DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on August 28, 2026 has been entered. Any rejections or objections not reiterated herein have been withdrawn. This action is made FINAL.
Applicants election of MYO7A, CDH23, and CLRN1 in the reply filed on January 20, 2026 is reiterated for the record. The claims have been amended to recite “at least a first gene associated with Usher syndrome and at least a second, different gene associated with a hereditary hearing loss syndrome other than Usher syndrome”. The election is no longer commensurate in scope with the claims because each of MYO7A, CDH23, and CLRN1 are associated with Usher syndrome and the claims as amended require a gene associated with a different hereditary hearing loss syndrome. After further consideration, the following genes have been rejoined: ADGRV1, CEP250, ESPN, GJB2, GJB6, KCNE1, KCNQ1, PCDH15, SLC26A4, USH1C, USH1G, and USH2A with the elected genes.
Claims 1-5, 7-8, 11-13, 15, 17-22 are currently pending.
Claims 2, 12, and 20-22 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected subject matter (a non-elected invention or non-elected species), there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on replies filed on October 31, 2025 and January 20, 2026.
The claims have been examined to the extent that the claims read on the elected combination of genes and the rejoined genes (CDH23, CLRN1, MYO7A, ADGRV1, CEP250, ESPN, GJB2, GJB6, KCNE1, KCNQ1, PCDH15, SLC26A4, USH1C, USH1G, and USH2A). The additionally recited genes have been withdrawn from consideration as being directed to non-elected subject matter. Prior to allowance of the claim, any non-elected subject matter that is not rejoined with any allowed elected subject matter will be required to be removed from the claims.
Duplicate Claim Warning
3. Applicant is advised that should claims 1 and 3-5 be found allowable, claims 11, 13, 15, and 17 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Claim Rejections - 35 USC § 101
4. 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, 3-5, 7-8, 11, 13, 15, and 17-19 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims recite a judical exception that is not integrated into a practical application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. The claim analysis is set forth below.
Step 1: The claims are directed to the statutory category of a process.
Step 2A, prong one: Evaluate Whether the Claim Recites a Judicial Exception
The instant claims recite a law of nature.
The claims recite the following limitation:
wherein the plurality of hereditary hearing loss-related genes comprises three or more of ABHD12, ADGRV1, ARSG, CDH23, CEP250, CEP78, CIB2, CLRN1, ESPN, FOX11, GJB2, GJB6, HARS2, KCNE1, KCNJ10, KCNQ1, MYO7A, PCDH15, PDZD7, SLC26A4, USH1C, USH1G, USH2A, and WHRN
The claims recite a correlation between the recited genes and hereditary hearing loss. This type of correlation is a consequence of natural processes, similar to the naturally occurring correlation found to be a law of nature by the Supreme Court in Mayo.
Step 2A, prong two: Evaluate Whether the Judicial Exception Is Integrated Into a Practical Application
The claims do NOT recite additional steps or elements that integrate the recited judicial exceptions into a practical application of the exception(s). For example, the claims do not practically apply the judicial exception by including one or more additional elements that the courts have stated integrate the exception into a practical application:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
An additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
An additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
An additional element effects a transformation or reduction of a particular article to a different state or thing; and
An additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological
environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
In addition to the judical exceptions the claims recite steps of “extracting” DNA, “generating” a library of bait captured gene sequences, and “detecting” a mutation in one of the bait captured gene sequences. These steps are NOT considered to integrate the judicial exception into a practical application because they merely add insignificant extra-solution activity (data gathering) to the judicial exception.
Step 2B: Evaluate Whether the Claim Provides an Inventive Concept
In addition to the judical exceptions the claims recite steps of “extracting” DNA, “generating” a library of bait captured gene sequences, and “detecting” a mutation in one of the bait captured gene sequences. These steps do NOT amount to significantly more because they simply append well understood, routine, and conventional activities previously known in the art, specified at a high level of generality, to the judicial exceptions.
The teachings in the specification demonstrate the well understood, routine, conventional nature of additional elements because it teaches that the additional elements are well known or commercially available. For example the specification teaches the following:
[0082] In some embodiments, the library is prepared using Agilent's SureSelect XT HS2 kit and sequenced on an Illumina platform (e.g. NextSeq 550Dx). In some embodiments, high throughput massive parallel sequencing is performed using pyrosequencing, reversible dye- terminator sequencing, SOLiD sequencing, Ion semiconductor sequencing, Helioscope single molecule sequencing, sequencing by synthesis, sequencing by ligation, or SMRT™ sequencing.
The prior art also demonstrates the well understood, routine, conventional nature of additional elements because it teaches that the additional elements are well known or commerically available.
For example Garcia (Genes 2020 11,1467 pages 1-25 ) teaches that they performed targeted next-generation sequencing (NGS) with a custom panel that included 59 genes associated with non-syndromic HL or syndromic HL (abstract). Garcia teaches a cohort of 128 patients from 118 families diagnosed with non-syndromic or syndromic hearing loss were evaluated. Garcia teaches that genomic DNA was obtained and purified using an automated DNA extractor. Garcia teaches that they designed a NGS panel for the analysis of hereditary hearing loss using the SureDesign tool (Agilent) (page 2). Garcia teaches that library preparation was carried out according to the Bravo NGS SureSelectQXT Automated Target Enrichment Protocol (Agilent) for Illumina Multiplexed Sequencing. Garcia teaches that the libraries were sequenced on a MiSeq instrument (page 3). As shown in Table 1 the panel included CDH23, CLRN1, MYO7A, ADGRV1, CEP250, ESPN, GJB2, GJB6, KCNE1, KCNQ1, PCDH15, SLC26A4, USH1C, USH1G, and USH2A. Table 2 discloses mutations were detected in GJB2, SLC26A4, MYO7A, CDH23, and ESPN.
Further it is noted that the courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity.
Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015);
Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017);
Immunizing a patient against a disease, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011);
Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
Freezing and thawing cells, Rapid Litig. Mgmt. 827 F.3d at 1051, 119 USPQ2d at 1375;
Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014)
For the reasons set forth above the claims are not directed to patent eligible subject matter.
Claim Rejections - 35 USC § 102
5. The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 3, 5, 11, 13, and 17 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Garcia (Genes 2020 11,1467 pages 1-25 ).
Regarding Claims 1 and 11 Garcia teaches that they performed targeted next-generation sequencing (NGS) with a custom panel that included 59 genes associated with non-syndromic HL or syndromic HL (abstract). Garcia teaches a cohort of 128 patients from 118 families diagnosed with non-syndromic or syndromic hearing loss were evaluated. Garcia teaches that genomic DNA was obtained and purified using an automated DNA extractor. Garcia teaches that they designed a NGS panel for the analysis of hereditary hearing loss using the SureDesign tool (Agilent) (page 2). Garcia teaches that library preparation was carried out according to the Bravo NGS SureSelectQXT Automated Target Enrichment Protocol (Agilent) for Illumina Multiplexed Sequencing. Garcia teaches that the libraries were sequenced on a MiSeq instrument (page 3). As shown in Table 1 the panel included CDH23, CLRN1, MYO7A, ADGRV1, CEP250, ESPN, GJB2, GJB6, KCNE1, KCNQ1, PCDH15, SLC26A4, USH1C, USH1G, and USH2A. Table 2 discloses mutations were detected in GJB2, SLC26A4, MYO7A, CDH23, and ESPN. Thus Garcia teaches a method comprising a) extracting genomic DNA from a biological sample obtained from a patient, b) generating a library comprising a plurality of bait-captured gene sequences corresponding to a plurality of hereditary hearing loss-related genes (the SureSelect library), wherein the plurality of hereditary hearing loss-related genes comprises CDH23, CLRN1, MYO7A, ADGRV1, CEP250, ESPN, GJB2, GJB6, KCNE1, KCNQ1, PCDH15, SLC26A4, USH1C, USH1G, and USH2A, and wherein generating the library comprises bait capturing gene sequences corresponding to genes associated with Usher syndrome (CDH23, MYO7A, PCDH15, USH1C, USH1G, ADGRV1, CLRN1, USH2A) and genes associated with hereditary hearing loss syndrome other than Usher syndrome (CEP250, ESPN, GJB2, GJB6, CDH23, MYO7A, PCDH15, SLC26A, USH1C, USH1G are associated with non-syndromic hearing loss, KCNE1 and KCNQ1are associated with Jervell and Lange-Nielsen syndrome, and SLC26A is associated with Pendred).
Regarding Claims 3 and 17 Garcia teaches a method wherein the detecting step is performed using high throughput massive parallel sequencing (MiSeq instrument from Illumina) (page 3).
Regarding Claims 5 and 13 Garcia teaches detection of disease causing variants in the GJB2 gene in samples obtained from patients having non-syndromic hearing loss (NSHL) that are 0 years old (page 5). Thus Garcia teaches a method wherein the biological sample is a human biological sample from an infant patient, the infant patient having a hereditary hearing loss disorder.
Claim Rejections - 35 USC § 103
6. 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.
7. Claims 4 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Garcia (Genes 2020 11,1467 pages 1-25 ) in view of Wei (Clinica Chimica Acta 11/20/2012 Vol 413 pages 1866-1871).
The teachings of Garcia are presented above.
Garcia does not teach a method wherein the biological sample is plasma, dried plasma, serum, dried serum, whole blood, or dried whole blood.
However Wei teaches performing next generation sequencing to detect mutations associated with Usher syndrome. Wei teaches that total genomic DNA from whole blood was extracted (page 1867).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Garcia by obtaining the genomic DNA from a whole blood sample as suggested by Wei. Based on the teachings of Wei it was known in the art that genomic DNA could be obtained from whole blood samples. One of skill in the art would have been motivated to obtain genomic DNA from whole blood since it was a known source of genomic DNA and blood collection is a routine medical procedure.
8. Claims 7-8 are rejected under 35 U.S.C. 103 as being unpatentable over Garcia (Genes 2020 11,1467 pages 1-25 ) in view of Hess (Biotechnology Advances 41 (2020) 107537).
The teachings of Garcia are presented above.
Garcia does not teach a method wherein an adaptor sequence is ligated to at least one end of the plurality of bait-captured gene sequences (clm 7). Garcia does not teach a method wherein an adaptor sequence is ligated to both ends of the plurality of bait-captured gene sequences (clm 8).
However Hess teaches that NGS can be roughly divided into the process elements of sample preprocessing, library preparation, sequencing itself and bioinformatics (Fig. 1). Regardless of the underlying principles of the respective sequencing method, all modern sequencing technologies require dedicated sample preparation to yield the sequencing library loaded onto the instrument (Goodwin et al., 2016; Metzker, 2010). Sequencing libraries consist of DNA fragments of a defined length distribution with oligomer adapters at the 5′ and 3′ end for barcoding, as well as the actual sequencing process. After sequencing, the generated data is analyzed using bioinformatics (page 1).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Garcia by putting adapters on both ends of the bait captured sequences as suggested by Hess. In the instant case Hess teaches that the use of adapters is standard in NGS. One of skill in the art would have been motivated to add adapters at both ends of the captured sequences to render the sequences compatible with the applied sequencing technique.
9. Claim 18 is rejected under 35 U.S.C. 103 as being unpatentable over Garcia (Genes 2020 11,1467 pages 1-25 ) in view of Lipson (US 11,118,213 Issued 9/14/2021)
The teachings of Garcia are presented above.
Garcia does not teach a method further comprising the use of at least 5,000 nucleic acid probes.
However Lipson teaches a method of using bait sequences to capture targets for nucleic acid sequencing. Lipson teaches that the bait set is greater than 5000 probes (Col 58, lines 28-32).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Garcia by using at least 5000 nucleic acid bait probes as suggested by Lipson. In the instant case Lipson teaches that any number of bait probes can be used. It would have been obvious to use 5000 probes for the benefit of being able to capture a larger number of target genes for sequencing.
10. Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Garcia (Genes 2020 11,1467 pages 1-25 ) in view of Lipson (US 11,118,213 Issued 9/14/2021) and Johnson (Res Pract Thromb Haemost 2018; 2:640-652)
The teachings of Krawitz and Lipson are presented above.
The combined references do not teach a method wherein at least one of the 5,000 nucleic acid probes comprises a region of complementarity to at least one of the plurality of hereditary hearing loss-related genes, the region of complementarity comprising a coding region and 10 bases of an untranslated region (UTR) of the at least one of the plurality of hereditary hearing loss-related genes.
However Johnson teaches that they have developed an IT specific gene panel as a prescreen for patients prior to WES using the Agilent SureSelectQXT system (abstract). Johnson teaches that the sequencing probes/baits were designed to cover the following regions: all coding exons ±10 bp flanking sequence from the intron-exon boundary and the 5′UTR and 3′UTR. Sequencing baits were designed with 2x density so that each desired region was covered by at least two overlapping probes. (page 642).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Krawitz and Lipson by using nucleic acid bait probes that are complementary to a coding region and 10 bases of an untranslated region (UTR) of the at least one of the plurality of hereditary hearing loss-related genes as suggested by Johnson. It would have been obvious to use bait probes complementary to the UTR for the benefit of being able to ensure higher quality coverage of the coding sequences.
Improper Markush Grouping Rejection
11. Claims 1, 3-5, 7-8, 11, 13, 15, and 17-19 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The claims recite the following Markush group:
wherein the plurality of hereditary hearing loss-related genes comprises three or more of ABHD12, ADGRV1, ARSG, CDH23, CEP250, CEP78, CIB2, CLRN1, ESPN, FOX11, GJB2, GJB6, HARS2, KCNE1, KCNJ10, KCNQ1, MYO7A, PCDH15, PDZD7, SLC26A4, USH1C, USH1G, USH2A, and WHRN (claims 1 and 11)
The Markush grouping is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons:
MPEP 2117(II) states that “A Markush claim may be rejected under judicially approved “improper Markush grouping” principles when the claim contains an improper grouping of alternatively useable members. A Markush claim contains an “improper Markush grouping” if either: (1) the members of the Markush group do not share a “single structural similarity” or (2) the members do not share a common use. Supplementary Guidelines at 7166 (citing In re Harnisch, 631 F.2d 716, 721-22, 206 USPQ 300, 305 (CCPA 1980)).
MPEP 2117(II) further state that alternatives (1) share a “single structural similarity” when they belong to the same recognized physical or chemical class or to the same art-recognized class and (2) share a common function or use when they are disclosed in the specification or known in the art to be functionally equivalent in the context of the claimed invention.
MPEP § 2117(II)(A) states that “A recognized physical class, a recognized chemical class, or an art-recognized class is a class wherein “there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention. In other words, each member could be substituted one for the other, with the expectation that the same intended result would be achieved”. Herein the members of the Markush grouping are all genes. These do not belong to the same recognized physical or chemical class or to the same art-recognized class because there is no expectation from the art that each of the recited genes would function in the same way in the claimed method. It is only in the context of this specification that it was disclosed that all members of this group may behave in the same way in the context of the claimed invention.
MPEP § 2117(II)(B) states that “Where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as explained in subsection IIA above, the members of the Markush grouping may still be considered to be proper where the alternatives share a substantial structure feature that is essential to a common use. Again the members of the Markush grouping are all genes. While they are all made up of nucleic acids, the structure of comprising nucleic acids is not essential to any asserted common use.
The genes are disclosed as having in common that are related to hereditary hearing loss. However, the specification teaches that the genes are associated with different types of herediatry hearing loss (see Tables 1 and 2). For example, some of the claimed genes are assoicated with Usher Syndrome, while other genes are assoicated with EVA, non-syndromic deafness, Jervell-Lange Nielson syndrome, and Romano Ward syndrome. Thus, the groups of genes do not all share a common use/function.
Following this analysis, the claims are rejected as containing an improper Markush grouping.
Response To Arguments- Improper Markush Group
12. In the response the Applicants traversed the improper Markush Group rejection. The Applicants argue that the genes form an art recognized class. They argue that the Examiner
identifies no listed gene that behaves differently in the claimed bait-capture and mutation-detection workflow and provides no reasoned explanation for the asserted absence of an expectation of equivalent behavior.
This argument has been fully considered but is not persuasive. Members of a Markush group share a “single structural similarity” when they belong to the same art recognized physical or chemical class or to the same art recognized class. MPEP 2117 (II)(A) states that”
A recognized physical class, a recognized chemical class, or an art-recognized class is a class wherein there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention. In other words, each member could be substituted one for the other, with the expectation that the same intended result would be achieved. For example, in the context of a claim covering a disposable diaper, a limitation "the fastener selected from the group consisting of a pressure sensitive adhesive and complementary release material, a complementary hook and loop structure, a snap, and a buckle" would likely be considered an art recognized class because a review of the prior art would establish that it was well known that each member could be substituted for each other with the expectation that the intended result (repositionable and refastenable) would occur.
In the instant case the Examiner has cited Garcia (Genes 2020 11,1467 pages 1-25), which establishes that CDH23, CLRN1, MYO7A, ADGRV1, CEP250, ESPN, GJB2, GJB6, KCNE1, KCNQ1, PCDH15, SLC26A4, USH1C, USH1G, and USH2A were well known in the prior art to be correlated with hereditary hearing loss. As such this combination could be considered an art recognized class.
However it is unknown based on the teachings in the specification if a review of the prior art would establish that it was well known that each of the non-examined genes (ABHD12, ARSG, CEP78, CIB2, FOX11, HARS2, KCNJ10, PDZD7, and WHRN) could be substituted for each other with the expectation that the intended result (detection of hereditary hearing loss) would occur. For this reason Applicants have not established that the recited genes are all from an art recognized class
13. Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMANDA HANEY whose telephone number is (571)272-8668. The examiner can normally be reached Monday-Friday, 8:15am-4:45pm 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, Wu-Cheng Shen can be reached at 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AMANDA HANEY/Primary Examiner, Art Unit 1682
Prosecution Insights