DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Status of claims
Canceled:
3-4
Pending:
1-2 and 5-10
Withdrawn:
5 and 8-10
Examined:
1-2 and 6-7
Independent:
1 and 7
Allowable:
none
Rejections applied
Abbreviations
x
112/b Indefiniteness
PHOSITA
"a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention"
112/b "Means for"
BRI
Broadest Reasonable Interpretation
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
x
102, 103
JE
Judicial Exception
x
101 JE(s)
112/a
35 USC 112(a) and similarly for 112/b, etc.
101 Other
N:N
page:line
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed on the 5/4/2022 filing receipt, this application claims priority to as early as 6/22/2021. At this point in examination, all claims have been interpreted as being accorded this priority date.
Withdrawal / revision of objections and/or rejections
In view of the amendment and remarks:
The previous objections are withdrawn, however new objections are applied.
The previous 112/b rejections are withdrawn, except as noted below, and new rejections are applied.
Rejections and/or objections not maintained from previous office actions are withdrawn. The following rejections and/or objections are either maintained or newly applied. They constitute the complete set applied to the instant application.
Claim rejections - 112/b
The following is a quotation of 35 USC 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.
Claims 1-2 and 6-7 are rejected under 112/b, as indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention. Claims depending from rejected claims are rejected similarly, unless otherwise noted, and any amendments in response to the following rejections should be applied throughout the claims, as appropriate. With regard to any suggested amendment below, for claim interpretation during the present examination it is assumed that each amendment suggested here is made. However equivalent amendments also would be acceptable. For compact prosecution and examination, similar withdrawn claims also should be amended.
The following issues cause the respective claims to be rejected under 112/b as indefinite:
Claim
Recitation
Comment (suggestions in bold)
1
a sample treatment step: using...;
using...
A list follows "sample treatment step:...," however
(i) the list lacks a grammatical conjunction, e.g. "and" vs. "or" such that the relationship among the list elements is unclear
(ii) each of the "using..." steps should appear on a new line with equal indentation
1, 7
to obtain...
..., a nitrous acid degradation array, respectively
It is unclear what is referenced by the recited "respectively." It is unclear how to interpret the term. This rejection is maintained.
1
using a liquid chromatography and a mass spectrometry
Not interpretable at least because "chromatography" and "spectrometry" should not, in this grammatical construction, be preceded by grammatical articles. That is, the preceding "a" in each instance is grammatically incorrect. This rejection might be overcome either by deleting these articles or amending to "chromatograph[[y]]" and "spectrometer[[y]]" which nouns are preceded by articles.
1
1,6-anhydro structure-including sequences - generation time;
The relationship is unclear between "generation time," the preceding "...sequences" and the rest of the claim.
1
1,6-anhydro structure-excluding sequences - generation time;
The relationship is unclear between "generation time," the preceding "...sequences" and the rest of the claim.
1
total sequences - sorted in decreasing order based on the content - generation time;
Not interpretable. Possibly the use of hyphens or dashes in this context should be revised / removed.
1
selected sequences - at least one of generation time
Not interpretable. Possibly the use of hyphens or dashes in this context should be revised / removed.
7
A sequencing system...
a data storage device, comprising:
a data processing unit, configured to calculate...
a sequence database building unit, configured to build...
a specific result output unit, configured to screen...
Claim 7 is to a 101 machine or manufacture, i.e. a "system" in this instance, limited according to its claimed physical structure, but it remains unclear what is the structure associated with the recited "data processing," "calculate IdoA/GlcA" and similar computational steps.
While the claim now recites a "data storage device," it remains unclear, regarding recitation of structure, as to how the recited process steps relate to the data storage device.
As previously noted, this rejection might be overcome by, for example, reciting instructions stored on the device and configured according to the recited elements and steps.
This rejection is maintained.
Claim rejections - 35 USC 103
In the event the determination of the status of the application as subject to AIA 35 USC 102 and 103 is incorrect, any correction of the statutory basis 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 USC 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 of this title, 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 USC 102(b)(2)(C) for any potential 35 USC 102(a)(2) prior art against the later invention.
Claims 1-2 and 7
Claims 1-2 and 7 are rejected under 35 USC 103 as unpatentable over Wang 2018 (as cited on the 10/20/2025 "Notice of References Cited" form 892) in view of Miller 2020 (as cited on the 10/20/2025 "Notice of References Cited" form 892).
Regarding claim 1, the recited sample preparation and treatment are taught as at least "Low molecular weight heparins (LMWHs)" (Wang: abstract; and entire document); "LMWHs are... exhaustively digested to disaccharides using a cocktail of heparinase I, II and III" (Wang: p. 83, 1st col., penultimate para.; and entire document) and "nitrous acid depolymerization" (Wang: §1; and entire document).
The recited chromatography and spectrometry are taught as "liquid chromatography (HPLC) and ESI–MS/MS approach to sequence... short oligosaccharides" (Wang: abstract; and entire document).
Wang does not teach the recited "IdoA/GlcA," but Miller does as "A library of standards representing features found in heparin and HS (including... IdoA/GlcA) was collected" (Miller: p. 2, 2nd col.; and entire document).
The recited database and screening read "identified from a HS oligosaccharide library screen" (Miller: abstract; and entire document).
Wang teaches "1,6-anhydro structure" (Wang: §1; and entire document).
The art is applied to claim 7 similarly to claim 1 above.
Claim 2 further specifies enzymatic digestion and nitrous acid degradation which read on Wang's "LMWHs are either exhaustively digested to disaccharides using a cocktail of heparinase I, II and III for" (Wang: p. 83, 1st col., penultimate para.; and entire document) and "nitrous acid depolymerization" (Wang: §1; and entire document).
Combining Wang and Miller
In the absence of a secondary consideration to the contrary, it would have been prima facie obvious for PHOSITA to modify the heparin analysis of Wang using the related teaching of Miller. As motivation to combine, an advantage taught by Miller of modifying methods such as those of Wang would have been the teaching of Miller that "We take advantage of a library of defined standards to build unique IMMS features that enable us to obtain unambiguous sequence information on both validated standards and unknown natural HS saccharides..." (Miller: p. 2, 1st col., penultimate para.). Thus, PHOSITA would have been motivated to modify Wang using the above techniques of Miller in order to achieve the above advantage. One would have had a reasonable expectation of success in doing so because Wang and Miller are generally drawn to related teaching, and PHOSITA would have understood how to and would have been motivated to apply the teaching of Miller to the related teaching of Wang.
Claim rejections - 101
35 USC 101 reads:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
For each rejection below, dependent claims are rejected similarly as not remedying the rejection, unless otherwise noted.
Judicial exceptions (JE) to 101 patentability
Claims 1-2 and 6-7 are rejected under 35 USC 101 because the claimed inventions are not directed to patent eligible subject matter. After consideration of relevant factors with respect to each claim as a whole, each claim is directed to one or more JEs (i.e. an abstract idea, a natural phenomenon, a law of nature and/or a product of nature), as identified below. Any elements or combination of elements beyond the JE(s) (i.e. "additional elements") are conventional and do not constitute significantly more than the JE(s). Thus, no claim includes additional elements amounting to significantly more than the JE(s), as explained below.
In Alice, citing Mayo and Bilski, two Mayo/Alice questions determine eligibility under 101: First, is a claim directed to a JE? And second, if so, does the claim recite significantly more than the JE?
MPEP 2106 organizes JE analysis into Steps 1, 2A (1st & 2nd prongs) and 2B as follows below.
MPEP 2106 and the following USPTO website provide further explanation and case law citations: www.uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter? -- MPEP 2106.I and 2106.03
[Step 1: claims 1-2 and 6-7: YES]
Step 2A, 1st prong: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea? -- abstract idea -- MPEP 2106.I and 2106.04
Preliminarily, in a 1st prong of Step 2A, elements of independent claim 1 are interpreted as directed to the abstract idea of building and screening a sequencing database including the JE elements of "calculating...," "building..." and "screening...," each of which, including all recitation within each listed element, in at least some embodiments within a BRI, involves only manipulation of data. While manipulation of data is not per se directed to an abstract idea, in this instance the above-identified elements are directed to the abstract ideas identified below.
BRIs of the claims are analogous to an abstract idea in the form of at least a mental process, at least equivalent to a computer-implemented process, including obtaining and comparing intangible data (e.g. Cybersource, Synopsys and Electric Power Group). In a BRI, it is not clear that the claim embodiments are limited so as to require complexity precluding analogy to a mental process.
BRIs of the claims also are analogous to an abstract idea in the form of a mathematical concept, including mathematical relationships and calculations, as found in the following case law, as cited and discussed above: collecting information, analyzing it, and displaying certain results of the collection and analysis (Electric Power Group) and/or obtaining and comparing intangible data (e.g. Cybersource, Ambry and Myriad CAFC) and/or execution of an algorithm to implement mathematical relationships and/or formulas, including image processing (e.g. TLI, Digitech, Benson, Flook, Diehr, FuzzySharp, In re Grams and In re Abele all as cited in MPEP 2106).
Instant examples of math concepts include calculating IdoA/GlcA and screening the sequence database according to input qualification information.
The preceding case law examples are cited for the basic form of their identified abstract ideas, and analogy to these example abstract ideas need not be within the same technology field, 101 analysis generally being assumed to be neutral with respect to technology field.
Regarding inherency of abstract ideas, MPEP 2106.04.II.A.1 includes: "the claims in Alice Corp. v. CLS Bank, 'described' the concept of intermediated settlement without ever explicitly using the words 'intermediated' or 'settlement'" (emphasis added, p. 1). Similarly, inherency can effectively be recitation, as in, for example, "By claiming simply 'crystalline paroxetine hydrochloride hemihydrate' with no reference to how it was produced, SKB effectively claimed 'crystalline paroxetine hydrochloride hemihydrate whether non-naturally occurring or arising through natural conversion.' Claim 1, as issued, therefore combines patentable and unpatentable subject matter, and is invalid under Section 101." (capitalization added, SmithKline Beecham Corp. v. Apotex Corp., 365 F.3d 1306, 1321-33, Fed. Cir. 2004).
In the instant type of data processing claims, the specification is not merely adding background explanation as to how a claimed process works, e.g. a physical process based on, involving or further explained by abstract ideas and natural laws. Rather, the specification is detailing the only disclosed way that a programmer may proceed from the recited inputs to the recited outputs, e.g. through actual performance of the disclosed judicial exceptions (JEs).
Regarding the "Meaning of 'Recites,'" MPEP 2106.04.II.A.1 states:
In Prong One examiners evaluate whether the claim recites a judicial exception, i.e. whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim. While the terms "set forth" and "described" are thus both equated with "recite", their different language is intended to indicate that there are two ways in which an exception can be recited in a claim. For instance, the claims in Diehr, 450 U.S. at 178 n. 2, 179 n.5, 191-92, 209 USPQ at 4-5 (1981), clearly stated a mathematical equation in the repetitively calculating step, and the claims in Mayo, 566 U.S. 66, 75-77, 101 USPQ2d 1961, 1967-68 (2012), clearly stated laws of nature in the wherein clause, such that the claims "set forth" an identifiable judicial exception. Alternatively, the claims in Alice Corp., 573 U.S. at 218, 110 USPQ2d at 1982, described the concept of intermediated settlement without ever explicitly using the words "intermediated" or "settlement."
While the "set forth" language approximates explicit recitation, it also is fundamental that all recitation must be interpreted and that to be patent eligible a claim must satisfy 101 according to its properly interpreted scope, e.g. for all embodiments on which the claim reads, e.g. according to any inherency pertinent to a given claim and disclosure accompanying that claim, i.e. consistent with the "described" meaning of "recites" as in the MPEP. Thus, within a BRI, the identified abstract idea elements read on one or more embodiments which only involve manipulation of data. It is not clear than any improvement argument clearly on the record causes a claim not to be directed to a JE for all embodiments within the scope of the claim.
As in Alice (at 306, as cited in the MPEP above) and Bilski (as cited in Alice, id), an abstract idea may comprise multiple abstract elements or steps (i.e. from Alice: "a series of steps" at 306) and need not be a single equation, relationship or principle.
It is not clear that the identified elements must represent other than an abstract idea according to any relevant analysis or case law.
[Step 2A, 1st prong, abstract idea: claims 1 and 7: YES]
Step 2A, 2nd prong: If the claims recite a judicial exception under the 1st prong, then is the judicial exception integrated into a practical application? -- MPEP 2106.I and 2106.04(d)
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
In Step 2A, 1st prong above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In Step 2B below, any remaining steps and/or elements are therefore in addition to the identified JE(s). Any such additional steps and additional elements are further discussed in Step 2B.
Here in Step 2A, 2nd prong, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
At this point in examination it is not yet the case that any of the Step 2A, 2nd prong considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of 1. an improvement, 2. treatment, 3. a particular machine or 4. a transformation is clear in the record.
For example, regarding the first consideration at MPEP 2106.04(d)(1), the record, including for example the specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field. The claims do not yet clearly result in such an improvement (e.g. specification: [40, 227]).
[Step 2A, 2nd prong: claims 1 and 7: NO]
Step 2B: Do the claims recite a non-conventional arrangement of additional elements in addition to the identified JEs? -- MPEP 2106.I and 2106.05
Addressing the second Mayo/Alice question, all elements of claims 1 and 7 are part of one or more identified JEs (as described above), except for elements identified here as conventional elements in addition to the above judicial exceptions:
The recited isolating, preparing, sequencing, chromatography and spectrometry are conventional elements of a laboratory and/or computing environment and/or conventional data gathering/input elements, as exemplified by Wang 2018 (as cited on the attached "Notice of References Cited" form 892), and generally it is understood that the examples in the reference are well-known and routine.
It is emphasized that, outside of an improvement argument, analysis of what is conventional generally pertains to the above-identified additional elements and not to elements identified as part of a JE.
[Step 2B: claims 1 and 7: NO]
Summary and conclusion regarding claims 1 and 7
Summing up the above analysis of claims 1 and 7, each viewed as a whole and considering all elements individually and in combination, no claim recites limitations that transform the claim, finally interpreted as directed to the identified JE(s), into patent eligible subject matter, and it is not clear that any claim is sufficiently analogous to controlling case law identifying an example of an eligible claim.
Remaining claims
Claim 6 adds elements which also are part of the identified JEs for the same reasons described above regarding the independent claims and therefore do not provide the something significantly more necessary to satisfy 101.
Elements of the following claims are additional elements but nonetheless are conventional elements of a laboratory or computing environment, conventional data gathering elements or conventional post-processing elements, as in the following specific examples which also are understood to be well-known and routine:
claim 2: "...digestion... with a mixture of heparinases I, II, and III...," are conventional elements of a laboratory and/or computing environment and/or conventional data gathering/input elements, as exemplified by Wang 2018, and generally it is understood that the examples in the reference are well-known and routine.
None of the dependent claim elements provides the something significantly more than the identified JE(s) necessary to satisfy 101.
Citations to art
In the above citations to documents in the art, rejections refer to the portions of each document cited as example portions as well as to the entirety of each document, unless otherwise noted in the situation of lengthy, multi-subject documents. Other passages not specifically cited within a document may apply as well.
Conclusion
No claim is allowed.
Applicant's amendments necessitated the new grounds for rejection in this action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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The examiner for this Office action, G. Steven Vanni, may be contacted at:
(571) 272-3855 Tu-F 8-7 (ET). If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D. Riggs, II, may be reached at (571) 270-3062.
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686
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