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 .
1. This action is in response to the communication filed on February 19, 2025. Claims 1-20 were originally received for consideration. No preliminary amendments for the claims have been received.
2. Claims 1-20 are currently pending consideration.
Information Disclosure Statement
3. Initialed and dated copies of Applicant’s IDS (form 1449), received on 8/28/2025 and 11/20/2025, are attached to this Office Action.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract idea without significantly more. The claim(s) recite(s) identifying a first potential IBD segment, comparing a first site of the first potential IBD segment to an end sight of a second potential IBD segment, determining that the end site of the second potential IBD segment and first potential IBD segment are within a threshold number of each other, and merging the first and second segments into a combined potential IBD segment. The steps of identifying, comparing, determining and merging can all be performed in the human mind and are therefore a mental process which is an abstract idea. The claim also discloses providing two or more haplotype strings for identification of IBDM segments in between, but this is merely insignificant presolution activity (data gathering). Claim 12 provides a processor and associated memory, but these are generic computing components that do not rescue the claim from being directed towards an abstract idea.
This judicial exception is not integrated into a practical application. The recited “providing two or more paired haplotypes” are conventional methods of a laboratory and/or computing environment and are merely insignificant presolution data gathering steps. The IBD segments are merely data strings with points in those data strings (first site and end sites) defined in the claims. They do not integrate the abstract idea into a practical application.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because none of the elements defined in the claims provide significantly more than the abstract idea. The recited “providing two or more paired haplotypes” are conventional methods of a laboratory and/or computing environment and are merely insignificant presolution data gathering steps. The IBD segments are merely data strings with points in those data strings (first site and end sites) defined in the claims. Claim 12 provides a processor and associated memory, but these are generic computing components that do not rescue the claim from being directed towards an abstract idea.
The dependent claims do not provide anything to rescue the claims from being an abstract idea. Claim 2 determines a phase switch error, which can be determined by the human mind. Claim 3 examines overlap, claim 4 determines if a span is within a threshold, claim 5 determines if the number of sites is within a range of SNPs, claim 6 provides determining and merging steps, and claim 7 determines a minimum length and stores the combined IBD segments which is merely insignificant postsolution activity. All these steps can be performed in the human mind and are therefore directed towards an abstract idea. None of the claims provide anything additional to integrate the abstract idea into a practical application or provide any elements that are significantly more than the abstract idea.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Browning et al. (“Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data”,Genetics 194.2 (2013): 459-471).
Regarding claim 1, Browning discloses:
A computer implemented method of processing haplotypes to reduce errors when determining identity-by-descent (IBD) segments between haplotypes, the method comprising:
providing two or more paired haplotype strings for identification of IBD segments therebetween (page 2, paragraph 4), each of the two or more paired haplotype strings representing a sequence of allele values at polymorphic sites in a haplotype of an organism (page 8, paragraph 3: SNPs); and
computationally iterating through the two or more paired haplotype strings (page 2, right column first paragraph: computationally iterating through multiple IBD segments) by:
(i) identifying a first potential IBD segment (Figure 1, shaded segments) between the two or more paired haplotype strings (Figure 1, white segments) by identifying matches among alleles of the haplotype strings (page 2, paragraph 2: each sampled haplotype matches to the same sequence of Hidden Markov Model States);
(ii) comparing a first site of the first potential IBD segment to an end site of a previously identified second potential IBD segment (page 2, right column, paragraph 3);
(iii) determining that the end site of the second potential IBD segment and the first site of the first potential IBD segment are within a threshold number of sites of each other (page 2, paragraph 4); and
(iv) merging the first potential IBD segment and the second potential IBD segment to form a combined potential IBD segment (paragraph 2, right column, paragraph 1: merging the segments occurs between the union (combined IBD) and subsequent IBD segments such as a third IBD).
Browning does not explicitly disclose computationally iterating through the two or more paired haplotype strings. However, it would have been obvious to one of ordinary skill in the art that performing multiple runs and merging IBD segments in the union (page 2, column 1), would be performed more efficiently if performed iteratively.
Claim 2 is rejected as applied above in rejecting claim 1. Furthermore, Browning discloses:
The computer implemented method of claim 1, wherein the first potential IBD segment and the second potential IBD segment are on different haplotypes, and wherein the method further comprises:
determining that a phase switch error occurred at a site between the first potential IBD segment and the second potential IBD segment (page 9, last paragraph).
Browning does not explicitly disclose swapping the haplotypes from a position of the phase switch error onward. However, Browning states that phasing of sequence data can have a high number of switch errors per centimorgan due to low-frequency variants (page 9, last paragraph) which effects the accuracy of the IBD analysis. It would have been obvious for one of ordinary skill in the art to have recognized that swapping the haplotypes for the individual from the position of the phase switch error onwards would have reduced this source of error with reasonable expectation of success.
Claim 3 is rejected as applied above in rejecting claim 1. Furthermore, Browning discloses:
The computer implemented method of claim 1, wherein the first potential IBD segment and the second potential IBD segment overlap (page 2, right column, page 1).
Claim 4 is rejected as applied above in rejecting claim 1. Furthermore, Browning discloses:
The computer implemented method of claim 1, wherein the first potential IBD segment and the second potential IBD segment each span at least the threshold number of sites (page 2, paragraph 1).
Claim 5 is rejected as applied above in rejecting claim 1. Furthermore, Browning discloses:
The computer implemented method of claim 1, wherein the threshold number of sites is between 1 and 500 SNPs (page 2, right column, paragraphs 4-5: Browning uses 64 markers (64 SNPs) corresponding to approximately .2cM and the threshold used is 1.0CM, corresponding to 320 SNPs which is in the range of 1-500).
Claim 6 is rejected as applied above in rejecting claim 1. Furthermore, Browning does not explicitly disclose determining a third potential IBD segment among phased haplotype data for a plurality of individuals, wherein the third potential IBD segment has a start site, determining that the end site of the combined potential IBD segment and the start site of the third potential IBD segments are within the threshold number of sites of each other and merging the combined potential IBD segments and the third potential IBD segments. However, Browning shoes in Figure 5 distributes IBD segments. It would have been obvious to one of ordinary skill in the art that there are more than IBD segments being considered for the data in the graph, and therefore, the method performed for two IBDM segments is performed again for a third IBD segment.
Claim 7 is rejected as applied above in rejecting claim 1. Furthermore, Browning discloses:
The computer implemented method of claim 1, further comprising:
determining that the combined potential IBD segments have a minimum length in centimorgans (page 5, last paragraph: calculates minimum segment lengths in centimorgans); and
storing the combined potential IBD segments as an IBD segment (Fig. 5, the IBD segments are stored for the plurality of individuals).
Regarding claim 8, Browning discloses:
A computer implemented method of determining identity-by-descent (IBD) segments, the method comprising:
determining first potential IBD segments among phased haplotype data for a plurality of individuals, wherein the first potential IBD segments have an end site (page 2, right column, paragraph 3: first potential IBD segment has an ending genome coordinate);
determining second potential IBD segments among haplotype data for the plurality of individuals, wherein the second potential IBD segments have a start site (page 2, right column, paragraph 3: the GERMLINE algorithm detects candidate IBD segments to include a second potential IBD segment among haplotype data for the plurality of individuals, wherein the second potential IBD segments have a starting genome coordinate);
determining that the end site of the first potential IBD segments and the start site of the second potential IBD segments are within a threshold number of sites of each other (page 2, paragraph 1: a merged tract is formed when the first and second IBD segments are within a threshold number of sites of each other); and
merging the first potential IBD segments and the second potential IBD segments to form a combined potential IBD segment (paragraph 2, right column, paragraph 1: merging the segments occurs between the union (combined IBD) and subsequent IBD segments such as a third IBD).
Browning does not explicitly disclose a threshold number of sites but it would have been obvious to one of ordinary skill in the art, using BRI, to use the comparing of the two IBD segments and comparing and determining if an end site of the first and the start site of the second site are adjacent in order to determine if they are a proper distance from each other.
Claim 9 is rejected as applied above in rejecting claim 8. Furthermore, Browning discloses:
The method of claim 8, wherein the first potential IBD segments and the second potential IBD segments are on different haplotypes for an individual of the plurality of individuals, and the method further comprises:
determining that a phase switch error occurred at a site between the first potential IBD segment and the second potential IBD segment for the individual (page 9, last paragraph).
Browning does not explicitly disclose swapping the haplotypes from a position of the phase switch error onward. However, Browning states that phasing of sequence data can have a high number of switch errors per centimorgan due to low-frequency variants (page 9, last paragraph) which effects the accuracy of the IBD analysis. It would have been obvious for one of ordinary skill in the art to have recognized that swapping the haplotypes for the individual from the position of the phase switch error onwards would have reduced this source of error with reasonable expectation of success.
Claim 10 is rejected as applied above in rejecting claim 8. Furthermore, Browning discloses:
The method of claim 8, wherein the first potential IBD segment and the second potential IBD segment each span at least the threshold number of sites (page 2, paragraph 1).
Claim 11 is rejected as applied above in rejecting claim 8. Furthermore, Browning discloses:
The method of claim 8, wherein the threshold number of sites is between 1 and 500 SNPs (page 2, right column, paragraphs 4-5: Browning uses 64 markers (64 SNPs) corresponding to approximately .2cM and the threshold used is 1.0CM, corresponding to 320 SNPs which is in the range of 1-500).
Regarding claim 12, Browning discloses:
A system for determining identity-by-descent (IBD) segments, the system comprising:
(a) one or more processors and associated memory (page 10, column 2, paragraph 1: all computation times are from runs on a 2.4-GHz computer); and
(b) computer readable instructions that, when executed by the one or more processors, cause the one or more processors to:
determine first potential IBD segments among phased haplotype data for a plurality of individuals, wherein the first potential IBD segments have an end site (page 2, right column, paragraph 3: first potential IBD segment has an ending genome coordinate);
determine second potential IBD segments among haplotype data for the plurality of individuals, wherein the second potential IBD segments have a start site (page 2, right column, paragraph 3: the GERMLINE algorithm detects candidate IBD segments to include a second potential IBD segment among haplotype data for the plurality of individuals, wherein the second potential IBD segments have a starting genome coordinate);
determine that the end site of the first potential IBD segments and the start site of the second potential IBD segments are within a threshold number of sites of each other (page 2, paragraph 1: a merged tract is formed when the first and second IBD segments are within a threshold number of sites of each other); and
merge the first potential IBD segments and the second potential IBD segments to form a combined potential IBD segment (paragraph 2, right column, paragraph 1: merging the segments occurs between the union (combined IBD) and subsequent IBD segments such as a third IBD).
Browning does not explicitly disclose a threshold number of sites but it would have been obvious to one of ordinary skill in the art, using BRI, to use the comparing of the two IBD segments and comparing and determining if an end site of the first and the start site of the second site are adjacent in order to determine if they are a proper distance from each other.
Claim 13 is rejected as applied above in rejecting claim 12. Furthermore, Browning discloses:
The system of claim 12, wherein the first potential IBD segments and the second potential IBD segments are on different haplotypes for an individual of the plurality of individuals, and wherein the computer readable instructions, when executed by the one or more processors, further cause the processor to:
determine that a phase switch error occurred at a site between the first potential IBD segment and the second potential IBD segment for the individual (page 9, last paragraph).
Browning does not explicitly disclose swapping the haplotypes from a position of the phase switch error onward. However, Browning states that phasing of sequence data can have a high number of switch errors per centimorgan due to low-frequency variants (page 9, last paragraph) which effects the accuracy of the IBD analysis. It would have been obvious for one of ordinary skill in the art to have recognized that swapping the haplotypes for the individual from the position of the phase switch error onwards would have reduced this source of error with reasonable expectation of success.
Claim 14 is rejected as applied above in rejecting claim 12. Furthermore, Browning discloses:
The system of claim 12, wherein the first potential IBD segments and the second potential IBD segments overlap for an individual of the plurality of individuals (page 2, right column, page 1).
Claim 15 is rejected as applied above in rejecting claim 12. Furthermore, Browning discloses:
The system of claim 12, wherein the first potential IBD segment and the second potential IBD segment each span at least the threshold number of sites (page 2, paragraph 1).
Claim 16 is rejected as applied above in rejecting claim 12. Furthermore, Browning discloses:
The system of claim 12, wherein the threshold number of sites is between 1 and 500 SNPs (page 2, right column, paragraphs 4-5: Browning uses 64 markers (64 SNPs) corresponding to approximately .2cM and the threshold used is 1.0CM, corresponding to 320 SNPs which is in the range of 1-500).
Claim 17 is rejected as applied above in rejecting claim 12. Furthermore, Browning discloses:
The system of claim 12, wherein the plurality of individuals do not share a parent-child relationship (page 2, last paragraph: cohort of data consist of unrelated data).
Claim 18 is rejected as applied above in rejecting claim 12. Furthermore, Browning does not explicitly disclose determining a third potential IBD segment among phased haplotype data for a plurality of individuals, wherein the third potential IBD segment has a start site, determining that the end site of the combined potential IBD segment and the start site of the third potential IBD segments are within the threshold number of sites of each other and merging the combined potential IBD segments and the third potential IBD segments. However, Browning shoes in Figure 5 distributes IBD segments. It would have been obvious to one of ordinary skill in the art that there are more than IBD segments being considered for the data in the graph, and therefore, the method performed for two IBDM segments is performed again for a third IBD segment.
Claim 19 is rejected as applied above in rejecting claim 18. Furthermore, Browning discloses:
The system of claim 18, wherein the combined potential IBD segment and the third potential IBD segment are on different haplotypes for an individual of the plurality of individuals, and the computer readable instructions, when executed by the one or more processors, further cause the one or more processors to:
determine that a phase switch error occurred at a site between the combined potential IBD segment and the third potential IBD segment for the individual (page 9, last paragraph).
Browning does not explicitly disclose swapping the haplotypes from a position of the phase switch error onward. However, Browning states that phasing of sequence data can have a high number of switch errors per centimorgan due to low-frequency variants (page 9, last paragraph) which effects the accuracy of the IBD analysis. It would have been obvious for one of ordinary skill in the art to have recognized that swapping the haplotypes for the individual from the position of the phase switch error onwards would have reduced this source of error with reasonable expectation of success.
Claim 20 is rejected as applied above in rejecting claim 12. Furthermore, Browning discloses:
The system of claim 12, wherein the computer readable instructions, when executed by the one or more processors, further cause the one or more processors to:
determine that the combined potential IBD segments have a minimum length in centimorgans (page 5, last paragraph: calculates minimum segment lengths in centimorgans); and
store the combined potential IBD segments as IBD segments for the plurality of individuals (Fig. 5, the IBD segments are stored for the plurality of individuals).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAVEH ABRISHAMKAR whose telephone number is (571)272-3786. The examiner can normally be reached M-F 9-5:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Jung Kim can be reached at 571-272-3804. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KAVEH ABRISHAMKAR/
08/29/2026Primary Examiner, Art Unit 2494
