DETAILED ACTION
The Applicant’s response, received 20 January 2026, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
Status of the Claims
Claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 are pending.
Claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 are rejected.
Priority
This application is a 371 of PCT/US2018/018092, filed 14 February 2018,
which claims priority to foreign applications:
United States of America PCT/US17/17842, filed 14 February 2017; and
United States of America PCT/US17/41591, filed 11 July 2017.
Claim Interpretation
Claims 13-28 include limitations that use the word “means” but are nonetheless not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, as previously noted in the Office action mailed 04 June 2024.
The term “descriptor(s)” in claims 1, 13-35, 37-39, 45, 49-51, 67, and 68 is interpreted to mean information of a specific type (Specification, page 17, lines 13-15; and page 47, lines 9-11).
The term “block” in claims 1, 13-35, 37-39, 45, 49-51, 67, and 68 is interpreted to mean a grouping, or structure of data organized by information type (Specification, page 3, lines 5-10).
The terms “block(s) of descriptors” in claims 1, 29, 31-34, 37-39, 45, 49-51, 67, and 68, and “descriptor block” in claims 1, 13-28, 31, and 45 are interpreted to mean a grouping or a collection of information types (Spec., page 12, lines 1-4).
The term “access unit(s)” in claims 1, 29-34, 37, 45, 67, and 68 is interpreted to mean a separately accessible data unit (Spec., page 17, lines 16-19).
The Applicant’s amendment received 20 January 2026 has been fully considered, however after further consideration, the claim interpretations raised under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, in the Office action mailed 18 September 2025 are maintained in view of the amendment.
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.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier.
Such claim limitation(s) are:
transforming, using a reference transformation unit, in claim 45;
a genomic encoder for encoding…configured to…, in claim 52; and
a genomic decoder for decoding…configured to…, in claim 58.
Because these claim limitation(s) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, they are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
The written description discloses a corresponding structure for:
a transformation unit at page 49, lines 1-7 in the Specification (hardware, software, firmware, or any combination thereof);
a genomic encoder at page 15, lines 1-3 in the Specification (at least one processor); and page 49, lines 1-7 in the Specification (hardware, software, firmware, or any combination thereof); and
a genomic decoder at page 15, lines 5-8 in the Specification (at least one processor); and page 49, lines 1-7 in the Specification (hardware, software, firmware, or any combination thereof).
If applicant does not intend to have these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Objections
The objections to claims 1, 14, 30, and 36 in the Office action mailed 18 September 2025 are withdrawn in view of the amendment received 20 January 2026.
Claim Rejections - 35 USC § 112
The rejection of claims 1, 8, 10-42, 44, 46-51, 67, and 68 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in the Office action mailed 18 September 2025 is withdrawn in view of the amendment received 20 January 2026.
The rejection of claims 40, 41, and 42 under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, in the Office action mailed 18 September 2025 is withdrawn in view of the amendment received 20 January 2026.
Claim Rejections - 35 USC § 101
The Applicant’s amendment received 20 January 2026 has been fully considered, however after further consideration, the rejection of claims 1, 8, 10-42, 44-52, 58, 64, 65, 67, and 68 under 35 U.S.C. 101 in the Office action mailed 18 September 2025 is maintained with modification, as noted below.
The rejection of claims 40-42 in the Office action mailed 18 September 2025 is withdrawn in view of the cancellation of these claims in the amendment received 20 January 2026.
35 U.S.C. 101 reads as follows:
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.
Claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter? Regarding the instant claims:
claims 1, 8, 10-39, 44, and 67 are directed to a computer-implemented method (i.e., a process) for encoding genome sequence data;
claims 45-51, and 68 are directed to a computer-implemented method (i.e., a process) for decoding encoded genomic data;
claim 52 is directed to a genomic encoder (i.e., a machine or manufacture);
claim 58 is directed to a genomic decoder (i.e., a machine or manufacture); and
claims 64 and 65 are directed to a non-transitory computer-readable medium (i.e., a machine or manufacture).
Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under Step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes 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.
Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
aligning said reads to one or more first reference sequences thereby creating aligned reads (i.e., mental processes);
classifying said aligned reads according to specified matching rules with said one or more first reference sequences into different classes, thereby creating classes of aligned reads (i.e., mental processes), the classifying comprising:
identifying an aligned read without any mismatch in the one or more first reference sequences as a first class P when no mismatches are present in the aligned read with respect to the reference sequence used for alignment (i.e., mental processes);
identifying an aligned read as a second class N when mismatches are only found in the positions where a sequencing machine was not able to call any base and the number of mismatches in each read does not exceed a given threshold (i.e., mental processes and mathematical concepts);
identifying an aligned read as a third class M when mismatches are found in the positions where the sequencing machine was not able to call any base, named n type mismatches, and/or it called a different base than a sequence in the one or more first reference sequences, named s type mismatches, and the number of mismatches does not exceed given thresholds for the number of mismatches of n type, of s type and a threshold obtained from a given function (f(n,$)) (i.e., mental processes and mathematical concepts);
identifying an aligned read as a fourth class I when they can possibly have the same type of mismatches of the third class M, and in addition at least one mismatch of type: insertion (i type), deletion (d type), soft clips (c type), and wherein the number of mismatches for each type does not exceed the corresponding given threshold and a threshold provided by a given function (w(n,s,i,d,c)) (i.e., mental processes and mathematical concepts);
encoding said classified aligned reads as a multiplicity of blocks of descriptors specific for and homogeneous within a respective class, wherein encoding said classified aligned reads as a multiplicity of blocks of descriptors comprises selecting said descriptors according to said classes of aligned reads (i.e., mental processes); and
structuring said blocks of descriptors with header information thereby creating successive access units (i.e., mental processes), wherein:
access units of the first class (class P) are built using blocks of descriptors for information on the mapping position, blocks of descriptors for information on the strandedness, i.e., the DNA strand the read was sequenced from, and flags for information on specific characteristics of the aligned read; and wherein in said access units of class P, pairing information of paired-end reads is encoded using a respective block of descriptors (i.e., mental processes);
access units of the second class (class N) are built using the same blocks of descriptors of an access unit of the first class (class P) plus a descriptor block for the information on the position of unknown bases (i.e., mental processes);
access units of the third class (class M) are built using the same blocks of descriptors of access units of the first class (class P) plus blocks of descriptors for information on position and type of substitutions (i.e., mental processes); and
access units of the fourth class (class I) are built using the same blocks of descriptors of access units of the first class (class P) plus blocks of descriptors for information on position and type of substitutions, insertions, deletions and clipped bases (i.e., mental processes); and the method further comprising:
identifying, as a fifth class (class U), aligned reads that do not find any classification in the first to fourth class (classes P, N, M, I) (i.e., mental processes);
constructing a set of second reference sequences using at least some of the reads of the fifth class (i.e., mental processes);
aligning said reads of the fifth class to the set of second reference sequences (i.e., mental processes);
encoding the reads of the fifth class as respective descriptors based on specified matching accuracy constraints with respect to the second reference sequences (i.e., mental processes); and
structuring said respective descriptors with header information thereby creating access units of a fifth class (i.e., mental processes);
wherein the method further comprises transforming said reference sequences into different reference sequences, wherein different transformations are applied to the one or more first reference sequences used for each class of data (i.e., mental processes),
wherein the one or more first reference sequences transformations are encoded as blocks of descriptors and structured with header information thereby creating successive access units (i.e., mental processes), and
wherein the encoding of said classified aligned reads and the related reference sequences transformations as multiplicity of blocks of descriptors comprises the step of associating a specific source model and a specific entropy coder to each descriptor block (i.e., mental processes),
wherein the different transformations applied to the one or more first reference sequences used for each data class are determined by analyzing the mismatches identified in each of the one or more first reference sequences and selecting a transformation that reduces an entropy of each of the blocks of descriptors (i.e., mental processes and mathematical concepts).
Independent claim 45 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
parsing access units access units containing said encoded genomic data (i.e., mental processes);
transforming, using a reference transformation unit, the reference transformation descriptors into a transformed reference (i.e., mental processes);
decoding said multiplicity of blocks of descriptors to extract reads according to specific matching rules defining their classification with respect to one or more reference sequences to produce genomic descriptors (i.e., mental processes), wherein:
if an access unit is of a first, second, third or fourth class, the blocks of descriptors are descriptive of the matching of said reads with respect to first reference sequences according to specified matching rules (i.e., mental processes);
an access unit is of the first class (class P) when it represents genomic reads for which no mismatches are present with respect to a one of the one or more reference sequences used for mapping (i.e., mental processes);
an access unit is of the second class (class N) when it represents genomic reads for which mismatches are only found in the positions where a sequencing machine was not able to call any base and the number of mismatches in each read does not exceed a given threshold (i.e., mental processes and a mathematical concepts);
an access unit is of the third class (class M) when it represents genomic reads for which mismatches are found in the positions where the sequencing machine was not able to call any base, named n type mismatches, and/or it called a different base than the one or more reference sequences, named s type mismatches, and the number of mismatches does not exceed given thresholds for the number of mismatches of n type, of s type and a threshold obtained from a given function (f(n,$)) (i.e., mental processes and a mathematical concepts);
an access unit is of the fourth class (class I) when it represents genomic reads which can possibly have the same type of mismatches of the third class (class M), and in addition at least one mismatch of type: Insertion (i type), deletion (d type), soft or hard clips (c type), and wherein the number of mismatches for each type does not exceed a corresponding given threshold and a threshold provided by a given function (w(n,s,i,d,c)) (i.e., mental processes and a mathematical concepts);
access units of the first class (class P) are built using blocks of descriptors for information on the mapping position, blocks of descriptors for information on the strandedness, i.e., the DNA strand the read was sequenced from, and flags for information on specific characteristics of the read (i.e., mental processes); and wherein in said access units of class P, pairing information of paired-end reads is encoded using a respective block of descriptors (i.e., mental processes);
access units of the second class (class N) are built using the same blocks of descriptors of an access unit of the first class (class P) plus a descriptor block for the information on the position of unknown bases (i.e., mental processes);
access units of the third class (class M) are built using the same blocks of descriptors of access units of the first class (class P) plus blocks of descriptors for information on position and type of substitutions (i.e., mental processes);
access units of the fourth class (class I) are built using the same blocks of descriptors of access units of the first class (class P) plus blocks of descriptors for information on position and type of substitutions, insertions, deletions and clipped bases (i.e., mental processes); and
if an access unit is of a fifth class, the blocks of descriptors are descriptive of the matching of said reads with respect to second reference sequences according to specified matching rules (i.e., mental processes); and
merging the genomic descriptors and the transformed reference to produce uncompressed reads of sequences (i.e., mental processes);
wherein the reference transformation unit analyzes mismatches identified in the genomic data and selects a transformation for each of the transformation descriptors that reduces an entropy of each of the transformation descriptors (i.e., mental processes and mathematical concepts).
Independent claim 52 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the encoding method of claim 1, as discussed above.
Independent claim 58 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the decoding method of claim 45, as discussed above.
Independent claim 64 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the encoding method of claim 1, as discussed above.
Independent claim 65 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the decoding method of claim 45, as discussed above.
Dependent claims 8, 10-39, 44, 46-51, 67, and 68 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 8 further recites:
wherein the reads of the genomic sequence to be encoded are paired (i.e., mental processes), and wherein said classifying further comprises identifying genomic reads as a sixth class HM as comprising all read pairs where one read belongs to class P, N, M or I, and the other read belongs to class U (i.e., mental processes).
Dependent claim 10 further recites:
identifying if the two mate reads are classified in the same class (each of: P, N, M, I, U) (i.e., mental processes), and then assigning the pair to the same identified class (i.e., mental processes);
identifying if the two mate reads are classified in different classes (i.e., mental processes), and in case none of them belongs to the class U, then assigning the pair of reads to the class with the highest priority defined according to the following expression: P < N < M < I, in which class P has the lowest priority and class I has the highest priority (i.e., mental processes); and
identifying if only one of the two mate reads has been classified as belonging to class U and classifying the pair of reads as belonging to the class HM sequences (i.e., mental processes).
Dependent claim 11 further recites:
wherein each class of reads N, M, I is further partitioned into two or more subclasses according to a vector of thresholds defined respectively for each class N, M and I, by the number of n type mismatches, the function f(n,s) and the function w(n,s,i,d,c) (i.e., mental processes and a mathematical concepts).
Dependent claim 12 further recites:
identifying if the two mate reads are classified in the same subclass, then assigning the pair to the same sub-class (i.e., mental processes);
identifying if the two mate reads are classified into sub-classes of different classes, then assigning the pair to the subclass belonging to the class of higher priority according to the following expression: N < M < I, where N has the lowest priority and I has the highest priority (i.e., mental processes);
identifying if the two mate reads are classified in the same class, and such class is N or M or I, but in different sub-classes, then assigning the pair to the sub-class with the highest priority according to the following expressions:
N1 < N2 <…< Nk;
M1 < M2 <…<Mj; and
I1 < I2 <…< Ih,
where the highest index has the highest priority (i.e., mental processes).
Dependent claim 13 further recites:
wherein information on the mapping position of each read is encoded by means of a pos descriptor block (i.e., mental processes).
Dependent claim 14 further recites:
wherein information on the strandedness (i.e., the DNA strand the read was sequenced from) of each read is encoded by means of a rcomp descriptor block (i.e., mental processes).
Dependent claim 15 further recites:
wherein pairing information of paired-end reads is encoded by means of a pair descriptor block (i.e., mental processes).
Dependent claim 16 further recites:
wherein additional alignment information such as if the read is mapped in proper pair, it fails platform/vendor quality checks, it is a PCR or optical duplicate or it is a supplementary alignment is encoded by means of a flags descriptor block (i.e., mental processes).
Dependent claim 17 further recites:
wherein information on unknown bases is encoded by means of a nmis descriptor block (i.e., mental processes).
Dependent claim 18 further recites:
wherein information on the position of substitutions is encoded by means of a snpp descriptor block (i.e., mental processes).
Dependent claim 19 further recites:
wherein information on the type of substitutions is encoded by means of a specific snpt descriptor block (i.e., mental processes).
Dependent claim 20 further recites:
wherein information on the position of mismatches of type substitutions, insertions or deletions is encoded by means of a indp descriptor block (i.e., mental processes).
Dependent claim 21 further recites:
wherein information on the type of mismatches such as substitutions, insertions or deletions is encoded by means of a indt descriptor block (i.e., mental processes).
Dependent claim 22 further recites:
wherein information on clipped bases of a mapped read is encoded by means of a indc descriptor block (i.e., mental processes).
Dependent claim 23 further recites:
wherein information on unmapped reads is encoded by means of a ureads descriptor block (i.e., mental processes).
Dependent claim 24 further recites:
wherein information on the type of reference sequence used for encoding is encoded by means of a rtype descriptor block (i.e., mental processes).
Dependent claim 25 further recites:
wherein information on multiple alignments of the mapped reads is encoded by means of a mmap descriptor block (i.e., mental processes).
Dependent claim 26 further recites:
wherein information on spliced alignments and multiple alignments of the same read is encoded by means of a msar descriptor block and a mmap descriptor block (i.e., mental processes).
Dependent claim 27 further recites:
wherein information on read alignment scores is encoded by means of a mscore descriptor block (i.e., mental processes).
Dependent claim 28 further recites:
wherein information on the class that the reads belong to is encoded by means of a rgroup descriptor block (i.e., mental processes).
Dependent claim 29 further recites:
wherein access units of class P are built using blocks of descriptors of type pos, rcomp and flags (i.e., mental processes).
Dependent claim 30 further recites:
wherein said access units of class P encodes pairing information of paired-end reads using a block of pair descriptors (i.e., mental processes).
Dependent claim 31 further recites:
wherein access units of class N are built using the same blocks of descriptors of an access unit of class P plus a nmis descriptor block for the information on the position of unknown bases (i.e., mental processes).
Dependent claim 32 further recites:
wherein access units of class M are built using the same blocks of descriptors of access units of class P plus blocks of the snpp and snpt descriptors for the information on position and type of substitutions (i.e., mental processes).
Dependent claim 33 further recites:
wherein access units of class I are built using the same blocks of descriptors of access units of class P plus blocks of the indp, indt and indc descriptors for the information on position and type of substitutions, insertions, deletions and clipped bases (i.e., mental processes).
Dependent claim 34 further recites:
wherein access units of class HM are built using the same blocks of descriptors of access units of class I for the mapped reads, and using blocks of the ureads descriptor for the unmapped reads (i.e., mental processes).
Dependent claim 35 further recites:
wherein information on multiple alignments is conveyed using blocks of the mmap and msar descriptor (i.e., mental processes).
Dependent claim 36 further recites:
wherein information on spliced alignments is conveyed using an extended cigar string comprising:
the symbol = to indicate matching bases (i.e., mental processes);
the symbol + to indicate insertions (i.e., mental processes);
the symbol - to indicate deletions (i.e., mental processes);
the symbol / to indicate a splice on the forward strand (i.e., mental processes);
the symbol % to indicate a splice on the reverse strand (i.e., mental processes);
the symbol * to indicate an undirected splice (i.e., mental processes);
a textual character from the IUPAC codes for DNA to indicate a substitution (i.e., mental processes);
the symbol (n) to indicate n soft clipped bases where n is an integer number (i.e., mental processes); and
the symbol [n] to indicate n hard clipped bases where n is an integer number (i.e., mental processes).
Dependent claim 37 further recites:
wherein said blocks of descriptors comprise a master index table, containing one section for each class and sub-class of aligned reads, said section comprising the mapping positions on said one or more reference sequences of the first read of each access unit of each class or sub-class of data (i.e., mental processes); and
jointly coding said master index table and said access unit data (i.e., mental processes).
Dependent claim 38 further recites:
wherein said blocks of descriptors further comprise information on the type of reference used (pre-existing or constructed), and the segments of the read that do not map on the reference sequence (i.e., mental processes).
Dependent claim 39 further recites:
wherein said reference sequences are first transformed into different reference sequences by applying substitutions, insertions, deletions and clipping, then the encoding of said classified aligned reads as a multiplicity of blocks of descriptors refers to the transformed reference sequences (i.e., mental processes).
Dependent claim 44 further recites:
wherein said entropy coder is one of a context adaptive arithmetic coder, a variable length coder or a golomb coder (i.e., mental processes and mathematical concepts).
Dependent claim 46 further recites:
decoding a master index table containing one section for each class of reads and the associated relevant mapping positions (i.e., mental processes).
Dependent claim 47 further recites:
decoding information related to the type of reference used: pre-existing, transformed or constructed (i.e., mental processes).
Dependent claim 48 further recites:
decoding information related to one or more transformations to be applied to the pre-existing reference sequences (i.e., mental processes).
Dependent claim 49 further recites:
wherein said block of descriptors are entropy decoded (i.e., mental processes and mathematical concepts).
Dependent claim 50 further recites:
wherein class P reads are obtained by decoding blocks of descriptors of type: pos, rcomp, flags and rlen (i.e., mental processes);
wherein class N reads are obtained by decoding blocks of descriptors of type: pos, rcomp, flags, rlen and nmis (i.e., mental processes);
wherein class M reads are obtained by decoding blocks of descriptors of type: pos, rcomp, flags, rlen, snpp and snpt (i.e., mental processes);
wherein class I reads are obtained by decoding blocks of descriptors of type: pos, rcomp, flags, rlen, indp, indt and indc (i.e., mental processes); and
wherein class U reads are obtained by decoding blocks of descriptors of type: pos, rcomp, flags, rlen, snpp, snpt, indc, ureads and rtype (i.e., mental processes).
Dependent claim 51 further recites:
wherein paired reads of: class P, N, M and I are obtained by also decoding blocks of descriptors of type: pair (i.e., mental processes); and
wherein paired reads of: class HM are obtained by decoding blocks of descriptors of type: pos, rcomp, flags, rlen, indp, indt, ndc, and ureads (i.e., mental processes).
Dependent claim 67 further recites:
wherein the access units of the fifth class are built using one or more of:
blocks of descriptors for information on the mapping position (i.e., mental processes);
blocks of descriptors for information on the strandedness, i.e. the DNA strand the read was sequenced from, and flags for information on specific characteristics of the sequence read (i.e., mental processes); and wherein pairing information of paired-end reads is encoded using a respective block of descriptors (i.e., mental processes);
blocks of descriptors for information on the position and type of substitutions (i.e., mental processes);
blocks of descriptors for information on parts of the reads that do not match with the second reference sequences (i.e., mental processes); and
blocks of descriptors to encode verbatim the reads that cannot be mapped on any reference sequence (i.e., mental processes).
Dependent claim 68 further recites:
wherein the access units of the fifth class are built using one or more of:
blocks of descriptors for information on the mapping position (i.e., mental processes);
blocks of descriptors for information on the strandedness, i.e. the DNA strand the read was sequenced from, and flags for information on specific characteristics of the sequence read (i.e., mental processes); and wherein pairing information of paired-end reads is encoded using a respective block of descriptors (i.e., mental processes);
blocks of descriptors for information on the position and type of substitutions (i.e., mental processes);
blocks of descriptors for information on parts of the reads that do not match with the second reference sequences (i.e., mental processes); and
blocks of descriptors to encode verbatim the reads that cannot be mapped on any reference sequence (i.e., mental processes).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., classifying sequence reads according to matching rules (Specification, pages 18-20); an access unit is a self-contained block of data that can be decoded independently of any other access unit (Specification, page 51, lines 1-11, and Figures 37 & 38); and reference sequence transformations can be modifications of the reference sequence resulting from changing the bases corresponding to the mismatches of a read in the bases actually present in the read (Specification, page 24, lines 12-15, and page 25, lines 12-19, and Figures 26 & 27)), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., probability models and associated entropy coders (Specification, page 17, lines 16-21; and page 48, lines 14-16)) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d); MPEP 2106.04(d)(I)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Dependent claims 8, 10-39, 44, 46-51, 67, and 68 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claims 1, 45, 52, 58, 64, and 65 include:
a computer (claims 1 and 45);
extract a multiplexed genomic stream (claim 45);
feeding, to a demultiplexer, the multiplexed genomic stream to produce multiple blocks of descriptors employing header information and reference transformation descriptors (claim 45); and
a non-transitory computer-readable medium and at least one processor (claims 64 and 65).
The additional elements of a computer (claims 1 and 45) and a non-transitory computer-readable medium and at least one processor (claims 64 and 65) invoke a computer and/or computer-related components merely as tools for use in the claimed process, such that they amount to no more than mere instructions to apply the exceptions using a generic computer (MPEP 2106.05(f)), and therefore are not an improvement to computer functionality itself, or an improvement to any other technology or technical field (see MPEP 2106.04(d)(1)).
The additional elements of a multiplexed bitstream (claim 45) and demultiplexing the multiplexed bitstream using a demultiplexer to produce the original separate bitstreams (claim 45), are activities incidental to the primary process that are merely a nominal or tangential addition to the claim, and therefore do not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
Thus, the additionally recited elements merely invoke computer technology as a tool, and/or amount to insignificant extra-solution data gathering activity, and as such, when all limitations in claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are searched for an inventive concept. An inventive concept is furnished by an element or combination of elements that is recited in the claim in addition to (beyond) the judicial exception, and is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception itself (MPEP 2106.05(I)). Therefore, evaluating additional elements to determine whether they amount to an inventive concept requires considering them both individually and in combination, such that the claim is considered as a whole.
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Dependent claims 8, 10-39, 44, 46-51, 67, and 68 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claims 1, 45, 52, 58, 64, and 65 are identified above, and carried over from Step 2A: Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A: Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional elements of a computer (claims 1 and 45) and a non-transitory computer-readable medium and at least one processor (claims 64 and 65) are conventional computer components and/or functions (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The additional elements of a multiplexed bitstream (claim 45) and demultiplexing the multiplexed bitstream using a demultiplexer to produce the original separate bitstreams (claim 45), are conventional. Evidence of conventionality is shown by:
Zhang (Data Communications in Distributed Control System, 2008, (Eds. Peng Zhang) In Industrial Control Technology, William Andrew Publishing, pp. 675-774, as cited in the Office action mailed 18 September 2026).
Zhang reviews data communication models for distributed control systems (Title; & Introduction) categorized in open and closed architectures and different network types (e.g., 6.1.1.2 and Figure 6.2; and 6.1.2.1 and Figure 6.3); further reviews the basics of data communications (Section 6.2) including multiplexing, i.e., sending multiple signals or streams of information on a carrier at the same time in the form of a single, complex signal and then recovering the separate signals at the receiving end (Section 6.2.3.6); further reviews multiplexer devices (Section 6.3.6) and demultiplexers (page 722, Section 6.3.6.1, para. 3); and further reviews data transmission protocols (Section 6.4) and data compression and decompression (Section 6.4.4) and data encoding and decoding (Section 6.4.2).
Therefore, when taken alone, all additional elements in claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Response to Arguments
The Applicant’s arguments/remarks received 20 January 2026 have been fully considered, but are not persuasive.
The Applicant states on page 18 (para. 2) of the Remarks that in previous amendments, the Applicant set forth extensive arguments evidencing why the claims are not directed to an abstract idea, how the claims incorporate any alleged abstract idea into a practical application, and how the claims recite significantly more than an abstract idea. The Applicant summarizes the analysis process of Step 2A Prong Two (para. 3) and provides a passage (para. 4) of the Office action mailed 18 September 2025 and states on page 19 (para. 2) of the Remarks that the claims as a whole are not directed to the abstract idea of a mental process and/or mathematical concept. The Applicant further states (para. 3) that the Office’s analysis parses each limitation in isolation and does not address how the elements operate together to constrain the alleged abstract idea and improve sequence encoding and decoding technology, and that this approach contradicts Prong Two’s “claim as a whole” requirement and the “individually and in combination” directive, and further states that the Patent Office’s own analysis demonstrates the piecemeal – rather than claim as a whole – approach (e.g., see Remarks, page 19, for the Applicant’s example from the previous Office action). The Applicant further states (para. 4) that simply containing a limitation that is alleged to be an abstract idea is not sufficient to find that the claim as a whole is directed to an abstract idea. The Applicant further summarizes (para. 5) analysis under Step 2A Prong Two and further states on page 20 (para. 1) that the claims as a whole are not directed to the abstract idea of a mental process and/or mathematical concepts.
These arguments are not persuasive, because first, the passage provided by the Applicant allegedly demonstrating the Office’s piecemeal – rather than claim as a whole – approach (e.g., see Remarks, page 19) is a passage from a brief summary following the analysis at Step 2A Prong One (i.e., “As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper…and therefore recite judicial exceptions from the mental process grouping of abstract ideas.”). The Applicant is reminded that Step 2A Prong One asks “does the claim recite an abstract idea, law of nature, or natural phenomenon? 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” (MPEP at 2106.04 II. A. 1.). Thus, it is sufficient for this analysis for the examiner to identify that the claimed concept (the specific claim limitation(s) that the examiner believes may recite an exception) aligns with at least one judicial exception (MPEP at 2106.04 I.). Second, Prong Two asks does the claim recite additional elements that integrate the judicial exception into a practical application? In Prong Two, examiners evaluate whether the claim as a whole integrates the exception into a practical application of that exception. If the additional elements in the claim integrate the recited exception into a practical application of the exception, then the claim is not directed to the judicial exception (MPEP at 2106.04 II. A. 2.). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception (MPEP 2106.04(d)), and as noted and discussed in the above rejection, the instant claims do not recite any additional elements that either apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. Third, and as noted and discussed in the above rejection, the additionally recited elements merely invoke computer technology as a tool, and/or amount to insignificant extra-solution data gathering activity, and as such, when all limitations in claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application.
The Applicant states on page 20 (para. 2) of the Remarks that the claims as a whole are not directed to the abstract idea of a mental process, and further states that the claims comprise elements that are not performed in the human mind alone, and thus are not directed to the abstract idea of a mental process. The provides an excerpt from the claims (claim 1) and further states (para. 3) that the human mind alone – with or without pen and paper – cannot transform reference sequences into different reference sequences (using the claimed method) such that the transformation reduces an entropy of each of the block of descriptors, because these limitations require execution of a specific process that requires at least significant computer memory, buffer management, and physical writing of data blocks, which are activities that cannot be performed mentally, and accordingly, the claim does not fall within the mental process grouping. The Applicant further states (para. 4) that a transformation where “first reference sequences transformations are encoded as blocks of descriptors and structured with header information thereby creating successive access units” is a concrete data-structuring and serialization operation in a computer system, and that, e.g., data blocks must be arranged into successive (ordered) access units, and each access unit requires the insertion of machine-parseable header information (e.g., fields/lengths/identifiers), the result of which is a computer-readable sequence of access units that downstream components can parse, index, and retrieve. The Applicant further states on page 21 (para. 1) that a human mind cannot practically perform these steps, and that mental reasoning cannot produce a machine-formatted bit/byte stream with precise head fields, lengths, offsets, and ordering in physical memory or storage, nor can a person mentally create successive access units that a computer can parse and use for retrieval, and accordingly, these steps fall outside the mental processes grouping.
These arguments are not persuasive, because first, the Applicant is reminded that claims can recite a mental process even if they are claimed as being performed on a computer (MPEP 2106.04(a)(2)(III)(C)). Second, regarding the Applicant’s argument that the claim “limitations require execution of a specific process that requires at least significant computer memory, buffer management, and physical writing of data blocks,” and are “a concrete data-structuring and serialization operation in a computer system,” the amount of data and/or the amount of time to perform the process steps, in and of themselves is not a limitation which takes a process out of the realm of the human mind. It is the process performed on that data which is the mental step, and mental steps identified in the claims do not have to be the fastest, most efficient, or require specialized computing elements. Thus, although the amount of data may be considered to be significantly large and take considerable time and effort to process manually, the use of a computer to perform the claimed method at a rate and accuracy that can far outstrip the mental performance of a skilled artisan does not change the nature of the activity being performed (i.e., an abstract idea), and therefore does not materially alter the patent eligibility of the claimed subject matter. Third, and as noted and discussed in the foregoing response to arguments, the additionally recited elements merely invoke computer technology as a tool, and/or amount to insignificant extra-solution data gathering activity, and as such, when all limitations in claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application.
The Applicant states on page 21 (para. 3) that the claims as a whole are not directed to a mathematical concept, e.g., the claims do not explicitly recite a mathematical process or equation. The Applicant further points page 7 of the “October 2019 Update: Subject Matter Eligibility” and states that all of these examples comprise a mathematical calculation but do not explicitly recite a mathematical process or equation. The Applicant further points (para. 4) to Example 38 and states that the Applicant draws the Patent Office’s attention to its own statement that while “some of the limitations may be based on mathematical concepts, the mathematical concepts are not recited in the claims.” The Applicant further points (para. 5) to Example 39 and states that the Patent Office finds that the claim does not recite a judicial exception because “the claim does not recite any mathematical relationships, formulas, or calculations” and that while “some of the limitations may be based on mathematical concepts, the mathematical concepts are not recited in the claims.” The Applicant further states on page 22 (para. 1) that in stark contrast to Examples 38 and 39, Example 41 clearly does recite a mathematical formula or calculation (including the step of “encoding each of the message block word signals MA to produce a ciphertext word signal CA, whereby CA=MAe (mod n)”), and this claim, the Patent Office holds, “is determined to recite a mathematical concept because the claim explicitly recites a mathematical formula or calculation.” The Applicant further states (para. 2) that notably, there is no mathematical formula or calculation explicitly recited in the present claims, and further states that the question “does the claim require mathematical calculations?” is not the proper test under 35 U.S.C. 101, but rather the proper test is whether the claims explicitly recite a mathematical relationship, formula, or calculation, and when that test is applied to Examples 38 and 39, the claims clearly do not fall within the mathematical concepts grouping of abstract ideas and therefore do not recite any of the judicial exceptions enumerated in the 2019 PEG, whereas in contrast, the claim in Example 41 does recite a mathematical relationship, formula, or calculation and therefore does fall within the mathematical concepts grouping of abstract ideas. The Applicant further provides a comparison of the aforementioned Examples (see Remarks at page 22) and further states (para. 3) that the steps in Examples 38 and 39 clearly require very intensive calculations performed by the respective computer systems, but have been found by the Patent Office to not recite a judicial exception. The Applicant further states that how “can it be that these steps in Examples 38 and 39 do not recite a mathematical relationship, formula, or calculation and yet certain identified steps in the present claims allegedly do recite a mathematical relationship, formula, or calculation?” The Applicant further states on page 23 (para. 1) that this cannot be reconciled, and accordingly, the claims are not directed to a judicial exception. The Applicant further provides the claim in Example 39 and provides a brief summary of the analysis of the example claim (para. 2) and states (para. 3) that the only difference between Examples 38/39 and Example 41 is that 41 explicitly recites a mathematical concept while Examples 38/39 do not, and the Patent Office cannot simply ignore the differences between these examples. The Applicant further states that these are examples provided by the Patent Office, and the Patent Office is bound by these examples, and what those Examples convey to Applicants and the Patent Bar, and therefore here, the only logical conclusion is that the present claims are similar to Examples 38/39 and dissimilar from Example 41. The Applicant further states (para. 4) that there is of course no requirement that claims being examined have a one-to-one correspondence to the claims in Examples 38, 39, and 41, and that it is the reasoning and analysis of the Examples that applies to claims under examination, and thus there is sufficient correspondence to utilize the Examples as informative guidelines. The Applicant further states that indeed, the Examples are provided for exactly that purpose; to provide guidance to applicants. The Applicant further states on page 24 (para. 1) that any argument that the claims under examination are not sufficiently similar to the claims in the Examples ignores the purpose of the Examples, and inaccurately dismisses the guidance provided by the Examples. The Applicant further states that the takeaway of the Examples, without any comparison to the present claims, is that the only difference between Examples 38/39 and Example 41 is that 41 explicitly recites a mathematical concept (i.e., a formula or equation) while Examples 38/39 do not, and that this takeaway is very easily and very simply applied to the present claims – that the present claims do not recite a mathematical concept, and are thus unlike Example 41 and similar to Examples 38/39, and accordingly, the claims as a whole are not directed to an abstract idea.
These arguments are not persuasive, because first, at Eligibility Step 2A 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. Furthermore, a mathematical concept need not be expressed in mathematical symbols, because words used in a claim operating on data to solve a problem can serve the same purpose as a formula, and still further, there is no particular word or set of words that indicates a claim recites a mathematical concept, that is, a claim does not have to recite the word “calculating” in order to be considered a mathematical calculation (MPEP 2106.04(a)(2)(I)). Second, the Eligibility Examples are hypothetical and only intended to be illustrative of the claim analysis performed using MPEP 2106, and of the particular issues noted in the Example. The Examples should be interpreted based on the fact patterns set forth in a particular Example, as other fact patterns may have different eligibility outcomes, as evidenced in the rejection of the instant claims. Third, with regard to Example 38, while some of the limitations may be based on mathematical concepts, the mathematical concepts are not recited in the claims, whereas, e.g., instant claim 49 recites “wherein said block of descriptors are entropy decoded” which is describing a fundamentally mathematical and statistical process. Fourth, with regard to Example 39, while some of the limitations may be based on mathematical concepts, the mathematical concepts are not recited in the claims, whereas, e.g., instant claim 49 recites “wherein said block of descriptors are entropy decoded” which is describing a fundamentally mathematical and statistical process. Fifth, the subject matter eligibility test for products and processes as described in the MPEP at 2106 does not show guidance for determining eligibility based on which set of Example claims (i.e., Examples 38, 39, or 41) more closely align with the instant claims. Sixth, the proper legal basis for construing the scope of the claims is not by analogizing them to USPTO training examples, but by interpreting the plain meaning of the claim language in light of the specification. As noted in the above rejection under 35 U.S.C. § 101, the plain meaning of the claim limitations recited in dependent claim 49, when read in light of the corresponding descriptions in the specification, recites mathematical concepts.
The Applicant summarizes the analysis at Step 2A Prong Two on page 24 (para. 3) and states (para. 4) that the claims are not directed to a judicial exception, and the claims incorporate any judicial exception into a practical application. The Applicant provides a passage from the previous Office action regarding Step 2A Prong Two, and the Applicant further states on page 25 (para. 2) that the Applicant disagrees with the Office’s conclusion, and further states that the Applicant maintains that the claims comprise a practical application, e.g., the claims integrate the alleged abstract idea into a practical application that improves computer functionality in the specific technological field of genomic data storage and retrieval. The Applicant further states that the method organizes descriptors into class-specific data blocks and structures them into access units with headers, among other functionality, and that this coordinated architecture improves storage efficiency and retrieval latency, thereby amounting to a practical application in a particular technological environment. The Applicant further states that the claims do not merely “store” or “organize” information in the abstract; they impose a specific data format and index keyed to genomic mapping positions and read classes that alters how a computer stores and retrieves data. The Applicant further states (para. 3) that, e.g., the specification clearly sets forth the technological problem that is solved by the technological advancements of the claimed methods, and points to paragraphs [0008] – [0016] of the Specification on pages 25-26 of the Remarks, and further points to paragraphs [0017] – [0020] of the Specification on pages 26-27 of the Remarks, states on page 27 (para. 2) that thus, the claims comprise a practical application.
These arguments are not persuasive, because first, as noted and discussed in the above rejection, and as noted and discussed in the foregoing responses to arguments, Step 2A Prong Two asks: does the claim recite additional elements that integrate the judicial exception into a practical application? In Prong Two, examiners evaluate whether the claim as a whole integrates the exception into a practical application of that exception. If the additional elements in the claim integrate the recited exception into a practical application of the exception, then the claim is not directed to the judicial exception (MPEP at 2106.04 II. A. 2.). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception (MPEP 2106.04(d)), and as noted and discussed in the above rejection, the instant claims do not recite any additional elements that either apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. Second, and as noted and discussed in the above rejection, the additionally recited elements merely invoke computer technology as a tool, and/or amount to insignificant extra-solution data gathering activity, and as such, when all limitations in claims 1, 8, 10-39, 44-52, 58, 64, 65, 67, and 68 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application.
The Applicant provides a brief summary of analysis at Step 2B on page 27 (para. 2) of the Remarks, and states (para. 3) that the claims recite significantly more than an abstract idea as they affect an improvement in the technology and/or technical field of resource usage in computing devices. The Applicant further states (para. 4) that the Specification describes the inventions of amended independent claims 1 and 45 such that the improvements (e.g., regarding improved methods of encoding and decoding genomic data) would be readily apparent to an individual ordinarily skilled in the art. The Applicant points to (para. 5) paragraphs [0014] and [0017] – [0020] of the Specification for examples that explicitly outline some of the benefits afforded by the inventions of amended claims 1 and 45. The Applicant further states on page 28 (para. 2) that as indicated above, the specification plainly outlines a number of improvements offered by the inventions of amended independent claims 1 and 45, and furthermore, the recitations of amended claims 1 and 45 incorporate a number of the improvements highlight above into the claims, e.g., as amended, independent claim 1 recites that “the different transformations applied to the one or more first reference sequences used for each data class are determined by analyzing mismatches identified in each of the one or more first reference sequences and selecting a transformation that reduces an entropy of each of the blocks of descriptors,” which directly enables the increased compression performance described in para. [0018] of the Specification, and similarly, amended independent claim 45 recites that “the reference transformation unit analyzes mismatches identified in the genomic data and selects a transformation for each of the transformation descriptors that reduces an entropy of each of the transformation descriptors,” which allows for the efficient reconstruction of original genomic sequences by leveraging the information carried by the reference transformation descriptors (e.g., at para. [0046] of the Specification). The Applicant further states (para. 3) that in this regard, it should be appreciated that the methods recited by claims 1 and 45 amount to significantly more than the judicial exception at least because they provide a clear improvement in terms of resource usage to compressing and storing genomic sequences. The Applicant further states (para. 4) that the MPEP makes specific reference in section 2106.05(a)(II)(iv) to the patentability of an improved, particular method of digital compression (i.e., DDR Holdings) and further states that the Federal Circuit has also established that the inventive concept may not be found within the allegedly abstract idea itself, which the Office action impermissibly asserts, and the Applicant further states on page 29 (para. 1) that more particularly, in Berkheimer, similarly to the instant claimed invention, the court found that an inventive concept of storing in a structured archive without substantial redundancy improves system operating efficiency and reduces storage costs, finding the claims invention eligible under the 35 U.S.C. 101 analysis. The Applicant further states that such is one of the purposes of the inventions of amended independent claims 1 and 45, especially as it relates to improvements in computer speed, efficiency, and resource usage for storing representations of genome sequence data, and that in this regard, it should be further noted that the Federal Circuit Court of Appeals has found that a data structure that improves performance, as described hereinabove and disclosed throughout the instant Specification in concert with the claimed embodiments, is sufficient subject matter to find patentable subject matter (see Enfish). The Applicant further states (para. 2) that the MPEP at 2106.05(c) notes that another consideration when determining whether a claim integrates a judicial exception into a practical application at Step 2A Prong Two and whether a claim recites significantly more in Step 2B is whether the claim effects a transformation or reduction of a particular article to a different state or thing. The Applicant further states (para. 3) that amended claims 1 and 45 qualify as particular transformations that are directed to patent eligible subject matter, because claim 1 recites transformations that are applied to the reference sequences used for each class of data, and the reference sequences transformations are encoded as blocks of descriptors and structured with header information thereby creating successive access units. The Applicant further states on page 30 (para. 1) that accordingly, it should be understood that the transformation of the refence transformation descriptors into transformed references, and the merging of the genomic descriptors and the transformed references, allows for the reconstruction of the genomic sequence described hereinabove. The Applicant further states (para. 2) that the transformations provided by amended claims 1 and 45 are an inventive aspect of amended independent claims 1 and 45 inasmuch as the transformations recited by independent claims 1 and 45 enable enhanced compression and reconstruction of genomic sequences, respectively, and for at least these reasons, the conditions of a particular transformation as set forth in MPEP 2106.05(c) are satisfied, and further states (para. 3) that at least for these reasons, the features of the pending claims amount to significantly more than an abstract idea itself and are directed to patent-eligible subject matter.
These arguments are not persuasive, because first, the search for an inventive concept at Step 2B requires determining whether a claim amounts to significantly more than the judicial exception itself, i.e., the “inventive concept” is furnished by an element or combination of elements that is recited in the claim in addition to (beyond) the judicial exception, and is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception itself (MPEP 2106.05 I.). In particular, Step 2B asks: Does the claim recite additional elements that amount to significantly more than the judicial exception? This question is answered by first identifying whether there are any additional elements (features/limitations/steps) recited in the claim beyond the judicial exception(s), and then evaluating those additional elements individually and in combination to determine whether they contribute an inventive concept (i.e., amount to significantly more than the judicial exception(s)). Second, and as noted in the rejection above, the claims do not recite any additional elements that amount to an inventive concept, because the additional elements of a computer, a non-transitory computer-readable medium and at least one processor and multiplexing and demultiplexing bitstreams, are conventional. Third, the purported improvements (e.g., regarding improved methods of encoding and decoding genomic data) recited by claims 1 and 45 and described in the Specification at the aforementioned paragraphs are not improvements to the additional elements recited in the claims, but rather, are purported improvements to the abstract ideas recited by the claims, e.g., “the different transformations applied to the reference sequences used for each data class are determined by analyzing the mismatches identified in each of the reference sequences and selecting a transformation that reduces an entropy of each of the blocks of descriptors.” The transformations that are applied to the reference sequences are manipulations of data (e.g., Figures 19, 26, 27, and 30), and therefore are a purported improvement in the abstract idea itself, and not an improvement in the functioning of a computer, or an improvement to any other technology or technical field (MPEP 2106.05(a)). Fourth, regarding the Applicant’s pointing to DDR Holdings, LLC v. Hotels.com, L.P. and also pointing to Intellectual Ventures v. Symantec Corp. as presented at MPEP 2106.05(a)(II)(iv), it is noted that with respect to DDR Holdings, LLC v. Hotels.com, the claims were found to include “additional features” (i.e., additional elements) that when taken together as an ordered combination, recite an invention that is not merely the routine or conventional use of the Internet. Regarding Intellectual Ventures v. Symantec Corp., it is noted that the claims at issue (the ‘050; ‘142; and ‘610 patents) were found to be not patent-eligible under § 101. Fifth, regarding Berkheimer v. HP INC, and Aatrix Software v. Green Shades Software, it is noted that whether a claim element or combination of claim elements is well-understood, routine, and conventional is a question of fact. It is further noted that the inventive concept cannot be the abstract idea itself, and further still, it is noted that the application must provide something inventive, beyond mere well-understood, routine, conventional activity. Regarding Berkheimer and the court’s finding of an inventive concept of storing in a structured archive without substantial redundancy, it is noted that the dependent claims at issue (claims 4-7) recite an additional element (storing object structures) that according to the specification, is an improvement over the conventional technology. The instant claims, however, and as noted in the rejection above and in the foregoing responses to arguments, do not recite any additional elements that provide an inventive concept. Sixth, regarding the Applicant’s attempt at analogizing the instant claims to Enfish, the instant claims are not analogous to the claims in Enfish, because the instant claims recite a process of manipulating genomic sequencing data to and from different representations of the original form (e.g., encoding and decoding) that is a purported improvement to the abstract idea itself, whereas the improvement recited in Enfish is found in a data structure that corresponds to a storage and retrieval structure configured in a computer memory comprising a self-referential table that is designed to improve the way a computer stores and retrieves data in memory, and thus is an improvement to computer functionality itself. Seventh, as noted at MPEP 2106.05(c), for data, mere "manipulation of basic mathematical constructs [i.e.,] the paradigmatic ‘abstract idea,’" has not been deemed a transformation. Therefore, the limitations reciting the transformation steps in the Applicant’s arguments do not recite a transformation or reduction of a particular article to a different state or thing, because 1), "transformation" of an article means that the "article" has changed to a different state or thing, and 2), that the “article” itself includes a physical object or substance, i.e., not data. Therefore, the instant limitations cannot be a particular transformation because the recited transformations to reference sequences are merely assignments of information to other information that serve as substitute representations of the information, and thus, the “transformed” reference sequences themselves do not result from a transformation or a reduction from another article that is a physical object or substance; and 3), even if the recited “transformed” reference sequences involved an article that is a physical object or substance being transformed or reduced to a different state or thing, the recitation of a “merging the genomic descriptors and transformed reference to produce uncompressed reads of sequences” does not recite a “particular” article that can be specifically identified.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687
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