Source: s3://data.kl3m.ai/documents/govinfo/USCOURTS/USCOURTS-cand-3_12-cv-00865/USCOURTS-cand-3_12-cv-00865-35/pdf.json

Nature of Suit Code: 830
Nature of Suit: Patent
Cause of Action: 35:145 Patent Infringement

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United States District Court

Northern District of California

UNITED STATES DISTRICT COURT

NORTHERN DISTRICT OF CALIFORNIA

VERINATA HEALTH, INC., et al.,

Plaintiffs,

v.

SEQUENOM, INC., et al.,

Defendants.

Case No. 12-cv-00865-SI 

ORDER DENYING CROSS MOTIONS 

FOR SUMMARY JUDGMENT AND 

STAYING CASE

On January 23, 2015 the Court heard argument on the parties’ cross motions for summary 

judgment. Having considered the arguments of the parties and the papers submitted, the Court 

hereby DENIES the parties’ motions for summary judgment. Additionally, the Court STAYS this 

proceeding as set forth below.

BACKGROUND

I. Factual Background

The innovations at issue involve methods to conduct non-invasive prenatal DNA testing. 

Fetal DNA testing can aid sex determination, blood typing and other genotyping, and detection of 

pre-eclampsia in the mother. It can also detect fetal aneuploidy, which is a disorder in which the 

fetus has an abnormal number of chromosomes, instead of the normal 23 pairs. Common 

aneuploidy disorders include Down syndrome (a third copy, or “trisomy,” of chromosome 21), 

Edwards syndrome (a third copy of chromosome 18), and Patau syndrome (a third copy of 

chromosome 13).

On February 15, 2011, the PTO issued the ′017 patent, entitled “Non-invasive Fetal 

Genetic Screening by Digital Analysis,” and on August 30, 2011, it issued the ′018 patent, entitled 

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“Determination of Fetal Aneuploidies by Massively Parallel DNA Sequencing.” The ′018 patent is 

a continuation of the ′017 patent, and has a nearly identical specification. Stanford is the patent 

owner and Verinata is the exclusive licensee of these patents. They previously alleged that 

Sequenom was infringing these patents. See Verinata I, infra. 

The patents explain that “[s]ince aneuploidies do not present a mutational change in 

sequence, and are merely a change in the number of chromosomes, it has not been possible to 

detect them in a fetus without resorting to invasive techniques,” because researchers believed that 

determining whether a fetus was carrying an extra chromosome required distinguishing fetal DNA 

from maternal DNA. The ′018 Patent, Abstract. However, the patent inventors discovered that 

“digital amplification allows the detection of aneuploidy using massively parallel amplification 

and detection methods.” Id. By using sophisticated molecular counting techniques, the researchers 

could determine small under or over-representations of a chromosome that would reveal fetal 

aneuploidy, without the need to distinguish between the maternal and fetal DNA. See id. 21:10–

30.

II. Procedural Background

This dispute began in 2011, when Ariosa1filed a declaratory relief action against 

Sequenom, seeking a declaration that Ariosa's “Harmony Test” does not infringe any claims of 

U.S. Patent No. 6,258,540 (“the ′540 patent”). Aria Diagnostics, Inc. v. Sequenom, Inc., C 11–

6391–SI (filed Dec. 19, 2011). Sequenom filed a counterclaim against Ariosa, asserting 

infringement of Sequenom's ′540 patent. Subsequently, two other companies, Natera and Verinata, 

also filed declaratory judgment actions in this Court seeking judgments that their products do not 

infringe Sequenom's ′540 patent and asserting that the ′540 patent is invalid. See Natera Inc. v. 

 

1

Formerly known as Aria Diagnostics, Inc.

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Sequenom, Inc., C 12–0132–SI (filed Jan. 6, 2012) (regarding Natera's “Non–Invasive Paternity 

Test”); Verinata Health, Inc. v. Sequenom, Inc. (Verinata I), C 12–0865–SI (filed Feb. 22, 2012) 

(regarding Verinata's “Verifi Prenatal Test”). Sequenom then filed counterclaims alleging that 

Natera, DNA Diagnostics Center, Verinata, and Stanford are infringing the ′540 patent. See id. On 

October 30, 2013, this Court held the ′540 patent to be invalid. Sequenom has appealed this ruling 

to the Federal Circuit, and that appeal is pending. C 11–cv–6391 SI, Docket No. 254.

In Verinata I, Verinata2and Stanford also alleged that Sequenom was infringing U.S. 

Patent Nos. 7,888,017 (“the ′017 patent”), 8,008,018 (“the ′018 patent”), and 8,195,415 (“the ′415 

patent”). In addition, Verinata and Stanford filed a case alleging that Ariosa and LabCorp are 

infringing U.S. Patent Nos. 8,296,076 (“the ′076 patent”) and 8,318,430 (“the ′430 patent”). See 

Verinata Health, Inc. v. Ariosa Diagnostics, Inc. (Verinata II), C 12–5501–SI (filed Oct. 25, 

2012). Finally, Illumina filed a case alleging that Ariosa is infringing U.S. Patent No. 7,955,794 

(“the ′794 patent”). See Illumina, Inc. v. Ariosa Diagnostics, Inc., C 14–1921–SI (filed April 25, 

2014). This final action was consolidated with Verinata II.

Verinata and Sequenom ultimately reached a settlement in Verinata I which resolved all of 

their respective claims, save the issue of written description of the ‘018 Patent and ‘833 

Application, Docket No. 320, which is the subject of the present motion.

Beginning in March 2013, the Patent Trial and Appeal Board (“PTAB”) declared three 

interferences between (1) patents and patent applications listing as inventors Drs. Yuk–Ming 

Dennis Lo, Rossa Wai Kwun Chiu, and Kwan Chee Chan of the Chinese University Hong Kong 

(“CUHK”) (collectively, “Lo”) and (2) patents and patent applications listing as inventors Drs. 

Stephen Quake and Hei–Mun Christina Fan of Stanford University, (collectively, “Quake”). On 

April 7, 2014, the PTAB issued orders finding that the claims of the ’018 Patent and ’833 

 

2

In January of 2013, Illumina acquired Verinata

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Application lack a sufficient written description as required by 35 U.S.C. § 112(a).3 Docket No. 

252, Bosch Decl. Exhs. 3-5. 

Stanford appealed the PTAB’s decision pursuant to 35 U.S.C. § 146. Now before the Court 

are Stanford and CUHK’s cross-motions for summary judgment on the issue of written 

description. Docket Nos. 252, 255. 

LEGAL STANDARDS

I. Summary Judgment

Summary judgment is proper if the pleadings, the discovery and disclosure materials on 

file, and any affidavits show that there is no genuine issue as to any material fact and that the 

movant is entitled to judgment as a matter of law. See Fed. R. Civ. P. 56(a). The moving party 

bears the initial burden of demonstrating the absence of a genuine issue of material fact. Celotex 

Corp. v. Catrett, 477 U.S. 317, 323 (1986). The moving party, however, has no burden to 

disprove matters on which the non-moving party will have the burden of proof at trial. The 

moving party need only demonstrate to the Court that there is an absence of evidence to support 

the non-moving party’s case. Id. at 325.

Once the moving party has met its burden, the burden shifts to the non-moving party to 

“set out ‘specific facts showing a genuine issue for trial.’” Id. at 324 (quoting then Fed. R. Civ. P. 

56(e)). To carry this burden, the non-moving party must “do more than simply show that there is 

some metaphysical doubt as to the material facts.” Matsushita Elec. Indus. Co., Ltd. v. Zenith 

Radio Corp., 475 U.S. 574, 586 (1986). “The mere existence of a scintilla of evidence . . . will be 

insufficient; there must be evidence on which the jury could reasonably find for the [non-moving 

party].” Anderson v. Liberty Lobby, Inc., 477 U.S. 242, 252 (1986). In deciding a summary 

 

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The ’018 Patent and ’833 Application share the same specification. Docket No. 255-3, Pl. 

Mot. at 1 nt. 1.

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judgment motion, the Court must view the evidence in the light most favorable to the non-moving 

party and draw all justifiable inferences in its favor. Id. at 255. “Credibility determinations, the 

weighing of the evidence, and the drawing of legitimate inferences from the facts are jury 

functions, not those of a judge . . . ruling on a motion for summary judgment.” Id. However, 

conclusory, speculative testimony in affidavits and moving papers is insufficient to raise genuine 

issues of fact and defeat summary judgment. Thornhill Publ’g Co., Inc. v. GTE Corp., 594 F.2d 

730, 738 (9th Cir. 1979). The evidence the parties present must be admissible. Fed. R. Civ. P. 

56(c)).

II. 35 U.S.C. § 146

“District court review of an interference proceeding under section 146 is an equitable 

remedy of long standing.” Gen. Instrument Corp. v. Scientific-Atlanta, Inc., 995 F.2d 209, 214 

(Fed. Cir. 1993), citing Standard Oil Co. v. Montedison S.p.A, 540 F.2d 611, 616-17 (3d 

Cir.1976). A Section 146 proceeding “is not a new claim, but an authorized phase of the 

interference proceeding that is conducted by the PTO and is subject to judicial review.” Vas–Cath, 

Inc. v. Curators of the Univ. of Mo., 473 F.3d 1376, 1382 (Fed.Cir.2007). If the parties present no 

new evidence, then the district shall review the factual findings of the PTAB for “substantial 

evidence.” Winner Int'l Royalty Corp. v. Wang, 202 F.3d 1340, 1345 (Fed. Cir. 2000), citing 

Dickinson v. Zurko, 527 U.S. 150, 162 (1999). However, as is the case here, if the parties present 

new evidence that was not before the PTAB, then the district court conducts de novo review of the 

PTAB’s factual findings. Winner Int'l Royalty Corp 202 F.3d at 1345. 

DISCUSSION

I. Cross Motions for Summary Judgment 

Both parties agree that claims in the ’018 Patent and ’833 Application recite a technique 

for random massive parallel sequencing (“MPS”). However, CUHK argues that the specification 

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only describes targeted sequencing techniques (such as PCR), and therefore does not meet the 

written description requirement for random MPS. Specifically, CUHK argues that the 

specification (1) does not describe, or even mention “random massively parallel sequencing,” or 

(2) disclose any examples or experiments using random MPS. Docket No. 252, CUHK Mot. at 11.

Conversely, Stanford argues that, when accounting for the knowledge of one skilled in the art,

there is ample discussion of random MPS to satisfy the written description requirement.

It is well established that a patent is presumed valid, and “the burden of persuasion to the 

contrary is and remains on the party asserting invalidity.” Ralston Purina Co. v. Far–Mar–Co, 

Inc., 772 F.2d 1570, 1573 (Fed.Cir.1985). To be valid, however, 35 U.S.C. § 112 requires that 

every patent contain a written description of the invention. The purpose of this requirement is to 

“ensure that the patent applicant was in full possession of the claimed subject matter on the 

application filing date.” TurboCare Div. of Demag Delaval Turbomachinery Corp. v. Gen. Elec. 

Co., 264 F.3d 1111, 1118 (Fed.Cir.2001). “The test requires an objective inquiry into the four 

corners of the specification from the perspective of a person of ordinary skill in the art. Based on 

that inquiry, the specification must describe an invention understandable to that skilled artisan and 

show that the inventor actually invented the invention claimed.” Ariad Pharms, Inc. v. Eli Lilly 

and Co., 598 F.3d 1336, 1351 (Fed.Cir.2010). While the written description requirement does not 

require that the original disclosure provide in haec verba support for the claimed subject matter at 

issue, Fujikawa v. Wattanasin, 93 F.3d 1559, 1570 (Fed.Cir.1996), the original disclosure must 

convey with reasonable clarity to those skilled in the art that the inventor was in possession of the 

invention. Vas–Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563–64 (Fed.Cir.1991). In a section 146 

proceeding, the party asserting invalidity must show, by a preponderance of the evidence, that the 

specification fails to meet the written description requirement. Streck, Inc. v. Research & 

Diagnostic Sys., Inc., 659 F.3d 1186, 1191-92 (Fed. Cir. 2011). 

A. PTAB Interference Orders

On April 7, 2014, the PTAB issued orders finding that the claims of the ’018 Patent and 

’833 Application lack a sufficient written description for the claimed random MPS technique. 

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Specifically, the Board found that while the specification included certain “isolated words and 

references” that could support the random MPS method, in light of the specification’s “main 

focus” on targeted sequencing methods (namely, PCR), “those of skill in the art would not have 

had a credible reason to interpret the isolated words and references as supporting a method using 

random [MPS].” Docket 252, Bosch Decl. Exh. 3 at 21. The interference order also found that the 

specification never discloses “a complete analysis of aneuploidy using random [MPS],” and that 

as a result those of skill in the art would not have understood the inventors to have put “these 

pieces together into a complete method of [random MPS].” Id. at 22. In sum, while the 

specification contained certain buzzwords related to random MPS, it failed to meet the written 

description requirement because it is never “explained with sufficient detail.” Id.

Both parties agree that the Court must conduct de novo review of the PTAB’s findings of 

fact. However, CUHK urges the Court to give weight to the PTAB’s orders, while Stanford 

maintains that the PTAB was “misled” into an “erroneous approach” and that the orders should 

therefore be ignored for purposes of the present motions. The PTAB interference orders presented 

a thorough and persuasive analysis of the issue now before the Court, and the Court may therefore 

consider the PTAB’s findings. However, Stanford is correct to stress that when new evidence is 

introduced in a Section 146 appeal, the Court must conduct a de novo review of the facts, and is 

not bound by the PTAB’s prior ruling. Furthermore, the Court notes that the PTAB’s conclusion

was based at least in part on its determination of the relative credibility and probative value of the 

evidence before it. See e.g. Bosch Decl. Exh. 3 at 19 (“we credit Dr. Gabriel’s testimony that those 

of skill in the art could have considered the references in the [specification] to Illumina products to 

indicate targeted sequencing.”). On summary judgment, the Court may not engage in such fact 

finding, and may only grant relief if there is no genuine issue of material fact that would preclude 

summary judgment.

B. Description of Random MPS

While the parties discuss various sections of the specification in arguing whether certain

discrete steps in the random MPS technique were adequately disclosed, much of the parties’ 

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disagreement centers on the following two paragraphs of the specification.

The genomic DNA from the tissue taken from the mother, i.e. the 

mixture of fetal and maternal genetic material, may be distributed 

into discrete samples which are anchored to a surface and 

sequenced or monitored by labeled probes to detect a target specific 

sequence, e.g., a unique region of chromosome 21, e.g., AML1. 

Further guidance for the preparation of chromosome 21-unique 

sequences may be found, for example, in Fuscoe et al., “An Efficient 

Method for Selecting Unique-Sequence Clones from DNA Libraries 

and Its Application To Fluorescent Staining of Human Chromosome 

21 Using in Situ Hybridization,” Genomics, vol. 5, 1989, pp. 100-

109. A methodology useful in the present invention platform is 

based on massively parallel sequencing of millions of fragments 

using attachment of randomly fragmented genomic DNA to a 

planar, optically transparent surface and solid phase 

amplification to create a high density sequencing flow cell with 

millions of clusters, each containing  ̃1,000 copies of template per 

sq. cm. These templates are sequenced using four-color DNA 

sequencing-by-synthesis technology. See, products offered by 

Illumina, Inc., San Diego Calif. Also, see US 2003/0022207 to 

Balasubramanian, et al., published Jan. 30, 2003, entitled “Arrayed 

polynucleotides and their use in genome analysis.”

Sequencing may be combined with amplification-based methods in 

a microfluidic chip having reaction chambers for both PCR and 

microscopic template-based sequencing. Only about 30 bp of 

random sequence information are needed to identify a sequence 

as belonging to a specific human chromosome. Longer sequences 

can uniquely identify more particular targets. An algorithm for 

designing unique sequences is described in Yamada, et al. 

“PrimerStation: a highly specific multiplex genomic PCR primer 

design server for the human genome,” Nucleic Acids Res., Jul. 1, 

2006; 34(Web Server issue): W665-W669, illustrative of software 

methods that can be used to identify a sequence in comparison 

to the known genome sequence. See, also Zhu et al., “Single 

molecule profiling of alternative pre-mRNA splicing,” Science. 

2003 Aug. 8; 301(5634):836-838, describing a single-moleculebased technology for studying mRNA.

The’ 018 Patent, 19:48-20:20 (emphasis added). 

Stanford seizes on the bolded passages to show that the specification describes random 

MPS. It points to testimony of CUHK’s expert, Dr. Gabriel, wherein she states that the phrase 

“randomly fragmented genomic data,” bolded supra, is associated with random rather than 

targeted sequencing. Docket No. 276-6 at 134:21-25. Dr. Gabriel has also noted that the 

Balasubramanian publication quoted above discloses a sequencing platform that can be used for 

either targeted or random sequencing. Docket No. 255-3, Stanford Mot. at 15. Stanford also points 

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to testimony from Dr. Gabriel and its own expert, Dr. Weinstock4, to show that the above excerpt 

amply discloses “alignment” and “comparison,” two necessary steps in the random MPS 

technique. Docket No. 255-3, Exh. 21 at 110:4-17; Docket No. 255-5 at 112:9-20. In particular, 

Stanford highlights that Dr. Gabriel’s definition of “alignment” is reflected in the passage of the 

specification which Stanford argues discloses alignment. See Stanford Opp’n at 17. Stanford also 

contends that its reference to “massively parallel sequencing of millions of fragments using 

attachment of randomly fragmented genomic DNA,” by its plain meaning, describes random MPS.

Stanford additionally points to a number of factors that would explain the relatively short 

description of random MPS in the specification. First, it points to testimony from Dr. Metzker,

Sequenom’s expert, showing that one of skill in the art would have understood that both targeted 

and random sequencing could be used with the claimed inventions. Docket No. 255, Exh. 25 at 

444:4-18. It also points to testimony from Dr. Gabriel that someone of skill in the art would be 

motivated to try different methods of detection in order to perform the entire scope of the 

invention, not just targeted sequencing methods. Docket No. 276-6, Exh. 37 at 95:1-18. Similarly, 

Stanford cites an article published by Drs. Quake and Fan in 2008 which describes random MPS 

as merely a “variant” of targeted sequencing. Stanford Opp’n at 11-12. Stanford therefore 

concludes that “[a]lthough the disclosure of random sequencing in the patent encompasses only a 

few paragraphs, this disclosure is more than adequate because the data gathering technique was 

well-within the competency of one of ordinary skill in the art.” Docket No. 275, Stanford Opp’n at 

 

4 CUHK argues that due to certain errors in his testimony and expert report, Dr. 

Weinstock’s opinions are “irrelevant” and should therefore be disregarded for purposes of ruling 

on these motions. CUHK Mot. at 22. First, CUHK points to testimony wherein Dr. Weinstock 

appears to admit that he applied the incorrect “clear and convincing” standard to whether the 

written description requirement was met, rather than the proper “preponderance” standard as 

required in Section 146 appeal. Bosch. Decl. Exh. 7 at 10:13-12:3. Stanford has failed to rebut this 

contention in its briefs, and it appears that it has made a similar error in its own motion. Stanford 

Mot. at 7. Second, CUHK points to testimony tending to show that Dr. Weinstock did not 

appreciate the difference between the requirements for written description and enablement. Bosch 

Decl. Exh. 7 at 109:10-16. Stanford has introduced evidence tending to show that Dr. Weinstock 

indeed did understand the difference between these two standards. Id. at 22:6-17. 

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9. 

CUHK argues that the passage from the specification quoted above must be read in light of 

the first two sentences (in italics), which describe targeted sequencing. Echoing the reasoning of 

the PTAB, it argues that while certain phrases that Stanford points to could describe random MPS, 

the first two sentences of the paragraph make clear that the subject of the entire passage is directed

toward targeted sequencing. CUHK points to testimony from Drs. Gabriel and Weinstock tending 

to show that they both agree that these two sentences indeed address targeted sequencing. CUHK 

Mot. at 16. In her expert report, Dr. Gabriel notes that the word “sequence,” and similar 

derivations, appear in only six paragraphs of the specification, and they all refer to targeted

sequencing. Docket No. 252, Gabriel Decl. Exh A. ¶ 70. Dr. Gabriel further notes that all working 

examples in the specification use PCR to detect target sequences in DNA. Id. ¶ 67. She also notes 

that the specification never discloses certain necessary steps in the random MPS process such as 

“alignment,” “sequence reads,” “fractional representation,” or “comparison” Id. ¶ 68, 71, 123, 

146. Dr. Gabriel also identified a number of terms that one skilled in the art would have used to 

describe random MPS, none of which appears in the specification of February, 2007. Gabriel 

Decl. Exh. A ¶ 71, Exh. B ¶¶ 49-50. Dr. Gabriel notes, however, that these terms do appear in a

later 2008 Quake publication on the subject of random MPS. Gabriel Decl. Exh. A ¶ 84. Stanford 

rebuts this by highlighting that many of Dr. Gabriel’s definitions of certain claim terms relating to 

random MPS are nearly identical to language disclosed in the specification. Stanford Opp’n at 13-

15.

While new evidence has been introduced since the PTAB decision, the parties essentially 

echo the arguments that they made before the Board. Stanford argues that the two paragraphs from 

the specification quoted supra, while relatively terse, are enough to satisfy the written description 

requirement when read in light of the knowledge of one skilled in the art. Conversely, CUHK 

contends that isolated buzzwords cannot be read to describe random MPS in light of the 

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specification’s focus on targeted sequencing.

No “length requirement exists for a disclosure to adequately describe an invention. While 

some inventions require more disclosure, the adequacy of the description of an invention depends 

on its content in relation to the particular invention, not its length.” In re Hayes Microcomputer 

Products, Inc. Patent Litig., 982 F.2d 1527, 1534 (Fed. Cir. 1992). However, in deciding whether 

the written description requirement is satisfied, “the specification as a whole must be considered.” 

In re Wright, 866 F.2d 422, 425 (Fed. Cir. 1989). It is not enough that an “invention is an obvious 

variant of that which is disclosed in the specification... all the limitations must appear in the 

specification.” Lockwood v. Am. Airlines, Inc., 107 F.3d 1565, 1572 (Fed. Cir. 1997). 

The PTAB examined the same question now before the Court. It conducted a thorough and 

reasoned analysis, which the Court finds to be compelling. However, the Board’s persuasive

exposition of the issues is not a sufficient basis to grant summary judgment. In light of the 

conflicting evidence presented by the parties – some of which was never presented to the PTAB –

the Court finds that the question of whether the specification would have adequately described the 

random MPS technique to one of ordinary skill in the art requires resolving questions of fact not 

suitable for summary judgment. Accordingly, the Court DENIES both parties’ motions for 

summary judgment.

II. Staying the Case

“Courts have inherent power to manage their dockets and stay proceedings.” Ethicon, Inc. 

v. Quigg, 849 F.2d 1422, 1426-27 (Fed. Cir. 1988) (citations omitted); see also Clinton v. Jones, 

520 U.S. 681, 706 (1997) (“The District Court has broad discretion to stay proceedings as an 

incident to its power to control its own docket.”). Courts often stay patent cases to “avoid 

inconsistent results, narrow the issues, obtain guidance from the PTO, or simply...avoid the 

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needless waste of judicial resources.” Pragmatus AV, LLC v. Facebook, Inc., No. 11-CV-02168-

EJD, 2011 WL 4802958, at *2 (N.D. Cal. Oct. 11, 2011) (internal citations omitted). 

On January 27, 2014, CUHK filed a notice of a pending Federal Circuit appeal which may 

affect the ultimate disposition of this case. Specifically, in Biogen Idec MA, Inc. v. Japanese 

Found. for Cancer Research, No. CIV. 13-13061-FDS, 2014 WL 2167677 (D. Mass. May 22, 

2014), the district court held that under the America Invents Act (“AIA”) of 2011, the proper 

forum for § 146 appeals from PTAB interference proceedings declared after September 16, 2012 

is the Federal Circuit, not a district court. The Biogen Idec case had been appealed, and the Federal 

Circuit is set to hear oral argument on March 4, 2015. Docket Nos. 342, 344. In an unrelated 

proceeding on December 26, 2014, the PTAB expressed approval of the Biogen court’s reasoning.

Docket No. 342, Exh. B.

The three interferences at issue here were all declared after September 16, 2012. A bench 

trial in this case is currently set for March 10, 2015. Should the Federal Circuit affirm in Biogen, it 

would deprive this Court of subject matter jurisdiction over this action. Therefore, in the interest 

of judicial economy, and to spare the parties the expense of prosecuting a trial that may ultimately 

prove to have been brought in the wrong forum, the Court hereby STAYS this action pending the 

resolution of the appeal of Biogen to the Federal Circuit. 

IT IS SO ORDERED.

Dated: February 2, 2015

______________________________________

SUSAN ILLSTON

United States District Judge

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