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 .
Claim Status
Claims 130-159 are newly added by Applicant.
Claims 1-129 are cancelled by Applicant.
Claims 130-159 are currently pending and are herein under examination.
Claims 130-159 are rejected.
Claims 130 and 158-159 are objected.
Information Disclosure Statement
The IDSs filed 05/12/2023, 05/15/2023, and 01/29/2024 follow the provisions of 37 CFR 1.97 and have been considered in full. A signed copy of the list of references cited from these IDSs is included with this Office Action.
Priority
The instant application claims domestic benefit as a continuation of U.S. Application No. 17/556,055 filed 01/06/2022, which claims domestic benefit to international application PCT/US2020/060899 filed 11/17/2020, which claims domestic benefit to U.S. Provisional Application No. 62/936,879 filed 11/18/2019. The claims to domestic benefit are acknowledged for claims 130-159. As such, the effective filing date for claims 130-159 is 11/18/2019.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: 110 and 112 in Figure 1.
Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objection
Claims 130 and 158-159 objected to because of the following informalities:
In claim 130 the lines beginning with “scoring each of the plurality …” and “assigning a plurality of weights …” should be indented to the same degree as “dividing the matched segment into …” because these limitations are all substeps of step (b).
In claim 130 step (d) should be indented to the same degree as steps (a)-(c) and step (iii) should be indented to the same degree as steps (i)-(ii).
In claim 158 step (iii) should be indented to the same degree as steps (i)-(ii).
In claim 159 steps (i)-(iii) should be indented relative to step (b) to indicate that they are subsets of step (b).
Appropriate correction is required.
Claim Rejections - 35 USC § 112
35 USC 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 130-159 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims dependent from a rejected claim are also rejected, unless otherwise noted.
Claim 130, step (a) and step (c)(i), recites the relative term “about”, which renders the claim indefinite. The term “about” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Because about is a subjective term, the metes and bounds of about 1,000 markers and about 100 kb is unclear.
Claim 130 step (c) recites the phrase “for each of the population of test individuals” which renders the claim indefinite. It is unclear if the phrase means the following: (i) “for each test individual in the population of test individuals”, (ii) “for the population of test individuals”, (iii) there is more than one population and for each population steps (c)(i)-(c)(iii) are performed, or (iv) the population contains just two 2 individuals, i.e., the first and second individuals. For examination purposes, the phrase is being interpreted as “for the population of test individuals”. To overcome this rejection, clarify the meaning of the phrase.
Claim 130 step (iii) recites “the plurality of discrete genomic intervals for the matched segment … the plurality of scores and the plurality of weights” which renders the claim indefinite. It is unclear which plurality of discrete genomic intervals, scores and weights for which matched segment is being referenced because steps (ii)-(iii) generate for each matched segment a plurality of genomic intervals, scores and weight. To overcome this rejection, clarify which matched segment is being referenced.
Claim 130 step (d) recites “the first individual and the second individual” which renders the claim indefinite. Steps (c)-(c)(i) require that for each test individual in the population segments between a first individual and a second individual are matched, resulting in multiple first/second individuals. Thus, it is unclear which first/second individual is being referenced in step (d). To overcome this rejection, clarify how steps (c) and (d) should be interpreted.
Claim 130 step (d) recites “the weighted sums of the matched segments” which renders the claim indefinite. It is unclear which weighted sums are being referenced because steps (ii)-(iii) generate a weighted sum for both the first and second individual. To overcome this rejection, clarify which weighted sums are being referenced.
Claim 132 recites “wherein the haplotype data is generated at least in part by processing” which renders the claim indefinite. It is unclear if this is an active step or a product by process that defines a process previously performed to derive the product of the haplotype data. For examination purposes, claim 132 is being interpreted as an active step. To overcome rejection, clarify interpretation.
Claim 134 is indefinite for similar reasons to claim 132 because it depends on claim 132, which is unclear whether there is an active step of processing the genotype data. Thus, it is also unclear if claim 134 is an active step or if it defines a process previously performed to acquire the genotype data that was used in a process previously performed to acquire the haplotype data. For examination purposes, claim 134 is being interpreted as an active step. To overcome rejection, clarify interpretation.
Claims 138-140 recite the relative term “about”, which renders the claims indefinite. The term “about” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Because about is a subjective term, the metes and bounds of about 10,000 markers, about 500 kb, and about 30 markers is unclear.
Claims 139-142 recite “the matched segments” which renders the claims indefinite. It is unclear which matched segments are being referenced because claim 130 creates matched segments for each individual in the test population. To overcome this rejection, clarify which segments are being referenced.
Claims 141-142 recite “the discrete genomic intervals of the plurality of discrete genomic intervals” which renders the claims indefinite. It is unclear which discrete genomic intervals are being referenced because in claim 130 each matched segment is divided into a plurality of discrete genomic intervals, resulting in multiple pluralities of discrete genomic intervals. To overcome this rejection, clarify which intervals are being referenced.
Claim 143 recites “the plurality of discrete genomic intervals” which renders the claim indefinite. It is unclear which plurality is being referenced because in claim 130 each matched segment is divided into a plurality of discrete genomic intervals. To overcome this rejection, clarify which intervals are being referenced.
Claim 145 recites “the plurality of scores” which renders the claim indefinite. It is unclear which plurality of scores is being referenced because claim 130 step (c)(ii) generates a plurality of scores for each matched segment. To overcome this rejection, clarify which scores are being referenced.
Claims 145-146 recite the relative term “consistency”, which renders the claims indefinite. The term “consistency” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Because consistency is a subjective term, it is unclear when a degree of homozygosity and pairwise matching is not consistent.
Claim 147, lines 1-2, recites “the plurality of weights to the plurality of discrete genomic intervals” which renders the claim indefinite. It is unclear which plurality of weights and which plurality of genomic intervals are being referenced because claim 130 step (c)(ii) assigns weights to intervals for each matched segment. To overcome this rejection, clarify which weights and which intervals are being referenced.
Claim 148, 2nd to last line, recites “the plurality of weights” which renders the claim indefinite. It is unclear which plurality of weights is being referenced because claim 130 step (c)(ii) assigns a plurality of weights to a plurality of intervals for each matched segment, and because claim 147 recites “the plurality of weights to the plurality of discrete genomic intervals” intervals for each matched segment. To overcome this rejection, clarify which plurality of weights is being referenced.
Claims 150 and 152, lines 1-2, recite “the weighted sum over the plurality of discrete genomic intervals of the matched segment” which renders the claims indefinite. It is unclear which weighted sum, intervals, and matched segment is being referenced because claim 130 recites a weighted sum for each matched segment. To overcome this rejection, clarify what it refers to.
Claims 150 and 152, line 4, recite “the genome length” which lacks antecedent basis. Provide antecedent basis.
Claims 150 and 152 are indefinite because the equations are not legible. To overcome this rejection, provide a legible copy of the equation in the claims.
Claim 158, step (a) and step (c)(i), and claim 159, lines 5-6 and step (c)(i), recite the relative term “about”, which renders the claim indefinite. The term “about” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Because about is a subjective term, the metes and bounds of about 1,000 markers and about 100 kb is unclear.
Claim 158 step (c) and claim 159 step (b) recite the phrase “for each of the population of test individuals” which renders the claims indefinite. It is unclear if the phrase means the following: (i) “for each test individual in the population of test individuals”, (ii) “for the population of test individuals”, (iii) there is more than one population, or (iv) the population contains just two 2 individuals, i.e., the first and second individuals. For examination purposes, the phrase is being interpreted as “for the population of test individuals”. To overcome this rejection, clarify the meaning of the phrase.
Claim 158 step (c)(iii) and claim 159 step (b)(iii) recite “the plurality of discrete genomic intervals for the matched segment … the plurality of scores and the plurality of weights” which renders the claims indefinite. It is unclear which plurality of discrete genomic intervals, scores and weights for which matched segment is being referenced because claim 158 step (ii)-(iii) and claim 159 step (ii)(iii) generate for each matched segment a plurality of genomic intervals, scores and weight. To overcome this rejection, clarify which matched segment is being referenced.
Claim 158 step (d) and claim 159 step (c) recite “the first individual and the second individual” which renders the claims indefinite. Claim 158 step (c)-(c)(i) and claim 159 step (b)-(b)(i) require that for each test individual in the population segments between a first individual and a second individual are matched, resulting in multiple first/second individuals. Thus, it is unclear which first/second individual is being referenced. To overcome this rejection, clarify which individuals are being referenced in claim 158 step (d) and in claim 159 step (c).
Claim 158 step (d) and claim 159 step (c) recite “the weighted sums of the matched segments” which renders the claims indefinite. It is unclear which weighted sums are being referenced because claim 158 steps (c)(ii)-(c)(iii) and claim 159 steps (b)(ii)-(b)(iii) generate a weighted sum for both the first and second individual. To overcome this rejection, clarify which weighted sums are being referenced.
35 USC 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 131 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 131 fails to further limit claim 130. Claim 131 limits the diploid population which is part of an intended use recited in the preamble of claim 130. To overcome this rejection, Applicant can further limit the “population of test individuals” which is not an intended use in claim 130.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 130-159 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1:
Step 1 asks whether the claims recite statutory subject matter. In the instant application, claims 130-157 recite a method, claim 158 recites a CRM, and claim 159 recites a computer system. As such, these claims recite statutory subject matter (Step 1: YES).
Step 2A, Prong 1:
Claims that recite statutory subject matter are analyzed under Step 2A, Prong 1 to determine if they recite any concepts that equate to an abstract idea, law of nature or natural phenomena. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claim 130 recites “… for estimating a degree of ancestral relatedness between two individuals of a diploid population … (b) dividing the haplotype data into segments based on the plurality of genetic markers; (c) for each of the population of test individuals: (i) based on the plurality of genetic markers, matching segments of the haplotype data that are identical-by-descent (IBD) between a first individual and a second individual among the population of test individuals, each of the matched segments having a size that is at least about 100 kilobase pairs (kbp); (ii) for each of the matched segments between the first individual and the second individual: dividing the matched segment into a plurality of discrete genomic intervals; scoring each of the plurality of discrete genomic intervals based on a degree of homozygosity matching of the discrete genomic interval within the first individual or the second individual, wherein the degree of homozygosity matching is a number of matching homozygous haplotypes within a discrete genomic interval within a single individual, thereby generating a plurality of scores; and assigning a plurality of weights to the plurality of discrete genomic intervals, based at least in part on the plurality of scores; and (iii) calculating a weighted sum over the plurality of discrete genomic intervals of the matched segment, based on the plurality of scores and the plurality of weights; and (d) estimating the degree of ancestral relatedness between the first individual and the second individual based on the weighted sums of the matched segments.”
Claim 131 recites “wherein the diploid population is a mammal population.”
Claim 132 recites “wherein the haplotype data is generated at least in part by processing genotype data of the population of test individuals using a haplotype phasing algorithm.”
Claim 133 recites “wherein the haplotype phasing algorithm comprises a reference-based haplotype phasing algorithm comprising a Hidden Markov Model (HMM)-based search.
Claim 137 recites “wherein the assaying further comprises aligning the plurality of sequencing reads to a reference genome.
Claim 139 recites “wherein each of the matched segments has a size that is at least about 500 kilobase pairs (kbp).
Claim 140 recites “wherein each of the matched segments comprises at least about 30 distinct genetic markers.
Claim 141 recites “further comprising dividing the matched segments such that the discrete genomic intervals of the plurality of discrete genomic intervals have an equal size.
Claim 142 recites “further comprising dividing the matched segments such that the discrete genomic intervals of the plurality of discrete genomic intervals have a variable size.
Claim 143 recites “wherein the variable size of a given discrete genomic interval of the plurality of discrete genomic intervals is determined based at least in part on a start position and an end position of IBD matches proximal to the given discrete genomic interval, a density of genetic markers in the given discrete genomic interval, a maximum number of markers for the given discrete genomic interval, a maximum length of the given discrete genomic interval, or a combination thereof.
Claim 144 recites “further comprising scoring each of the plurality of discrete genomic intervals based on the degree of homozygosity matching and a degree of pairwise matching of the discrete genomic interval between the first individual and the second individual, wherein the degree of pairwise matching is a number of matching haplotypes within a discrete genomic interval between two individuals.
Claim 145 recites “further comprising correcting the plurality of scores based on a consistency between degree of homozygosity matching and degree of pairwise matching.
Claim 146 recites “further comprising correcting pairwise matching scores based on a consistency with a corresponding homozygosity matching score.
Claim 147 recites “further comprising assigning the plurality of weights to the plurality of discrete genomic intervals, based at least in part on a plurality of identity states for two alleles in two diploid individuals, wherein zero weights are assigned to discrete genomic intervals with identity states indicative of no pairwise matching between two diploid individuals, and wherein non-zero weights are assigned only to discrete genomic intervals with identity states indicative of non-zero pairwise matching between two diploid individuals.
Claim 148 recites “wherein the plurality of identity states comprises identity states selected from the recited table: wherein the first individual x has alleles a and b, wherein the second individual y has alleles c and d, wherein horizontal lines of the nine identity states indicate homozygosity in an individual from identity by descent, and wherein the plurality of weights are assigned further based on a plurality of contributions to the relatedness rxy.”
Claim 149 recites “wherein the degree of ancestral relatedness comprises a coefficient of relatedness.”
Claim 150 recites “further comprising calculating the weighted sum over the plurality of discrete genomic intervals of the matched segment, wherein the weighted sum is expressed by:
PNG
media_image1.png
63
478
media_image1.png
Greyscale
wherein 1, 2, 3, and 4 represent the sum total of the genome length assigned to one of the four match count states State 1, State 3, State 7, and State 8, respectively, wherein State 1 = {Pairwise = 4, Homozygous = 2}, wherein State 3 = {Pairwise = 2, Homozygous = 1}, wherein State 7 = {Pairwise = 2, Homozygous = 0}, wherein State 8 = {Pairwise = 1, Homozygous = 0}, and wherein L is the total length of the genome considered.”
Claim 151 recites “wherein the degree of ancestral relatedness comprises a coefficient of kinship.”
Claim 152 recites “further comprising calculating the weighted sum over the plurality of discrete genomic intervals of the matched segment, wherein the weighted sum is expressed by:
PNG
media_image2.png
70
502
media_image2.png
Greyscale
wherein 1, 2, 3, and 4 represent the sum total of the genome length assigned to one of the four match count states State 1, State 3, State 7, and State 8, respectively, wherein State 1 = {Pairwise = 4, Homozygous = 2}, wherein State 3 = {Pairwise = 2, Homozygous = 1}, wherein State 7 = {Pairwise = 2, Homozygous = 0}, wherein State 8 = {Pairwise = 1, Homozygous = 0}, and wherein L is the total length of the genome considered.”
Claim 153 recites “wherein estimating the degree of ancestral relatedness between the first individual and the second individual comprises determining a degree of inbreeding of the first individual or the second individual.”
Claim 154 recites “further comprising determining a familial relationship between the first individual and the second individual based at least in part on the degree of inbreeding of the first individual and the second individual.”
Claim 155 recites “wherein the familial relationship is a parent-child relationship, a sibling relationship, an aunt/uncle-nephew/niece relationship, a cousin relationship, or a grandparent-grandchild relationship.
Claim 156 recites “further comprising generating a social connection between a first person associated with the first individual and a second person associated with the second individual, based at least in part on the estimated degree of ancestral relatedness between the first individual and the second individual.
Claim 157 recites “further comprising identifying a familial relationship between the first individual and the second individual based at least in part on the degree of ancestral relatedness, wherein the familial relationship is a parent-child relationship, a sibling relationship, an aunt/uncle-nephew/niece relationship, a cousin relationship, or a grandparent- grandchild relationship.
Claim 158 recites “(b) dividing the haplotype data into segments based on the plurality of genetic markers; (c) for each of the population of test individuals: (i) based on the plurality of genetic markers, matching segments of the haplotype data that are identical-by-descent (IBD) between a first individual and a second individual among the population of test individuals, each of the matched segments having a size that is at least about 100 kilobase pairs (kbp); (ii) for each of the matched segments between the first individual and the second individual: dividing the matched segment into a plurality of discrete genomic intervals; scoring each of the plurality of discrete genomic intervals based on a degree of homozygosity matching of the discrete genomic interval within the first individual or the second individual, wherein the degree of homozygosity matching is a number of matching homozygous haplotypes within a discrete genomic interval within a single individual, thereby generating a plurality of scores; and assigning a plurality of weights to the plurality of discrete genomic intervals, based at least in part on the plurality of scores; and (iii) calculating a weighted sum over the plurality of discrete genomic intervals of the matched segment, based on the plurality of scores and the plurality of weights; and (d) estimating the degree of ancestral relatedness between the first individual and the second individual based on the weighted sums of the matched segments.
Claim 159 recites “(a) divide the haplotype data into segments based on the plurality of genetic markers; (b) for each of the population of test individuals: (i) based on the plurality of genetic markers, match segments of the haplotype data that are identical-by-descent (IBD) between a first individual and a second individual among the population of test individuals, each of the matched segments having a size that is at least about 100 kilobase pairs (kbp); (ii) for each of the matched segments between the first individual and the second individual: divide the matched segment into a plurality of discrete genomic intervals; score each of the plurality of discrete genomic intervals based on a degree of homozygosity matching of the discrete genomic interval within the first individual or the second individual, wherein the degree of homozygosity matching is a number of matching homozygous haplotypes within a discrete genomic interval within a single individual, thereby generating a plurality of scores; and assign a plurality of weights to the plurality of discrete genomic intervals, based at least in part on the plurality of scores; and (iii) calculate a weighted sum over the plurality of discrete genomic intervals of the matched segment, based on the plurality of scores and the plurality of weights; and (c) estimate the degree of ancestral relatedness between the first individual and the second individual based on the weighted sums of the matched segments.”
Limitations reciting a mental process.
Claims 130, 137, 141-142, 144-154 and 157-159 contain limitations recited at such a high level of generality that they equate to a mental process because they are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), which the courts have identified as concepts that can be practically performed in the human mind. The paragraphs below discuss the broadest reasonable interpretation (BRI) of the limitations in these claims that recite a mental process.
Regarding claims 130 and 158-159, step (b) includes writing down sequences into segments. Step (c)(i) includes aligning segmented sequences to determine if they match. Step (c)(ii) includes dividing the segments, calculating a score includes calculations described in specification para. [104], and assigning weights which can be done on pen and paper. Step (d) includes calculating a coefficient of relationship as recited in specification para. [117].
Claim 137 includes manually aligning sequences on pen and paper. Claim 141-142 include writing down sequences on pen and paper and segmenting them. Claim 144 includes scoring by adding values related to degree of homozygosity and pairwise matching. Claims 145-146 include manipulating numerical values and relationships as shown in specification para. [110-117]. Claim 147 includes assigning a value to an interval which includes mental determinations. Claim 148 includes calculating probabilities. Claims 149 and 151 include calculating a coefficient. Claims 150 and 152 include performing calculations using the given equation. Claim 153 includes calculating a fraction as recited in specification para. [30]. Claims 154 and 157 include analyzing data and making a determination.
Limitations reciting a mathematical concept.
Claims 130, 132-133, 144-146, 148-153, and 158-159 recite limitations that equate to a mathematical concept because they are similar to the concepts of organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)), which the courts have identified as mathematical concepts. The paragraphs below discuss the broadest reasonable interpretation (BRI) of the limitations in these claims that recite a mathematical concept.
In claims 130 and 158-159 steps (c)(ii)-(c)(iii) and (d) include calculating scores, weights and coefficients. Claims 132-133 includes performing calculations using a Hidden Markov Model to model probabilities of haplotype configurations. Claim 144 includes adding degrees to calculate a score. Claims 145-146 include manipulating numerical values and relationships as shown in specification para. [110-117]. Claim 148 includes calculating probabilities. Claims 149 and 151 include calculating a coefficient. Claims 150 and 152 include performing calculations using the given equation. Claim 153 includes calculating a fraction as recited in specification para. [30].
Limitations reciting organizing human activity.
The BRI of claim 156 includes a human arranging for two people to meet. This limitation equates to organizing human activity because it is similar to managing personal behavior or relationships or interactions between people (See MPEP 210604(a)(2).II.C).
Limitations included in the recited judicial exception.
Claims 139-140, 143 and 155 further limit the following limitations that are part of the recited judicial exception: matched segments, variable size, and familial relationship.
Regarding claim 131, as discussed above in section 35 USC 112(d), claim 131 further limits the intended use recited in the preamble of claim 130 and as such is not required by the claim.
As such, claims 130-159 recite an abstract idea (Step 2A, Prong 1: YES).
Additional Elements:
Once limitations have been identified that recite a judicial exception, the claims are evaluated for additional elements. The additional elements are then analyzed under Step 2A, Prong 2 then Step 2B. The instant claims recite the following additional elements:
Claim 130 recites “A computer-implemented method … comprising: (a) receiving haplotype data for a population of test individuals, the haplotype data comprising a plurality of genetic markers shared among the population of test individuals, wherein the plurality of genetic markers comprises at least about 1,000 distinct genetic markers;”
Claim 134 recites “wherein the genotype data is obtained at least in part by assaying biological samples obtained from the population of test individuals or derivatives thereof.”
Claim 135 recites “wherein the assaying further comprises use of array hybridization.”
Claim 136 recites “wherein the assaying further comprises sequencing the biological samples to generate a plurality of sequencing reads.”
Claim 138 recites “wherein the plurality of genetic markers comprises at least about 10,000 distinct genetic markers.”
Claim 158 recites “A non-transitory computer readable medium comprising machine-executable code that, upon execution by one or more computer processors, implements a method for estimating a degree of ancestral relatedness between two individuals of a diploid population, the method comprising: (a) receiving haplotype data for a population of test individuals, the haplotype data comprising a plurality of genetic markers shared among the population of test individuals, wherein the plurality of genetic markers comprises at least about 1,000 distinct genetic markers;”
Claim 159 recites “A computer system for estimating a degree of ancestral relatedness between two individuals of a diploid population, comprising: a database that is configured to store haplotype data for a population of test individuals, the haplotype data comprising a plurality of genetic markers shared among the population of test individuals, wherein the plurality of genetic markers comprises at least about 1,000 distinct genetic markers; and one or more computer processors operatively coupled to the database, wherein the one or more computer processors are individually or collectively programmed to:”
These above recited additional elements are analyzed below under both Step 2A, Prong 2 and Step 2B:
Step 2A, Prong 2:
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to a computer, technology, or technical field (MPEP § 2106.04(d)(1) and 2106.5(a)), require a particular treatment or prophylaxis for a disease or medical condition (MPEP § 2106.04(d)(2)), implement the recited judicial exception with a particular machine that is integral to the claim (MPEP § 2106.05(b)), effect a transformation or reduction of a particular article to a different state or thing (MPEP § 2106.05(c)), nor provide some other meaningful limitation (MPEP § 2106.05(e)). Rather, the claims include limitations that equate to an equivalent of the words “apply it” and/or to instructions to implement an abstract idea on a computer (MPEP § 2106.05(f)) and to insignificant extra-solution activity (MPEP § 2106.05(g)). The paragraphs below discuss the additional elements recited above in the instant claims.
The computer-implemented method of claims 130-157, the CRM being executed by processors in claim 158, and the computer system comprising a database and processors in claim 159 equate to a generic computer. Therefore, these limitations equate to mere instructions to implement an abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp. 573 U.S. at 223, 110 USPQ2d at 1983. These limitations invoke computers as a tool to perform an existing process such as receiving, storing, or transmitting data (MPEP 2106.05(f)(2)).
Regarding step (a) in claims 130 and 158, the database in claim 159, and claims 134-136 and 138, these limitations equate to extra-solution activity of necessary data gathering. They gather data necessary to perform the judicial exceptions in steps (b)-(d).
As such, claims 130-159 are directed to an abstract idea (Step 2A, Prong 2: NO).
Step 2B:
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions to apply the recited exception in a generic way and/or in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The paragraphs below discuss the additional elements recited above in the instant claims.
The computer-implemented method of claims 130-157, the CRM being executed by processors in claim 158, and the computer system comprising a database and processors in claim 159 equate to a generic computer. Therefore, these limitations equate to instructions to implement an abstract idea on a generic computing environment, which the courts have established does not provide an inventive concept in Intellectual Ventures I LLC v. Capital One Bank (USA), 792 F.3d 1363, 1367, 115 USPQ2d 1636, 1639 (Fed. Cir. 2015).
Regarding step (a) in claims 130 and 158, this limitation equates to receiving/transmitting data over a network, which the courts have established as WURC limitation of a generic computer in buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014). Claim 138 also equates to transmitting/receiving data because it further limits the type of data being transmitted/received.
Regarding a CRM storing instructions in claim 158 and a database configured to store data in claim 159, these limitations equate to storing information in memory, which the courts have established as a WURC function of a generic computer in Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015).
The additional elements in claims 130, 134-136 and 158-159 when viewed in combination are WURC as taught by Browning et al. (“Browning”; Nature Reviews Genetics 12, no. 10 (2011): 703-714). Browning reviews haplotype phasing (abstract). Haplotypes are generated from unphased genotypes acquired from SNP arrays and sequencing data using computational algorithms such as FastPHASE and BEAGLE (pg. 703, col. 1, para. 1-2) (pg. 704, sec. Computational phasing). This indicates that assaying biological samples using array hybridization or sequencing to generate genotype data, which is then used for haplotype phasing by a computational algorithm is WURC in combination with generic computer functions/components.
When these additional elements are considered individually and in combination, they do not provide an inventive concept because they equate to WURC functions/components of a generic computer and to WURC limitations of haplotype phasing as taught by Browning. Therefore, these additional elements do not transform the claimed judicial exception into a patent-eligible application of the judicial exception and do not amount to significantly more than the judicial exception itself (Step 2B: No).
As such, claims 130-159 are not patent eligible.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 130-159 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-27 of U.S. Patent No. 11,501,851 B2 (hereinafter “Patent ‘851”).
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are anticipated by the claims in Patent ‘851. The following table shows claims in Patent ‘851 that anticipate the claims of the instant application:
Instant Application claims
Patent ‘851
130, 144
1
131
2
132
3
133
4
134
5
136
6
138
7
139
9
140
10
141
11
142
12
143
13
145-146
14
147
15
148
16
149
17
150
18
151
19
152
20
153
21
154
22
155
23
156
24
157
25
158
26
159
27
Conclusion
No claims are allowed.
Notable, but not relied upon, prior art includes: Gusev et al. (NPL ref. 6 on IDS filed 05/12/2023) disclose GERMLINE a pairwise segmental sharing algorithm to detect identify by descent (IBD) and a match likelihood scoring function that prioritizes matches with most indicative IBD (abstract) (pg. 21, last para.). Browning et al. (Annual review of genetics 46, no. 1 (2012): 617-633) review detection and application of identity by descent between distant relatives (abstract). Howrigan et al. (BMC genomics 12, no. 1 (2011): 460) detect runs of homozygosity to determine relatedness (abstract). Ceballos et al. (Nature Reviews Genetics 19, no. 4 (2018): 220-234) reviews runs of homozygosity (abstract). Browning et al. (The American Journal of Human Genetics 88, no. 2 (2011): 173-182) disclose FastIBD for IBD between individuals (abstract). Choi et al. (PLoS genetics 14, no. 4 (2018): e1007308) review phasing strategies for whole human genomes (abstract). Miyazawa et al. (The American Journal of Human Genetics 80, no. 6 (2007): 1090-1102) uses homozygosity haplotypes to identify shared autosome segments between patients (abstract).
Claims 130-159 are free from the prior art because the prior art does not teach or fairly suggest the following limitations in claims 130 and 158-159: “(ii) for each of the matched segments between the first individual and the second individual: dividing the matched segment into a plurality of discrete genomic intervals; scoring each of the plurality of discrete genomic intervals based on a degree of homozygosity matching of the discrete genomic interval within the first individual or the second individual, wherein the degree of homozygosity matching is a number of matching homozygous haplotypes within a discrete genomic interval within a single individual”. The closest prior art is Barber et al. (“Barber”; US 2017/0220738 A1; ref. 14 on IDS filed 05/12/2023) and Howrigan et al. (“Howrigan”; BMC genomics 12, no. 1 (2011): 460).
Barber estimates a degree of ancestral relatedness between two diploid individuals using haplotype data (abstract) [33]. Barber recites “To estimate the ancestral relatedness of two individuals methods include receiving haplotype data from a population of individuals. The haplotype data include a plurality of genetic markers that are shared among the individuals in the population” [7] and “partitioning module 130 divides 104 the haplotype data into segment windows based on the genetic markers” [34]. Barber “divides the observed SNPs into K windows of equal size d, with each window, for example, including 96 SNPs. Other examples for window sizes include 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150 or any number that falls within the range of 50 to 500” [41]. Barber “includes for each individual in the population, based on the genetic markers, matching 106 segments of the haplotype data that are identical between the individual and any other individual in the population” [44]. The matches are IBD [24]. Each matched segment contains a predefined centimorgan (cM) widths [8][45][99].
However, Barber does not further divide each matched segment into a plurality of discrete genomic intervals within an individual to score each interval based on a number of matching homozygous haplotypes.
Howrigan detects autozygosity through runs of homozygosity (abstract). Howrigan discloses “The principal use of GERMLINE is identity by descent (IBD) mapping between individuals, where ROH analysis is the special case of IBD within an individual … GERMLINE breaks up SNP data into non-overlapping windows of a user-specified length in SNPs (default is 128 SNPs) … If several tagged windows are in a row and surpass a user-defined length threshold in terms of genetic (cM) or physical (kb) distance, the region is called a ROH … To accommodate various genetic distances, we set the window size threshold to be the expected number of SNPs for a given genetic distance” (pg. 7, col. 1, para. 2 – col. 2, para. 1).
However, Howrigan does not render obvious further segmenting the matched segments in Barber into discrete genomic intervals, wherein each genomic interval is scored based on a number of homozygous haplotypes.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Noah A. Auger whose telephone number is (703)756-4518. The examiner can normally be reached M-F 7:30-4:30 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz Skowronek can be reached at (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685