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Case 1:04-cv-00901-JJF Document 325 Filed 08/16/2006 Page1 0f3
IN THE UNITED STATES DISTRICT COURT
FOR THE DISTRICT OF DELAWARE
I AFFYMETRIX, INC., :
Plaintiff, ;
v. ; Civil Action No. 04-901 JJF
ILLUMINA, INC., E
D Defendant. 3
O R D E R
At Wilmington, this_jQL Day of August, 2006, for the
reasons set forth in the Memorandum Opinion issued this date,
IT IS HEREBY ORDERED that for the purposes of the United
States Patents at issue in this case, the following terms and
phrases are construed as follows:
l. The phrase “said beads being coded with an encoding
system,” as used in the claims of U.S. Patent No. 6,355,432,
means “said beads having a property associated with each bead
(separate from the binding polymer) that can be used to
distinguish one bead from another;”
2. The term “target specific sequence,” as used in the
claims of U.S. Patent No. 6,355,432, means “a known polymer
sequence that has affinity for another sequence;”
3. The term “substrate,” as used in the claims of U.S.
Patent No. 6,646,243, means “a material having a rigid or semi-
rigid surface;”

Case 1:04-cv-00901-JJF Document 325 Filed 03/16/2006 Page 2 of 3
4. The term “target nucleic acids,” as used in the claims
of U.S. Patent No. 6,646,243, means “nucleic acids that are
deliberately exposed to the nucleic acids attached to the
substrate;”
5. The term “probe array," as used in the claims of U.S.
Patent No. 5,545,531, means “a collection of probes, at least
two of which are different, arranged in a spacially defined and
physically addressable manner;”
6. The phrase “arranged in a spacially defined and
physically addressable manner,” as used in the claims of U.S.
Patent No. 5,545,531, means “looated in a particular location
and capable of being addressed;"
7. The phrase “biological polymers immobilized on a
surface,” as used in the claims of U.S. Patent No. 6,399,365,
means “two or more surface—immobilized biological polymers that
are recognized by a particular target;”
B. The term “housing,” as used in the claims of U.S.
Patent No. 6,399,365, means “a structure that covers, protects,
and supports the probe array;”
9. The term “probe,” as used in the claims of U.S. Patent
No. 5,795,716, means “a nucleic acid of known sequence that is
capable of hybridizing to its complementary sequence;”
10. The term “probe intensity,” as used in the claims of
U.S. Patent No. 5,795,716, means “intensity from a labeled
sample nucleic acid hybridized to a probe location;”

Case 1:04-cv-00901-JJF Document 325 Filed 08/16/2006 Page30f3
11. The phrase “corresponding to probe intensities for a
plurality of nucleic acid probes,” as used in the claims of U.S.
Patent No. 5,795,716, does not require further construction
12. The phrase “indicating an extent of hybridization,” as
used in the claims of U.S. Patent No. 5,795,716, means
“indicating the relative strength of binding;”
13. The phrase “comparison of said plurality of probe
intensities to each other,” as used in the claims of U.S. Patent
No. 5,795,716, means “an examination of the probe intensities of
two or more probes in relation to each other;”
14. The phrase “generates a base call identifying said
unknown base,” as used in the claims of U.S. Patent No.
5,795,716, means “determines which nucleotide is most likely to
be present at a particular position in a nucleic acid sequence;”
15. The phrase “generates a base call . . . according to
results of said comparison and said sequences of said nucleic
acid probes,” as used in the claims of U.S. Patent No.
5,795,716, does not require further construction.
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