DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Drawings
New corrected drawings in compliance with 37 CFR 1.121(d) are required in this application because:
Figure(s) 1(a) – 9(c) is/are not properly labeled. See 37 CFR 1.84(u)(1).
The margins are not of proper size in Figure(s) 1(a) – 9(c). See 37 CFR 1.84(g).
Each panel in FIG. 1(a)-1(), 3(a) – 4(d), and 8(a) – 9(c) needs to be labeled in accordance with 37 CFR 1.84(u)(1) and (2),
The numbering of the sheets of drawings bearing FIG(s). 1(a) – 9(c) is not in compliance with all aspects of 37 CFR 1.84(t).
Applicant is advised to employ the services of a competent patent draftsperson outside the Office, as the U.S. Patent and Trademark Office no longer prepares new drawings. The corrected drawings are required in reply to the Office action to avoid abandonment of the application. The requirement for corrected drawings will not be held in abeyance.
INFORMATION ON HOW TO EFFECT DRAWING CHANGES
Replacement Drawing Sheets
Drawing changes must be made by presenting replacement sheets which incorporate the desired changes and which comply with 37 CFR 1.84. An explanation of the changes made must be presented either in the drawing amendments section, or remarks, section of the amendment paper. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). A replacement sheet must include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of the amended drawing(s) must not be labeled as “amended.” If the changes to the drawing figure(s) are not accepted by the examiner, applicant will be notified of any required corrective action in the next Office action. No further drawing submission will be required, unless applicant is notified.
Identifying indicia, if provided, should include the title of the invention, inventor’s name, and application number, or docket number (if any) if an application number has not been assigned to the application. If this information is provided, it must be placed on the front of each sheet and within the top margin.
Annotated Drawing Sheets
A marked-up copy of any amended drawing figure, including annotations indicating the changes made, are required by the examiner. The annotated drawing sheet(s) must be clearly labeled as “Annotated Sheet” and must be presented in the amendment or remarks section that explains the change(s) to the drawings.
Timing of Corrections
Applicant is required to submit acceptable corrected drawings within the time period set in the Office action. See 37 CFR 1.85(a). Failure to take corrective action within the set period will result in ABANDONMENT of the application.
If corrected drawings are required in a Notice of Allowability (PTOL-37), the new drawings MUST be filed within the THREE MONTH shortened statutory period set for reply in the “Notice of Allowability.” Extensions of time may NOT be obtained under the provisions of 37 CFR 1.136 for filing the corrected drawings after the mailing of a Notice of Allowability.
Claim Rejections - 35 USC § 112, (b) / Second Paragraph
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-9 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1, 5, and 6 are indefinite with respect to what constitutes the metes and bounds of “facing”. For example, can the cytosine be immediately/adjacent to the “terminal guanine”, id est, 3’ or 5’, or is this to mean that the cytosine is hybridized to the terminal guanine, or is some other meaning to be ascribed? It is also unclear if the probe has some form of secondary structure, and if so, just what forms of secondary structure are encompassed and how such relates to one nucleotide “facing” another.
Claims 1, 5, and 6 are indefinite with regard to what constitutes the metes and bounds of the “interaction” that occurs between the fluorescent dye and a guanine For example, is the fluorescent signal produced by the dye quenched by the guanine, and/or does the guanine comprise a quencher moiety and that it is this moiety that is quenching the “fluorescent dye”.
Claims 2-4, which depend from claim 1, and claims 7-9, which depend from claim 6, fail to overcome the above-identified issues and are similarly rejected.
Claim Rejections - 35 USC § 112 - Enablement
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Standard for Enablement
As set forth in the unanimous U.S. Supreme Court decision in Amgen Inc., et al. v. Sanofi et al. 598 U.S. ___ (2023):
Our decisions in Morse, Incandescent Lamp, and Holland Furniture reinforce the simple
statutory command. If a patent claims an entire class of processes, machines,
manufactures, or compositions of matter, the patent’s specification must enable a person skilled in the art to make and use the entire class. In other words, the specification must enable the full scope of the invention as defined by its claims. The more one claims, the more one must enable. See §112(a); see also Continental Paper Bag Co. v. Eastern Paper Bag Co., 210 U. S. 405, 419 (1908) (“[T]he claims measure the invention.”). (Emphasis added)
***
To be fair, Amgen does not dispute this much. It freely admits that it seeks to claim for
itself an entire universe of antibodies. Still, it says, its broad claims are enabled because scientists can make and use every undisclosed but functional antibody if they simply follow the company’s “roadmap” or its proposal for “conservative substitution.” We cannot agree. These two approaches amount to little more than two research assignments… Whether methods like a “roadmap” or “conservative substitution” might suffice to enable other claims in other patents—perhaps because, as this Court suggested in Incandescent Lamp, the inventor identifies a quality common to every functional embodiment, supra, at 13—they do not here. They leave a scientist about where Sawyer and Man left Edison: forced to engage in “painstaking experimentation” to see what works. 159 U. S., at 475. That is not enablement. More nearly, it is “a hunting license.” Brenner v. Manson, 383 U. S. 519, 536 (1966). (Emphasis added)
Standard for Enablement
As set forth in the unanimous U.S. Supreme Court decision in Amgen Inc., et al. v. Sanofi et al. 598 U.S. ___ (2023):
Our decisions in Morse, Incandescent Lamp, and Holland Furniture reinforce the simple
statutory command. If a patent claims an entire class of processes, machines,
manufactures, or compositions of matter, the patent’s specification must enable a person skilled in the art to make and use the entire class. In other words, the specification must enable the full scope of the invention as defined by its claims. The more one claims, the more one must enable. See §112(a); see also Continental Paper Bag Co. v. Eastern Paper Bag Co., 210 U. S. 405, 419 (1908) (“[T]he claims measure the invention.”). (Emphasis added)
***
To be fair, Amgen does not dispute this much. It freely admits that it seeks to claim for
itself an entire universe of antibodies. Still, it says, its broad claims are enabled because scientists can make and use every undisclosed but functional antibody if they simply follow the company’s “roadmap” or its proposal for “conservative substitution.” We cannot agree. These two approaches amount to little more than two research assignments… Whether methods like a “roadmap” or “conservative substitution” might suffice to enable other claims in other patents—perhaps because, as this Court suggested in Incandescent Lamp, the inventor identifies a quality common to every functional embodiment, supra, at 13—they do not here. They leave a scientist about where Sawyer and Man left Edison: forced to engage in “painstaking experimentation” to see what works. 159 U. S., at 475. That is not enablement. More nearly, it is “a hunting license.” Brenner v. Manson, 383 U. S. 519, 536 (1966). (Emphasis added)
Attention is directed to MPEP 2111 Claim Interpretation; Broadest Reasonable Interpretation [R-10.2019]. As stated therein:
During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification." The Federal Circuit’s en banc decision in Phillips v. AWH Corp., 415 F.3d 1303, 1316, 75 USPQ2d 1321, 1329 (Fed. Cir. 2005) expressly recognized that the USPTO employs the "broadest reasonable interpretation" standard:
The Patent and Trademark Office ("PTO") determines the scope of claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction "in light of the specification as it would be interpreted by one of ordinary skill in the art." In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364[, 70 USPQ2d 1827, 1830] (Fed. Cir. 2004). Indeed, the rules of the PTO require that application claims must "conform to the invention as set forth in the remainder of the specification and the terms and phrases used in the claims must find clear support or antecedent basis in the description so that the meaning of the terms in the claims may be ascertainable by reference to the description." 37 CFR 1.75(d)(1). (Emphasis added).
Holding and Rationale
Claims 1-9 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Claims 1-9 are drawn to “a method for detecting a target nucleic acid”. The type of nucleic acid and the source of same are undefined in the claims.
Applicant, at page 14, paragraph [0029], asserts:
[0029] The source of the target nucleic acid is not particularly limited and the
target nucleic acid may be a nucleic acid derived from an animal, a plant, a
fungus, a microorganism, or a virus. (Emphasis added)
In applying the broadest reasonable interpretation, the claimed method has been construed as encompassing the detection of any nucleic acid, be it DNA or RNA, as found in any organism. Such nucleic acids are deemed to encompass any and all manner of sequences in the human Y chromosome as well as the nucleic acids found in the different strains and variants of the coronavirus that was responsible for the COVID-19 pandemic.
It is noted that the subject application claims benefit of a priority date of 09 February 2016. By way of comparison, the human Y chromosome was not fully sequenced until 2023.1 It is also noted that the first strain of the SARS-CoV-2 virus that causes COVID-19 was not detected until December 2019, which is some 3 years subsequent to applicant’s priority date. It is also noted that numerous strains and variants have been found through 2023.2
Attention is directed to the following publications which teach of the enormity of the genera of virus, plants, insects, bacteria, mammals, and species encompassed by the subfamily Murinae as the detection of any and all genes from all members of the various genera are encompassed by the instant claims.
“Viruses” (Wikipedia.com, accessed 08 September 2023), teaches:
An enormous variety of genomic structures can be seen among viral species; as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. There are millions of different types of viruses, although fewer than 7,000 types have been described in detail. (Emphasis added)
“How many species of bacteria are there” (wisegeek.com; accessed 21 January 2014) teaches:
Currently, estimates of the total number of species of bacteria range from about 10 million to a billion, but these estimates are tentative, and may be off by many orders of magnitude. By comparison, there are probably between 10 and 30 million species of animals, the vast majority of them insects. The number of scientifically recognized species of animals is about 1,250,000. There are almost 300,000 recognized species of plants.
“Fungi,” (Wikipedia.com; accessed 08 September 2023), teaches:
As of 2020, around 148,000 species of fungi have been described by taxonomists,[6] but the global biodiversity of the fungus kingdom is not fully understood.[48] A 2017 estimate suggests there may be between 2.2 and 3.8 million species.[5]
“Plant,” (Wikipedia.com; accessed 08 September 2023) teaches:
There are about 380,000 known species of plants, of which the majority, some 260,000, produce seeds.
“Mammal,” (Wikipedia.com; accessed 08 September 2023) teaches:
According to Mammal Species of the World, which is updated through periodic editions, 5,416 species were identified in 2006. These were grouped into 1,229 genera, 153 families and 29 orders.[5]
“Murinae,” (Wikipedia.com, accessed 08 September 2023) teaches:
The Old World rats and mice, part of the subfamily Murinae in the family Muridae, comprise at least 519 species. Members of this subfamily are called murines. In terms of species richness, this subfamily is larger than all mammal families except the Cricetidae and Muridae, and is larger than all mammal orders except the bats and the remainder of the rodents.
“Fish,” (Wikipedia.com, accessed 08 September 2023) teaches:
Fish are abundant in most bodies of water. They can be found in nearly all aquatic environments, from high mountain streams (e.g., char and gudgeon) to the abyssal and even hadal depths of the deepest oceans (e.g., cush-eels and snailfish), although no species has yet been documented in the deepest 25% of the ocean.[4] At 34,300 described species, fish exhibit greater species diversity than any other group of vertebrates.[5]
“Archaea,” Wikipedia.com (accessed 08 September 2023), teaches:
The classification of archaea into species is also controversial. Ernst Mayr defined a species as a group of interbreeding organisms which are reproductively isolated, but this is of no help since archaea only reproduce asexually.[37]
Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma.[38] On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. Some researchers question whether such species designations have practical meaning.[40]
Current knowledge on genetic diversity is fragmentary, so the total number of species cannot be estimated with any accuracy.[22] (Emphasis added)
“Algae,” Wikipedia.com (accessed 03-04-2016) teaches:
The most recent estimate suggests 72,500 algal species worldwide.
“Protozoa,” Wikipedia.com (accessed 05-11-2016), teaches:
The classification of protozoa has been and remains a problematic area of taxonomy. Where they are available, DNA sequences are used as the basis for classification; however, for the majority of described protozoa, such material is not available. (Emphasis added)
For purposes of examination, the claimed method have been construed as encompassing the detection of any and all manner of sequences, be it DNA and/or RNA, as found in all of the millions of different organisms.
A review of the disclosure does locate a Sequence Listing. The Sequence Listing is found to comprise some 50 sequences, all of which are identified as being DNA. Those sequences with SEQ ID NO. 1-22, 24, 25, and 27-50 are all identified as being an “Artificial Sequence”.
SEQ ID NO. 23 is identified as being a 425 nucleotide sequence of Mycoplasma pneumoniae. SEQ ID NO. 26 is identified as being a 664 nucleotide sequence of Mycobacterium tuberculosis.
The disclosure has not been found to provide the nucleotide sequence for any virus, much less any variant of the coronavirus responsible for the COVD-19. Likewise, the disclosure has not been found to disclose the nucleotide sequence for the human Y chromosome. Further, the disclosure has not been found to disclose the nucleotide sequence for any plant, much less any RNA sequence that is found in any organism. Clearly, the nucleotide sequence for target sequences, be they DNA or RNA, as well as the “nucleic acid probe” required to perform the claimed methods, are essential material.3
As evidenced above, it is well settled that applicant must enable the full scope of that which is claimed. Applicant’s non-disclosure of such essential material has not been found to constitute enablement of the full scope of the claimed methods.
In view of the above analysis and in the absence of convincing evidence to the contrary, claims 1-9 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement.
Claim Rejections - 35 USC § 112 – Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Standard for Written Description.
Attention is directed to MPEP 2163.02 Standard for Determining Compliance With the Written Description Requirement [R-07-2022]:
An objective standard for determining compliance with the written description requirement is, "does the description clearly allow persons of ordinary skill in the art to recognize that he or she invented what is claimed." In re Gosteli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989). Under Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991), to satisfy the written description requirement, an applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention, and that the invention, in that context, is whatever is now claimed. (Emphasis added)
Attention is also set directed to MPEP 2161.01 I [R-07-2022], wherein is stated:
For instance, generic claim language in the original disclosure does not satisfy the written description requirement if it fails to support the scope of the genus claimed. Ariad, 598 F.3d at 1349-50, 94 USPQ2d at 1171 ("[A]n adequate written description of a claimed genus requires more than a generic statement of an invention’s boundaries.") (citing Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1405-06); Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 968, 63 USPQ2d 1609, 1616 (Fed. Cir. 2002) (holding that generic claim language appearing in ipsis verbis in the original specification did not satisfy the written description requirement because it failed to support the scope of the genus claimed); Fiers v. Revel, 984 F.2d 1164, 1170, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) (rejecting the argument that "only similar language in the specification or original claims is necessary to satisfy the written description requirement").
As set forth in Fiers v. Revel 25 USPQ2d 1601, 1604-5 (CAFC, January 1993):
We thus determined that, irrespective of the complexity or simplicity of the method of isolation employed, conception of a DNA, like conception of any chemical substance, requires a definition of that substance other than by its functional utility.
Fiers' attempt to distinguish Amgen therefore is incorrect. We also reject Fiers' argument that the existence of a workable method for preparing a DNA establishes conception of that material. (Emphasis added)
Conception of a substance claimed per se without reference to a process requires conception of its structure, name, formula, or definitive chemical or physical properties...
The difficulty that would arise if we were to hold that a conception occurs when one has only an idea of a compound, defining it by its hoped-for function, is that would-be inventors would file patent applications before they had made their inventions and before they could describe them. That is not consistent with the statute or the policy behind the statute, which is to promote disclosure of inventions.
As set forth in the en banc decision in Ariad Pharmaceuticals Inc. v. Eli Lilly and Company, 94 USPQ2d 1161 (Fed. Cir. 2010) at 1171:
We held that a sufficient description of a genus instead requires the disclosure of either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can “visualize or recognize” the members of the genus. Id. at 1568-69. We explained that an adequate written description requires a precise definition, such as by structure, formula, chemical name, physical properties, or other properties, of species falling within the genus sufficient to distinguish the genus from other materials. Id. at 1568 (quoting Fiers v. Revel, 984 F.2d 1164, 1171 [25 USPQ2d 1601] (Fed. Cir. 1993)). We have also held that functional claim language can meet the written description requirement when the art has established a correlation between structure and function. See Enzo, 323 F.3d at 964 (quoting 66 Fed. Reg. 1099 (Jan. 5, 2001)). But merely drawing a fence around the outer limits of a purported genus is not an adequate substitute for describing a variety of materials constituting the genus and showing that one has invented a genus and not just a species.
***
In Fiers, we rejected the argument that “only similar language in the specification or original claim is necessary to satisfy the written description requirement.” 984 F.2d at 1170 (emphasis added). Rather, we held that original claim language to “a DNA coding for interferon activity” failed to provide an adequate written description as it amounted to no more than a “wish” or “plan” for obtaining the claimed DNA rather than a description of the DNA itself. Id. at 1170-71. That Fiers applied § 112, first paragraph, during an interference is irrelevant for, as we stated above, the statute contains no basis for ignoring the description requirement outside of this context. And again in Enzo we held that generic claim language appearing in ipsis verbis in the original specification does not satisfy the written description requirement if it fails to support the scope of the genus claimed. 323 F.3d at 968. We concluded that “[a] claim does not become more descriptive by its repetition, or its longevity.” Id. at 969.
***
The written description requirement also ensures that when a patent claims a genus by its function or result, the specification recites sufficient materials to accomplish that function—a problem that is particularly acute in the biological arts.
Attention is also directed to MPEP 2163 Guidelines for the Examination of Patent Applications Under the 35 U.S.C. 112(a) or Pre-AIA 35 U.S.C. 112, first paragraph, “Written Description” Requirement [R-07.2022], at part II iii):
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus (see i)(C) above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. (Emphasis added)
Attention is also directed to the decision of University of California v. Eli Lilly and Co. (CA FC, July 1997) 43 USPQ2d 1398 wherein is stated:
In claims involving chemical materials, generic formulas usually indicate with specificity what the generic claims encompass. One skilled in the art can distinguish such a formula from others and can identify many of the species that the claims encompass. Accordingly, such a formula is normally an adequate written description of the claimed genus. In claims to genetic material, however, a generic statement such as “vertebrate insulin cDNA” or “mammalian cDNA,” without more, is not an adequate written description of the genus because it does not distinguish the claimed genus from others, except by function. It does not specifically define any of the genes that fall within its definition. It does not define any structural features commonly possessed by members of the genus that distinguish them from others. One skilled in the art therefore cannot, as one can do with a fully described genus, visualize or recognize the identity of the members of the genus. A definition by function, as we have previously indicated, does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is See Fiers, 984 F.2d at 1169-71, 25 USPQ2d at 1605-06 (discussing Amgen). It is only a definition of a useful result rather than a definition of what it achieves as a result. Many such genes may achieve that result. The description requirement of the patent statute requires a description of an invention, not an indication of a result that one might achieve if one made that invention. See In re Wilder, 736 F.2d 1516, 222 USPQ 369, 372-373 (Fed. Cir. 1984) (affirming rejection because the specification does “little more than outlin[e] goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate.”). Accordingly, naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not a description of that material.
Thus, as we have previously held, a cDNA is not defined or described by the mere name cDNA,” even if accompanied by the name of the protein that it encodes, but requires a kind of specificity usually achieved by means of the recitation of the sequence of nucleotides that make up the cDNA. See Fiers, 984 F.2d at 1171, 25 USPQ2d at 1606.
Holding and Rationale
Claims 1-9 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1-9 are drawn to “a method for detecting a target nucleic acid”. The type of nucleic acid and the source of same are undefined in the claims.
Applicant, at page 14, paragraph [0029], asserts:
[0029] The source of the target nucleic acid is not particularly limited and the
target nucleic acid may be a nucleic acid derived from an animal, a plant, a
fungus, a microorganism, or a virus. (Emphasis added)
In applying the broadest reasonable interpretation, the claimed method has been construed as encompassing the detection of any nucleic acid, be it DNA or RNA, as found in any organism. Such nucleic acids are deemed to encompass any and all manner of sequences in the human Y chromosome as well as the nucleic acids found in the different strains and variants of the coronavirus that was responsible for the COVID-19 pandemic.
It is noted that the subject application claims benefit of a priority date of 09 February 2016. By way of comparison, the human Y chromosome was not fully sequenced until 2023.4 It is also noted that the first strain of the SARS-CoV-2 virus that causes COVID-19 was not detected until December 2019, which is some 3 years subsequent to applicant’s priority date. It is also noted that numerous strains and variants have been found through 2023.5
Attention is directed to the following publications which teach of the enormity of the genera of virus, plants, insects, bacteria, mammals, and species encompassed by the subfamily Murinae as the detection of any and all genes from all members of the various genera are encompassed by the instant claims.
“Viruses” (Wikipedia.com, accessed 08 September 2023), teaches:
An enormous variety of genomic structures can be seen among viral species; as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. There are millions of different types of viruses, although fewer than 7,000 types have been described in detail. (Emphasis added)
“How many species of bacteria are there” (wisegeek.com; accessed 21 January 2014) teaches:
Currently, estimates of the total number of species of bacteria range from about 10 million to a billion, but these estimates are tentative, and may be off by many orders of magnitude. By comparison, there are probably between 10 and 30 million species of animals, the vast majority of them insects. The number of scientifically recognized species of animals is about 1,250,000. There are almost 300,000 recognized species of plants.
“Fungi,” (Wikipedia.com; accessed 08 September 2023), teaches:
As of 2020, around 148,000 species of fungi have been described by taxonomists,[6] but the global biodiversity of the fungus kingdom is not fully understood.[48] A 2017 estimate suggests there may be between 2.2 and 3.8 million species.[5]
“Plant,” (Wikipedia.com; accessed 08 September 2023) teaches:
There are about 380,000 known species of plants, of which the majority, some 260,000, produce seeds.
“Mammal,” (Wikipedia.com; accessed 08 September 2023) teaches:
According to Mammal Species of the World, which is updated through periodic editions, 5,416 species were identified in 2006. These were grouped into 1,229 genera, 153 families and 29 orders.[5]
“Murinae,” (Wikipedia.com, accessed 08 September 2023) teaches:
The Old World rats and mice, part of the subfamily Murinae in the family Muridae, comprise at least 519 species. Members of this subfamily are called murines. In terms of species richness, this subfamily is larger than all mammal families except the Cricetidae and Muridae, and is larger than all mammal orders except the bats and the remainder of the rodents.
“Fish,” (Wikipedia.com, accessed 08 September 2023) teaches:
Fish are abundant in most bodies of water. They can be found in nearly all aquatic environments, from high mountain streams (e.g., char and gudgeon) to the abyssal and even hadal depths of the deepest oceans (e.g., cush-eels and snailfish), although no species has yet been documented in the deepest 25% of the ocean.[4] At 34,300 described species, fish exhibit greater species diversity than any other group of vertebrates.[5]
“Archaea,” Wikipedia.com (accessed 08 September 2023), teaches:
The classification of archaea into species is also controversial. Ernst Mayr defined a species as a group of interbreeding organisms which are reproductively isolated, but this is of no help since archaea only reproduce asexually.[37]
Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma.[38] On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. Some researchers question whether such species designations have practical meaning.[40]
Current knowledge on genetic diversity is fragmentary, so the total number of species cannot be estimated with any accuracy.[22] (Emphasis added)
“Algae,” Wikipedia.com (accessed 03-04-2016) teaches:
The most recent estimate suggests 72,500 algal species worldwide.
“Protozoa,” Wikipedia.com (accessed 05-11-2016), teaches:
The classification of protozoa has been and remains a problematic area of taxonomy. Where they are available, DNA sequences are used as the basis for classification; however, for the majority of described protozoa, such material is not available. (Emphasis added)
For purposes of examination, the claimed methods have been construed as encompassing the detection of any and all manner of sequences, be it DNA and/or RNA, as found in all of the millions of different organisms.
A review of the disclosure does locate a Sequence Listing. The Sequence Listing is found to comprise some 50 sequences, all of which are identified as being DNA. Those sequences with SEQ ID NO. 1-22, 24, 25, and 27-50 are all identified as being an “Artificial Sequence”.
SEQ ID NO. 23 is identified as being a 425 nucleotide sequence of Mycoplasma pneumoniae. SEQ ID NO. 26 is identified as being a 664 nucleotide sequence of Mycobacterium tuberculosis.
The disclosure has not been found to provide the nucleotide sequence for any virus, much less any variant of the coronavirus responsible for the COVD-19. Likewise, the disclosure has not been found to disclose the nucleotide sequence for the human Y chromosome. Further, the disclosure has not been found to disclose the nucleotide sequence for any plant, much less any RNA sequence that is found in any organism. Clearly, the nucleotide sequence for target sequences, be they DNA or RNA, as well as the “nucleic acid probe” required to perform the claimed methods, are essential material.
Applicant’s non-disclosure of such essential material has not been found to satisfy the written description requirement.
In view of the above analysis ad in the absence of convincing evidence to the contrary claims 1-9 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-9 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3-8 of U.S. Patent No. 11,434,533 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the claims in the ‘533 patent are to “a method for detecting a target nucleic acid” which is based in part on measuring fluorescent intensity.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Standard for Obviousness
As set forth in the US Supreme Court decision in KSR International Co. v. Teleflex Inc., et al.(550 U.S. 398, April 30, 2007):
The question is not whether the combination was obvious to the patentee but whether the combination was obvious to a person with ordinary skill in the art Under the correct analysis, any need or problem known in the field of endeavor at the time of invention and addressed by the patent can provide a reason for combining the elements in the manner claimed.
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The same constricted analysis led the Court of Appeals to conclude, in error, that a patent claim cannot be proved obvious merely by showing that the combination of elements was "obvious to try." Id., at 289 (internal quotation marks omitted). When there is a design need or market pressure to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely the product not of innovation but of ordinary skill and common sense. In that instance the fact that a combination was obvious to try might show that it was obvious under 103.
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We build and create by bringing to the tangible and palpable reality around us new works based on instinct, simple logic, ordinary inferences, extraordinary ideas, and sometimes even genius. These advances, once part of our shared knowledge, define a new threshold from which innovation starts once more. And as progress beginning from higher levels of achievement is expected in the normal course, the results of ordinary innovation are not the subject of exclusive rights under the patent laws. Were it otherwise patents might stifle, rather than promote, the progress of useful arts. See U.S. Const., Art. I, 8, cl. 8. These premises led to the bar on patents claiming obvious subject matter established in Hotchkiss and codified in 103. Application of the bar must not be confined within a test or formulation too constrained to serve its purpose.
Holding and Rationale
Claims 1-9 are rejected under 35 U.S.C. 103 as being unpatentable over US 2013/0143212 A1 (Hosomi).
Hosomi, at paragraph [0121] – [0124] teaches of designing probes that not only bear a fluorescent label, but that the fluorescent label attached to the cytosine, and that upon hybridization, the cytosine is opposite (applicant’s facing) a guanine, and that the guanine quenches the fluorescent signal. As disclosed therein:
[0121] From the standpoint of the detection efficiency, it is preferred that the detection probes are labeled probes having a labeling substance.
[0122] Specific examples of the labeling substance in the labeled probes include fluorescent dyes and fluorophores and specific preferred examples of the labeled probes include probes that are labeled with a fluorescent dye and emit fluorescence by themselves and whose fluorescence is decreased (e.g., quenched) upon formation of a hybrid. (Emphasis added)
[0123] Probes utilizing this kind of fluorescence quenching phenomenon are generally referred to as "fluorescence quenching probes". Thereamong, as the detection probes, those in which a base in the 3'-region (e.g., 3'-end) or the 5'-region (e.g., 5'-end) of the oligonucleotide is labeled with a fluorescent dye are preferred, and it is preferred that the base to be labeled is cytosine (C). In this case, in the detection target sequences to which the labeled probes hybridize, it is preferred that the base sequence of the respective labeled probes are designed such that the base forming a pair with the terminal base C of the labeled probe or a base which is positioned at 1 to 3 bases away from the base forming a pair, is guanine (G). Such a probe is generally referred to as a "guanine quenching probe" and is known as a "Q Probe". (Emphasis added)
[0124] When this kind of guanine quenching probe hybridizes to a detection target sequence, the terminal cytosine (C) labeled with a fluorescent dye approaches the guanine (G) in the detection target sequence, resulting in the phenomenon of decreased fluorescence of the fluorescent dye (decrease in the fluorescence intensity). By using such a probe, hybridization and dissociation can be easily verified based on the signal fluctuation. Further, the labeled substance is usually, for example, capable of binding to a phosphate group of a nucleotide. (Emphasis added)
[0125] In addition to this kind of detection method where a Q Probe is used, any known detection method may be applied, and examples thereof include Taq-Man Probe methods and RFLP methods.
Hosomi, at paragraph [0013], teaches:
The method according to any one of [1] to [11], in which at least one of the at least two genes is a reference gene whose abundance in the nucleic acids contained in the subject sample is known in advance and at least one other gene of the at least two genes is a target gene whose abundance in the nucleic acids contained in the subject sample is to be measured. [13] The method according to [12], which includes determining the abundance of the target gene in the nucleic acids contained in the subject sample by comparing the detection signal of an amplification product derived from the reference gene with a detection signal of an amplification product derived from the target gene
Hosomi, at paragraph [0158], teaches:
[0158] FIG. 1(A) shows a melting curve which represents the relationship between the temperature of an arbitrary nucleic acid mixture of a target gene and a reference gene and a detection signal such as absorbance or fluorescence intensity, and FIG. 1(B) shows a melting curve (also referred to as a "differential melting curve") which represents the relationship between the temperature and the differential detection signal value.
Hosomi, at paragraph [0177], teaches:
[0158] FIG. 1(A) shows a melting curve which represents the relationship between the temperature of an arbitrary nucleic acid mixture of a target gene and a reference gene and a detection signal such as absorbance or fluorescence intensity, and FIG. 1(B) shows a melting curve (also referred to as a "differential melting curve") which represents the relationship between the temperature and the differential detection signal value. (Emphasis added)
Hosomi, in claim 13, claims a method of measuring target gene abundance where one takes uses an amplification product. As stated therein:
13. The method according to claim 12, comprising determining the abundance of the target gene in the nucleic acids contained in the subject sample by comparing the detection signal of an amplification product derived from the reference gene with a detection signal of an amplification product derived from the target gene.
In view of the detailed teachings of the prior art, it would have been obvious to one of ordinary skill in the art at the time of the invention to detect target nucleic acids via a method whereby the target, which can be the result of an amplification reaction, is detected by the interaction of both a complementary probe, and the quenching of fluorescent signal when the probe is hybridized to the target and wherein the terminal C of the probe bears a fluorescent label and that, upon hybridization of the probe to the target, the fluorescently-labeled C is within 1-3 bases of a guanine, which will quench the fluorescent signal.
It would have also been obvious to said ordinary artisan to evaluate the signal, and any decrease/quenching of same, by performing melting curve analysis.
In view of the well-developed state of the art, the detailed guidance provided, said ordinary artisan would have not only been well motivated, but would have also had a most reasonable expectation of success. In view of the above analysis and in the absence of convincing evidence to the contrary, claims 1-9 are rejected under 35 U.S.C. 103 as being unpatentable over US 2013/0143212 A1 (Hosomi).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Bradley L. Sisson whose telephone number is (571)272-0751. The examiner can normally be reached Monday to Thursday, from 6:30 AM to 5 PM..
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Shen can be reached on 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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