Applera Corp.-Applied Biosystems Group v. Illumina, Inc. (PDF)
2008 U.S. Dist. LEXIS 16712
Decided Feb. 21, 2008
Judge Alsup

Judge Alsup construes six terms in this patent infringement lawsuit:

1) initializing oligonucleotide probe
2) ligating an extension oligonucleotide probe to said extendable probe terminus
3) extended oligonucleotide probe
4) identifying
5) just-ligated extension probe
6) repeating steps (b), (c) and (d) until a sequence of nucleotides in the target polynucleotide is determined.

The terms were construed as follows:

1) the oligonucleotide to which the first extension oligonucleotide probe is first ligated
2) forming a covalent bond between an extension oligonucleotide probe and the extendable probe terminus of either an initializing oligonucleotide or an extended oligonucleotide probe while hybridized to a target polynucleotide
3) an initializing oligonucleotide probe effectively extended by one or more nucleotides
4) within each cycle determining the identity of a base in the target polynucleotide
5) the extension oligonucleotide probe or an extended oligonucleotide probe in the present cycle of the method
6) construed as ordinary and plain meaning