Ex Parte Yakhini et al

Patent Trial and Appeal Board

Jun 8, 2016

10817244 (P.T.A.B. Jun. 8, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
10/817,244 0410312004
22878 7590 06/10/2016
Agilent Technologies, Inc, in care of:
CPA Global
P. 0. Box 52050
Minneapolis, MN 55402
FIRST NAMED INVENTOR
Zohar Y akhini
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
10020503-2 3028
EXAMINER
NEGIN, RUSSELL SCOTT
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
06/10/2016 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):
IPOPS.LEGAL@agilent.com
Agilentdocketing@cpaglobal.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ZOHAR Y AKHINI,
ROBERT KINCAID, AMIR BEN-DOR,
LESLIE A. LEONARD, and NICHOLAS M. SAMP AS
Appeal2013-004406 1
Application 10/81 7 ,244
Technology Center 1600
Before DONALD E. ADAMS, DEMETRA J. MILLS, and
FRANCISCO C. PRATS, Administrative Patent Judges.
PRATS, Administrative Patent Judge.
DECISION ON APPEAL
This appeal under 35 U.S.C. § 134(a) involves claims to computer
implemented methods for overlaying gene-related data onto chromosome
maps. The Examiner rejected the claims for obviousness.
We have jurisdiction under 35 U.S.C. § 6(b). We reverse.
1 Agilent Technologies, Inc., is the real party in interest. App. Br. 1.
Appeal2013-004406
Application 10/81 7 ,244
STATEMENT OF THE CASE
Claim 1 illustrates the appealed subject matter, and reads as follows
(App. Br. 37):
1. A computer-implemented method for overlaying gene-
or protein-related data on chromosome maps to provide at least
one data-enhanced chromosome map as an output, said method
compnsmg:
receiving said chromosome maps as a first input to a
computer;
receiving a list comprising a plurality of gene- or protein-
related data items as a second input to said computer, each data
item including data other than data specifying a genetic location
on said chromosome maps;
providing an identifier specifying a genetic location for
each of said data items on said chromosome maps;
matching said identifiers with predefined identifiers on at
least one of said chromosome maps;
reordering said data items to an order matching the order
of said predefined identifiers on said at least one of said
chromosome maps; and
displaying said data items on said at least one
chromosome map at locations determined by said reordered
data items to provide said data-enhanced output, wherein said
receiving, matching, reordering and displaying are carried out
automatically by said computer.
The following rejections are before us for review:
(1) Claims 1-3, 12-15, 21-23, 29, 55, and 56, under 35 U.S.C.
§ 103(a), for obviousness over Haefliger,2 Willecke,3 Cuticchia,4 Ledley,5
and Metaphase Chromosome Spread6 (Final Action 3-10);7
2 Jacques-Antoine Haefliger et al., Four Novel Members of the Connexin
Family of Gap Junction Proteins, 267 J. Biol. Chem. 2057-2064 (1992).
2
Appeal2013-004406
Application 10/81 7 ,244
(2) Claims 4--10, under 35 U.S.C. § 103(a), for obviousness over
Haefliger, Willecke, Cuticchia, Ledley, Metaphase Chromosome Spread,
and Koleszar8 (Final Action 13-15);
(3) Claim 11, under 35 U.S.C. § 103(a), for obviousness over
Haefliger, Willecke, Cuticchia, Ledley, Metaphase Chromosome Spread,
Koleszar, and Corcoran9 (Final Action 16-17);
(4) Claims 16-18, 24--28, 30, 32, and 33, under 35 U.S.C. § 103(a),
for obviousness over Haefliger, Willecke, Cuticchia, Ledley, Metaphase
Chromosome Spread, and Golub 10 (Final Action 17-21 );
(5) Claims 19, 31, 34, 35, 80, and 81, under 35 U.S.C. § 103(a), for
obviousness over Haefliger, Willecke, Cuticchia, Ledley, Metaphase
Chromosome Spread, Golub, Lowe, 11 and Schultz12 (Final Action 23-25);
3 Klaus Willecke et al., Six genes of the human connexin gene family coding
for gap junctional proteins are assigned to four different human
chromosomes, 53 Eur. J. Cell. Biol. 275-280 (1990).
4 A.J. Cuticchia et al., CMAP: contig mapping and analysis package, a
relational database for chromosome reconstruction, 8 CABIOS 467--474
(1992).
5 US Patent No. 4,656,594 (issued Apr. 7, 1987).
6 Definition of "metaphase chromosome spread," Dictionary of
Developmental Biology and Embryology (2002)
(http://www. credoreference. com/ entry /wileydevbio/
metaphase_chromosome_spread).
7 Final Action entered April 6, 2012.
8 US Patent No. 6,519,583 Bl (issued Feb. 11, 2003).
9 US Patent App. Pub. No. 2003/0224419 Al (published Dec. 4, 2003).
10 T. R. Golub et al., Molecular Classification of Cancer: Class Discovery
and Class Prediction by Gene Expression Monitoring, 286 Science 531-537
(1999).
11 US Patent App. Pub. No. 2002/0081597 Al (published June 27, 2002).
12 US Patent No. 6,391,551 Bl (issued May 21, 2002).
3
Appeal2013-004406
Application 10/81 7 ,244
(6) Claims 44, 45, 47, 48, 90, 93, 94, and 101, under 35 U.S.C.
§ 103(a), for obviousness over Haefliger, Willecke, Cuticchia, Ledley,
Metaphase Chromosome Spread, Golub, Lowe, Schultz, and Pollack13
(Final Action 27-29); and
(7) Claims 46 and 92, under 35 U.S.C. § 103(a), for obviousness over
Haefliger, Willecke, Cuticchia, Ledley, Metaphase Chromosome Spread,
Golub, Lowe, Schultz, Pollack, and Vanhooydonck14 (Final Action 30-31 ).
OBVIOUSNESS
The Examiner's Position
The Examiner cited Haefliger as disclosing a study of rat connexin
(gap junction) proteins, in which each of four newly discovered connexin
proteins was distinctly identified according to molecular weight, and their
corresponding gene locations placed on mouse chromosomal maps. Final
Action 4--5 (citing Haefliger, Fig. 6). The Examiner noted that Haefliger
also placed, on those chromosomal maps, identifiers of the corresponding
human genes, as well as identifiers providing the locations of the human
genes on the human chromosomes. Id. at 5. The Examiner noted also that
Haefliger cited Willecke as its source of information regarding the human
connexin genes, and the Examiner cited Willecke for its disclosure of the
human chromosomal locations of the corresponding human connexin genes.
Id. at 6.
13 Jonathan R. Pollack et al., Genome-wide analysis of DNA copy-number
changes using cDNA microarrays, 23 Nature Genetics 41--46 (1999).
14 US Patent No. 6,682, 172 B2 (issued Jan. 27, 2004).
4
Appeal2013-004406
Application 10/81 7 ,244
While the Examiner found that Haetliger and Willecke at least
suggested claim 1 's step of reordering data items, the Examiner conceded
that those reference "do not teach inputting the chromosomal maps into a
computer. Haefliger et al. and Willecke et al. do not teach the computer
limitations of the instantly rejected claims." Id.
To address those deficiencies, the Examiner cited Ledley and
Cuticchia. Id. at 6-7. As to Ledley, the Examiner contended:
It would have been ... obvious to one of ordinary skill
in the art at the time of the instant invention to modify the
mouse chromosomal maps of Haefliger et al. and the human
chromosomal mapping of Willecke et al. by use of function of
inputting chromosomal maps into computer systems as in
Ledley wherein the motivation would have been that entering
chromosomal maps into a computerized system facilitates
automated chromosomal analysis and interaction with the
operator of the computer [column 3, line 59 to column 4, line
24 of Ledley].
Tri <>f 0
_LU. UL _/ •
As to Cuticchia, the Examiner contended:
It would have been further obvious to one of ordinary
skill in the art at the time of the instant invention to modify the
mouse chromosomal maps of Haefliger et al., the human
chromosomal mapping of Willecke et al., and the inputting of
chromosomal maps of Ledley by use of the computer
equipment of Cuticchia et al. wherein the motivation would
have been that the computers of Cuticchia et al. automate and
expedite results [the first two paragraphs under "System and
methods" on pages 467 to 468 of Cuticchia et al.].
Id. at 9-10.
5
Appeal2013-004406
Application 10/81 7 ,244
Analysis
As stated in In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992):
[T]he examiner bears the initial burden . . . of presenting a
prim a facie case of unpatentability ....
After evidence or argument is submitted by the applicant
in response, patentability is determined on the totality of the
record, by a preponderance of evidence with due consideration
to persuasiveness of argument.
In the instant case, we are not persuaded that the preponderance of the
evidence supports the Examiner's prima facie case of obviousness.
Independent claims 1 and 80 recite a computer implemented method that
includes a step of receiving chromosome maps as a first input into a
computer, and both of those claims recite that the receiving step is "carried
out automatically by said computer." App. Br. 37, 42. The other
independent claim on appeal, claim 101, similarly recites:
receiving a list comprising a plurality of gene- or protein-
related data items as an input to a computer, each data item
having identifiers specifying a genetic location for each of said
data items on said chromosome maps . . ., wherein said
receiving ... [is] carried out automatically by said computer ...
Id. at 43.
As seen above, the Examiner relied initially on Ledley as providing
the methodology and motivation for automatically inputting Haefliger's
chromosome map, which included Willecke' s human connexin gene data,
into a computer, as required by independent claims 1, 80, and 101. We
agree with Appellants (App. Br. 18) that the Examiner has not explained
adequately why an ordinary artisan would have applied the teachings of
Ledley to the Haefliger' s chromosomal maps.
6
Appeal2013-004406
Application 10/81 7 ,244
As is evident, Haetliger's chromosomal maps consist of vertical lines
along which are indicated the relative chromosomal positions of the genes
encoding the connexin proteins that were discovered, as well as the positions
on the human chromosome of the corresponding human genes. Haefliger,
2062 (Fig. 6). Haefliger, thus explains that "[t]he position of loci in human
chromosomes, determined in previously reported studies, are shown to the
right of the chromosome maps." Id. (Fig. 6 legend).
In contrast to Haefliger' s use of maps to schematically depict
chromosomes and the location of specific genes on those chromosomes,
Ledley describes methods that automate the process of producing a
karyotype, which involves generating direct visual images of chromosomes
when viewed from a microscope. Ledley, col. 1, 11. 8-14; id. at col. 3, 1. 45
through col. 4, 1. 23. Ledley's invention seeks to improve the karyotyping
process by providing an automated detector that detects, from an image of
chromosomes obtained from the tested individual, a chromosome spread
suitable for karyotyping:
When a good metaphase spread comes into view under the
microscope and TV camera 24 (via optical path 36), presence of
the good metaphase spread is detected by metaphase detector
30 (connected to the microscope and TV camera 24 via optical
path 44), and the computer system 20 is notified by metaphase
detector 30 via the generation of output 46.
Id. at col. 3, 11. 59---65 (bolding omitted).
We are not persuaded that the Examiner has adequately explained
why Ledley's teachings, directed to automated visual recognition of
chromosome metaphase spreads using a microscope, with no mention of
being able to locate the positions of any specific genes on the chromosome,
7
Appeal2013-004406
Application 10/81 7 ,244
would have prompted an ordinary artisan to automatically input, into a
computer, Haefliger's maps, which schematically depict chromosomes and
the location of specific genes on those chromosomes. As noted above, the
Examiner contends that "the motivation would have been that entering
chromosomal maps into a computerized system facilitates automated
chromosomal analysis and interaction with the operator of the computer
[column 3, line 59 to column 4, line 24 of Ledley]." Final Action 9. The
Examiner does not direct us, however, to any evidence in that passage or any
other portion of Ledley suggesting that Ledley's system is capable of, or
suitable for, analyzing the type of data presented in the chromosomal maps
of Haefliger.
As noted above, the Examiner also appears to rely on Cuticchia as
suggesting the automated step of receiving Haefliger's chromosomal maps
as an input to a computer, as required by claims 1, 80, and 101, the
independent claims under appeal. Final Action 9-10; see also Ans. 7
("[T]he documents of Ledley and Cuticchia et al. not only teach obviousness
of automation of such a plot [as Figure 6 of Haefliger], but the documents
also teach obviousness of inputting and outputting data from related
diagrams into computer systems.").
While the Examiner directs us to certain passages within Cuticchia to
support his indicated rationale, the Examiner does not identify or discuss
specifically which teachings within those passages support that rationale, or
suggest the automated step of receiving Haefliger's chromosomal maps as
an input to a computer. In particular, the Examiner contends that "the
motivation would have been that the computers of Cuticchia et al. automate
8
Appeal2013-004406
Application 10/81 7 ,244
and expedite results [the first two paragraphs under 'System and methods'
on pages 467 to 468 of Cuticchia et al.]."
We acknowledge that the cited passage on pages 467--468 of
Cuticchia discusses how users may input gene sequence data into a database
to create a sequential map of clones or gene fragments. Cuticchia 468
("Once an order of fragments has been reached, CMAP [the contig mapping
and analysis package] can update 'to' and 'from' clone pointers via SQL
[structured query language] to create the linear arrangement representing the
contig map within the database."); see also id. at 4 72, left column
(discussing how users input sequence data into the database).
The Examiner does not, however, explain with adequate specificity
how or why these passages of Cuticchia, or any other portions of the
reference, suggest that the results of Haefliger' s chromosomal mapping of
connexin genes might be expedited or automated, as the Examiner posits.
The Examiner also does not explain specifically why an ordinary artisan
would have viewed the nucleotide sequence-related techniques described in
Cuticchia as being applicable to the chromosomal mapping experiments
described in Haefliger, or how, specifically, Haefliger would have been
modified to incorporate Cuticchia's teachings to arrive at a process including
the automated step of receiving chromosomal maps as an input to a
computer, as required by independent claims 1, 80, and 101 under appeal
herein.
Accordingly, we are not persuaded that the Examiner has adequately
explained why the combination of Haefliger, Willecke, Ledley, and
Cuticchia, as posited, teaches or suggests the automated step of receiving
chromosomal maps as an input to a computer, as required by claims 1, 80,
9
Appeal2013-004406
Application 10/81 7 ,244
and 101, the independent claims under appeal. Because we are not
persuaded that the Examiner has adequately explained why the combination
of Haefliger, Willecke, Ledley, and Cuticchia teaches or suggests all of the
steps required by claims 1, 80, and 101, and because each of the Examiner's
rejections relies ultimately on that combination of references to render
obvious the processes recited in those claims, we reverse each of the
Examiner's rejections.
SUMMARY
For the reasons discussed, we reverse each of the Examiner's
obviousness rejections.
REVERSED
10