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 .
Applicant Response
Applicant's response, filed 01/29/2026, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
The Applicant initiated interview request submitted 02/20/2026 was denied because no power of attorney was filed for the only tentative participant listed (Blaine T. Bettinger) in the request.
The claim objections and rejections under 35 U.S.C. 112(b) are newly applied after further consideration.
It is suggested that applicant cancel the withdrawn claims.
Election/Restrictions
Claims 1-44, 76, 78-79, and 81-82 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected inventions, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 07/05/2023.
Terminal Disclaimer
The terminal disclaimer filed on 03/27/2025 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of any patent granted on Application Number 16/485670 was reviewed and accepted in the office action mailed 07/29/2025. The terminal disclaimer has been recorded.
Claim Status
Claims 46-47, 49-56, and 59-71 are canceled.
Claims 1-45, 48, 57-58, and 72-82 are pending.
Claims 1-44, 76, 78-79 and 81-82 are withdrawn.
Claims 45, 48, 57-58, 72-75, 77 and 80 are under examination herein.
Claims 45, 48 and 58 are objected to.
Claims 45, 48, 57-58, 72-75, 77 and 80 are rejected.
Priority
The instant application is a National Stage entry of PCT/US2017/066863 , International Filing Date: 12/15/2017, which claims priority to PCT/US2017/041579, filed 07/11/2017 and PCT/US2017/017842, filed 02/14/2017. As such, the effective filing date of claims 1-45, 48, 57-58, and 72-82 is 02/14/2017.
Drawings
The drawings were accepted in the office action mailed 09/27/2024.
Claim Objections
NEW OBJECTIONS:
Claims 45, 48 and 58 are objected to because of the following informalities:
In claim 45, “genome sequence data” should be “genomic data” for consistency.
In claim 45, “access unit” should be “Access Unit” for consistency.
In claim 45, “named Class” should be “
In claim 48, “pair descriptor… are paired unreads descriptor …a reference sequence;” should be:
“pair descriptor… are paired;
unreads descriptor …a reference sequence;” for proper delineation of claim steps.
In claim 48, in the rftp descriptor step, “wherein positions of mismatches are terminated by a special terminator character;” should be “wherein the positions of mismatches are terminated by a special terminator character;”
In claims 48 and 58, “to signal” should be ”for signaling” for consistency.
In claim 58, “to this encoding parameters” should be “to this encoding
In claim 58, the parameters should all have “parameter” following the parameter name, for consistency. For example, “a dataset type” should be “a dataset type parameter”.
In claim 58, “the number of classes for signaling the number of data classes encoded in all Access Units referring to said configuration parameters;” step is repeated twice.
In the last step of claim 58,”when set to 0 no spliced reads are present” should be ”when set to 0, no spliced reads are present”.
Appropriate correction is required. These objections are newly recited after further consideration.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
In the instant claims, the following limitation is interpreted under 35 U.S.C. 112f, sixth paragraph because it uses “means” coupled with functional language without reciting sufficient structures to achieve the function in claim 77:
decoding means for implementing the decoding method of claim 45
In the Applicant’s Arguments filed 04/30/2024, the applicant states on page 13 that “in view of specification page 71, lines 26-33, the individual aspects of the decoding apparatus would be understood by one of skill in the art to be implemented in software according to the application method instructions on the hardware structures which are well known in the art and listed in the following paragraph.”
Claim Rejections - 35 USC § 112
NEW REJECTIONS:
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 45, 48, 57-58, 72-75, 77 and 80 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. These rejections are newly recited after further consideration.
There is insufficient antecedent basis for the following limitations in the claims:
In claim 45, and all claims dependent thereon, there is insufficient antecedent basis for the following limitations:
“the number of positions in which a sequencing machine generating the read was not able to call any base” in step 4, sub-step 2;
“the number of positions in which the sequencing machine generating the one or more aligned reads was not able to call any base” and “the one present” in step 4, sub-step 5;
“the DNA or RNA strand”, “the position of mismatches”, “the types of mismatches”, and “the associated positions” in the sub-steps for the descriptors for the first to third classes.
In claim 48, and all claims dependent thereon, there is insufficient antecedent basis for the following limitations:
“the length” in rlen descriptor step;
“the identification” and “the existence” in msar descriptor step’
“the subset” in the rtype descriptor step;
“the position” in rftp descriptor step;
“the type” in rftt descriptor step.
In claim 58, and all claims dependent thereon, there is insufficient antecedent basis for the following limitations:
“the type” in the dataset type step;
“length” in the reads length step;
“the number of Quality Values” in the quality values depth parameter step;
“the number of alignments scores” the alignment score depth step;
“the size” in the terminator size step;
“the value” in the terminator value step;
“the number of classes” in step 7;
“the coding modes” in the coding mode identifiers step;
“the number of different values” and “the current encoding” in the number of groups parameter step;
“the presence of multiple alignments” in the multiple alignment flag step;
“the presence of spliced reads” in the spliced read flag step.
In claim 72, and all claims dependent thereon, there is insufficient antecedent basis for the following limitations:
“the use” in line 2.
In claim 73, and all claims dependent thereon, there is insufficient antecedent basis for the following limitations:
“the size” in line 2.
In claim 74, and all claims dependent thereon, there is insufficient antecedent basis for the following limitations:
“the number of bits” in line 2 and “the exponent” in line 3.
In claim 75, and all claims dependent thereon, there is insufficient antecedent basis for the following limitations:
“the fractional part” in line 3.
Claim Rejections - 35 USC § 101
The rejections of claims 45, 48, 57-58, 72-75, 77 and 80 under 35 U.S.C. 101 are withdrawn in view of Applicant’s Arguments filed 01/29/2026, which were found to be persuasive. Specifically, applicant stated any judicial exceptions are integrated into practical application, by providing an improvement in computer performance and resource usage by enabling partial decoding and selective access directly in the compressed domain, reducing I/O and compute through selective reconstruction without full decompression and reduced entropy coding for performance, thereby providing an improvement to computer functionality (Applicant’s Arguments, p 23, para 4-p 25, para 4).
Claim Rejections - 35 USC § 102 and 35 USC § 103
The rejection of claims under 35 U.S.C. 102(a)(1) and 35 U.S.C. 103 were withdrawn in the office action mailed 06/13/2024 in view of claim amendments filed 04/30/3034, as the prior art to Joint Call for Proposals for Genomic Information Compression and Storage (ISO/IEC JTC 1/SC 29/WG 11 N16320, ISO/TC 276/WG 5 N99, Geneva, CH 2016; previously cited) does not appear to teach or suggest classifying the data into the classes, the information conveyed by the descriptors or the how the entropy decoding and de-binarization is used for the descriptors as disclosed by instant claim 45.
Double Patenting
The provisional rejections of claim 45, 77 and 80 on the ground of nonstatutory double patenting as being unpatentable over claim 45, 49-50, 58, 65 and 68 of copending Application No. 16/485,670 in view of Panneel (IDS filed 04/07/2020, NPL reference 11, 81 pgs; previously cited) were withdrawn in the office action mailed 07/29/2025 in view of the Terminal Disclaimer filed 03/27/2025 and the Applicant’s Arguments filed 03/27/2025 requesting reconsideration.
Conclusion
No claims are allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NIDHI DHARITHREESAN whose telephone number is (571)272-5486. The examiner can normally be reached Monday - Friday 9:00 - 5:00.
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/N.D./ Examiner, Art Unit 1686
/Karlheinz R. Skowronek/ Supervisory Patent Examiner, Art Unit 1687