Reply Brief — Ariosa Diagnostics, Inc., et al., Petitioners v. Illumina, Inc., et al.

No. 20-892

IN THE

Supreme Court of the United States

ARIOSA DIAGNOSTICS, INC., ROCHE SEQUENCING

SOLUTIONS, INC., ROCHE MOLECULAR SYSTEMS, INC.,

Petitioners,

v.

ILLUMINA, INC., SEQUENOM, INC.,

Respondents.

ON PETITION FOR A WRIT OF CERTIORARI TO THE

UNITED STATES COURT OF APPEALS

FOR THE FEDERAL CIRCUIT

REPLY BRIEF FOR PETITIONERS

ROBERT J. GUNTHER, JR.

CHRISTOPHER R. NOYES

OMAR A. KHAN

WILMER CUTLER PICKERING

HALE AND DORR LLP

7 World Trade Center

250 Greenwich Street

New York, NY 10007

THOMAS G. SPRANKLING

WILMER CUTLER PICKERING

HALE AND DORR LLP

2600 El Camino Real, Suite 400

Palo Alto, CA 94306

Attorneys for Roche Molecular

Systems, Inc. and Roche

Sequencing Solutions, Inc.

DARALYN J. DURIE

Counsel of Record

DURIE TANGRI LLP

217 Leidesdorff Street

San Francisco, CA 94111

(415) 362-6666

ddurie@durietangri.com

KIRA A. DAVIS

DURIE TANGRI LLP

953 East 3rd Street

Los Angeles, CA 90013

Attorneys for Ariosa

Diagnostics, Inc.

TABLE OF CONTENTS

Page

TABLE OF AUTHORITIES ........................................... ii

ARGUMENT ....................................................................... 2

I.

THE FEDERAL CIRCUIT’S RULING CANNOT

BE SQUARED WITH MYRIAD OR EXISTING

SECTION 101 DOCTRINE MORE BROADLY ................. 2

II. THIS CASE PRESENTS AN EXCELLENT

VEHICLE TO RESOLVE THE QUESTION

PRESENTED ................................................................... 9

CONCLUSION ................................................................. 12

ii

TABLE OF AUTHORITIES

CASES

Page(s)

Alice Corp. Pty. Ltd. v. CLS Bank

International, 573 U.S. 208 (2014) ................... 1, 2, 11

Ariosa Diagnostics, Inc v. Sequenom, Inc,

788 F.3d 1371 (Fed. Cir. 2015) ................................ 2, 8

Association for Molecular Pathology v.

Myriad Genetics, Inc., 569 U.S. 576 (2013) ..... 1, 3, 11

Mayo Collaborative Services.v. Prometheus

Laboratories, Inc., 566 U.S. 66 (2012) ............. 4, 5, 11

Merritt v. Welsh, 104 U.S. 694 (1881) ............................... 9

Parker v. Flook, 437 U.S. 584 (1978) ................................ 5

Rapid Litigation Management Ltd. v.

CellzDirect, Inc., 827 F.3d 1042 (Fed. Cir.

2016) ............................................................................... 8

Virginia Uranium, Inc. v. Warren, 139 S. Ct.

1894 (2019) ..................................................................... 9

STATUTORY PROVISIONS

35 U.S.C. § 101 ..................................... 1, 2, 3, 6, 7, 9, 10, 11

This Court has held that “separating [a] gene from

its surrounding genetic material is not an act of invention” under 35 U.S.C. § 101. Association for Molecular

Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 591

(2013). The panel majority, however, came to the opposite conclusion. It held that a patent claim that involves

separating larger naturally-occurring human DNA

from smaller naturally-occurring human DNA is patentable under Section 101—without any consideration

of whether the patented method itself provides an innovative process for achieving that result (i.e., an inventive concept).

Respondents’ only argument for why the panel majority’s ruling does not violate Myriad is that this case

involves method claims and Myriad did not. But Myriad explained that the patentee “could possibly have

sought a method patent” only if the patentee had “created an innovative method of manipulating genes.” 569

U.S. at 595-596 (emphasis added). And Respondents’

insistence that the claims here are directed to eligible

subject matter because they involve a “process” cannot

be reconciled with Alice v. Corp. Pty. Ltd. v. CLS Bank

Int’l, 573 U.S. 208, 216 (2014), which not only established the governing framework but applied it to invalidate a claim to a process—the same kind of claim at

issue here.

Myriad further held that the central idea of the patents in this case—separating human DNA from surrounding genetic material—is “not an act of invention.”

Myriad, 569 U.S. at 591. But here, the panel majority

did not even consider whether the patented method

was innovative and, if anything, reinforced the district

court’s conclusion that it was not. See Pet. 15. Respondents’ vague warning that reversing the panel majority’s ruling would “cast a cloud of uncertainty” over

2

patents on “purifying water” and “cleaning air” (Opp.

17) rings hollow. If such patents described an innovative way of purifying or cleaning, Section 101 would

pose no obstacle. To the contrary, it is the panel majority’s holding—that a process for separating one naturally occurring substance from another is patentable without any consideration of whether the process is innovative—that wreaks havoc on existing doctrine.

The petition for a writ of certiorari should be

granted.

ARGUMENT

I.

THE FEDERAL CIRCUIT’S RULING CANNOT BE

SQUARED WITH MYRIAD OR EXISTING SECTION 101

DOCTRINE MORE BROADLY

As Petitioners have explained, the panel majority’s

ruling conflicts with Myriad and Ariosa Diagnostics,

Inc v. Sequenom, Inc, 788 F.3d 1371 (Fed. Cir. 2015).

Pet. 12-22. Respondents have no persuasive response.1

A. Respondents’ sole argument regarding Myriad

is that Myriad involved composition claims (i.e., claims

to isolated DNA itself) rather than, like here, methods

of separating and analyzing DNA. Opp. 7, 13-14. But

this rigid distinction between composition and method

claims makes little sense (Pet. 13), and this Court has

already held in Alice and other cases that Section 101

applies to method claims, Alice, 573 U.S. at 217.

1

Respondents incorrectly allege that Petitioners’ Federal

Circuit brief “recognized that neither [Myriad or Ariosa] was directly on point.” Opp. 12. Respondents do not cite any such

statement about Myriad. Moreover, Respondents rely on Petitioners’ statement that Ariosa “closely resembles” this case (id.

(emphasis added))—hardly a concession that Ariosa was not on

point.

3

Indeed, almost any DNA composition claim could

be rewritten to be a method for isolating that DNA.

For example, the composition claims for the breast cancer genes at issue in Myriad easily could have been rewritten to cover a generic two-step process:

(1) separating the breast cancer genes from other genetic material and (2) analyzing the breast cancer

genes. This method claim would grant the same effective control over the relevant genes as the composition

claim invalidated by this Court and thus would raise

the same concerns about “inhibit[ing] future innovation” that the Myriad Court warned against. Pet. 13.

Respondents have no answer.

As discussed above, moreover, Myriad indicated

that an “innovative” method for isolating DNA might

have been patent eligible. 569 U.S. at 595-596. That

standard is not met here. Myriad was clear that the

mere act of separating DNA from genetic material

(which is essentially all that is claimed here) is not an

“act of invention” sufficient to justify patent eligibility

under Section 101. Id. at 591. In any event, the panel

majority here did not even consider whether Respondents’ techniques for separating smaller DNA from larger DNA fragments were innovative because it did not

reach step two of the Alice test. Pet. 13-14. Again, Respondents have no answer.

B. Unable to distinguish Myriad, Respondents

urge this Court to ignore it and instead apply the “settled two-part test” laid out in Alice. Opp. 7. But both

cases apply here. Myriad informs the Alice step-one

analysis—a patent is necessarily directed to unpatentable subject matter (i.e., a law of nature) if it merely

claims separating a gene from its genetic material. See

Myriad, 568 U.S. at 591 (describing patents at issue as

“f[alling] squarely within the law of nature exception”).

4

In other words, Respondents are simply wrong that

this case involves the “factbound” application of the Alice standard. Opp. 15. To the contrary, the panel majority ignored the important legal principle outlined in

Myriad and did so in a way that will have serious ramifications—making it easier to patent human DNA and

generally allowing clever drafters to evade the substantive limits on patentability set forth in Myriad.

Pet. 22-25.

Respondents also argue that it is overly simplistic

to describe the patents as directed to the idea of separating smaller DNA fragments from larger ones. Opp.

9-10. Rather, Respondents assert, the patents claim

the “selective removal of longer DNA from a maternal

sample to enrich the fraction in [smaller] fetal DNA, for

use in fetal genetic testing.” Id. But that is simply another way of saying the smaller fragments of DNA are

separated. See Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 77-78 (2012) (“If a law of

nature is not patentable, then neither is a process reciting a law of nature, unless that process has additional

features that provide practical assurance that the process is more than a drafting effort designed to monopolize the law of nature itself.”).

To the extent Respondents are suggesting that limiting the patents to the specific context of genetic testing somehow alters the analysis, they are wrong. As

the Mayo Court explained, Einstein could not patent

E=mc2 simply by claiming a process by which he told

“linear accelerator operators” to apply it, “[n]or could

Archimedes have secured a patent for his famous principle of flotation” by claiming a process by which he

told “boat builders” to apply the principle. Mayo, 566

U.S. at 78.

5

Respondents relatedly assert that the patents are

not directed to a natural law because they specify two

different size thresholds that should be used as part of

the separation process—500 base pairs and 300 base

pairs. Opp. 10. But as Petitioners have pointed out

(and Respondents ignore), the patents themselves state

that the 500 and 300 base pair thresholds reflect the

naturally occurring size of fetal DNA and the use of

conventional techniques to separate it. Pet 16-17. For

example, both patents explain that on average, the inventors “found” fetal DNA “to be smaller in size (approximately 500 base pairs or less)” than “maternal

DNA (greater than approximately 500 base pairs)”—a

“finding that forms the basis of the” invention claimed

in the patents. See Id. 16 n.5. In one experiment,

moreover, the patentees found that “DNA fragments

originating from the fetus were almost completely of

sizes smaller than 500 base pairs with around 70% being … sizes smaller than 300 bases.” Id.

While Respondents point out (at 10-11) that the

size of fetal DNA fragments may vary somewhat from

woman to woman, this is a red herring. The question is

not whether separating DNA at the 500/300 base pair

thresholds will achieve some desired (but unclaimed)

level of enrichment of fetal DNA for all people; the

question is whether the size distribution of DNA existed in nature before it was described in the patents (and

under Alice Step two, whether the inventors added anything inventive to it). See Mayo, 566 U.S. at 77 (“[A]

patent that simply describes [a naturally occurring] relation[ship] sets forth a natural law.”); Parker v. Flook,

437 U.S. 584, 593 n.5 (1978) (invention that merely “reveals a relationship that has always existed” is not patentable). The patents themselves admit that the

500/300 base-pair thresholds did in fact exist in nature.

6

See Pet. 16-17. Indeed, the patents report that the

claimed methods were used to study that natural distribution. Id. In addition, Respondents tellingly do not

dispute that the 300/500 base pair thresholds were in

use before the patents issued, as those values derive

from the fragment sizes used in off-the-shelf DNA kits.

Id. 17.

Respondents also contend that even if the patents

are directed to a law of nature at Alice step one, they

describe an inventive concept at Alice step two because

the 500/300 base pair limitation does not preempt the

basic principle that fetal DNA tends to be smaller than

maternal DNA. Opp. 11-12. Respondents’ Alice step

two argument is not only wrong but reinforces the need

for review. The panel majority’s decision in this case

conflicts with Myriad and other Section 101 precedent

precisely because it held that the separation of smaller

fetal DNA from larger maternal DNA survived Section

101 review at Alice step one without considering

whether the process claimed was innovative or nonconventional under Alice step two.

Had the panel majority reached the issue, it almost

certainly would have joined the district court and dissent in concluding that the patents do not claim an inventive concept because the patents merely apply conventional tools to naturally occurring materials. Pet.

14-15. It is also troubling that Petitioners were granted multiple patents claiming different size thresholds.

This means that (if the panel majority’s logic is upheld)

Petitioners could have sought dozens of other patents,

each claiming a different threshold—effectively

preempting all efforts to separate DNA based on the

naturally occurring size distribution of fetal DNA. Indeed, the panel majority’s step-one-focused reasoning

would allow for patents that undisputedly preempt

7

basic building blocks of scientific knowledge to survive

Section 101 review, as preemption is only an issue at

Alice step two.

Finally, Respondents contend that an altered version of Petitioners’ hypothetical about filtering pondwater to study a microorganism would survive Section

101 review. Compare Pet. 15 with Opp. 16-17. But Respondents’ modified hypothetical—using “an approximately 5-micron diameter filter on water from a specific kind of brackish pond to enrich the proportion of a

particular microorganism”—suffers from the same

flaws as the patents here. The use of a specific filter

size that reflects the average size of the microorganism

to be filtered adds nothing inventive to the law of nature at issue—the discovery of the size of the microorganism itself, which is akin to the discovery of the

500/300 base-pair thresholds here. Nor is there anything inventive about looking for “a particular microorganism” in a “brackish pond” where those are known

facts—just as the presence of cell-free DNA in maternal blood was already known here (App. 2a). If such a

claim were to be patent eligible, it would have to be because, under Alice step two, it includes an inventive

concept beyond that natural law. But that second-step

inquiry into the existence of an inventive concept is exactly what the Federal Circuit failed to perform here.

Step two of the Alice test also refutes Respondents’ warning that application of the Myriad principle

will “cast a cloud of uncertainty over” patents on processes like purifying water or cleaning air. Opp. 17. If

those processes include an inventive concept under Alice step two that goes beyond an underlying law of nature, Section 101 poses no obstacle. This Court created

a two-step test for a reason and should not allow the

Federal Circuit to collapse the framework it created.

8

C. In addition to conflicting with this Court’s

guidance, the panel majority’s decision creates incoherence in the Federal Circuit’s own jurisprudence. Respondents argue that the Federal Circuit’s decision in

Ariosa v. Sequenom, is distinguishable, adopting the

panel majority’s explanation without further analysis.

Opp. 14. As the Petition explained, however, the distinctions drawn by the panel majority make little sense

because (1) the “method of preparation” category was

created out of whole cloth, and (2) the “enrichment” of

the sample in Ariosa through selectively copying DNA

to create new molecules in the laboratory was, if any,

further from nature than the “enrichment” here

through mere separation of DNA already present in a

blood sample. Pet. 19-21. Tellingly, Respondents do

not even attempt to address Petitioners’ arguments.2

Respondents also contend that “even if there were

tension” between the panel majority’s ruling and Ariosa, “that would not warrant this Court’s review.”

Opp. 14. Respondents, however, never explain why

this is so. To the contrary, resolving a conflict between

this case and Ariosa would serve the important purpose of eliminating confusion in the Federal Circuit, the

district courts, and the Patent and Trademark Office.

2

Respondents do argue (at 13-14) that this case resembles

Rapid Litigation Management Ltd. v. CellzDirect, Inc., 827 F.3d

1042 (Fed. Cir. 2016). But the panel majority itself recognized that

CellzDirect is “not directly on point.” Pet. App. 15a. This is because CellzDirect involved a patent claiming a “new and useful

cryopreservation technique”—rather than the patents here, which

merely “apply[] a known laboratory technique to a newly discovered natural phenomenon.” Id. 30a (Reyna, J., dissenting); see also

Pet. C.A. Br. 27-30. And regardless of any similarity to CellzDirect, the Federal Circuit’s decision in this case still conflicts with

Ariosa, which is more directly on point.

9

Pet. 18, 21-22. Because the Federal Circuit is the only

appellate court that resolves patent law issues and it

has declined to grant en banc review in this case, this

confusion will linger unless and until this Court acts.

Respondents do not deny that the Federal Circuit itself

has expressed its confusion and called for this Court’s

help. Id. 24-25.

D. Finally, Respondents repeatedly suggest that

because the patents ostensibly claim a “process,” they

necessarily survive review under Section 101. Opp. 4,

7, 8-9, 11, 12, 16, 18. They cite no authority in support

of such a rule and for good reason: This Court has held

for nearly 170 years that an invention is not patentable

if it claims a “law of nature, natural phenomena, [or]

abstract idea[].” Pet. 5. There is no exception to that

longstanding rule for inventions that can be described

as a “process.”3 Indeed, Respondents acknowledge that

the two-step analysis laid out in Alice is the “settled

legal test” under Section 101. Opp. 15; see also id. 5

(Alice is the “well-settled test” for Section 101), id. 7

(Alice provides the “settled two-part test”). More accurately, it was the settled test until the panel majority’s ruling in this case.

II. THIS CASE PRESENTS AN EXCELLENT VEHICLE TO RESOLVE THE QUESTION PRESENTED

This case provides a strong, straightforward vehicle to reaffirm Myriad’s holding that the mere act of

separating a gene from surrounding genetic material is

not patentable under Section 101. First, the issue is

3

The only cases Respondents cite (at 8-9) are not even patent

cases. See Virginia Uranium, Inc. v. Warren, 139 S. Ct. 1894, 1900

(2019) (preemption); Merritt v. Welsh, 104 U.S. 694, 696 (1881)

(sugar import duties).

10

cleanly presented because the Federal Circuit’s decision rested solely on its conclusion that the patents-insuit are not directed to a law of nature—the Federal

Circuit did not identify any alternative grounds that

would support its holding. Second, the opinion below is

published and provides a detailed (although erroneous)

analysis to support its holding. If this case is allowed to

stand, subsequent decisions will likely be unpublished

and will contain less reasoning for this Court to review.

Respondents identify three purported reasons why

this case is a poor vehicle, none of which is persuasive.

First, Respondents argue that even if the panel majority’s decision is reversed, they might prevail on remand

under Alice step two. Opp. 18. This misses the point.

The primary reason for this Court to grant review is

that the Federal Circuit truncated the analysis at step

one and created an end-run around Myriad’s holding as

a matter of law. The hypothetical possibility that Respondents could prevail at step two on remand—

although unlikely—does nothing to detract from the

importance of reversing the legal error that is currently binding precedent in the appellate court with exclusive national jurisdiction over patent law matters.

Second, and relatedly, Respondents assert that applying the proper Myriad/Alice standard would not resolve whether all of the dependent claims are invalid.

Opp. 19. But the panel majority did not suggest that a

different analysis would apply to the dependent claims;

rather, in a short footnote, the majority “note[d], without deciding” that Respondents had “argue[d]” that

one dependent claim employed a novel methodology.

Pet. App. 16a n.1 (emphasis added). Notably, the district court held—and Judge Reyna would have held—

that all the asserted claims (including the dependent

claims) were invalid under Section 101. Id. 88a (district

11

court); id. 35a (Reyna, J., dissenting). Regardless, the

primary reason for this Court to review is to fix the legal error at Alice step one—there is no need for this

Court to make a ruling on the patentability of the dependent claims.

Finally, Respondents argue it would “depart from

… ordinary practice” to take this case up because it

arose in an interlocutory, summary judgment posture.

Opp. 17-18. This ignores that each of the Court’s last

three Section 101 rulings also arose in a summary

judgment posture. See Alice, 573 U.S. at 214; Mayo,

566 U.S. at 76; Myriad, 569 U.S. at 586. If anything,

this Court’s “ordinary practice” in the Section 101 context is to grant review of summary judgment rulings.

12

CONCLUSION

The petition for a writ of certiorari should be

granted.

Respectfully submitted.

ROBERT J. GUNTHER, JR.

CHRISTOPHER R. NOYES

OMAR A. KHAN

WILMER CUTLER PICKERING

HALE AND DORR LLP

7 World Trade Center

250 Greenwich Street

New York, NY 10007

THOMAS G. SPRANKLING

WILMER CUTLER PICKERING

HALE AND DORR LLP

2600 El Camino Real, Suite 400

Palo Alto, CA 94306

Attorneys for Roche Molecular

Systems, Inc. and Roche

Sequencing Solutions, Inc.

MAY 2021

DARALYN J. DURIE

Counsel of Record

DURIE TANGRI LLP

217 Leidesdorff Street

San Francisco, CA 94111

(415) 362-6666

ddurie@durietangri.com

KIRA A. DAVIS

DURIE TANGRI LLP

953 East 3rd Street

Los Angeles, CA 90013

Attorneys for Ariosa

Diagnostics, Inc.