Cornell University, et al. v. Illumina Inc., C.A. No. 10-433 – LPS-MPT, May 6, 2016. 

Claim construction opinion issues regarding thirty-three terms from eleven patents.  A Markman hearing took place on February 22, 2016.

Thynge, C.M. J. The disputed technology relates to methods for determining whether a certain DNA sequence is present in a sample. The following terms were considered:

1. “oligonucleotide probe set(s)”
2. “primer-specific portion”
3. “ligation product sequence(s)” “ligation products”
4. “composite oligonucleotide”
5. “solid support”
6. “an array of positions”
7. “linker”
8. “immobilized”
9. “attached”
10. “suitable for attachment”
11. “coupled to”
12. “capture oligonucleotide probes” “capture oligonucleotide(s)”
13. “capturing said one or more amplification products to a solid support”
14. “each [type of] capture oligonucleotide hybridizes to a nucleic acid molecule comprising a complementary nucleotide sequence the capture oligonucleotides hybridize to complementary portions of the target nucleic acid molecules”
15. “one or more target nucleic acid molecules hybridized [to complementary portions of the capture oligonucleotides on the solid support]”
16. “each type of capture oligonucleotide . . .hybridizes to its complement”
17. “wherein the zip code portion of each of the composite oligonucleotides . . .hybridizes to its complement”
18. “the capture oligonucleotides hybridize to the complementary portions of the nucleic acid molecules”
19. “each capture oligonucleotide probe of the array differs in sequence from its adjacent capture oligonucleotide probe, when aligned to each other by at least 25%”
20. “each capture oligonucleotide probe of the array differs in sequence from its adjacent capture oligonucleotide probe, when aligned to each other by at least 25%”
21. “each type of capture oligonucleotide . . .differs in nucleotide sequence, when aligned to another type of capture oligonucleotide that is located on an adjacent position of said solid support, by at least 25%”
22. “each type of capture oligonucleotide . . .differs in nucleotide sequence, when aligned to another type of capture oligonucleotide, by at least 25%” “each type of capture oligonucleotide . . . differs by at least 25% in nucleotide sequence, when aligned to another type of capture oligonucleotide” “comprises a nucleotide sequence that differs from the nucleotides sequence of other types of capture oligonucleotides in the collection by at least 25% when aligned each type of capture oligonucleotide . . . comprising nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotide of the collection by at least 25% when aligned each type of capture nucleotide . . . with a nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotides on the solid support by at least 25% when aligned”
23. “uniform hybridization conditions”
24. “addressable array specific portion”
25. “address-specific portion”
26. “zip code portion”
27. “unique nucleotide sequence” “unique nucleotide portion”
28. “ligase detection reaction”
29. “suitable for ligation together”
30. “ligase detection reaction cycles”
31. “ligase detection reaction mixture” “ligation detection reaction mixture” “reaction mixture”
32. “polymerase chain reaction (PCR) mixture PCR mixture”
33. “target-specific portion(s)”