James Yen et al.

Patent Trials and Appeals Board

Dec 9, 2020

2020001659 (P.T.A.B. Dec. 9, 2020)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
12/963,272 12/08/2010 James Yen ZYMO.P0007US 2527
108197 7590 12/09/2020
Parker Highlander PLLC
1120 South Capital of Texas Highway
Bldg. 1, Suite 200
Austin, TX 78746
EXAMINER
STRZELECKA, TERESA E
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
12/09/2020 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
docket@phiplaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte JAMES YEN and XIYU JIA
Appeal 2020-001659
Application 12/963,272
Technology Center 1600
Before JOHN E. SCHNEIDER, RYAN H. FLAX, and
RACHEL H. TOWNSEND Administrative Patent Judges.

SCHNEIDER, Administrative Patent Judge.
DECISION ON APPEAL
STATEMENT OF THE CASE
Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the
Examiner’s decision to reject claims 1–9 and 13–31.2 We have jurisdiction
under 35 U.S.C. § 6(b).
We AFFIRM.

1 We use the word Appellant to refer to “applicant” as defined in 37 C.F.R.
§ 1.42(a). Appellant identifies the real party in interest as Zymo Research
Corporation. Appeal Br. 3.
2 Oral arguments were heard on November 16, 2020. A copy of the hearing
transcript (“Tr.”) has been made part of the record.
Appeal 2020-001659
Application 12/963,272
2
CLAIMED SUBJECT MATTER
The claims are directed to methods for genomic DNA
hydroxymethylation analysis. Claim 1, reproduced below, is illustrative of
the claimed subject matter:
1. A method of performing locus specific quantification of
glucosylated DNA in a sample comprising:
(i) performing quantitative polymerase chain reaction
(PCR) amplification on a first portion of a DNA sample
comprising both DNA having a glucosylated
hydroxymethylation position and DNA that does not include a
glucosylated hydroxymethylation position; and
(ii) comparing the results of the amplification to a control
amplification to determine the glucosylated
hydroxymethylation at said locus.
The Examiner has rejected claims 1–9 and 13–31 under 35 U.S.C.
§ 112, first paragraph for failure to comply with the written description
requirement.
OPINION
Issue
The issue on appeal is whether the Examiner has correctly determined
that the present disclosure does not reasonably convey to those skilled in the
art that the inventor had possession of the claimed subject matter as of the
filing date so as to comply with the written description requirement under
35 U.S.C. § 112.
The Examiner finds that the claims are directed to locus specific
quantification of glucosylated DNA in a sample using quantitative
polymerase chain reaction (“qPCR”) amplification. Non-Final Act. 9. The
Examiner contends that only examples 6 and 7 of the present disclosure
relate to qPCR and that the disclosure does not show that the amount of
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Application 12/963,272
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glucosylated DNA nucleotides can be determined using qPCR. Id. The
Examiner finds that the present disclosure fails to give sufficient details to
demonstrate that the applicants had invented the claimed method. See id. at
8–9. The Examiner also finds that the present disclosure is limited to
hydroxymethylated cytosine and that there is no evidence that the invention
can be used for other hydroxymethylated nucleotides such as
hydroxymethyluracil. Id. at 9–10.
Appellant contends that, although the examples in the present
specification do not set forth the specific enzymes used or instructions for
the procedure, qPCR was well-known at the time of filing and one skilled in
the art would “have [had] no problem employing” the technique. Appeal Br.
4–5. With respect to the term “locus specific quantification” Appellant
contends that the term only refers to a region of a chromosome and not a
specific nucleotide position and that the claimed method need not yield
quantity data for a specific location. Id. at 6. Appellant also contends that the
recited method provides relative quantitative values for glucosylated DNA
which is a suitable proxy for detection of hydroxymethylated DNA. Id. at 7–
8.
Legal Principles
“[T]he examiner bears the initial burden, on review of the prior art or
on any other ground, of presenting a prima facie case of unpatentability. If
that burden is met, the burden of coming forward with evidence or argument
shifts to the applicant.” In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992).
In addition providing an enabling disclosure, a description adequate to
satisfy 35 U.S.C. § 112, first paragraph, “must ‘clearly allow persons of
ordinary skill in the art to recognize that [the inventor] invented what is
claimed.’ In other words, the test for sufficiency is whether the disclosure of
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Application 12/963,272
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the application relied upon reasonably conveys to those skilled in the art that
the inventor had possession of the claimed subject matter as of the filing
date.” Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir.
2010) (en banc) (citation omitted, alteration in original).
“[T]he 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.” Id.
“[W]hile the description requirement does not demand any particular
form of disclosure, or that the specification recite the claimed invention in
haec verba, a description that merely renders the invention obvious does not
satisfy the requirement.” Id. at 1352.
Analysis
We have considered the arguments presented by the Appellant and the
Examiner’s determinations, as well as the evidence of record, and conclude
that the present disclosure would not have reasonably conveyed to one
skilled in the art that the inventors had in their possession the invention
recited in the claims.
Claim 1 recites a method for “locus specific quantification of
glucosylated DNA in a sample.” Appeal Br. 9 (Claims App’x.). The
Examiner contends that the term “locus specific” refers to quantification at a
specific position in a DNA sample. See Non-Final Act. 8; Ans. 15. Appellant
responds by contending that the term as used in the art refers to a region of a
chromosome, such as a certain number of base pairs of a chromosome and
not a specific nucleotide position. Appeal Br. 6. We find that the Examiner
has the better position.
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Application 12/963,272
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Although we agree with Appellant that one definition of “locus
specific” may refer generally to a region of a chromosome representing the
locus of a gene, that does not appear to be the meaning of the term as used in
the present application.3 “[A] claim must be read in view of the
specification of which it is a part.” Renishaw PLC v. Marposs Societa per
Azioni, 158 F.3d 1243, 1248 (Fed. Cir. 1998). As the Examiner points out,
claim 13 refers to comparing specific glucosylated hydroxymethylation
positions. Ans. 15; Appeal Br. 10. Moreover the Specification teaches that
the disclosed method is directed to site specific quantification. For example
the Specification teaches that the disclosed technique can be used to
determine “which DNA positions comprise 5'mC and which comprise
5'hmC.” Spec. 3–4. The Specification also teaches “[t]hus, protection of
5'hmC positions provides a method for specific analysis of
hydroxymethylation versus cytosine positions that are methylat[ed] or lack
modification.” Id. at 10. Based on the foregoing, we agree with the
Examiner that the term locus specific is used in the instant claims in
reference to positon specific quantification.
Using that construction we agree with the Examiner that the written
description fails to support the claims. We discern nothing in the present
disclosure that shows the inventors ever determined the quantity of
glucosylated DNA at a specific positon within a given sample. Example 7,
which purports to show that qPCR can be used for locus specific

3 Appellant asks that we take judicial notice that the term locus specific refer
to a location on a chromosome, such as a genetic locus, and not a specific
nucleotide site. Appeal Br. 6. We decline to do so. As shown above, our
construction of the term is not based on a dictionary definition. Rather our
construction is based on how the term is used in the context of the
Specification.
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Application 12/963,272
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quantification of 5'-hydroxymethylcytosine does not report quantification for
any specific positon. Spec. 21–22.
The Specification also does not support the claim limitation calling for
“a DNA sample comprising both DNA having a glucosylated
hydroxymethylation position and DNA that does not include a glucosylated
hydroxymethylation position.” Appeal Br. 9 (Claims App’x.). Example 7,
which purports to show quantification of glucosylated DNA describes the
testing of two samples, a “Control DNA” from Example 5 (FIG. 5),
containing methylated cytosines in CpG context and a “+ Tet” DNA sample,
containing glucosyl-5'-hydroxymethylcytosine. Spec. 21. The
Specification’s Table 2, reproduced below, reports Cp data on two Tet1
samples as well as two control samples. Id. at 22.

Table 2 from the present Specification showing the quantification data for
example 7.

We discern nothing in Example 7, which is the portion of the Specification
pointed to by Appellant as disclosing quantifying (see Appeal Br. 6–7), that
teaches quantification of a sample having both DNA having a glucosylated
hydroxymethylation position and DNA that does not include a glucosylated
hydroxymethylation position.
During oral argument, Appellant contended that Figure 5, which
appears to show a portion of unreacted DNA in the glucosylated sample
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Application 12/963,272
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supports the limitation calling for DNA having a glucosylated
hydroxymethylation position and DNA that does not include a glucosylated
hydroxymethylation position. Tr. 18. We are not persuaded by this
argument.
Although Example 7 describes using the methylated DNA from
Figure 5 as a control, we do not read the example as teaching that the
glucosylated sample was combined with the methylated cytosine control
sample and then digested. Moreover, in its Appeal Brief, Appellant argues
that all of the DNA in the glucosylated sample was glucosylated. Appeal Br.
5. Similarly, Appellant argued that “detection of the glucosylated 5hmC
DNA is also a suitable proxy for detection of hydroxymethylated DNA, as
essentially all hydroxymethylated DNA is glucosylated as evidenced by
FIGS. 2A-B.” Id. at 7. This would lead one skilled in the art to the
conclusion that the samples tested did not contain DNA that does not include
a glucosylated hydroxymethylation position as required by the claims.
Conclusion
Based on the foregoing we conclude that the Examiner properly found
that the present disclosure does not reasonably convey to those skilled in the
art that the inventor had possession of the claimed subject matter as of the
filing date.
CONCLUSION
The Examiner’s rejection under 35 U.S.C. § 112, first paragraph for
failure to comply with the written description requirement is affirmed.
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Application 12/963,272
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DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1–31 112 Written
Description
1–31

TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R.
§ 1.136(a)(1)(iv).
AFFIRMED