Claim Construction: Foundation Medicine, Inc. v. Guardant Health, Inc.(FMI)

03-06-2017 – The parties have filed their proposed claim constructions in Foundation Medicine, Inc. v. Guardant Health, Inc.

 

Case 2:16-cv-00523-JRG-RSP   Document 65-1   Filed 03/02/17   Page 1 of 2 PageID #:  739 EXHIBIT A

FOUNDATION MEDICINE, INC. v.

GUARDANT HEALTH, INC.,

E.D. Texas No. 2:16-cv-00523-JRG-RSP

 

AGREED CLAIM CONSTRUCTIONS

United States Patent No. 9,340,830

Term Agreed Construction
preamble

Claims 1 and 65

The parties agree that the preamble to claims 1 and 65 is limiting.
sample

Claims 1, 26, 65

“a collection of similar cells obtained from a tissue, or circulating cells, of a subject or patient”
tumor cells “cells possessing characteristics typical of cancer-causing cells, such as uncontrolled proliferation, immortality, metastatic potential, rapid growth and proliferation rate, and certain characteristic morphological features”
tumor sample

Claims 1, 26, 65

“a ‘sample’ that includes ‘tumor cells’”
library

Claims 1, 26, 65

“a collection of members”
tumor member

Claims 1, 65

Claims 1, 65

“a member having sequence from a tumor cell”
member “a nucleic acid molecule that is in a library”

 

 

Case 2:16-cv-00523-JRG-RSP   Document 65-1   Filed 03/02/17   Page 2 of 2 PageID #:  740

 

Term Agreed Construction
subgenomic interval

Claims 1, 8, 9, 15,

16, 19, 44, 45, 47,

48, 65, 72, 73, 83,

84

“a portion of a genomic sequence”
coverage depth

Claims 2, 66

“the average number of sequencing reads that align to a base or bases in  a reference nucleotide sequence”

 

 

2

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 1 of 19 PageID #:  741 Exhibit B

FOUNDATION MEDICINE, INC. v.

GUARDANT HEALTH, INC.,

E.D. Texas No. 2:16-cv-00523-JRG-RSP

 

PARTIES’ PROPOSED PRELIMINARY CLAIM CONSTRUCTIONS

United States Patent No. 9,340,830

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence[1] Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
bait set that selects a highlevel target

 

Claims 1, 65

Plaintiff contends that this term need not be construed because it is self-defined by claims 1 and 65. Intrinsic Evidence

Claims 1 and 65 (Col.

227:39-43; col. 239:1822)

‘830 patent col.

13:20-29; col.

67:66-col 68:5; col.

93:59-94:4; col.

110:29-42; col. 116:8-21; col.

133:41-48; col.

140:9-18; col.

238:3-8; col.

235:33-38

 

File History of U.S.

Patent App. No.

“bait set tailored to capture a target for which the deepest coverage is required” Intrinsic Evidence

 

Claims 1 and 65.

 

‘830 patent 2:33-37;

12:6-9; 13:20-29;

14:24-37; 66:64-67;

67:66-68:5; 69:1-

15; 93:59-94:4;

110:29-42; 116:8-

21;  133:41-48;  140:9-18; 238:3-8; 235:33-38.

 

File History, Notice of

Allowance, April 4, 2016;

Applicant’s Remarks,

December 16, 2015;

Declaration of Doran

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 2 of 19 PageID #:  742

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    13/339, 986,  Claim 14(e)(i); Response to Office Action pp. 26-28 (dated

Mar. 27, 2015)

 

Extrinsic Evidence

Testimony of Stacey Gabriel, Ph.D., concerning what this term would mean to one of ordinary skill in the art, in light of the term’s usage in claims 1 and 65 and in light of the specification of the ‘830 patent.

  Lipson, December 16, 2015.

 

Extrinsic Evidence

 

GUARD00035285.

 

Testimony of John Quackenbush, Ph.D., concerning what this term would mean to one of ordinary skill in the art in light of the specification and prosecution history.

 

References including intrinsic and extrinsic evidence cited in

Declaration of John

Quackenbush, Ph.D.

bait set that selects a midlevel target

 

Claims 1, 65

Plaintiff contends that this term need not be construed because it is self-defined by claims 1 and 65. Intrinsic Evidence

Claims 1 and 65 (Col.

227:44-48; col. 239:2327)

‘830 patent col.

13:30-40; col. 68:916; col. 94:5-17; col. 110:46-52; col.

116:25-31; col.

“bait set tailored to capture a target for which high coverage is required” Intrinsic Evidence

 

Claims 1 and 65

 

‘830 patent at 2:37-41;

12:11-14; 13:30-40;

14:24-27; 14:38-46; 67:15; 68:9-19; 69:1-4; 69:1524; 94:4-16; 110:46-52; 116:25-31; 238:9-14.

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 3 of 19 PageID #:  743

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    238:9-14

 

File History of U.S.

Patent App. No. 13/339,

986,  Claim 14(e)(ii);

Response to Office

Action pp. 26-28 (dated Mar. 27, 2015)

Extrinsic Evidence

Testimony of Stacey Gabriel, Ph.D. concerning what this term would mean to one of ordinary skill in the art, in light of the term’s usage in claims 1 and 65 and in light of the specification of the ‘830 patent.

   

File History, Notice of

Allowance, April 4, 2016;

Applicant’s Remarks,

December 16, 2015;

Declaration of Doran Lipson, December 16, 2015.

 

Extrinsic Evidence

 

GUARD00035285.

 

Testimony of John Quackenbush, Ph.D., concerning what this term would mean to one of ordinary skill in the art in light of the specification and prosecution history.

 

References including intrinsic and extrinsic evidence cited in

Declaration of John

Quackenbush, Ph.D.

bait set that selects a lowlevel target

 

Plaintiff contends that this term need not be construed because it is self-defined by claims 1 Intrinsic Evidence

Claims 1 and 65 (Col.

227:49-59; col. 239:28-

“bait set tailored to capture a target for which low-medium coverage is required” Intrinsic Evidence

 

Claims 1 and 65.

 

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 4 of 19 PageID #:  744

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
  and 65. 38)

‘830 patent col.

13:41-53; col.

68:20-34; col.

83:34-53; col.

94:18-30; col.

110:61-111:6; col.

116:40-52; col.

238:16-24

 

File History of U.S. Patent App. No.

13/339, 986,  Claim 14(e)(iii); Response to Office Action pp. 26-28 (dated

Mar. 27, 2015)

 

Extrinsic Evidence

Testimony of Stacey Gabriel, Ph.D. concerning what this term would mean to one of ordinary skill in the art, in light of the term’s usage in claims 1 and 65 and in light of the specification of the ‘830 patent.

  ‘830 patent at 2:42-48;

12:15-23; 13:41-53;

14:47-62; 67:6-15; 69:1-

4; 69:25-40; 68:20-34;

84:34-53; 94:18-30; 110:61-111:6; 116:40-52; 238:16-24.

 

File History, Notice of

Allowance, April 4, 2016;

Applicant’s Remarks,

December 16, 2015;

Declaration of Doran Lipson, December 16, 2015.

 

Extrinsic Evidence

 

GUARD00035285.

 

Testimony of John Quackenbush, Ph.D., concerning what this term would mean to one of ordinary skill in the art in light of the specification and prosecution history.

 

References including intrinsic and extrinsic

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 5 of 19 PageID #:  745

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
        evidence cited in

Declaration of John

Quackenbush, Ph.D.

efficiency for

selection

 

Claims 1, 2, 65,

66

Plaintiff contends that this term need not be construed because the longer term “wherein each bait set of said plurality has a unique preselected efficiency for selection for its target as compared with the other bait sets in the plurality” should be construed.

 

Intrinsic Evidence

Claims 1 and 65 (Col.

227:37-38; col. 227:6466; col. 239:16-17; col. 44-46)

‘830 patent col. 11:30-32; col. 11:58-63; col. 11:6612:3; col. 14:17-19; col. 14:21-16:63; col. 64:1727; col. 66: 22-29; col. 66:51-61; col. 68:61-63; col. 68:65-67; col. 69:17:11; col. 96:13-37

Extrinsic Evidence

Testimony of Stacey Gabriel, Ph.D. concerning what this term would mean to one of ordinary skill in the art, in light of the specification of the ‘830 patent

 

“level or depth of sequence coverage as it is adjusted to a target subgenomic interval(s)” Intrinsic Evidence

 

Claims 1 and 65.

 

‘830 patent at 11:25-35;

11:58-65; 11:67-12:3;

14:17-62; 14:63-15:54;

15:55-16:25; 16:26-54; 16:55-17:28; 64:1765:27; 66:22-29: 66:4756; 68:61-67; 69:1-6770:11; 71:3-11; 96:13-37.

 

Extrinsic Evidence

 

GUARD00035285.

 

Testimony of John Quackenbush, Ph.D., concerning what this term would mean to one of ordinary skill in the art in light of the specification and prosecution history.

 

References including intrinsic and extrinsic

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 6 of 19 PageID #:  746

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
        evidence cited in

Declaration of John

Quackenbush, Ph.D.

preselected

 

Claims 1,65

Plaintiff contends that this term need not be construed because it has a plain and ordinary meaning readily apparent to one of skill in the art. Intrinsic Evidence

Claims 1 and 65 (Col.

227:64-66; col. 239:4446)

‘830 patent col. 3:51-52; col. 11:30-32; col. 11:58col. 12:3; col. 14:17-62; col. 66:22-29; col. 66:5157;col. 68:61-63; col. 69:1-40.

Extrinsic Evidence

Testimony of Stacey Gabriel, Ph.D. concerning what this term would mean to one of ordinary skill in the art, in light of the specification of the

‘830 patent

“selected prior to performing the method” Intrinsic Evidence

 

Claims 1 and 65.

 

‘830 patent at 3:45-47;

3:51-53;  14:16-15:54;

16:28-17:21; 17:23-25;

31:4-15; 37:36-45; 42:6-

10; 44:6-29; 50:3-7;

66:22-29; 69:1-70:10; 71:3-11; 71:50-73:21;

77:47-52; 84:36-43; 87:1-

67; 96:13-37; 129:61130:15; 131:11-132:46; 134:28-46; 140:9-18.

 

File History, Notice of

Allowance, April 4, 2016;

Applicant’s Remarks,

December 16, 2015;

Declaration of Doran Lipson, December 16, 2015.

wherein each bait set of said plurality has a unique “wherein at least two bait sets have distinct preselected efficiencies for selecting their targets” Intrinsic Evidence

‘830 patent Fig 2.; col.

14:17-62; col. 66:51-59

Defendant contends that only the terms “preselected” and

“efficiency for selection”

Intrinsic Evidence

 

See above for

Defendant’s Intrinsic and

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 7 of 19 PageID #:  747

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
preselected efficiency for selection for its target as

compared with

the other bait sets

in the plurality

 

Claims 1 and 65

  col. 199:29-33; col. 199:66-col. 200:23; col. 227:37-38; col. 239:1617.

File History of U.S. Patent App. No.

13/339, 986,  Claim 14; Response to Office Action pp.

26-28 (dated Mar.

27, 2015)

Extrinsic Evidence

Testimony of Stacey Gabriel, Ph.D. concerning what this term would mean to one of ordinary skill in the art, in the context of claims 1 and 65 and in light of the specification of the ‘830 patent

need to be construed from this phrase, and that the remaining terms in this phrase have their plain and ordinary meaning.

 

Extrinsic Evidence supporting the terms

“preselected” and

“efficiency for selection,” all of which are incorporated herein by reference.

somatic mutation that appears at a frequency of about 5% or less of the cells from

the tumor sample

 

Plaintiff contends one of ordinary skill in the art would understand the scope of this term with reasonable certainty. Intrinsic Evidence

‘830 patent col. 3:31-52; col. 7:21-25; col. 7:29-33; col. 7:35-40; col. 7:45-56; col. 7:51-56; col. 8:9-15; col. 8:20-27; col. 8:35-56;

Defendant contends this term is indefinite. Intrinsic Evidence

 

Claims 1 and 65.

 

‘830 patent at 2:33-41;

3:45-47; 3:51-53; 12:614; 13:20-40; 14:16-15:4;

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 8 of 19 PageID #:  748

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
Claims 1, 65   col. 9:12-39; col. 19:5862; col. 22:64-23:1; col. 24:60-63; col. 27:24-25; col. 30:43-45; col. 31:4954; col. 32:33-33:12; col. 33:25-27; col. 33:30-36; col. 34:30-31; col. 41:5852; col. 44:37-47:21; col. 92:23-24; col. 104:65-67; col. 105:15-18; col.

105:30-34; col. 105:5660; col. 106:15-18; col.

106:43-47; col. 106:6166; col. 110:33-43; col. 110:46-59; col. 116:12-

22; col. 116:25-28; col

119:4-120:44; col. 121:3122:3; col. 129:41-45; col. 129:48-53; col. 129:55-60; col. 129:64130:8; col. 130:28-32; col. 130:37-43; col.

130:51-131:5; col.

131:20-54; col. 132:4346; col. 132:51-54; col. 133:41-51; col. 133:5264; col. 140:9-18; col.

140:19-30; col. 140:62141:6; col. 141:36-44; col. 143:16-21; col.

  16:28-17:25; 31:4-15;

37:36-45; 42:6-10; 44:6-

29; 50:3-7; 66:22-29;

66:64-67:5; 67:66-68:19;

67:47-8; 69:1-70:10;

71:3-30; 71:50-73:21;

74:28-34; 77:47-52;

84:36-43; 87:1-67; 93:59-

94:3; 96:13-37; 110:29-

111:25; 116:8-31;

129:61-130:15; 131:11-

132:46; 133:40-51; 134:28-46;140:9-18; 235:33-38; 238:3-14.

 

File History, Notice of

Allowance, April 4, 2016;

Applicant’s Remarks,

December 16, 2015;

Declaration of Doran Lipson, December 16, 2015.

 

Extrinsic Evidence

Testimony of John Quackenbush, Ph.D., that this claim term, read in light of the specification and the prosecution

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 9 of 19 PageID #:  749

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    142:23-26; col. 143:9-21; col. 143:28-37; col. 143:32-38; col. 144:5-13; col. 151:19-21; col. 151:25-26; col. 151:5051; col. 152:2-5; col. 152:7-10; col. 154:44-49; col. 155:27-40; col. 156:1-18; col. 157:19-22; col. 175:13-15; col. 199:15-55; col. 199:66200:23; col. 200:34-37; col. 201:16-21; col.

202:58-61; col. 203:4346; col. 204:41-42; col. 204:53-57; col. 205:9-11; col. 205:15-18; col.

205:35-39; col. 205:4346; col. 205:61-64; col. 205:66-67; col. 206:3-5; col. 206:56-59; col. 207:11-18; col. 207:2836; col. 207:50-208:9; col. 208:16-19; Claim 9;

Claim 20; Claim 21;

Claim 28; Claim 55;

Claim 73; Figure 1B;

Figure 1C; Figure 1D;

Figure 1E; Figure 2;

Figure 3; Table 1; Table

  history, fails to inform, with reasonable certainty, those skilled in the art  about the scope of the invention.

References including intrinsic and extrinsic evidence cited in

Declaration of John Quackenbush, Ph.D.

 

Plaintiff’s Infringement Contentions and references cited therein.

 

Guardant further reserves the right to rely on the intrinsic and extrinsic evidence cited by

Plaintiff to show that the term is indefinite.

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 10 of 19 PageID #:  750

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    1A; Table 1B; Table 2;

Table 3; Table 4; Table 5; Table 6; Table 9; Table 12; Table 13.

File History of U.S.

Patent App. No. 13/339,

986,  Claim 5(iii); Claim

5(iv); Claim 11; Claim 23

(dated Dec. 29, 2011);

Claim 37; Claim 39;

Claim 40 (dated Apr. 08,

2013); Claim 6; Claim

10; Claim 14; Claim 27

(dated Mar. 09, 2015);

Response to Office Action pg. 27; Claim 38;

Claim 82(i) (dated Mar.

27, 2015); Claim 86;

Claim 92; Claim 100

(dated Dec. 16, 2015);

Response to Office Action pg. 8; pgs. 34-35; pg. 38 (dated Dec. 16, 2015); Declaration of Doron Lipson pg. 2; pgs. 3-4; pg. 5; pg. 6 (dated Dec. 15, 2015).

Drilon et al., Clin. Cancer

Res. 2015; 21(16):3631-

   

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 11 of 19 PageID #:  751

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    3639.

Extrinsic Evidence

Stratton et. al.; Nickerson et. al.; Lanman et. al.; Ono. et. al.; Nature.com 

Testimony of Stacey Gabriel, Ph.D. concerning how one of ordinary skill in the art would understand the meaning and scope of this term, in light of the specification of the ‘830 patent.

   
somatic mutation that appears at a frequency of about 10% or higher of the cells from the tumor sample

 

Claims 1, 65

 

Plaintiff contends one of ordinary skill in the art would understand the scope of this term with reasonable certainty. Intrinsic Evidence

‘830 patent col. 3:31-52; col. 32:33-33:12; col. 33:25-27; col. 33:30-36; col. 34:30-31; col. 44:3747:21; col. 92:23-24; col. 104:65-67; col. 105:1518; col. 105:30-34; col.

105:56-60; col. 106:1518; col. 106:43-47; col. 106:61-66; col. 119:4120:44; col. 121:3-122:3; col. 129:41-45; col.

Defendant contends this term is indefinite. Intrinsic Evidence

 

Claims 1 and 65.

 

‘830 patent at 2:33-41;

3:45-47; 3:51-53; 12:614; 13:20-40; 14:16-15:4;

16:28-17:25; 31:4-15;

37:36-45; 42:6-10; 44:6-

29; 50:3-7; 66:22-29;

66:64-67:5; 67:66-68:19;

67:47-8; 69:1-70:10;

71:3-30; 71:50-73:21;

74:28-34; 77:47-52;

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 12 of 19 PageID #:  752

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    129:48-53; col. 129:64130:8; col. 130:28-32; col. 130:37-43; col. 132:43-46; col. 132:5154; col. 140:62-141:6; col. 141:36-44; col. 142:23-26; col. 143:9-21; col. 143:28-37; col. 143:32-38; col. 144:5-13; col. 151:19-21; col. 151:25-26; col. 151:5051; col. 152:2-5; col. 152:7-10; col. 154:44-49; col. 155:27-40; col. 156:1-18; col. 157:19-22; col. 175:13-15; col. 199:15-33; col. 199:4055; col. 199:66-200:23; col. 200:34-37; col.

201:16-21; col. 202:5861; col. 203:43-46; col.

204:41-42; col. 204:5357; col. 204:65-67; col. 205:9-11; col. 205:15-18; col. 205:35-39; col.

205:43-46; col. 205:6164; col. 205:66-67; col. 206:3-5; col. 206:56-59; col. 207:11-18; col. 207:28-36; col. 208:16-

  84:36-43; 87:1-67; 93:59-

94:3; 96:13-37; 110:29-

111:25; 116:8-31;

129:61-130:15; 131:11-

132:46; 133:40-51; 134:28-46;140:9-18; 235:33-38; 238:3-14.

 

File History, Notice of

Allowance, April 4, 2016;

Applicant’s Remarks,

December 16, 2015;

Declaration of Doran Lipson, December 16, 2015.

 

Extrinsic Evidence

Testimony of John Quackenbush, Ph.D., that this claim term, read in light of the specification and the prosecution history, fails to inform, with reasonable certainty, those skilled in the art  about the scope of the invention.

References including

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 13 of 19 PageID #:  753

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    19; Claim 20(i); Claim

21; Claim 73; Claim 9;

Figure 1B; Figure 1C; Figure 1D; Figure 1E;

Figure 2; Figure 3; Table 1; Table 13; Table 1A;

Table 1B; Table 2; Table 3; Table 4; Table 5; Table 6; Table 9.

File History of U.S.

Patent App. No.

13/339,986 Claim 5(iii);

Claim 5(iv); Claim 11;

Claim 23 (dated Dec. 29,

2011); Claim 37; Claim

38; Claim 39; Claim 38;

Claim 40 (dated Apr. 08,

2013); Claim 6; Claim

10; Claim 14; Claim 27

(dated Mar. 09, 2015);

Response to Office Action pg. 27; Claim 38; Claim 82(ii) (dated Mar.

27, 2015); Claim 86;

Claim 92; Claim 100

(dated Dec. 16, 2015);

Response to Office Action pg. 8; pgs. 34-35; pg. 38 (dated Dec. 16, 2015); Declaration of

  intrinsic and extrinsic evidence cited in

Declaration of John Quackenbush, Ph.D.

 

Plaintiff’s Infringement Contentions and references cited therein.

 

Guardant further reserves the right to rely on the intrinsic and extrinsic evidence cited by

Plaintiff to show that the term is indefinite.

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 14 of 19 PageID #:  754

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    Doron Lipson pg. 2; pgs. 3-4; pg. 5; pg. 6 (dated Dec. 15, 2015).

Drilon et al., Clin. Cancer Res. 2015; 21(16):36313639.

Extrinsic Evidence

Stratton et. al.; Nickerson et. al.; Lanman et. al.; Ono. et. al.; Nature.com

Testimony of Stacey Gabriel, Ph.D. concerning how one of ordinary skill in the art would understand the meaning and scope of this term, in light of the specification of the ‘830 patent.

   
a genomic SNP

or locus that is used to assess copy number

gains or losses of genomic DNA

and loss-ofheterozygosity

Plaintiff contends one of ordinary skill in the art would understand the scope of this term with reasonable certainty. Intrinsic Evidence

‘830 patent col. 2:45-48; col. 2:56-63; col. 12:1923; col. 12:32-42; col. 13:49-52; col. 13:6114:5; col. 19:16-21; col.

19:28-32; col. 22:9-10;

Defendant contends this term is indefinite. Intrinsic Evidence

 

Claims 1and 65.

 

Guardant further reserves the right to rely on the intrinsic and extrinsic evidence cited by

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 15 of 19 PageID #:  755

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
(LOH)

 

Claims 1 and 65

  col. 33:7-11; col. 35:1-6; col. 49:49-53; col. 55:3545; col. 61:1-13; col. 67:9–34; col. 68:28-34; col. 68:43-49; col. 83:5462; col. 84:52-59; col. 85:33-40; col. 85:44-51; col. 86:28-36; col. 94:2530; col. 94:38-44; col. 111:1-6; col. 111:17-25; col. 116:47-52; col. 116:63-117:4; col. 134:38; col. 134:19-27; col.

140:35-40; col. 140:4956; col. 141:36-41; col. 146:32-45; col. 157:24158:8; col. 199:40-46; col. 200:32-33; col. 206:3-13; col. 207:11-23; Figure 1D; Table 1B.

File History of U.S.

Patent App. No.

13/339,986, Claim 13(e)

(dated Dec. 29, 2011);

Response to Office

Action Claim 82 (dated Mar. 27, 2015); Response to Office Action pg. 35 (dated Dec. 16, 2015);

Declaration of Doron

  Plaintiff to show that the term is indefinite.

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 16 of 19 PageID #:  756

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    Lipson pg. 5 (dated Dec. 15, 2015).

Extrinsic Evidence

Zhang et. al.; Ramoni;

Nature.com; Strachan &

Read; Lasko et. al.; Linblad-Toh; McCarroll et. al; Beroukhim et. al.;

Thompson & Thompson

Testimony of Stacey Gabriel, Ph.D. concerning how one of ordinary skill in the art would understand the meaning and scope of this term, in light of the specification of the ‘830 patent.

 

   
step (b)

 

Claims 2 and 66

Plaintiff contends one of ordinary skill in the art would understand the scope of this term with reasonable certainty. Intrinsic Evidence

‘830 patent, claims 1-2, 65-66; col. 11:37-39; col. 66: 30-33.

Extrinsic Evidence

Defendant contends this term is indefinite. Intrinsic Evidence

 

Claims 1, 2, 65 and 66.

 

Guardant further reserves the right to rely on the intrinsic and extrinsic evidence cited by

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 17 of 19 PageID #:  757

Term Plaintiff’s Proposed Construction Plaintiffs’ Intrinsic and Extrinsic Evidence* Defendant’s Proposed Construction Defendant’s Intrinsic and Extrinsic Evidence*
    Testimony of Stacey Gabriel, Ph.D. concerning how one of ordinary skill in the art would understand the meaning and scope of this term, in light of the specification of the ‘830 patent.

 

  Plaintiff to show that the term is indefinite.

 

Plaintiffs’ Identification of Sources for Extrinsic Evidence

The sources listed below are identified as containing extrinsic evidence supporting Plaintiffs’ preliminary claim constructions.

  1. Bach et. al., Identification of deep intronic variants in 15 haemophilia A patients by next generation sequencing of the whole factor VIII gene, Thrombosis and Haemostasis, October 2005; 114(4): 757-767

 

  1. Beroukhim et al, The landscape of somatic copy-number alteration across human cancers, Nature, 463(7283): 899–905

(2010)

 

  1. Drilon et al., Broad, Hybrid Capture-Based Next-Generation Sequencing Identifies Actionable Genomic Alterations in Lung Adenocarcinomas Otherwise Negative for Such Alterations by Other Genomic Testing Approaches, Cancer Res. 2015; 21(16):3631-3639

 

  1. Lanman et al., Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-free Circulating Tumor DNA, PLOS One, 10(10): e0140712 (2015)

 

  1. Lasko et al., Loss of Constitutional Heterozygosity in Human Tumors, Annu. Rev. Genet. 25, 281, 286-87, 290 (1991)

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 18 of 19 PageID #:  758

 

  1. McCarroll et. al., Copy-number variation and association studies of human diseases, Nature Genetics, Vol. 39, S37, S38 (2007)

 

  1. Molnar et. al., Correcting Illumina data, Briefings in Bioinformatics Vol. 16 No. 4 588-599, September 2014

 

  1. com Definition, Allele frequency, available at http://www.nature.com/scitable/definition/allele-frequency-298

 

  1. com Definition, SNP, at http://www.nature.com/scitable/definition/single-nucleotide-polymorphism-snp-295.

 

  1. Nickerson, et al., Improved Identification of von Hippel-Lindau Gene Alterations in Clear Cell Renal Tumors, Clin. Cancer Res. 14(15): 4726 (2008)

 

  1. Ono, et al., Mutant allele frequency predicts the efficacy of EGFR-TKIs in lung adenocarcinoma harboring the L858R mutation, Annals of Oncology, 25: 1948 (2014)

 

  1. Ramoni, Human Variations, Genes, Genotypes and Generations, Presentation at Harvard-MIT Division of Health Sciences and Technology, at 2 (2005)

 

  1. Tom Strachan & Andrew P. Read, Human Molecular Genetics (3d Ed. 2004)

 

  1. Stratton et. al., The cancer genome, Nature, Vol. 458, No. 9 719-723 (2009)

 

  1. Talkowski et. al., Next-Generation Sequencing Strategies Enable Routine Detection of Balanced Chromosome Rearrangements for Clinical Diagnostics and Genetic Research, The American Journal of Human Genetics 88, 469-81 (April 8, 2011)

 

  1. Thompson & Thompson, Genetics in Medicine (7th 2007)

 

  1. Zhang, et al., Copy Number Variation in Human Health, Disease, and Evolution, Annu. Rev. Genomics Hum. Genet., 10, 451, 452 (2009)

 

Case 2:16-cv-00523-JRG-RSP   Document 65-2   Filed 03/02/17   Page 19 of 19 PageID #:  759

Plaintiff reserves the right to identify and rely on additional extrinsic evidence in rebuttal to Defendant’s identification of extrinsic evidence, including testimony from rebuttal expert witnesses.  Plaintiffs reserve the right to rely on extrinsic evidence cited by Defendants in their P.R. 4-2 submission dated February 2, 2017 to rebut Defendants’ proposed claim constructions.

Defendant’s Identification of Sources for Extrinsic Evidence

The sources listed below are identified as containing extrinsic evidence supporting Defendant’s preliminary claim constructions.

  • GUARD00035285
  • Declaration of John Quackenbush, Ph.D. and references cited therein
  • Plaintiff’s Infringement Contentions and references cited therein

Defendant reserves the right to identify and rely on additional extrinsic evidence in rebuttal to Plaintiffs’ identification of extrinsic evidence, including testimony from rebuttal expert witnesses.  Defendant reserves the right to rely on extrinsic evidence cited by Plaintiffs in their P.R. 4-2 submission dated February 2, 2017 to rebut Plaintiffs’ proposed claim constructions.

 

 

 

[1] See Plaintiff’s and Defendant’s Identifications of Sources for Extrinsic Evidence below.

 

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