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’s Amendment/Request for Reconsideration-After Non-Final Rejection, filed 6/1/2026, has been entered and fully considered
Status of Claims
Claims 3, 16, 19 and 20 are cancelled.
Claims 1-2, 4-15, 17-18 and 21-24 are pending and are examined on the merits.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application 62/402,873 filed 09/30/2016 is acknowledged.
Withdrawn Rejections/Objections
The rejections to claims 1, 3, 7, 11, 15-16 and 20 on the ground of nonstatutory double patenting in the Office action mailed 10 March 2026 are withdrawn in view of claims amendments filed 1 June 2026 and Applicant’s persuasive argument in the Remarks filed 1 June 2026 (pages 8-9).
The rejections to claims 1, 3-11, 13-15 and 20 under 35 U.S.C. 103 in the Office action mailed 10 March 2026 are withdrawn in view of claims amendments filed 1 June 2026 and Applicant’s persuasive argument in the Remarks filed 1 June 2026 (pages 16-20).
The objection to claim 14 in the Office action mailed 10 March 2026 is withdrawn in view of claims amendments filed 1 June 2026.
Regarding 35 USC 103
The claims are free of the analogous art at least because close art, e.g. as cited
on the 3/10/2026 Office action as well as art found in the search histories, either individually or in obvious combination, does not teach the recited combination of:
computing a signature for a first read from the plurality of reads, the signature being a bit string generated in part by a set of k-grams within the first read, wherein computing the signature comprises:
dividing the first read into two or more sub-reads;
finding all k-grams for each of the two or more sub-reads;
encoding the k-grams as bit strings, wherein the encoding comprises, for each of the two or more sub-reads, generating a bit string having a bit position for each of all possible substrings of length k and setting each bit position to a first value if the corresponding substring is present in the sub-read and to a second value if the corresponding substring is absent from the sub-read; and
concatenating the bit strings into the signature.
As recited in independent claim 1, and
separating the plurality of DNA reads into a plurality of buckets;
clustering DNA reads in one of the plurality of buckets into clusters based at least in part on edit distance between respective pairs of the DNA reads, wherein the edit distance is approximated by a Hamming distance between a binary signature of a first DNA read of the plurality of DNA reads and a binary signature of a second DNA read of the plurality of DNA reads;
determining that the Hamming distance is between a first threshold and a second threshold;
calculating the edit distance for the first DNA read of the plurality of DNA reads and the second DNA read of the plurality of DNA reads;
determining that the edit distance is less than an edit-distance threshold; and
placing the first DNA read of the plurality of DNA reads and the second DNA read of the plurality of DNA reads in a same cluster.
As recited in independent claim 14.
Additionally, the interview agreement of 1 May 2026, and Applicant's 6/1/2026 Remarks at p. 16-20 support the withdrawal of the 103 rejection.
Claim Rejections - 35 USC § 101
This rejection is maintained from a previous Office action. Modifications are necessitated by claim amendments.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 1-10 recite a series functional steps, so a process.
Claims 11-20 recite a series functional steps, so another process.
Step 2A Prong One: Identification of Abstract Ideas
The claim(s) recite:
1. Computing a signature for a first read from the plurality of reads, the signature being a bit string generated in part by a set of k-grams within the first read, wherein computing the signature comprises:
dividing the first read into two or more sub-reads;
finding all k-grams for each of the two or more sub-reads;
encoding the k-grams as bit strings, wherein the encoding comprises, for each of
the two or more sub-reads, generating a bit string having a bit position for each of all possible substrings of length k and setting each bit position to a first value if the corresponding substring is present in the sub-read and to a second value if the corresponding substring is absent from the sub-read; and
concatenating the bit strings into the signature (claim 1).
This step recites generating a signature (based on the k-grams) out of the first read and convert the signature into a bit string. The whole process (such as dividing the first read into two or more sub-reads; finding all k-grams for each of the two or more sub-reads; encoding the k-grams as bit strings, and concatenating the bit strings into signatures) can be achieved in human mind with perhaps the aid of a pen and paper. Further, “encoding” is classified by the court as abstract ideas ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016)). The step hence equates to an abstract idea of mental processes.
2. Generating a hash for the first read, the hash based at least in part on a sequence of the first read (claim 1).
Under a broadest reasonable interpretation (BRI), this step is interpreted as using the first read as hash key and assign a value to the hash key. The whole process can be achieved in human mind with perhaps the aid of a pen and paper. The step hence equates to an abstract idea of mental processes.
3. Grouping the first read with a second read having a same hash into a same bucket (claim 1).
Under a BRI, this step is interpreted as moving two reads into a same folder (here the bucket) or labeling the two reads with the same bucket. The whole process can be achieved in the human mind with perhaps the aid of a pen and paper. The step hence equates to an abstract idea of mental processes.
4. Computing an edit distance between the first read and the second read (claim 1).
This step recites computing an edit distance, which explicitly recites a mathematical calculation. Therefore the step is directed to an abstract idea of mathematical concepts.
5. Determining that the edit distance is below a threshold value (claim 1).
This step recites comparing a value to the threshold, which can be achieved in human mind. Therefore the step is directed to an abstract idea of mental processes.
6. Merging a first cluster containing the first read with a second cluster containing the second read into a third cluster (claim 1).
This step recites merging two clusters into a third cluster, which is interpreted as a data manipulation that can be achieved in human mind. Therefore the step is directed to an abstract idea of mental processes.
7. Separating a plurality of DNA reads into a plurality of buckets (claim 11).
Under a BRI, this step is interpreted as moving reads folders (here the buckets) or label the reads with different bucket labels. The whole process can be achieved in human mind. The step hence equates to an abstract idea of mental processes.
8. Clustering DNA reads in one of the plurality of buckets into clusters based at least in part on edit distance between respective pairs of the DNA reads (claim 11).
Under a BRI, this step is interpreted as moving reads in a same folder (here the bucket) or of a same bucket label into different clusters, after comparing the edit distance between respective pairs of the DNA reads. The whole process can be achieved in human mind with perhaps the aid of a pen and paper. The step hence equates to an abstract idea of mental processes.
Step 2A Prong Two: Consideration of Practical Application
The claims result in a process of assigning reads into clusters, which is directed to data analysis and manipulation. The claims do not recite any additional elements that integrate the abstract idea/judicial exception into a practical application.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses 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.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
“providing a DNA sample pool to a polynucleotide sequencer” (claim 1);
“receiving a plurality of reads from the polynucleotide sequencer, the plurality of reads including errors introduced by the polynucleotide sequencer” (claim 1); and
“generating a single consensus output sequence from the third cluster that has less error than individual reads in the third cluster” (claim 1).
“generating a single consensus output sequence from each of the cluster” (claim 20).
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional elements recited are directed to insignificant extra-solution activity of inputting/outputting data.
The claims do not include additional elements that are sufficient to amount for significantly more than the judicial exception because it is routine and conventional to perform the acts of acquiring a plurality of reads from a polynucleotide sequencer and outputting consensus sequence from each of the cluster to the pertinent industry. Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Applicant’s Argument
Applicant's arguments filed on 1 June 2026 have been fully considered but they are not persuasive. Particularly:
In the Remarks, Applicant argued (page 10, 1st para) that “Applicant's claimed invention represents an improvement to a technology or technical field-specifically polynucleotide sequencing. Inventions of this type may be found patent eligible at either Step 2A Prong Two or Step 2B”.
In response, Applicant’s argument is not persuasive. As discussed above over the 101 analysis, the claims as a whole, are directed to data analysis and new data generation. There might be some unique ways that data is analyzed in the instant claims, however, the alleged technological improvements which are rooted in data analysis is not applied by, captured in and reflected by any elements additional to judicial exceptions (here the data analysis). There is no indication that the polynucleotide sequencer is a particular machine. As recited, it is a generic, commercially available sequencer.
There is no unconventional arrangement in additional elements.
Hence, at Step 2A/Prong two and Step 2B, the claims are not eligible under 35 USC 101.
In the Remarks, Applicant argued (page 10, last para through page 11, 2nd para) that “The Amended Claims Tie the Recited Methods to a Particular Machine”.
In response, Applicant’s argument is not persuasive. The polynucleotide sequencer as recited, is a generic, commercially available sequencer. There is no indication that the polynucleotide sequencer is a particular machine. Hence, at Step 2A/Prong two, the claims are not integrated into a practical application.
In the Remarks, Applicant argued (page 11, 3rd para through page 12, 1st para) that “The Amended Claims Recite a Tangible Technological Improvement with Evidentiary Support in the Specification”.
In response, Applicant’s argument is not persuasive. As discussed above over the 101 analysis, the claims as a whole, are directed to data analysis and new data generation. The alleged improvement in sequencing accuracy (or “less error”) is nothing more than a good data analysis, which is still part of the judicial exceptions. There might be some unique ways that data is analyzed in the instant claims, however, the alleged technological improvements which are rooted in data analysis is not applied by, captured in and reflected by any elements additional to judicial exceptions (here the data analysis). Hence, at Step 2A/Prong two, the claims are not integrated into a practical application through a technological improvement.
In the Remarks, Applicant argued (page 12, 2nd para through page 13, 2nd para) that “The Specific Computational Techniques Recited in the Amended Claims Are Themselves Non-Conventional”.
In response, Applicant’s argument is not persuasive. The argued elements, such as:
"dividing the first read into two or more sub-reads," "finding all k-grams for each of the two or more sub-reads,"
"encoding the k-grams as bit strings, wherein the encoding comprises, for each of the two or more sub-reads, generating a bit string having a bit position for each of all possible substrings of length k and setting each bit position to a first value if the corresponding substring is present in the sub-read and to a second value if the corresponding substring is absent from the sub-read",
"a Hamming distance between a binary signature of a first DNA read and a binary signature of a second DNA read,"
"determining that the Hamming distance is between a first threshold and a second threshold," and
"calculating the edit distance" against an "edit-distance threshold",
are all directed to abstract ideas as they are all part of the data analysis. As to the additional elements recited in the claims, as discussed above over the 101 rejection, there is no unconventional arrangement in additional elements.
Hence, at Step 2B, the claims are not eligible under 35 USC 101.
In summary, the claims are not eligible under 35 USC 101.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office 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 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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/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635
Prosecution Insights