*** Confidential portions omitted and filed
separately with the Commission.
EXHIBIT 10.56
NOTE: Portions of this Exhibit
are the subject of a Confidential Treatment Request by the
Registrant to the Securities and Exchange Commission (the
“Commission”). Such portions have been redacted and are
marked with a “[***]” in place of the redacted
language. The redacted information has been filed separately with
the Commission.
AMENDMENT NO. 2 TO SECOND
AMENDED AND RESTATED
COLLABORATION, LICENSE AND SUPPLY
AGREEMENT
THIS AMENDMENT NO. 2 TO SECOND
AMENDED AND RESTATED COLLABORATION, LICENSE AND SUPPLY AGREEMENT
(the “2 nd Amendment”), is entered into
as of December 31, 2005 (the “2 nd Amendment Date”) by and
between EPOCH BIOSCIENCES, INC., with offices at 21720 23
rd
Drive S.E., Suite 150,
Bothell, WA ( “Epoch”), a wholly owned subsidiary of
Nanogen, Inc., with offices at 10398 Pacific Center Ct., San Diego,
CA 92121 (“Nanogen”); and APPLERA CORPORATION, through
its Applied Biosystems group, with offices at 850 Lincoln Centre
Drive, Foster City, CA 94404 (“ABG”). Each of Epoch and
ABG is individually referred to as a “Party” and,
collectively, as “Parties”.
RECITALS
WHEREAS, Epoch and ABG are parties
to that certain Second Amended and Restated Collaboration, License
and Supply Agreement (the “Collaboration Agreement”)
dated August 17, 2000 (the “Effective Date”), as
amended by that certain First Side Agreement dated October 31,
2001, and that certain Amendment No. 1 to Second Amended and
Restated Collaboration, License and Supply Agreement dated
July 26, 2002 (the “First Amendment, and collectively
with the First Side Agreement and the Collaboration Agreement, the
“MGB Agreement”); and
WHEREAS, Epoch and ABG have entered
into that certain Quencher License and Supply Agreement dated
September 2, 2003, as amended (the “Quencher
Agreement”), and
WHEREAS, the Parties now wish to
amend the MGB Agreement pursuant to the terms and conditions of
this 2 nd Amendment.
NOW, THEREFORE, in consideration of
the foregoing and other good and valuable considerations, the
sufficiency of which is hereby acknowledged, the Parties agree as
follows.
AGREEMENT
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1.
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Article II of
the MGB Agreement is hereby amended to add the following
sections:
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A.
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2.36
“Control” and its cognates means in-licensed with the
ability to grant sublicenses.
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B.
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2.37 “MGB
Intermediates Manufacturing Know-How” means all know-how,
technical information, trade secrets, data, technology, software
and protocols that are owned or Controlled by Epoch, as of the
Effective Date or thereafter, relating to the manufacture of MGB
Intermediates including, but not limited to, the information set
forth in Exhibit D attached hereto and incorporated
herein.
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C.
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2.38
“Modified Base Know-How” means all know-how, technical
information, trade secrets, data, technology, software and
protocols owned or Controlled by Epoch, as of the Effective Date or
thereafter, relating to Modified Bases or the manufacture of
Modified Bases.
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2.
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Each Section of
Article II of the MGB Agreement set forth below is hereby amended
as follows:
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A.
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2.05
“Licensed Patents” means (1) U.S. Patent
No. 5,801,155 titled Covalently Linked Oligonucleotide Minor
Groove Binder Conjugates, issued September 1, 1998;
(2) U.S. Patent No. 6,084,102 titled Covalently Linked
Oligonucleotide Minor Groove Binder Conjugates, issued July 4,
2000; (3) any patent covering Collaboration Intellectual
Property; and (4) any patent which is owned or Controlled by
Epoch as of the Effective Date or thereafter covering the making,
using, or selling of one or more of the following (alone or in
combination): (a) a minor groove binding moiety, (b) an
MGB Intermediate, (c) a product comprising an oligonucleotide
having a minor-groove binding moiety covalently attached thereto,
with or without a fluorescent label and/or a fluorescence quencher,
(d) a fluorescence quencher (with or without a fluorescent
label), (e) fluorescent label (with or without a fluorescence
quencher) and (f) Modified Bases (whether or not contained the
products in (a) through (e) are part of an
oligonucleotide).
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B.
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2.06
“Related Patents” means all patents or patent
applications owned, held, or Controlled, in whole or in part by
Epoch that: (a) disclose and/or claim substantially the same
subject matter as the Licensed Patents; (b) disclose and/or
claim improvements to inventions disclosed or claimed in a Licensed
Patent and require rights under the Licensed Patent to exploit such
improvements; (c) claim priority to any of the Licensed
Patents, including but not limited to continuation applications and
patents, continuation-in-part applications and patents, divisional
applications and patents, reexamination applications and patents,
reissue applications and patents, and continuing prosecution
applications and patents; (d) are a parent or sibling of the
Licensed Patents, or (e) are foreign equivalents of a Licensed
Patent or any patent or patent application in (a) through
(d) above.
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C.
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2.13
“Valid Claim” means a claim of an issued and unexpired
Licensed Patent or Related Patent (or any pending patent
application, that has not been held unpatentable in a final
decision by an appropriate administrative agency, which patent
application is within the Related Patents but limited to claims
thereof that claim minor groove binders or MGB Intermediates as
compositions of matter or methods of using such minor groove
binders or MGB Intermediates) that has not been held permanently
invalid or otherwise unenforceable by a court or other
administrative agency of competent jurisdiction in an unappealable
decision or a decision not appealed within the time allowed for
appeal.
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D.
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2.17
“Non-Exclusive Licensed Field” means all fields outside
of the 5’-Nuclease Assay Field and outside of the Human In
Vitro Diagnostics Field including, without limitation, the
following: (1) use of MGB Oligonuclotides as ligation probes
in an
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2
oligonuclotide ligation assay,
generally as described in U.S. Patent No. 4,883,750; (2) use of MGB
Oligonuclotides in an assay employing a [***]; (3) use of MGB
Oligonuclotides as primers in a primer extension reaction,
including but not limited to a PCR reaction or a DNA sequencing
reaction; and (4) use of MGB Oligonuclotides in the Real-Time
Nucleic Acid Monitoring Field, to the extent that (1), (2), (3) and
(4) are practiced outside of the Exclusive Licensed
Field.
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E.
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2.32
“Modified Base” (or in the plural, “Modified
Bases”) means any modified nucleotide, including but not
limited to pyrazolopyrimidine (ppn) nucleotide analogs, e.g., ppA
and ppG analogs and any other analogs of A, T, G, or C nucleotides,
including methods for making or using such modified
nucleotides.
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3.
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Section 4.01 of the MGB Agreement is hereby
amended to read in its entirety as follows:
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4.01 Exclusive License . As
of the Effective Date, Epoch hereby grants to ABG a world-wide,
exclusive license under Licensed Patents, Related Patents, MGB
Intermediates Manufacturing Know-How, Modified Base Know-How, and
Licensed Know-How to make, have made, use, offer to sell, sell and
import Licensed Products in the Exclusive Licensed Field (but not
the right to sell Modified Bases or MGB Intermediates that are not
incorporated into oligonucleotides).
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4.
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Section 4.02 of the MGB Agreement is hereby
amended to read in its entirety as follows:
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4.02
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Non-Exclusive Licenses .
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(a) MGB Probe Non-Exclusive License.
As of the Effective Date, Epoch hereby grants to ABG a world-wide,
non-exclusive license under Licensed Patents, Related Patents, MGB
Intermediates Manufacturing Know-How, Modified Base Know-How and
Licensed Know-How to make, have made, use, offer to sell, sell and
import Licensed Products in the Non-Exclusive Licensed Field (but
not the right to sell Modified Bases or MGB Intermediates that are
not incorporated into oligonucleotides).
(b) HIVD Field Customer
Licenses . Epoch shall grant to ABG’s customers, whether
referred by ABG, identified to Epoch by name, or otherwise
presenting evidence of having purchased Licensed Products from ABG
(“Customers”) a non-exclusive, world-wide,
royalty-bearing license to use Licensed Products purchased from ABG
in the HIVD Field (each, an “HIVD Field Customer
License”). Such royalty shall be [***]percent ([***]%) of
Customer Net Revenues from providing services in the HIVD Field.
“Net Revenues” shall mean all moneys received by a
Customer, less refunds, for or on account of laboratory services
provided using Licensed Products. Without limiting the foregoing,
at ABG
