a third oligonucleotide specific for a junction region within the translocation to the amplified target under conditions in which the third oligonucleotide specifically hybridizes to the junction region,
• wherein the third oligonucleotide comprises a third capture tag;
• (e) extending the first, second, and third hybridized oligonucleotide sequences to produce a first, second, and third labeled extended oligonucleotide;
• (f) hybridizing the first, second, and third oligonucleotides to a first, a second, and a third address tag on a solid support under conditions in which the first, second, and third labeled extended oligonucleotides specifically hybridize to the first, second, and third address tag;
• and
• (g) detecting the presence of the first, second, and third labeled extended oligonucleotides on the solid support, thereby detecting the presence of the chromosome translocation.

A method of detecting a chromosome translocation, the method comprising:

• (a) amplifying a target nucleic acid sequence from a biological sample;
• (b) hybridizing a first oligonucleotide specific for a first region of the translocation to the amplified target under conditions in which the first oligonucleotide specifically hybridizes to the first region of the translocation,
• wherein the first oligonucleotide comprises a label;
• (c) hybridizing a second oligonucleotide specific for a second region of the translocation to the amplified target under conditions in which the second oligonucleotide specifically hybridizes to the second region of the translocation,
• wherein the second oligonucleotide comprises a capture tag;
• (d) ligating the first and second oligonucleotide to each other;
• (e) hybridizing the first and second oligonucleotides to an address tag on a solid support under conditions in which the address tag specifically hybridizes to the capture tag;
• and
• (f) detecting the presence of the ligated first and second oligonucleotides on the solid support, thereby detecting the presence of the chromosome translocation.