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