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IN THE UNITED STATES DISTRICT COURT

FOR THE DISTRICT OF DELAWARE

CORNELL UNIVERSITY, CORNELL
RESEARCH FOUNDATION, INC., LIFE
TECHNOLOGIES CORPORATION AND
APPLIED BIOSYSTEMS, LLC,

Plaintiffs,

v.

ILLUMINA, INC.,

Defendant.

C.A. No. 10-433-LPS

DEMAND FOR JURY TRIAL

FIRST AMENDED COMPLAINT

Plaintiffs Cornell University and Cornell Research Foundation, Inc. (collectively,

“Cornell”), and Life Technologies Corporation and Applied Biosystems, LLC (collectively,

“Life Technologies”) allege as follows:

I.

NATURE OF THE ACTION

1.

This is an action arising under the patent laws of the United States (35 U.S.C.

§271 et seq.) based upon infringement by Defendant Illumina, Inc. (“Illumina”) of patents owned

by Cornell. Exclusive rights in and to each of the patents-in-suit have been granted to Life

Technologies. Plaintiffs seek a preliminary injunction, damages for Defendant’s infringement,

and a permanent injunction restraining Defendant from further infringement.

4851-4986-9578.1

II.

THE PARTIES

2.

Plaintiff Cornell University is a private university located in Ithaca, New York.

Plaintiff Cornell Research Foundation, Inc. is a New York non-profit corporation, having its

principal place of business at 395 Pine Tree Road, Suite 310, Ithaca, New York 14850. Cornell

Research Foundation, Inc. is a wholly owned subsidiary of Cornell University, whose mission is

to manage the intellectual property invented by Cornell University employees under Cornell

University’s Inventions and Related Property Rights Policy, including obtaining patent,

trademark or copyright protection where appropriate and licensing intellectual property for

commercial development and use.

3.

Plaintiff Life Technologies Corporation is a Delaware corporation with a principal

place of business at 5791 Van Allen Way, Carlsbad, California 92008. Plaintiff Applied

Biosystems, LLC is a wholly-owned subsidiary of Life Technologies Corporation. Life

Technologies serves the life science industry and research community by developing and

marketing instrument-based systems, consumables, software, and services. Its customers use

these tools to analyze nucleic acids (DNA and RNA), small molecules, and proteins to make

scientific discoveries and develop new pharmaceuticals. Life Technologies’ products also serve

the needs of some markets outside of life science research, in applied markets, such as the fields

of: human identity testing (forensic and paternity testing); “biosecurity,” which refers to products

needed in response to the threat of biological terrorism and other malicious, accidental, and

natural biological dangers; and quality and safety testing, for example in the food and drug

environment.

4851-4986-9578.1

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4.

Upon information and belief, Illumina, Inc., is a Delaware corporation, with its

principal place of business located at 9885 Towne Centre Drive, San Diego, CA 92121-1975.

III.

JURISDICTION AND VENUE

5.

This is an action for patent infringement arising under the patent laws of the

United States, Title 35 of the United States Code.

6.

7.

This Court has subject matter jurisdiction under 28 U.S.C. § 1331 and 1338(a).

Venue is proper in this judicial district under 28 U.S.C. §§ 1391 and 1400(b)

because, upon information and belief, Illumina has, among other things, committed infringing

acts in this district and does business in this district generally.

IV.

BACKGROUND

8.

United States Patent No. 6,797,470 (“the ‘470 Patent”), entitled “Detection of

Nucleic Acid Sequence Differences Using Coupled Ligase Detection and Polymerase Chain

Reactions,” was issued by the United States Patent and Trademark Office (“PTO”) on September

28, 2004. A copy of the ‘470 Patent is attached hereto as Exhibit A.

9.

The ‘470 Patent issued in the names of Francis Barany, Matthew Lubin, George

Barany, and Robert P. Hammer.

10.

Cornell is the assignee of all right, title and interest in and to the ‘470 Patent. Life

Technologies is the exclusive licensee of the ‘470 Patent.

11.

United States Patent No. 7,083,917 (“the ‘917 Patent”), entitled “Detection Of

Nucleic Acid Sequence Differences Using The Ligase Detection Reaction With Addressable

4851-4986-9578.1

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Arrays,” was issued by the PTO on August 1, 2006. A copy of the ‘917 Patent is attached hereto

as Exhibit B.

12.

The ‘917 Patent issued in the names of Francis Barany, George Barany, Robert P.

Hammer, Maria Kempe, Herman Blok, and Monib Zirvi, and contains claims to instruments.

13.

Cornell is the assignee of all right, title and interest in and to the ‘917 Patent. Life

Technologies is the exclusive licensee of the ‘917 Patent.

14.

United States Patent No. 7,166,434 (“the ‘434 Patent”), entitled “Detection of

Nucleic Acid Sequence Differences Using Coupled Ligase Detection and Polymerase Chain

Reactions,” was issued by the PTO on January 23, 2007. A copy of the ‘434 Patent is attached

hereto as Exhibit C.

15.

The ‘434 Patent issued in the names of Francis Barany, Matthew Lubin, George

Barany, and Robert P. Hammer.

16.

Cornell is the assignee of all right, title and interest in and to the ‘434 Patent. Life

Technologies is the exclusive licensee of the ‘434 Patent.

17.

United States Patent No. 7,312,039 (“the ‘039 Patent”), entitled “Detection of

Nucleic Acid Sequence Differences Using Coupled Ligase Detection and Polymerase Chain

Reactions,” was issued by the PTO on December 25, 2007. A copy of the ‘039 Patent is attached

hereto as Exhibit D.

18.

The ‘039 Patent issued in the names of Francis Barany, Matthew Lubin, George

Barany, and Robert P. Hammer.

19.

Cornell is the assignee of all right, title and interest in and to the ‘039 Patent. Life

Technologies is the exclusive licensee of the ‘039 Patent.

4851-4986-9578.1

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20.

United States Patent No. 7,320,865 (“the ‘865 Patent”), entitled “Detection of

Nucleic Acid Sequence Differences Using Coupled Ligase Detection and Polymerase Chain

Reactions,” was issued by the PTO on January 22, 2008. A copy of the ‘865 Patent is attached

hereto as Exhibit E.

21.

The ‘865 Patent issued in the names of Francis Barany, Matthew Lubin, George

Barany, and Robert P. Hammer.

22.

Cornell is the assignee of all right, title and interest in and to the ‘865 Patent. Life

Technologies is the exclusive licensee of the ‘865 Patent.

23.

United States Patent No. 7,332,285 (“the ‘285 Patent”), entitled “Detection of

Nucleic Acid Sequence Differences Using Coupled Ligase Detection and Polymerase Chain

Reactions,” was issued by the PTO on February 19, 2008. A copy of the ‘285 Patent is attached

hereto as Exhibit F.

24.

The ‘285 Patent issued in the names of Francis Barany, Matthew Lubin, George

Barany, and Robert P. Hammer.

25.

Cornell is the assignee of all right, title and interest in and to the ‘285 Patent. Life

Technologies is the exclusive licensee of the ‘285 Patent.

26.

United States Patent No. 7,364,858 (“the ‘858 Patent”), entitled “Detection of

Nucleic Acid Sequence Differences Using Coupled Ligase Detection and Polymerase Chain

Reactions,” was issued by the PTO on April 29, 2008. A copy of the ‘858 Patent is attached

hereto as Exhibit G.

27.

The ‘858 Patent issued in the names of Francis Barany, Matthew Lubin, George

Barany, and Robert P. Hammer.

4851-4986-9578.1

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28.

Cornell is the assignee of all right, title and interest in and to the ‘858 Patent. Life

Technologies is the exclusive licensee of the ‘858 Patent.

29.

United States Patent No. 7,429,453 (“the ‘453 Patent”), entitled “Detection of

Nucleic Acid Sequence Differences Using Coupled Ligase Detection and Polymerase Chain

Reactions,” was issued by the PTO on September 30, 2008. A copy of the ‘453 Patent is

attached hereto as Exhibit H.

30.

The ‘453 Patent issued in the names of Francis Barany, Matthew Lubin, George

Barany, and Robert P. Hammer.

31.

Cornell is the assignee of all right, title and interest in and to the ‘453 Patent. Life

Technologies is the exclusive licensee of the ‘453 Patent.

32.

United States Patent No. 7,892,746 (“the ‘746 Patent”), entitled “Detection Of

Nucleic Acid Sequence Differences Using The Ligase Detection Reaction With Addressable

Arrays,” was issued by the PTO on February 22, 2011. A copy of the ‘746 Patent is attached

hereto as Exhibit I.

33.

The ‘746 Patent issued in the names of Francis Barany, George Barany, Robert P.

Hammer, Maria Kempe, Herman Blok, and Monib Zirvi.

34.

Cornell is the assignee of all right, title and interest in and to the ‘746 Patent. Life

Technologies is the exclusive licensee of the ‘746 Patent.

35.

United States Patent No. 7,892,747 (“the ‘747 Patent”), entitled “Detection Of

Nucleic Acid Sequence Differences Using The Ligase Detection Reaction With Addressable

Arrays,” was issued by the PTO on February 22, 2011. A copy of the ‘747 Patent is attached

hereto as Exhibit J.

4851-4986-9578.1

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36.

The ‘747 Patent issued in the names of Francis Barany, George Barany, Robert P.

Hammer, Maria Kempe, Herman Blok, and Monib Zirvi.

37.

Cornell is the assignee of all right, title and interest in and to the ‘747 Patent. Life

Technologies is the exclusive licensee of the ‘747 Patent.

38.

United States Patent No. 7,893,233 (“the ‘233 Patent”), entitled “Detection Of

Nucleic Acid Sequence Differences Using The Ligase Detection Reaction With Addressable

Arrays,” was issued by the PTO on February 22, 2011. A copy of the ‘746 Patent is attached

hereto as Exhibit K.

39.

The ‘233 Patent issued in the names of Francis Barany, George Barany, Robert P.

Hammer, Maria Kempe, Herman Blok, and Monib Zirvi.

40.

Cornell is the assignee of all right, title and interest in and to the ‘233 Patent. Life

Technologies is the exclusive licensee of the ‘233 Patent.

41.

Defendant’s genetic analysis products and services infringe at least one claim of

each of the ‘470, ‘917, ‘434, ‘039, ‘865, ‘285, ‘858, ‘453, ‘746, ‘747 and ‘233 Patents (the

“Patents-in-Suit”).

42. With the exception of the ‘917 and ‘233 Patents, which contains claims to

instruments, all of the other Patents-In-Suit contain claims to polymerase chain reaction (“PCR”)

methods.

4851-4986-9578.1

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V.

FIRST CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘470 PATENT)

Plaintiffs incorporate ¶¶ 1-42 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

43.

44.

reagents, kits and services for genetic analysis, including detection of single nucleotide

polymorphisms (“SNPs”), within the United States, thereby infringing, both directly and

indirectly, at least one claim of the ‘470 Patent. Illumina’s infringing activities include, without

limitation, the making, using, selling and offering to sell instruments, reagents and kits to

perform the Illumina GoldenGate Genotyping Assay and the Illumina “cDNA-mediated

Annealing, Selection, Extension and Ligation Assay” (the “DASL Assay”) and services using the

Illumina GoldenGate Genotyping Assay and the Illumina DASL Assay. The GoldenGate

Genotyping Assay and DASL Assay detect nucleic acid sequence differences using an improved

PCR method that includes a ligase detection reaction, in a manner which infringes one or more

claims of the ‘470 Patent.

45.

Illumina provides to its customers instructions for the use of Illumina instruments,

reagents and kits to perform the GoldenGate Genotyping Assay and DASL Assay. For example,

these instructions recite the steps of: providing a nucleic acid sample; adding oligonucleotide

probe sets designed to detect specific SNP loci; allowing said oligonucleotide probes to

hybridize to the sample nucleic acid and ligation of said probes; amplifying said ligated

oligonucleotide probes using PCR; hybridizing amplification products to Illumina’s Sentrix

Array Matrix, BeadChip or VeraCode beads; and detecting said products using Illumina’s

BeadStation, BeadArray Reader, iScan, HiScanSQ, BeadLab or BeadXpress Reader.

4851-4986-9578.1

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VI.

SECOND CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘917 PATENT)

Plaintiffs incorporate ¶¶ 1-45 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

46.

47.

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘917 Patent.

Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments for the detection of nucleic acid sequence differences using

addressable arrays. The Sentrix Array Matrix, BeadChip, VeraCode beads, BeadStation,

BeadArray Reader, iScan, HiScanSQ, BeadLab and BeadXpress Reader are instruments for the

detection of nucleic acid sequence differences which infringe one or more claims of the ‘917

Patent.

48.

49.

VII.

THIRD CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘434 PATENT)

Plaintiffs incorporate ¶¶ 1-47 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘434 Patent.

Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments, reagents and kits to perform the Illumina GoldenGate Genotyping

Assay and the DASL Assay and services using the Illumina GoldenGate Genotyping Assay and

4851-4986-9578.1

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the Illumina DASL Assay. The GoldenGate Genotyping Assay and DASL Assay detect nucleic

acid sequence differences using an improved PCR method that includes a ligase detection

reaction, in a manner which infringes one or more claims of the ‘434 Patent.

VIII.

FOURTH CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘039 PATENT)

Plaintiffs incorporate ¶¶ 1-49 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

50.

51.

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘039 Patent.

Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments, reagents and kits to perform the Illumina GoldenGate Genotyping

Assay and the Illumina DASL Assay and services using the Illumina GoldenGate Genotyping

Assay and the Illumina DASL Assay. The GoldenGate Genotyping Assay and DASL Assay

detect nucleic acid sequence differences using an improved PCR method that includes a ligase

detection reaction, in a manner which infringes one or more claims of the ‘039 Patent.

IX.

FIFTH CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘865 PATENT)

Plaintiffs incorporate ¶¶ 1-51 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

52.

53.

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘865 Patent.

4851-4986-9578.1

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Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments, reagents and kits to perform the Illumina GoldenGate Genotyping

Assay and the Illumina DASL Assay and services using the Illumina GoldenGate Genotyping

Assay and the Illumina DASL Assay. The GoldenGate Genotyping Assay and DASL Assay

detect nucleic acid sequence differences using an improved PCR method that includes a ligase

detection reaction, in a manner which infringes one or more claims of the ‘865 Patent.

X.

SIXTH CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘285 PATENT)

Plaintiffs incorporate ¶¶ 1-53 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

54.

55.

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘285 Patent.

Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments, reagents and kits to perform the Illumina GoldenGate Genotyping

Assay and the Illumina DASL Assay and services using the Illumina GoldenGate Genotyping

Assay and the Illumina DASL Assay. The GoldenGate Genotyping Assay and DASL Assay

detect nucleic acid sequence differences using an improved PCR method that includes a ligase

detection reaction, in a manner which infringes one or more claims of the ‘285 Patent.

XI.

SEVENTH CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘858 PATENT)

56.

Plaintiffs incorporate ¶¶ 1-55 of this Complaint here.

4851-4986-9578.1

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57.

Illumina has been and is making, using, selling, and offering to sell instruments,

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘858 Patent.

Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments, reagents and kits to perform the Illumina GoldenGate Genotyping

Assay and the Illumina DASL Assay and services using the Illumina GoldenGate Genotyping

Assay and the Illumina DASL Assay. The GoldenGate Genotyping Assay and DASL Assay

detect nucleic acid sequence differences using an improved PCR method that includes a ligase

detection reaction, in a manner which infringes one or more claims of the ‘858 Patent.

XII.

EIGHTH CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘453 PATENT)

Plaintiffs incorporate ¶¶ 1-57 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

58.

59.

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘453 Patent.

Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments, reagents, kits and services to perform the Illumina GoldenGate

Genotyping Assay and the Illumina DASL Assay and services using the Illumina GoldenGate

Genotyping Assay and the Illumina DASL Assay. The GoldenGate Genotyping Assay and

DASL Assay detect nucleic acid sequence differences using an improved PCR method that

includes a ligase detection reaction, in a manner which infringes one or more claims of the ‘453

Patent.

4851-4986-9578.1

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XIII.

NINTH CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘746 PATENT)

Plaintiffs incorporate ¶¶ 1-59 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

60.

61.

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘746 Patent.

Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments for the detection of nucleic acid sequences. Illumina’s Array Matrix,

BeadChip, VeraCode beads, BeadStation, BeadArray Reader, iScan, HiScan, HiScanSQ,

BeadLab and BeadXpress Reader are instruments for the detection of nucleic acid sequences

which infringe one or more claims of the ‘746 Patent.

XIV.

TENTH CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘747 PATENT)

Plaintiffs incorporate ¶¶ 1-61 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

62.

63.

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘747 Patent.

Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments for the detection of nucleic acid sequences. Illumina’s BeadChip,

BeadStation, BeadArray Reader, iScan, HiScan, HiScanSQ, and BeadLab are instruments for the

detection of nucleic acid sequences which infringe one or more claims of the ‘747 Patent.

4851-4986-9578.1

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64.

Illumina provides to its customers instructions for the use of Illumina instruments,

reagents and kits to perform Illumina Infinium Assays (including the Infinium II Whole-Genome

Genotyping Assay, Infinium HD Assay and Infinium DNA Analysis Assay). For example, these

instructions recite the steps of: providing a nucleic acid sample; fragmenting said nucleic acid

sample; hybridizing said fragments to oligonucleotide probes of Illumina’s BeadChip; labeling

said oligonucleotide probes that have hybridized to said fragments; and detecting and

distinguishing said labeled probes using Illumina’s BeadStation, BeadArray Reader, iScan,

HiScan, HiScanSQ, or BeadLab.

XV.

ELEVENTH CLAIM FOR RELIEF

(INFRINGEMENT OF THE ‘233 PATENT)

Plaintiffs incorporate ¶¶ 1-64 of this Complaint here.

Illumina has been and is making, using, selling, and offering to sell instruments,

65.

66.

reagents, kits and services for genetic analysis, including SNP detection, within the United

States, thereby infringing, both directly and indirectly, at least one claim of the ‘233 Patent.

Illumina’s infringing activities include, without limitation, the making, using, selling and

offering to sell instruments for the detection of nucleic acid sequences. Illumina’s Array Matrix,

BeadChip, VeraCode beads, BeadStation, BeadArray Reader, iScan, HiScan, HiScanSQ,

BeadLab and BeadXpress Reader are instruments for the detection of nucleic acid sequences

which infringe one or more claims of the ‘233 Patent.

XVI.

PRAYER FOR RELIEF

1. That Illumina be adjudged to have infringed the Patents-in-Suit;

4851-4986-9578.1

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2. That Illumina, its officers, agents, servants, employees, attorneys, and those persons in

active concert or participation with any of them, be preliminarily and permanently

restrained and enjoined from infringing in any manner the Patents-in-Suit;

3. An accounting for damages by virtue of Illumina’s infringement of the Patents-in-Suit;

4. An assessment of pre-judgment and post-judgment interest and costs against Illumina,

together with an award of such interest and costs, in accordance with 35 U.S.C. § 284;

and

5. That Plaintiffs have such other and further relief as this Court may deem just and proper.

DATED: August 19, 2011

YOUNG CONAWAY STARGATT &
TAYLOR, LLP

/s/ Karen E. Keller
_________________________________
Adam W. Poff (No. 3390)
Karen E. Keller (No. 4489)
The Brandywine Building
1000 West Street, 17th Floor
Wilmington, DE 19801
(302) 571-6600
[email protected]

OF COUNSEL:

Francis M. Wikstrom (UT Bar 3462)
Kristine E. Johnson (UT Bar 7190)
Parsons Behle & Latimer
201 South Main, #1800
Salt Lake City, UT 84111
(801) 532-1234
[email protected]
[email protected]

Attorneys for Plaintiffs

4851-4986-9578.1

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Rip Finst (admitted pro hac vice)
Kurtis D. MacFerrin (admitted pro hac vice)
Life Technologies Corporation
5791 Van Allen Way
Carlsbad, CA 92008
(760) 603-7200

Attorney for Life Technologies Corp. &
Applied Biosystems, LLC

4851-4986-9578.1

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CERTIFICATE OF SERVICE

I, Karen E. Keller, Esquire, hereby certify that on August 19, 2011, I caused to be

electronically filed a copy of the foregoing document with the Clerk of the Court using

CM/ECF, which will send notification that such filing is available for viewing and

downloading to the following counsel of record:

Steven J. Balick, Esquire
Lauren E. Maguire, Esquire
Caroline Hong, Esquire
Andrew Colin Mayo, Esquire
Ashby & Geddes
500 Delaware Avenue
P.O. Box 1150
Wilmington, DE 19899
[email protected]
[email protected]
[email protected]
[email protected]


I further certify that on August 19, 2011, I caused a copy of the foregoing


document to be served by e-mail on the above-listed counsel and on the following non-

registered participants:

David G. Hanson, Esquire
Amy L. Lindner, Esquire
Reinhart Boerner Van Deuren
1000 North Water Street, Suite 2100
Milwaukee, WI 53202
[email protected]
[email protected]




























YCST01:10152207.1





























YOUNG CONAWAY STARGATT
& TAYLOR, LLP
/s/ Karen E. Keller
Adam W. Poff (No. 3990)
Karen E. Keller (No. 4489)
The Brandywine Building
1000 West Street
Wilmington, Delaware 19801
(302) 571-6600
[email protected]
Attorney for Plaintiffs



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