Thursday, July 23, 2015

Columbia University's nucleotide sequencing patents handled roughly at CAFC in Illumina case

concerns the affirmance, by the CAFC,
of invalidity for obviousness determinations by PTAB, of several patents
assigned to Columbia University.

The nonprecedential opinion written by Judge Wallach has a large discussion
of DNA science and of legal obviousness.
In March 2012, Columbia University sued Illumina
for infringement of five DNA sequencing patents. Inter partes reviews followed.

** An NSF Grant Announcement comes into play in the "obviousness" analysis:

The tendency of simultaneous invention to weigh in
favor of obviousness would, of course, be negated if the
purported simultaneous invention was not made
independently of the claimed invention. Perhaps with
this in mind, Columbia University asserts the Solexa
patent was filed “months after features of Dr. Ju’s SBS
method were disclosed in a public National Science
Foundation Grant Announcement.” Reply Br. 6–7.

However, Columbia University asserts that at the time of
Solexa’s disclosure, “Solexa . . . thought that a nucleotide
with the requisite combination of features was
patentable.” Id. It makes a similar assertion with respect
to Amersham. Id. In so asserting, Columbia University
undermines its own argument: If Solexa and Amersham
had copied their purported simultaneous inventions from
the grant announcement, they would have had no basis to
believe their simultaneous inventions were patentable.

Columbia University also argues Amersham’s
activities did not constitute simultaneous invention
because the chemical configuration it described was
“useless as a chain terminator.” Reply Br. 7. It points out
that Illumina did not present its simultaneous invention
argument to the PTAB. Because the record is not fully
developed, the evidence of simultaneous invention as a
whole weighs only modestly in favor of obviousness.

As to copying:

Columbia University asserts “Manteia, a company
whose intellectual property was later acquired by
Illumina’s predecessor-in-interest Solexa, copied Dr. Ju’s
invention” as reflected in a 2003 presentation.
Appellant’s Br. 12. The 2003 presentation cites Dr. Ju’s
publication. See J.A. 3894. Illumina responds that the
asserted copying is irrelevant because the only elements
shown to be copied were disclosed in Tsien, Dower, and
Stemple, and that the presentation does not disclose a
deazapurine and therefore does not reflect copying of the
claimed invention. Appellee’s Br. 57.

The Kinetic Concepts case is cited as to skill level
of the "person having ordinary skill in the art" {PHOSITA}:

In general, the higher
the PHOSITA’s skill level, the more likely the PHOSITA
would find an invention obvious. Kinetic Concepts, Inc. v.
Smith & Nephew, Inc., 688 F.3d 1342, 1366 (Fed. Cir.
2012) (“[I]t is generally easier to establish obviousness
under a higher level of ordinary skill in the art.”).

Of relevance to Columbia's arguments:

Because the PTAB found the claims would have been
obvious to a PHOSITA not necessarily possessing the
additional skill Columbia University proposed, the claims
would have also been obvious to a PHOSITA with a
higher level of knowledge and ability.

As to "reduction to practice":

Columbia University asserts that if “Tsien disclosed
such nucleotides in 1991,” then it is difficult to explain the
“decade-long SBS research efforts that followed.”5 Reply
Br. 29; see also Appellant’s Br. 61. However, Illumina
points out that Dr. Ju’s invention “was not reduced to
practice until six years later using important changes not
disclosed in the patents at issue.” Appellee’s Br. 53; see
also J.A. 4130–31. Although the record does not provide a
conclusive explanation for either of these long lags, some
testimony suggests large capital investments may provide
a partial answer. See J.A. 3581.

Footnote 5 observes

Although this argument might appropriately have
been raised in support of the secondary consideration of
long-felt need, Columbia University did not assert long-felt

As to emails, and licensing:

Columbia University cites several emails from
Illumina showing an interest in “collaborating with Dr. Ju
from Columbia University on his reversible terminators,”
and stating “Professor Jingyue Ju purportedly has solved
the reversible terminator cleavable dye label issue.” J.A.
3993–95. Although these emails demonstrate an interest
in Dr. Ju’s work, none of the emails mentions the ’698,
’575, or ’869 patents or clearly indicates the subject
matter sought to be licensed fell within the claims of those
patents. In re GPAC, 57 F.3d 1573, 1580 (Fed. Cir. 1995)
(“Because, in affidavits reciting the licensing history of
the ’111 patent, GPAC did not establish which claim(s) of
the patent the licensing program incorporates, GPAC has
not shown that licensing . . . arose out of recognition and
acceptance of the subject matter claimed in the ’111
patent.”). This factor therefore provides only modest
evidence of nonobviousness.

As to commercial success:

Columbia University asserts Illumina’s sales were
significant and embody the claims of the ’698, ’869, and
’575 patents. Appellant’s Br. 59 (citing J.A. 3879–85);
Appellant’s Br. (-1548) 57; Appellant’s Br. (-1550) 57.
Illumina responds that “the very features proclaimed by
Columbia [University] to be the reason for Illumina’s
commercial success (attachment of the label to the base
via a cleavable linker) were already known in Tsien,
Dower, and Stemple,” and that Columbia University did
not assert the deazapurine contributed to commercial
Appellee’s Br. 54.

Commercial success does not favor nonobviousness.
“[I]f the feature that creates the commercial success was
known in the prior art, the success is not pertinent.”
Ormco Corp. v. Align Tech., Inc., 463 F.3d 1299, 1312
(Fed. Cir. 2006). Here, each of the features claimed to be
responsible for the commercial success of the invention
was disclosed in a single prior art reference, Tsien.
In addition, Columbia University does not itself sell
its patented invention. Although reliance on a
defendant’s or third party’s sale of a patented invention to
demonstrate commercial success may be probative of
nonobviousness in some cases, it is not particularly
helpful in the present matter because it is unclear
whether any success was attributable to developments in
the field that led to simultaneous invention (which would
tend to show the invention was obvious) or to copying
(which would tend to show the invention was nonobvious).

As to unexpected results:

Unexpected results “‘must be shown to be unexpected
compared with the closest prior art.’” Kao Corp. v.
Unilever U.S., Inc., 441 F.3d 963, 970 (Fed. Cir. 2006)
(quoting In re Baxter Travenol Labs., 952 F.2d 388, 392
(Fed. Cir. 1991)). The PTAB found pyrosequencing was
not the closest prior art. Columbia University argues
pyrosequencing was the closest prior art because it was
“the only commercial embodiment of SBS at the time of
Dr. Ju’s invention.” Appellant’s Br. 63. However, there is
no requirement that the closest prior art be
See In re Merchant, 575 F.2d 865, 869
(CCPA 1978) (“In In re Wright . . . , failure of a particular
reference to constitute the commercial standard did not
diminish its position as the closest prior art.”) (internal
quotation marks and citation omitted); see also In re
Chupp, 816 F.2d 643, 644 (Fed. Cir. 1987) (“To rebut the
prima facie case of obviousness, Chupp submitted a
declaration discussing the results of tests comparing the
herbicidal activity of the claimed compound with that of
the closest prior art compounds and with two commercial
herbicides . . . . It is undisputed that the claimed
compound gave superior results . . . .”) (emphases added).
Evidence of unexpected results in comparison to
pyrosequencing is therefore not probative of

As to anticipation by a genus:

However, “when a genus is so limited
that a person of ordinary skill in the art can at once
envisage each member of this limited class, . . . a
reference describing the genus anticipates every species
within the genus.
” Abbvie Inc. v. Mathilda & Terrence
Kennedy Inst. of Rheumatology Trust, 764 F.3d 1366, 1379
(Fed. Cir. 2014) (internal quotation marks and citation
omitted). This court agrees with the PTAB that an
embodiment comprising a 3’-OH-capped nucleotide, baselabel,
and cleavable linker could be “envisaged clearly by
one of ordinary skill in the art upon reading the Tsien
disclosure.” J.A. (-1548) 10.

As to the interplay between enablement / written description and obviousness:

However, as already
explained, if novel and nonobvious chemistry was needed
to practice the claimed inventions, Dr. Ju would have
been obligated to disclose this chemistry in the patent.
See 35 U.S.C. § 112(1) (2000).7

The matter of inability to amend (in inter partes reviews) arose:

In Appeal 2014-1548, Columbia University argues the
PTAB’s denial of its motion to amend its claims was
erroneous, and that the error was not harmless:
Columbia’s amendments would have rewritten
claim 15 in independent form and added the
deazapurine limitation to the other challenged
claims. . . .
The [PTAB’s] failure to enter Columbia’s
amendment led it to address the critical dispute
over the scope of Tsien’s and Stemple’s disclosures
first in the context of anticipation, where the
issues were (in the [PTAB’s] mistaken view)
uncontested. When the [PTAB] turned to the
obviousness of claims 15 and 16, it had already
decided that Tsien and Stemple disclosed a
nucleotide with a 3’-OH cap and a label attached
to the base by a cleavable linker, and it asked
whether adding a deazapurine was obvious.
Appellant’s Br. (-1548) 62–63.


Because the PTAB did not clearly err in its determination
of what Tsien teaches, Columbia University’s argument
based on its contrary assertion does not establish
patentability over the prior art, and is therefore rejected.
See Microsoft Corp. v. Proxyconn, Inc., No. 2014-1542,
2015 WL 3747257, at *13 (Fed. Cir. June 16, 2015)
(explaining that motions to amend may properly be
denied where the patentee has failed to establish
patentability over the prior art of record).

UPDATE on August 5. Some commentary at PatentDocs was of interest:

Not sure if I just misfollowed your comments, but bumping up the skill level to find obviousness is exactly the wrong way to apply the PHOSITA standard.

The higher you go up that level of capability, the more will be "obvious" and that is reason enough NOT to conflate the levels and what is "obvious" at the different levels.

This appears to be nothing other than the outlawed "Flash of Genius."

Maybe I am just not following what you were trying to say...

Posted by: Skeptical | August 04, 2015 at 06:01 AM

Dear Skeptical,

Thank you for pointing out that my explanation related to the PHOSITA was less than clear. Basically, the PTAB had concluded that a PHOSITA would have found the claimed invention obvious, and the fact that they did not make an explicit finding regarding the level of skill was not necessarily reversible error. The Federal Circuit then pointed out that Columbia’s argument was basically doomed, because if the PTAB had used Illumina’s expert’s definition instead of Columbia’s expert’s definition, then Columbia’s argument that the level of skill should have been found to be higher would only make the invention more obvious, not less. However, reading between the lines, I think Columbia’s main argument was that Illumina’s expert should be discounted because he was not a PHOSITA (because of the lack of Chemistry experience). But, because the Federal Circuit deferred to the Board, this argument was a non-starter. I hope that clears it up (but I remain . . . )


Posted by: Andrew Williams | August 04, 2015 at 08:42 AM

I laughed at your closing Andrew.

The quantum of error that is "reversible" or not is an interesting one.

And as here, shifting the proper establishment of one of the factors of PHOSITA working against the arguments one side is making may be seen as saying that the error was self-induced.

But I do not think a court should make its judgment on an error-induced PHOSITA - no matter which side introduces that error. It is the function of the court in applying PHOSITA to get that set-up right, and I do not think the quantum of reversible error should be judged against the error-prone argument, poorly made.

Even if the Federal Circuit defers to the Board, the "shortcuts" of not explicating the proper foundations of applying the law are problematic. Shall we revisit eBay for a quick lesson?

Posted by: Skeptical | August 05, 2015 at 06:52 AM



Post a Comment

<< Home