Paper No. ______
`Filed July 7, 2014
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`Filed on behalf of: Sequenom, Inc.
`
`By: Michael J. Wise (mwise@perkinscoie.com)
`
`Patrick D. Morris (pmorris@perkinscoie.com)
`Perkins Coie LLP
`1888 Century Park East, Suite 1700
`Los Angeles, CA 90067-1721
`Telephone: (310) 788-3210
`Facsimile: (310) 788-3399
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`UNITED STATES PATENT AND TRADEMARK OFFICE
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`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
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`
`
`SEQUENOM, INC.
`Petitioner
`
`v.
`
`THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR
`UNIVERSITY
`Patent Owner
`
`
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`
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`
`
`SEQUENOM LISTING OF EXHIBITS AS OF JULY 7, 2014
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`
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`
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`Case IPR2013-00390
`Patent 8,195,415
`
`
`
`
`Filed July 7, 2014
`
`
`
`
`Filed on behalf of: Sequenom, Inc.
`
`By: Michael J. Wise (mwise@perkinscoie.com)
`
`Patrick D. Morris (pmorris@perkinscoie.com)
`Perkins Coie LLP
`1888 Century Park East, Suite 1700
`Los Angeles, CA 90067-1721
`Telephone: (310) 788-3210
`Facsimile: (310) 788-3399
`
`
`
`
`
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`
`
`
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`
`
`
`
`
`SEQUENOM, INC.
`Petitioner
`
`v.
`
`THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR
`UNIVERSITY
`Patent Owner
`
`
`
`
`
`
`
`SEQUENOM LISTING OF EXHIBITS AS OF JULY 7, 2014
`
`
`
`
`
`
`
`
`
`
`
`
`Case IPR2013-00390
`Patent 8,195,415
`
`
`
`
`
`IPR2013-00390
`Patent 8,195,415
`
`Exhibit
`
`Number
`
`Description
`
`1001
`
`1002
`
`1003
`
`1004
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`1005
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`1006
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`1007
`
`1008
`
`1009
`
`1010
`
`1011
`
`1012
`
`1013
`
`1014
`
`1015-1085
`
`1086
`
`U.S. Patent No. 8,195,415 to Fan and Quake.
`U.S. Patent Application Publication No. 2009/0029377 to Lo
`et al. ("Lo II").
`U.S. Provisional Patent Application No. 60/951,438 to Lo et
`al. ("Lo I").
`U.S. Patent Application Publication No. 2005/0221341 to
`Shimkets et al. ("Shimkets").
`Tian-Li Wang et al., "Digital karyotyping," Proc. Natl. Acad.
`Sci. USA, 99(25):16156-61 ("Wang").
`LaDeana W. Hillier, "Whole-genome sequencing and variant
`discovery in C. elegans," Nature Methods, 5(2):183-88 (and
`on-line supplementary information) ("Hillier").
`Juliane C. Dohm et al., "Substantial biases in ultra-short read
`data sets from high-throughput DNA sequencing," Nucleic
`Acids Res., 36(16):e105 ("Dohm").
`U.S. Patent No. 7,888,017 to Quake and Fan ("Quake")
`Andrew D. Smith et al., "Using quality scores and longer
`reads improves accuracy of Solexa read mapping," BMC
`Bioinformatics, 9:128 ("Smith").
`Declaration of Dr. Stacey Bolk Gabriel dated June 26, 2013.
`
`Curriculum Vitae of Dr. Stacey Bolk Gabriel.
`
`Affidavit of Michael J. Malecek dated January 13, 2014.
`Transcript of telephone conference call held on January 6,
`2014, in Case IPR2013-00390.
`Transcript of telephone conference call held on February 21,
`2014, in Case IPR2013-00390.
`Not used
`
`Declaration of J. Chris Detter, Ph.D. dated July 31, 2013 from
`Interference Nos. 105,920, 105,923, and 105,924
`(submitted by Party Quake as Exhibit 2049 in Interference
`Nos. 105,920, 105,923, and 105,924)
`
`
`
`-1-
`
`
`
`IPR2013-00390
`Patent 8,195,415
`(referenced as Exhibit 2049 in Deposition Transcript of John
`Christopher Detter, Ph.D. dated July 1, 2014 (Exhibit 1090,
`see below))
`Declaration of J. Chris Detter, Ph.D. dated July 31, 2013 from
`Interference No. 105,922
`(submitted by Party Quake as Exhibit 2050 in Interference
`Nos. 105,920, 105,922, 105,923, and 105,924)
`Decision on Motions dated April 7, 2014 in Interference
`105,922 (Paper 101)
`Deposition Transcript of Hei-Mun Christina Fan, Ph.D. dated
`June 25, 2014
`Deposition Transcript of John Christopher Detter, Ph.D. dated
`July 1, 2014
`(internal references to Exhibit 2049 refer to Exhibit 1086 in
`the present proceeding (see above))
`Elliott H. Margulies et al., "Comparative sequencing provides
`insights about the structure and conservation of marsupial and
`monotreme genomes," Proc Natl Acad Sci USA, 102(9):3354-
`3359 (2005) ("Margulies")
`Eldar Giladi et al., "SST: an algorithm for finding near-exact
`sequence matches in time proportional to the logarithm of the
`database size," Bioinformatics, 18(6):873-879 (2002)
`("Giladi")
`Mario A. Fares et al., "A sliding window-based method to
`detect selective constraints in protein-coding genes and its
`application to RNA viruses," J Mol Evol 55:509-521 (2002)
`("Fares")
`Anthony G. Brickner et al., "Genomic sequence comparison of
`the human and mouse adenosine deaminase gene regions,"
`Mamm Genome 10(2):95-101 (1999) ("Brickner")
`Heng Li et al., "Mapping short DNA sequencing reads and
`calling variants using mapping quality scores," Genome
`Research, 18(11):1851-1858 (2008) ("Li")
`Not used
`
`Fan Priority Statement dated July 31, 2013 in Interference No.
`105,922 (Paper 24)
`Eric S. Lander et al., "Initial sequencing and analysis of the
`human genome," Nature 409:860-921 (2001) ("Lander")
`
`-2-
`
`1087
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`1088
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`1089
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`1090
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`1091
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`1092
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`1093
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`1094
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`1095
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`1096-1099
`
`1100
`
`1101
`
`
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`
`
`IPR2013-00390
`Patent 8,195,415
`
`1102-1104
`
`1105
`
`Not used
`
`Supplementary Materials from Lander et al. Nature 409:860-
`921 (2001)
`
`
`
`Dated: July 7, 2014
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`
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`By:
`
`
`
`Respectfully submitted,
`Perkins Coie LLP
`
`/Michael J. Wise/
`Michael J. Wise, Reg. No. 34,047
`Patrick D. Morris, Reg. No. 53,351
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`-3-
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`IPR2013-00390
`Patent 8,195,415
`
`CERTIFICATE OF SERVICE
`I certify that a true and correct copy of the foregoing SEQUENOM
`
`LISTING OF EXHIBITS AS OF JULY 7, 2014 and EXHIBITS 1086-1095,
`
`1100, 1101, AND 1105 were served electronically via email on the Patent Owner
`through its attorneys of record on this 7th day of July, 2014 as follows:
`
`R. Danny Huntington, Esq. (dhuntington@rfem.com)
`Sharon E. Crane, Ph.D., Esq. (scrane@rfem.com)
`Rothwell, Figg, Ernst & Manbeck, PC
`607 14th Street, NW, Suite 800
`Washington, DC 20005
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`/Patrick D. Morris/
`Patrick D. Morris
`Registration No. 53,351
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