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 .
Claims 1, 2, 4-17, 21-24 are pending and under examination.
Applicant’s amendments and response, filed 9/22/2025 have been entered, and carefully considered, but are not completely persuasive.
The IDS filed 9/22/2025 and 10/08/2025, and the associated fee assertion statements, have been entered and considered.
Claim Interpretation
The claims in this application are given their broadest reasonable interpretation (BRI) 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.
Claim Rejections - 35 USC § 101
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 1-2, 4-17 and 21-24 remain rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental steps, mathematic concepts, organizing human activity, or a natural law without significantly more.
Claim 21 is the only claim that has been amended in the most recent response.
Applicant is directed to MPEP 2106 and the Federal Register notice (FR89, no 137 (7/17/2024) p 58128-58138) for the most current and complete guidelines in the analysis of patent- eligible subject matter. The current MPEP is the primary source for the USPTO’s patent eligibility guidance.
With respect to step (1): YES. The claims are drawn to statutory categories: a system comprising a sequencer and a processor, and computer implemented methods.
With respect to step (2A) (1): YES. The claims recite an abstract idea, law of nature and/or natural phenomenon. (See MPEP 2106.07(a)). The claims explicitly recite elements that, individually and in combination, constitute one or more judicial exceptions (JE).
Mathematic concepts, Mental Processes or Elements in Addition (EIA) in the claim(s) include:
1. (Previously Presented) A method, implemented using a computer system comprising one or more processors and system memory, for determining the presence or absence of a repeat expansion of a repeat sequence in a test sample comprising nucleic acids, wherein the repeat sequence comprises repeats of a repeat unit of nucleotides, the method comprising:
(EIA- preamble setting forth the goal, using a general-purpose computer, and defining a repeat expansion [0047-0049].)
(a) providing a genomic location of the repeat sequence and obtaining at least 100,000 paired end reads of the test sample, wherein the paired end reads have been processed to align to a reference sequence comprising the repeat sequence;
(EIA- data gathering step, acquiring / providing/ obtaining/ identifying target region information, and obtaining/ providing/ acquiring/ identifying routine laboratory process results: paired end sequence reads, and a description of the sequence read data collected. This is not an active step of sequencing, but a step of acquiring information generated outside the bounds of the claim by “paired end sequencing.” [0064, 0068] site or location; [0091] “The paired read ends obtained… may then be aligned to the reference sequences… As such the relative location and direction of a pair of reads are known.” [0039, 0050, 0090] “the practice of the methods and systems disclosed herein involves conventional techniques and apparatus commonly used in molecular biology… and DNA sequencing, and recombinant DNA fields that are within the skill of the art”. [0050] paired read ends. [0090] “In some embodiments the paired read ends may be obtained by Illumina’s sequencing by synthesis platforms.” [0051-0054] alignment; prior art known process ELAND. “Alignment can be done manually, although it is typically implemented by a computer algorithm…”)
(b) comparing, by the one or more processors, genomic locations of the at least 100,000 paired end reads to the genomic location of the repeat sequence to identify anchor and anchored reads in the paired end reads, wherein the anchor reads are aligned reads having genomic locations that are the same as or near the genomic location of the repeat sequence, and the anchored reads are unaligned reads that are paired with the anchor reads; and
(Mental process, performed in a computing environment, of comparing locations of aligned reads to the provided location (not the entire genome), and making a judgement as to whether anchor or anchored reads are present, and definitions of anchor and anchored reads. [0051-0054] alignment; prior art known process ELAND, “distributed as part of the Illumina Genomics Analysis pipeline.” “Alignment can be done manually, although it is typically implemented by a computer algorithm…”; Alternatively, a mathematic concept of set membership testing [0051] “a tool that provides this information may be called a set membership tester.” This includes a Bloom filter. [0052])
(c) determining if the repeat expansion is likely to be present in the test sample based at least in part on numbers of repeats of the repeat unit in the anchored reads.
(Mental step of judgement as to whether a repeat expansion is “likely to be present” based on the numbers of repeats; alternately a mathematic calculation of a number of repeats, and a likelihood determination. [0092] “The distribution of a test sample may be compared to an empirically or theoretically derived criterion separated unaffected samples from affected samples. In this way one may determine whether or not the test sample has the repeat expansion…”)
2. (Previously Presented) The method of claim 1, wherein (c) comprises determining if the repeat expansion is likely to be present in the test sample based on the anchor reads and the anchored reads.
(Modifying the mental step/ mathematic concept of step c), defining the basis for the comparison, or calculation without specifying how that basis is determined, or judged.)
4. (Previously Presented) The method of claim 1, wherein (c) comprises
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obtaining the number of identified reads that are high-count reads, wherein the high- count reads comprise reads having more repeats than a threshold value; and comparing the number of high-count reads in the test sample to a call criterion.
(EIA- data gathering AND a Mental Process/ mathematic concept: the number of high-count reads is provided by the Illumina sequence analysis pipeline [0051-0054]. Mental step/ or mathematic concept of comparison of a value to a criterion and making a judgement as to whether a call should be made. [0006] “threshold value... is at least about 80%... 90%... the call criterion is obtained from a distribution of high count reads in control samples… calculated from the length of the paired read ends, a length of a sequence having the repeat expansion and a sequencing depth…is calculated from the distance between the first and last observation of the repeat sequences within the reads…”)
5. (Previously Presented) The method of claim 4, wherein the threshold value for high-count reads is at least about 80% of the maximum number of repeats, which maximum is calculated from the length of the paired end reads and the length of the repeat unit.
(Mental step/ or mathematic concept of comparison of a value to a criterion and making a judgement as to whether a call should be made. [0006] “threshold value… is at least about 80%... 90%... the call criterion is obtained from a distribution of high count reads in control samples… calculated from the length of the paired read ends, a length of a sequence having the repeat expansion and a sequencing depth…is calculated from the distance between the first and last observation of the repeat sequences within the reads…”)
6. (Previously Presented) The method of claim 5, wherein the threshold value for high-count reads is at least about 90% of the maximum number of repeats.
(Mental step/ or mathematic concept of comparison of a value to a criterion and making a judgement as to whether a call should be made. [0006] “threshold value... is at least about 80%... 90%... the call criterion is obtained from a distribution of high count reads in control samples… calculated from the length of the paired read ends, a length of a sequence having the repeat expansion and a sequencing depth…is calculated from the distance between the first and last observation of the repeat sequences within the reads…”)
7. (Previously Presented) The method of claim 4, wherein the call criterion is obtained from a distribution of high-count reads of control samples.
(Mental step/ or mathematic concept of comparison of a value to a criterion and making a judgement as to whether a call should be made. [0006] “threshold value... is at least about 80%... 90%... the call criterion is obtained from a distribution of high count reads in control samples… calculated from the length of the paired read ends, a length of a sequence having the repeat expansion and a sequencing depth…is calculated from the distance between the first and last observation of the repeat sequences within the reads…”)
8. (Previously Presented) The method of claim 1, wherein the anchor reads are aligned to or within about 5 kb of the repeat sequence.
(Mental process/ mathematic concept: modifying step (b), alignment [0007], setting a parameter for alignment)
9. (Previously Presented) The method of claim 1, wherein the anchor reads are aligned to or within about 1 kb of the repeat sequence.
(Mental process/ mathematic concept: - modifying step (b), alignment [0007], setting a parameter for alignment)
10. (Previously Presented) The method of claim 1, wherein the unaligned reads comprise reads that cannot be aligned or are poorly aligned to the reference sequence.
(Mental process/ mathematic concept: modifying step (b), setting a parameter for alignment/unalignment. [0054] “when a read is aligned to a reference sequence with a number of mismatched bases above a certain criterion, the read is considered poorly aligned…”)
11. (Previously Presented) The method of claim 1, wherein (c) comprises comparing a distribution of numbers of repeats of the repeat unit in the identified reads for the test sample and a distribution of numbers of repeats for one or more control samples.
(Mental Process/ mathematic calculation: comparing a distribution between sample and control, and making a judgement. [0091] “in some implementations comparing the distribution for the test sample... includes using a Mann-Whitney rank test…”)
12. (Previously Presented) The method of claim 11, wherein comparing the distribution for the test sample to the distribution for the control samples comprises using a Mann-Whitney rank test to determine if the distribution of the test sample statistically significantly differs from the distribution of the control samples.
(mathematic concept: modifying step c) using a mathematic algorithm to determine the comparison. [0091] “in some implementations comparing the distribution for the test sample... includes using a Mann-Whitney rank test…”)
13. (Previously Presented) The method of claim 12, further comprising determining that the repeat expansion is likely present in the test sample if the test sample's distribution is skewed more towards higher numbers of repeats than the control samples, and the p value for the Mann-Whitney rank test is smaller than about 0.0001.
(Mathematic concept of calculating skew, and statistical significance of the result [0091].)
14. (Previously Presented) The method of claim 13, further comprising determining that the repeat expansion is likely present in the test sample if the test sample's distribution is skewed more towards higher numbers of repeats than the control samples, and the p value for the Mann-Whitney rank test is smaller than about 0.00001.
(Mathematic concept of calculating skew, and statistical significance of the result [0091].)
15. (Previously Presented) The method of claim 1, wherein the numbers of repeats are numbers of in-frame repeats.
(mathematic concept: modifying step c) to identify the repeats to be counted.)
16. (Previously Presented) The method of claim 1, further comprising using a sequencer to generate paired end reads from the test sample.
(EIA- use of a routine piece of laboratory equipment to generate the paired end sequence reads in the data gathering step. [0039, 0050, 0090] “the practice of the methods and systems disclosed herein involves conventional techniques and apparatus commonly used in molecular biology… and DNA sequencing, and recombinant DNA fields that are within the skill of the art”. [0050] paired end reads. [0090] “In some embodiments the paired read ends may be obtained by Illumina’s sequencing by synthesis platforms.”)
17. (Previously Presented) The method of claim 1, further comprising extracting the test sample from an individual.
(EIA- modifying the data gathering to include taking any type of sample, in any manner. [0011] “In some implementations, the test sample is a blood sample, a urine sample, a saliva sample, or a tissue sample. In some implementations, the test sample includes fetal and maternal cell-free nucleic acids.” See also [00122-00129] “samples”)
22. (Previously Presented) The method of claim 1, wherein the repeat sequence is a clinically- relevant sequence.
(EIA- modifying the preamble and the data gathering and modifying the mental step of judgement/ mathematic calculation of step c) to analyze repeat sequences that are “clinically-relevant,” a modification of the mental step of judgement. [0070] “The term "clinically-relevant sequence" herein refers to a nucleic acid sequence that is known or is suspected to be associated or implicated with a genetic or disease condition. Determining the absence or presence of a clinically-relevant sequence can be useful in determining a diagnosis or confirming a diagnosis of a medical condition, or providing a prognosis for the development of a disease.”)
23. (Previously Presented) The method of claim 1, further comprising (d) diagnosing a clinical condition of an individual associated with the test sample based on determining if the repeat expansion is likely to be present in the test sample.
(Mental process of judgement as to whether the presence or absence of a repeat expansion should result in a diagnosis, without specifying how the diagnosis is determined, with any particularity. [0070] “The term "clinically-relevant sequence" herein refers to a nucleic acid sequence that is known or is suspected to be associated or implicated with a genetic or disease condition. Determining the absence or presence of a clinically-relevant sequence can be useful in determining a diagnosis or confirming a diagnosis of a medical condition, or providing a prognosis for the development of a disease.”)
24. (Previously Presented) The method of claim 1, wherein the reference sequence is a portion of a reference genome.
(Mental Process- modifying the alignment of the paired end reads to a reference, to some amount less than a complete genome. [0065-0069] “the term "reference genome" or "reference sequence" refers to any particular known genome sequence, whether partial or complete, of any organism or virus which may be used to reference identified sequences from a subject.”)
The BRI of claim 1 is a method, implemented in a computer system, for “determining the presence of absence of a repeat sequence” which is defined as “repeats of a repeat unit of nucleotides” by providing a known location of a repeat sequence, and obtaining/providing “paired end sequence read data” which were previously aligned to a reference outside the bounds of the claim to obtain location data for each aligned read. Mental processes of comparison (matching the location of the sequence read to the provided “known” location) and judgement (to identify paired read ends which are anchor or anchored reads) and mental steps of judgement as to whether the expansion is likely to be present based on a number of repeats. As set forth above, the comparison of location data can be a mathematic process, and the mathematic concept of “counting” repeat units can be involved in the mental concept of determining the presence or absence of the repeat unit. The limitations of comparison and judgement do not require any particular element for which the human mind is not equipped. (MPEP 2106.04(a))
The computer system recited in the preamble is generically described with no particular interactions between data, and specific structures of the computer. (MPEP 2106.04(d), 2106.05(f))
Providing known repeat unit locations in step a), for the purpose of comparing locations from aligned sequence read data in step b), is a data gathering step, required to carry out step b). The provision of the known repeat unit location serves to reduce the number of comparisons required for each identified location from the sample. All locations of the reads from the sample are compared to “the genomic location of the repeat sequence.” (i.e. a single location), instead of comparing all reads to all known genomic locations of repeat sequences from a genome. (MPEP2106.05(g))
Providing/ obtaining paired end sequence read data from the sample in step a), which were previously processed to align to a reference to generate location data for each read, (outside the bounds of the claim) is a data gathering step required to carry out step b), to identify the presence or absence of the repeat unit in the particular sample (according to the goal of the preamble). The paired-end sequence read data was produced outside the bounds of the claim, and the obtained, aligned paired-end sequence read data as recited in the claim has no particular features or structure. One of skill was aware of paired-end sequence read data, and that the data generally encompasses pairs of sequence data strings, location information (after alignment to the reference), quality information, and certain other automatically provided results of Illumina paired-end sequencing processes. Any paired-end sequence read data appears to meet this data gathering limitation, as no particular paired-end processes are recited or required. (MPEP 2106.05(g)).
Comparing location information, for the purpose of identifying anchor and anchored reads, is a mental process of comparison of the location data of each read to “the genomic location”, and judgement as to whether the matched location data indicates “anchor” “anchored” or “neither”. Whether this mental process is carried out in the human mind, using a pen and paper, or in a computing environment does not change the identification of a mental process. This process is carried out one location comparison at a time, for each location of each sequence read, whether it is 100,000 or 1,000,000 reads. Matching or comparing genomic coordinate data between “the genomic location of the repeat sequence” (a single location) and lists or tables with the locations of each paired end read does not require any specific element for which the human mind is not equipped. (MPEP 2106.04(a))
The examiner notes that only aligned paired-end sequence read data is obtained in step a) from the sample, but somehow unaligned sequence read data is also acquired, to identify “anchored” reads which “are unaligned reads that are paired with the anchor reads…”
The Examiner reviewed the specification and determined that the comparing of genomic locations CAN be interpreted as a mathematic concept, using set membership testing. “Alternatively, a mathematic concept of set membership testing [0051] “a tool that provides this information may be called a set membership tester.” This includes a Bloom filter. [0052]” (MPEP 2106.04(a))
Identifying/ determining/ judging whether the sample contains the repeat unit expansion comprises both the mathematic concept of “counting” and the mental step of comparison and judgement. The number of repeat units is observed and used to make the judgement. Dependent claims set forth thresholds, “maximum” numbers of repeats, the use of “high count reads”, et al. to which the number of repeat units are to be compared. Neither the counting nor the comparison and judgement require any specific element for which the human mind is not equipped. (MPEP 2106.04(a))
21. (Previously Presented) A sequencer for determining the presence or absence of a repeat expansion of a repeat sequence in a test sample comprising nucleic acids, wherein the repeat sequence comprises repeats of a repeat unit, the sequencer comprising:
a processor; and
one or more computer-readable storage media having stored thereon instructions for execution on the processor to evaluate copy number in the test sample by:
(EIA- a “sequencer”, comprising a processor, and storage media, and the intended use of the sequencer. The sequencer was well known. [0090] “In some embodiments the paired read ends may be obtained by Illumina’s sequencing by synthesis platforms.” [00141-00163] describe routine sequencers and sequencing protocols that are widely known in the literature and/or are commercially available, such as those by Affymetrix, Illumina/ Solexa, Helicos Biosciences, Pacific Biosciences and Oxford Nanopore. [00164-00184] describe routine sequencers to carry out the method.)
(a) providing a genomic location of the repeat sequence and causing the sequencer to sequence nucleic acids of the test sample to generate at least 100,000 paired end reads of the test sample, wherein the paired end reads have been processed to align to a reference sequence comprising the repeat sequence;
(EIA- data gathering step, acquiring/ providing/ obtaining/ identifying target region information, and a data gathering step of performing routine laboratory processes of “paired end sequencing” to achieve certain results: paired end sequence reads, and a description of the sequence read data collected. [0064, 0068] site or location; [0091] “The paired read ends obtained… may then be aligned to the reference sequences… As such the relative location and direction of a pair of reads are known.” [0039, 0050, 0090] “the practice of the methods and systems disclosed herein involves conventional techniques and apparatus commonly used in molecular biology… and DNA sequencing, and recombinant DNA fields that are within the skill of the art”. [0050] paired read ends. [0090] “In some embodiments the paired read ends may be obtained by Illumina’s sequencing by synthesis platforms.” [0051-0054] alignment; prior art known process ELAND. “Alignment can be done manually, although it is typically implemented by a computer algorithm…”)
(b) comparing, by the one or more processors, genomic locations of the at least 100,000 paired end reads to the genomic location of the repeat sequence to identify anchor and anchored reads in the paired end reads, wherein the anchor reads are aligned reads having genomic locations that are the same as or near the genomic location of the repeat sequence, and the anchored reads are unaligned reads that are paired with the anchor reads; and
(Mental process, performed in a computing environment, of comparing and aligning sequences to the provided location, and making a judgement as to whether anchor or anchored reads are present. [0051-0054] alignment; prior art known process ELAND, “distributed as part of the Illumina Genomics Analysis pipeline.” “Alignment can be done manually, although it is typically implemented by a computer algorithm…”; Alternatively, a mathematic concept of set membership testing [0051] “a tool that provides this information may be called a set membership tester.” This includes a Bloom filter. [0052])
(c) determining if the repeat expansion is likely to be present in the test sample based at least in part on numbers of repeats of the repeat unit in the anchored reads.
(Mental step of judgement as to whether a repeat expansion is “likely to be present” based on the numbers of repeats; alternately a mathematic calculation of a number of repeats, and a likelihood determination. [0092] “The distribution of a test sample may be compared to an empirically or theoretically derived criterion separated unaffected samples from affected samples. In this way one may determine whether or not the test sample has the repeat expansion…”)
The BRI of claim 21: this analysis only addresses the differences with respect to the analysis of claim 1. Claim 21 is directed to a “sequencer”, which is a piece of laboratory machinery, comprising a processor and computer-storage-media comprising instructions, with the intended use: “for determining the presence of absence of a repeat sequence” in a sample and the repeat sequence is defined as “repeats of a repeat unit of nucleotides.” The stored instructions cause the processor to perform the following: providing a known location of a repeat sequence, and generating “paired end sequence read data” from a sample, and generating location data for each aligned read. (MPEP 2106.05(b))
The sequencer recited in the preamble is generically described and appears to act the same as any other “sequencer” of the prior art at the time of filing. It has no particular structure, or set of elements beyond the presence of the processor and stored instructions. [0166] of the specification states that “the sequencer is configured to perform next generation sequencing (NGS).” [0090] of the specification: “In some embodiments the paired read ends may be obtained by Illumina’s sequencing by synthesis platforms.” [00141-00163] describe routine sequencers and sequencing protocols that are widely known in the literature and/or are commercially available, such as those by Affymetrix, Illumina/ Solexa, Helicos Biosciences, Pacific Biosciences and Oxford Nanopore. [00164-00184] describe routine sequencers to carry out the method. The sequencer itself is not changed by carrying out the limitations of the JE. (MPEP 2106.05(b))
The sequencer acts as it was designed, to “sequence nucleic acids of the test sample to generate at least 100,000 paired end reads of the test sample” with no other specific instruction, process, or requirement. (MPEP 2106.05(b))
Generating paired end sequence read data from the sample in step a), and generating location data for each read, is a data gathering step required to carry out step b) and c), to identify the presence or absence of the repeat unit in the particular sample, to achieve the intended use of the sequencer from the preamble. The aligned paired-end sequence read data as recited in the claim has no particular features or structure. One of skill was aware of paired-end sequence read data, and that the data generally encompasses pairs of sequence data strings, location information (after alignment to the reference), quality information, and certain other results of Illumina paired-end sequencing processes. Any generation or process of sequencing the sample that generates paired-end sequence read data appears to meet this data gathering limitation, as no particular paired-end processes are recited or required. (MPEP 2106.05(b))
The remainder of the analysis is the same as that for claim 1.
With respect to step 2A (2): NO the claims are not integrated into a practical application. The claims were examined further to determine whether they integrated any JE into a practical application (MPEP 2106.04(d)). The claimed additional elements are analyzed alone, or in combination to determine if the JE is integrated into a practical application (MPEP 2106.05(a-c, e, f and h)).
MPEP 2106: “Limitations the courts have found indicative that an additional element (or combination of elements) may have integrated the exception into a practical application include:
• An improvement in the functioning of a computer, or an improvement to other technology or technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
• Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
• Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
• Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
• Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
The courts have also identified limitations that did not integrate a judicial exception into a practical application:
• Merely reciting the words "apply it" (or an equivalent) with the judicial exception, or merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f);
• Adding insignificant extra-solution activity to the judicial exception, as discussed in MPEP § 2106.05(g); and
• Generally linking the use of a judicial exception to a particular technological environment or field of use, as discussed in MPEP § 2106.05(h).”
With respect to step 2A-2 and independent claims 1 and 21:
The claims do not clearly provide an improvement in the functioning of the computer itself.
The claims do not clearly provide an improvement to a technology of paired end sequencing, or a technical field of paired end sequencing. The paired end sequencing carried out in claim 21 has no particular steps, actions or processes beyond the sequencing, and generating the location data. The paired end sequence read data acquired for claim 1 has no particular structure, beyond the sequence read pairs and the location information and could be met by any “paired end sequencing process”. The application of the data to the JE does not change any aspect of the paired end sequence read data, or location data and does not affect the technology/ technical field of paired end sequencing.
The claims do not provide a particular treatment or prophylaxis. Dependent claims assert that the repeats may be “clinically relevant” and could be used in diagnosis, however this is not the provision of a particular treatment or prophylaxis, and the repeat units identified in the claims are not specifically related to any diagnosis, illness or condition.
Claim 1 does not use a specific or particular machine integral to the claim. Claim 1 employs a general-purpose computer acting in the way it was designed. Claim 21 recites a “sequencer” with a processor, and instructions, wherein the sequencer and processor are described at a high level, having no particular structural or functional elements integral to carrying out the JE. The sequencer generates the data to be acted upon by the JE, but is not changed by the JE and it is not otherwise affected by carrying out the stored instructions.
The claims do not effect a transformation or reduction of a particular article.
The claims generally link the use of paired end sequencing technology to the JE as a particular technological environment without other meaningful integration. Claim 1 uses a computer as a tool to perform an abstract idea. Claim 21 uses computer elements within a sequencer to perform the abstract idea after the use of the sequencing-process-specific elements.
The claims add data gathering steps which are extra-solution activity to the JE.
Claims 1, 4, 16, 17, 21 and 22 each recite EIA related to data gathering, or a description of the data gathered.
In claim 1 the data gathered comprises: “a genomic location of the repeat sequence” and
“at least 100,000 paired end reads of the test sample… processed to align to a reference sequence comprising the repeat sequence” (a dataset) which provides the genomic location of each paired end read.
In claim 21, the data gathered comprises “a genomic location of the repeat sequence” and generating “at least 100,000 paired end reads of the test sample… processed to align to a reference sequence comprising the repeat sequence” using the sequencer, and the genomic location of each paired end read.
Data gathering steps are not an abstract idea, they are extra-solution activity, as they collect the data needed to carry out the JE. The data gathering does not impose any meaningful limitation on the JE, or how the JE is performed. The additional limitation (data gathering) must have more than a nominal or insignificant relationship to the identified judicial exception. (MPEP 2106.04/.05, citing Intellectual Ventures LLC v. Symantec Corp, McRO, TLI communications, OIP Techs. Inc. v. Amason.com Inc., Electric Power Group LLC v. Alstrom S.A.).
Claim(s) 1, 16 and 21 recite the additional non-abstract element (EIA) of a general-purpose computer system or parts thereof, including “a sequencer”.
Claim 1 sets forth a computer-implemented method where the general-purpose computer has no particular structure. Claim 21 sets forth the use of a generically described “sequencer” which comprises a processor, and stored instructions.
MPEP 2106: “T[t]he specificity of the claim limitations is relevant to the evaluation of several considerations including the use of a particular machine, particular transformation and whether the limitations are mere instructions to apply an exception. See MPEP §§ 2106.05(b), 2106.05(c), and 2106.05(f).”
The sequencer of claim 21 is a routine piece of laboratory equipment used to process the sample, to provide routine paired end sequence read data. No particular details are recited about the sequencer and it acts in the way in which it was designed. The sequencer performs no non-routine steps. The sequencer is not changed by carrying out the method. The “sequencing” aspect of the sequencer carries out the sequencing, whether or not the JE is subsequently applied to the sequence read datasets. The aspects of the sequencer that carry out the analysis steps of the method after the step of sequencing, are the processor and instructions, as in claim 1.
The computer-implementation of claim 1 requires nothing more than a general-purpose computer to perform the functions that constitute the judicial exceptions. The claims do not provide improvements to the functioning of the computer itself (as in DDR Holdings, LLC v. Hotels.com LP); they do not provide improvements to any other technology or technical field (as in Diamond v. Diehr); nor do they utilize a particular machine (as in Eibel Process Co. v. Minn. & Ont. Paper Co.). Hence, these are mere instructions to apply the JE using a computer, and therefore the claim does not recite integrate that JE into a practical application.
Dependent claim(s) 2-15, 23-24 recite(s) an abstract limitation to the JE reciting additional mathematic concepts, or mental processes. Additional abstract limitations cannot provide a practical application of the JE as they are a part of that JE.
In combination, the limitations of data gathering, for the purpose of carrying out the JE, using a general-purpose computer and/or a sequencer in the way it which it was designed merely provide extra-solution activity, and fail to integrate the JE into a practical application.
With respect to step 2B: NO the claims do not provide a specific inventive concept. The claims recite a JE, do not integrate that JE into a practical application, and thus are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). The additional elements were considered individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to claim(s) 1, 4, 16, 17, 21, 22: The limitation(s) identified above as non-abstract elements (EIA) related to data gathering do not rise to the level of significantly more than the judicial exception.
Illumina (2013) discloses obtaining a sample, sequencing the sample and obtaining the required amount of paired end reads, and alignment to a given location (Fig 4-5, p7-9).
Kural (US 2015/0199474 A1: of record, PTO 1449) disclosed obtaining a sample [0116-0119], sequencing the sample [0120-0134], and obtaining at least 10,000 paired end reads. [0066-0067] provide details on the paired end sequencing, and [0068+] disclose alignment of paired read ends to a given location [0038], for the same purpose of identifying a repeat expansion.
Cao (2014) disclosed obtaining a sample, sequencing the sample, and obtaining the required amount of paired end reads, as set forth at page 4/11. Cao discloses alignment to a given location at page 2/11, Fig 1.
Zavodna (2014) disclosed obtaining a sample (p4/14), sequencing the sample using multiple NGS platforms (p5/14) and Sanger sequencing (p7/14), obtaining the required amount of paired end reads and aligning them to the provided location (p4-5/14, p6/14).
Zhang (2013) disclosed obtaining a sample (p614), sequencing the sample using Illumina sequencing platforms to generate paired end reads (p614). The paired end reads are aligned to a given location (Fig 1, p615).
These elements meet the BRI of the identified data gathering limitations. As such, the prior art recognizes that this data gathering element is routine, well understood and conventional in the art (as in Alice Corp., CyberSource v. Retail Decisions, Parker v. Flook).
In the specification at [0011, 0039, 0050, 0090 0122-0129, 0141-0163] it is disclosed that the steps identified as data gathering (obtaining a sample, sequencing the sample and obtaining the required amount of paired end reads) can be met using well known prior art known kits, pipelines, processes or commercially available products/ equipment of companies such as Affymetrix, Illumina/ Solexa, Helicos Biosciences, Pacific Biosciences and Oxford Nanopore.
These elements meet the BRI of the identified data gathering limitations. As such, the specification supports the assertion that this data gathering element is routine, well understood and conventional in the art (as in Alice Corp., CyberSource v. Retail Decisions, Parker v. Flook).
With respect to claims 1, 16 and 22: the limitations identified above as non-abstract elements (EIA) related to general-purpose computer systems or the sequencer do not rise to the level of significantly more than the judicial exception.
Illumina (2013) provides sequencer laboratory equipment, the MiSeq™ and the HiSeq™ at page 4/12, Table 1. The analysis of the sequence read data is performed by processors within the equipment or using linked general-purpose computers.
Kural (2015) disclosed a variety of general-purpose computer systems (fig 10-11) [0073-0114], and sequencers, including commercially available systems from Illumina, Life Technologies, Roche, Applied Biosystems, Helicos, Pacific Biosciences, Oxford Nanopore, et al.
Cao (2014) disclosed general purpose computers (throughout), and a sequencer by Illumina (p4/11).
Zadovna (2014) disclosed sequencers from Illumina, a Sanger Sequencer (4-7) and general-purpose computers, throughout.
Each of these meet the BRI of the claimed computer system or computer system elements, comprising input, output/ display, a processor, and memory, and the required sequencer. As such, the prior art recognizes that these computing elements were routine, well understood and conventional in the art.
The specification, at [0164-0184] discloses the use of routine general-purpose computers for carrying out the invention, and/or the use of commercially available computer system elements. The specification notes at [0090, 0141-0163], that sequencers from Affymetrix, Illumina/Solexa, Helicos Biosciences, Pacific Biosciences and Oxford Nanopore are all useful in performing paired end sequencing.
Each of these meet the BRI of the claimed computer system or computer system elements, comprising input, output/ display, a processor, and memory, and the required sequencer. As such, the specification supports the assertion that these elements are routine, well understood and conventional in the art.
Dependent claim(s) 2-15, 23-24 each recite a limitation requiring additional mathematic concepts or mental processes. Additional abstract limitations cannot provide significantly more than the JE as they are a part of that JE (MPEP 2106.05).
In combination, the data gathering steps providing the information required to be acted upon by the JE, performed in a generic computer or generic computing environment fail to rise to the level of significantly more than that JE. The data gathering steps either provide the dataset or sequence the sample to provide the data for the JE, which is carried out by the general-purpose processor elements. No non-routine step or element has clearly been identified.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Applicant’s arguments:
Applicant’s arguments have been carefully considered but are not persuasive.
The examiner acknowledges Applicant’s arguments which set forth that the claims lead to an improvement in the identification of repeat expansions in paired end sequence read data. According to the guidance set forth in MPEP 2106, this is an improvement to the judicial exception itself, and is not reflected back into a specific technological environment or practically applied process.
The identification of the presence or absence of a repeat expansion in the sample is provided by the steps identified as mental processes and/or mathematic concepts (steps b) and c)).
In claim 1, the mental processes /mathematic concepts act on a dataset that comprises 1) “the genomic location of the repeat expansion” and 2) paired end sequence read data, and locations. In claim 1, the comparison and determination of the known location to the sample locations does not depend on how the dataset was generated, nor does the analysis of the data change any aspect of the data collected. The output (presence or absence) is not further applied to any particular process.
In claim 21, the sequencer acts as it was designed “to sequence” the sample, and generate paired end sequence read information, and location information. The location information from the sample is compared to the “genomic location of the repeat expansion”. The comparison does not depend on how the data was generated, nor does the analysis of the data change any aspect of the sequencing process, or the sequence read dataset. The sequencing is carried out whether or not the JE is applied to the resulting dataset. The result (presence or absence) is not further applied to any particular process.
Carrying out the claimed methods does not change the technology of next generation sequencing, or any type of sequencing that can generate paired end sequence read data. The technology of carrying out paired end sequencing is not changed or affected. The technology of receiving data is not changed or affected. The improvement is within the JE itself, which is insufficient to provide patent-eligibility.
MPEP 2106: “The courts have also found that improvements in technology beyond computer functionality may demonstrate patent eligibility. In McRO, the Federal Circuit held claimed methods of automatic lip synchronization and facial expression animation using computer-implemented rules to be patent eligible under 35 U.S.C. 101, because they were not directed to an abstract idea. McRO, 837 F.3d at 1316, 120 USPQ2d at 1103… The McRO court indicated that it was the incorporation of the particular claimed rules in computer animation that "improved [the] existing technological process", unlike cases such as Alice where a computer was merely used as a tool to perform an existing process. 837 F.3d at 1314, 120 USPQ2d at 1102. The McRO court also noted that the claims at issue described a specific way (use of particular rules to set morph weights and transitions through phonemes) to solve the problem of producing accurate and realistic lip synchronization and facial expressions in animated characters, rather than merely claiming the idea of a solution or outcome, and thus were not directed to an abstract idea. 837 F.3d at 1313, 120 USPQ2d at 1101.
Consideration of improvements is relevant to the eligibility analysis regardless of the technology of the claimed invention. That is, the consideration applies equally whether it is a computer-implemented invention, an invention in the life sciences, or any other technology. See, e.g., Rapid Litigation Management v. CellzDirect, Inc., 827 F.3d 1042, 119 USPQ2d 1370 (Fed. Cir. 2016)… Notably, the court did not distinguish between the types of technology when determining the invention improved technology. However, it is important to keep in mind that an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. For example, in Trading Technologies Int’l v. IBG, 921 F.3d 1084, 1093-94, 2019 USPQ2d 138290 (Fed. Cir. 2019), the court determined that the claimed user interface simply provided a trader with more information to facilitate market trades, which improved the business process of market trading but did not improve computers or technology.”
Arguments that the claims provide an improvement in the computer itself are not persuasive, as no changes to the computer itself are provided, nor is there any specific interaction between specific elements of the computer or processor with the gathered data.
MPEP 2106: “To show that the involvement of a computer assists in improving the technology, the claims must recite the details regarding how a computer aids the method, the extent to which the computer aids the method, or the significance of a computer to the performance of the method. Merely adding generic computer components to perform the method is not sufficient. Thus, the claim must include more than mere instructions to perform the method on a generic component or machinery to qualify as an improvement to an existing technology. See MPEP § 2106.05(f)”
MPEP 2106: “Examples that the courts have indicated may not be sufficient to show an improvement to technology include:…
ii. Using well-known standard laboratory techniques to detect enzyme levels in a bodily sample such as blood or plasma, Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1355, 1362, 123 USPQ2d 1081, 1082-83, 1088 (Fed. Cir. 2017);
iii. Gathering and analyzing information using conventional techniques and displaying the result, TLI Communications, 823 F.3d at 612-13, 118 USPQ2d at 1747-48;…”
Claim 21 uses standard laboratory techniques and equipment to sequence the sample, to provide paired end sequence read data, that has been processed to align to a reference sequence comprising the repeat unit, and a known genomic location of a repeat. Next generation sequencing was a conventional, well understood, routine process as identified by the specification, and multiple prior art references.
Claim 1 uses data generated by standard laboratory techniques, which comprises paired end sequence read data processed to align to a reference sequence, and a known location of a repeat. Datasets comprising this data from routine next generation sequencing protocols and equipment were well known, routine and conventional in the art as identified in the specification, and multiple prior art references.
As previously set forth, an improvement in the judicial exception itself is not an improvement in the technology. For example, in In re Board of Trustees of Leland Stanford Junior University, 989 F.3d 1367, 1370, 1373 (Fed. Cir. 2021) (Stanford I), Applicant argued that the claimed process was an improvement over prior processes because it ‘‘yields a greater number of haplotype phase predictions,’’ but the Court found it was not ‘‘an improved technological process’’ and instead was an improved ‘‘mathematical process.’’ The court explained that such claims were directed to an abstract idea because they describe ‘‘mathematically calculating alleles’ haplotype phase,’’ like the ‘‘mathematical algorithms for performing calculations’’ in prior cases. Notably, the Federal Circuit found that the claims did not reflect an improvement to a technological process, which would render the claims eligible (FR89 no.137, p58137, 7/17/2024).
Similarly, in the rejected claims, with the interpretation that the steps of comparing and determining include mathematic concepts, the mathematic comparison of the distributions of the anchor and anchored reads, using a Mann-Whitney rank test is an improvement in the mathematic process of identifying a repeat expansion.
Even if limited to the identification of mental processes comprising comparison and judgement, the improvement in the identification of repeat expansions is an improvement in the mental steps of comparing location data, and judging whether or not the locations indicate the presence or absence of a repeat element, based on the observation of the number of repeat units counted.
The improvement in the identification of repeat expansions in paired end sequence read data (carried out by the judicial exception) does not provide an improvement in the technology of obtaining a sample, sequencing the sample using paired-end read technology, or obtaining the paired end sequence read data. The steps of obtaining the sample, and carrying out paired-end sequencing, are carried out, unchanged, whether or not the judicial exception is applied. (Cleveland Clinic Foundation: using well-known or standard laboratory techniques is not sufficient to show an improvement (MPEP2106.05(a)).
The improvement in the identification of repeat expansions in paired end sequence read data (achieved by the judicial exception) does not require a non-conventional interaction with a specific element of a computer as was required in Enfish. The disputed claims in Enfish were patent-eligible because they were "directed to a specific improvement to the way computers operate, embodied in [a] self-referential table." Enfish, 822 F.3d at 1336. The court found that the "plain focus of the claims" there was on an improvement to computer functionality itself-a self-referential table for a computer database, designed to improve the way a computer carries out its basic functions of storing and retrieving data- not on a task for which a computer is used in its ordinary capacity. Id. at 1335-36. The court noted that the specification identified additional benefits conferred by the self-referential table (e.g., increased flexibility, faster search times, and smaller memory requirements), which further supported the court's conclusion that the claims were directed to an improvement of an existing technology. Id. at 1337 (citation omitted).
Applicant's claim merely uses general-purpose computer components (e.g., a processor and memory) that operate in their normal, expected manner in the analysis of the dataset.
The improvement in the identification of repeat expansions in paired end sequence read data (carried out by the judicial exception) does not improve the functionality of the computer itself as in Finjan, Visual Memory, BASCOM, or Data Engine Tech., LLC. (MPEP 2106.05(a))
In Finjan, the courts found that a method that generates a security profile that identifies both hostile and potentially hostile operations, and can protect the user against both previously unknown viruses and "obfuscated code," was an improvement over traditional virus scanning. (Finjan Inc. v. Blue Coat Systems, 879 F.3d 1299, 1304, 125 USPQ2d 1282, 1286 (Fed. Cir. 2018)) In contrast, in the rejected claims, no elements are present dealing with online security, or virus protection, or code are present.
In Visual Memory, the courts found that particular recited details of a memory system with programmable operational characteristics, configurable based on the type of processor, provided an improvement in the computer itself (Visual Memory, LLC v. NVIDIA Corp., 867 F.3d 1253, 1259-60, 123 USPQ2d 1712, 1717 (Fed. Cir. 2017)). In contrast, no aspect of the computer is specifically set forth in the rejected claims.
In BASCOM, the claims recited a "specific method of filtering Internet content" requiring "the installation of a filtering tool at a specific location, remote from the end-users, with customizable filtering features specific to each end user." BASCOM, 827 F.3d at 1345--46, 1350. The installation of a filtering tool at a specific location, remote from the end users, with customizable filtering features specific to each end user, provided an inventive concept in that it gave the filtering tool both the benefits of a filter on a local computer and the benefits of a filter on the ISP server. Id. at 1350. In contrast, the rejected claims do not recite any analogous non-conventional, non generic arrangement of known, conventional physical elements within a computer system. That is the claims do not recite any physical element positioned in an unconventional manner in the system.
In Data Engine Tech, LLC, the courts found that a specific interface and implementation for navigating complex three-dimensional spreadsheets using techniques unique to computers provided an improvement to the computer itself. (Data Engine Techs., LLC v. Google LLC, 906 F.3d 999, 1009, 128 USPQ2d 1381, 1387 (Fed. Cir. 2018)). In contrast, the rejected claims do not use any techniques unique to computers to carry out the JE.
The process of characterizing tandem repeat expansion is not a technological process; it is information evaluation.
In the claims, the EIA identified as data gathering steps do not affect how the steps of the abstract idea are performed, they provide the data which is acted upon by the limitations of the JE. The JE can act on any dataset which comprises paired end sequence read data, which have been aligned to a reference genome, and the provided known genomic location of the repeat. These data gathering steps do not apply, rely on, or use the steps identified as making up the JE. Rather, the claims avail themselves of the data gathered. The data gathering in the claims constitutes insignificant pre-solution activity. See MPEP § 2106.05(g):
MPEP2106.05(g). “The term "extra-solution activity” can be understood as activities incidental to the primary process or product that are merely a nominal or tangential addition to the claim...”
“An example of pre-solution activity is a step of gathering data for use in a claimed process, e.g., a step of obtaining information about credit card transactions, which is recited as part of a claimed process of analyzing and manipulating the gathered information by a series of steps in order to detect whether the transactions were fraudulent.”
See also CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1372 (Fed. Cir. 2011) ("[E]ven if some physical steps are required to obtain information from the database ... such data-gathering steps cannot alone confer patentability.").
Claim 1 sets forth the element in addition (EIA) to the JE of a general-purpose computing system. The computing system limitations are recited at such a high level of generality, they can be met by a general-purpose computer system and is not considered a particular machine or manufacture integral to the claim (MPEP 2106.05(b)). Routine computer elements acting upon the data in a manner consistent to and according to their design are not considered to be sufficient to provide eligibility. (see, for example MPEP 2106.04(d): Gottschalk v. Benson “‘held that simply implementing a mathematical principle on a physical machine, namely a computer, was not a patentable application of that principle.”) The processor is recited generically as simply a "processor" and the activity performed by that generic processor is normal computer functionality. The requirement of using a computer processor is not sufficient to establish integration of the JE into a practical application. One of the "examples in which a judicial exception has not been integrated into a practical application" is when "[a]n additional element ... merely includes instructions to implement an abstract idea on a computer, or merely uses a computer as a tool to perform an abstract idea." Guidance 84 Fed. Reg. at 55 (emphasis added); FairWarning, 839 F.3d at 1096 ("[T]he use of generic computer elements like a microprocessor or user interface do not alone transform an otherwise abstract idea into patent-eligible subject matter.").
That the claimed system may result in faster and more accurate identifications in large data sets does not take the claim out of the realm of the abstract.
"[R]elying on a computer to perform routine tasks more quickly or more accurately is insufficient to render a claim patent eligible." OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363 (Fed. Cir. 2015); see also Intellectual Ventures I LLC v. Erie Indemnity Co., 711 F. App'x 1012, 1017 (Fed. Cir. 2017) (unpublished) ("Though the claims purport to accelerate the process of finding errant files and to reduce error, we have held that speed and accuracy increases stemming from the ordinary capabilities of a general-purpose computer 'do[] not materially alter the patent eligibility of the claimed subject matter."'); see also Bancorp Servs., L.L.C. v. Sun Life Assurance Co. of Can. (US.), 687 F.3d 1266, 1278 (Fed. Cir. 2012) ("[T]he fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter.").
In claim 21, with respect to the sequencer and the use to perform paired end sequencing processes, having no particular qualities or requirements, does not take the claim out of the realm of the abstract. The sequencer is recited at a high level of generality, and acts completely in the way it was designed. No non-routine aspect of the sequencer is claimed. The “sequencer” aspects perform the next generation sequencing or paired end sequencing processes, and the general-purpose processor then analyzes the data. Sequencers were shown to be routine, well understood and conventional through citation of the specification and multiple prior art references. In particular the Illumina equipment (cited in the specification, and in the prior art) was shown to comprise a processor capable of storing instructions that meets the BRI of “the sequencer.”
Whether examined individually or in combination, the EIA in the claims beyond the JE, i.e., data collection and computer implementation including routine laboratory equipment, are insufficient to establish that the abstract ideas recited are integrated into a practical application nor do the EIA provide significantly more than the JE.
The EIA identified as data gathering, the use of general-purpose computers, and the use of a “sequencer” were each shown, by citation of prior art references, to be well-understood, routine, and conventional limitations in bioinformatics.
Illumina (2013) discloses obtaining a sample, sequencing the sample and obtaining the required amount of paired end reads, and alignment to a given location (Fig 4-5, p7-9). This disclosure provides sequencer laboratory equipment, the MiSeq™ and the HiSeq™ at page 4/12, Table 1. The analysis of the sequence read data is performed by onboard processors or linked general purpose computers.
Kural (US 2015/0199474 A1: of record, PTO 1449) disclosed obtaining a sample [0116-0119], sequencing the sample [0120-0134], and obtaining at least 10,000 paired end reads. [0066-0067] provide details on the paired end sequencing, and [0068+] disclose alignment of paired read ends to a given location [0038] using general purpose computers, for the same purpose of identifying a repeat expansion.
Cao (2014) disclosed obtaining a sample, sequencing the sample, and obtaining the required amount of paired end reads, as set forth at page 4/11. Cao discloses alignment to a given location at page 2/11, Fig 1, using general-purpose computers.
Zavodna (2014) disclosed obtaining a sample (p4/14), sequencing the sample using multiple NGS platforms (p5/14) and Sanger sequencing (p7/14), obtaining the required amount of paired end reads and aligning them to the provided location (p4-5/14, p6/14) using general purpose computers.
Zhang (2013) disclosed obtaining a sample (p614), sequencing the sample using Illumina sequencing platforms to generate paired end reads (p614). The paired end reads are aligned to a given location (Fig 1, p615) using general-purpose computer systems.
With respect to the arguments related to the novelty of the improvement: "Even assuming [the claimed invention is novel], it does not avoid the problem of abstractness." Affinity Labs of Tex., LLC v. DIRECTV, LLC, 838 F.3d 1253, 1263 (Fed. Cir. 2016). That is because the inventive concept must be significantly more than the abstract idea itself. Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1151 (Fed. Cir. 2016) ("[A] claim for a new abstract idea is still an abstract idea.")
As discussed above, the additional elements recited in the claims, beyond the abstract idea to which it is directed, are the data-gathering step of obtaining a sample, sequencing the sample and obtaining paired end sequence read data as well as the routine sequencer and the use of a general-purpose computer and/or a “sequencer”. Applicant's Specification supports the Examiner's conclusion that these additional elements are well-understood, routine, and conventional:
Employment of known data gathering steps meeting the BRI of those identified above, a known routine sequencer and a known computer system are each sufficient to carry out the JE as set forth in the specification:
In the specification at [0011, 0039, 0050, 0090 0122-0129, 0141-0163] it is disclosed that the steps identified as data gathering (obtaining a sample, sequencing the sample and obtaining the required amount of paired end reads) can be met using well known prior art known kits, pipelines, processes or commercially available products/ equipment of companies such as Affymetrix, Illumina/ Solexa, Helicos Biosciences, Pacific Biosciences and Oxford Nanopore.
The specification, at [0164-0184] discloses the use of routine general-purpose computers for carrying out the invention, and/or the use of commercially available computer system elements. The specification notes at [0090, 0141-0163], that sequencers from Affymetrix, Illumina/Solexa, Helicos Biosciences, Pacific Biosciences and Oxford Nanopore are all useful in performing paired end sequencing.
The paired end sequence read data required can be obtained from publicly available sources as set forth in the specification at [0153]: “other sources of public sequence information include GenBank, dbEST, ebSTS, EMBL… and the DDBJ.”
The repeat unit data and location required can be obtained from publicly available sources, as set forth in the specification at [0048]: Richards (2001) Human Molecular Genetics Vol 10, no 20, p2187-2194. [0081] McLennan et al. (2011) Fragile X syndrome, Current Genomics vol 12 no 3, p216-224.
In light of the foregoing, the examiner concludes that the claims are directed to no more than judicial exceptions to Section 101 and do not recite the "significantly more" requisite to transform the nature of the claim into a patent-eligible application.
Further, with respect to the arguments regarding the alleged improvement, it is unclear that the independent claims recite all the necessary and sufficient steps required to achieve that improvement. MPEP 2106.05(a): “An important consideration in determining whether a claim improves technology is the extent to which the claim covers a particular solution to a problem or a particular way to achieve a desired outcome, as opposed to merely claiming the idea of a solution or outcome. McRO, 837 F.3d at 1314-15, 120 USPQ2d at 1102- 03; DDR Holdings, 773F.3d at 1259, 113 USPQ2d at 1107.”
The MPEP sets forth that “if the examiner concludes the disclosed invention does not improve technology, the burden shifts to applicant to provide persuasive arguments supported by any necessary evidence to demonstrate that one of ordinary skill in the art would understand that the disclosed invention improves technology. Any such evidence submitted under 37 CFR 1.132 must establish what the specification would convey to one of ordinary skill in the art and cannot be used to supplement the specification.” Applicant’s arguments cannot take the place of evidence.
Conclusion
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY K ZEMAN whose telephone number is 5712720723. The examiner can normally be reached on 8am-2pm M-F. Email may be sent to mary.zeman@uspto.gov if the appropriate permissions have been filed.
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/MARY K ZEMAN/ Primary Examiner, Art Unit 1686