DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Status of Claims / Response to Amendment
This office action is in response to an Applicant's Request for Reconsideration-After Non-Final Rejection filed on September 05, 2025.
Claims 102-121 were previously pending. Aside from updating claim status identifiers, the applicant made no changes to the claims.
Claims 102-121 are currently pending, with claims 110 and 114-115 withdrawn.
Claims 102-109, 111-113, 116-121 are under examination.
Claim 102 is improper for having incorrect status identifier. The claim is incorrectly identified as "(Previously Amended)" when "(Previously presented)" should be used. Amendments to the claims filed on or after July 30, 2003 must comply with 37 CFR 1.121(c) which states:
"The claim listing, including the text of the claims, in the amendment document will serve to replace all prior versions of the claims, in the application. In the claim listing, the status of every claim must be indicated after its claim number by using one of the following identifiers in a parenthetical expression: (Original), (Currently amended), (Canceled), (Withdrawn), (Previously presented), (New), and (Not entered)."
In the interest of compact prosecution, however, the examiner will consider the claim listing on its merits. MPEP 714.03 (“Where an amendment substantially responds to the rejections, objections, or requirements in a non-final Office action (and is a bona fide attempt to advance the application to final action) but contains a minor deficiency . . . , the examiner may simply act on the amendment and issue a new (non-final or final) Office action.”) The examiner reserves the right to send a PTOL-324 Notice of Noncompliant Amendment in the event of more severe deficiencies, which may result in loss of patent term.
No rejection has been overcome. Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Response to Arguments
Applicant's arguments filed on Sept 5, 2025 have been fully considered.
35 U.S.C. § 103 rejection
In the Non-Final Office Action mailed on 06/09/2025:
Claims 102-109 and 116-121 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over HALLE, in view of RAYBUCK and Bonetta;
Claim 111 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over
HALLE, in view of RAYBUCK and Bonetta, as applied to claim 102 above and further in view of FEJGIN;
Claims 112-113 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over HALLE, in view of RAYBUCK, and Bonetta as applied to claim 102 above and further in view of TERSTAPPEN.
These rejections are maintained in this Office Action for reasons below.
Applicant argues that the rejections above should be withdrawn (Remarks, page 1-5). Applicant's arguments have been fully considered but are not found persuasive.
1: Applicant argues part of the obviousness rationale lacks support in the reference.
First, Applicant expresses disagreement with the previously set forth obviousness rationale in the 103 rejection for independent claim 102, and argues on the basis that:
"Halle does not describe reducing contamination from maternal cells as "a known issue," as alleged by the Office.
None of the paragraphs cited by the Office relate to this issue. The closest disclosure of these paragraphs in Halle cited by the Office is paragraph 0021, which merely recites the known fact that only a few fetal cells are found in maternal circulation, and thus there is a need to select and enrich the fetal cells, and then provides several methods to do so. The remaining paragraphs cited by the Office relate to selecting and enriching fetal cells from maternal blood or cfDNA." (Remarks, page 2).
This argument is not persuasive, as it mischaracterizes the previously set forth rejection.
The complete obviousness rationale can be found in the prior Non-Final Office Action (at pages 7-11), and is maintained in the current Office Action.
As stated in the rejection:
"It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the method taught by HALLE with the selective lysis technique of RAYBUCK because both references are in the same field of prenatal genetic testing. A skilled artisan, aiming to improve methods for fetal cell analysis, would likely encounter both references in their search.
The person of ordinary skill would have had a reasonable expectation of success in combining these teachings because RAYBUCK provides a specific technique for improving the purity of fetal cell DNA by isolating fetal nuclei with reduced contamination from maternal cells -- a known issue in the methods described by HALLE (see [0014][0021[[0174][0178]). RAYBUCK provides a detailed approach to selective lysis, which is technically compatible with the method taught by HALLE. This integration would have predictably yielded a cleaner sample with increased fetal DNA purity for subsequent DNA analysis, crucial for accurate and reliable prenatal diagnosis.
The skilled artisan would have been motivated to combine these teachings to further minimize DNA contamination from maternal cells and achieve economic and technical efficiencies in effective prenatal testing, as suggested by RAYBUCK."
Thus, Applicant incorrectly characterizes the rejection. The rejection does not state that HALLE identifies "reducing contamination from maternal cells" as a known issue. Rather, the rejection notes that maternal cell contamination is a known issue in the field, and that HALLE acknowledges this concern by both explicitly recognize the risk of maternal cell contamination in fetal cell DNA assays ([0014] line 13) and highlighting the need to enrich fetal cells or fetal cell DNA due to the large presence of maternal cells in maternal blood ([0021][0174][0178]).
HALLE teaches that "Only a few fetal cells (trophoblasts, lymphocytes and nucleated red blood cells) are found in maternal circulation, therefore there is a need to select and enrich for these cells." ([0021] lines 1-3). This indicates an inherent problem of sample contamination, as maternal DNA represents background noise in the detection of fetal DNA. A skilled artisan in the relevant field of assay development would understand the basic principle of single-to-noise ratio ꟷ that reducing background noise (maternal DNA) improves the ability to detect the target signal (fetal DNA).
RAYBUCK teaches a selective cell lysis technique that further improves fetal DNA purity by separating fetal nuclei from maternal cell components. This complements the enrichment approach of HALLE by providing a method to further reduce material DNA contamination in the sample.
Accordingly, it would have been obvious to combine the prenatal testing method of HALLE with the selective lysis technique of RAYBUCK. This integration would have predictably yielded a cleaner sample with increased fetal DNA purity for subsequent DNA analysis, crucial for accurate and reliable prenatal diagnosis.
The skilled artisan would have been motivated to combine these teachings to further minimize DNA contamination from maternal cells and achieve economic and technical efficiencies in effective prenatal testing, as suggested by RAYBUCK (RAYBUCK, pages 13-14).
2: Applicant argues cited references, individually, do not teach or suggest certain features.
Following the point above, applicant then asserts:
"Thus, there is no suggestion in Halle to use selective lysis of either fetal or maternal cells as a way in which to isolate or enrich fetal cells, and no disclosure or suggestion in Raybuck that its methods could be used in the methylation analysis method of Halle to detect an alteration in a locus copy number." (Remarks, page 2)
This argument is not persuasive.
The requirements for a proper response to a rejection may be found in 37 CFR 1.111(b) and MPEP §714.02; see also MPEP §707.07(a).
In this instance case, it is unclear what specific point is being raised in this argument, as it appears to assert that HALLE does not teach or suggest the selective lysis technique disclosed by RAYBUCK, and that RAYBUCK does not describe the method of HALLE.
The remarks do not provide any specific reasons as to why either the findings of fact or the legal conclusion of obviousness is allegedly in error. Thus, the remarks in response to the 103 rejections do not comply with 37 CFR 1.111(b) and MPEP § 714.02. However, Applicant’s reply is considered to be a bona fide attempt at a response and is being accepted as a complete response.
Also, Applicant is reminded one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. In reKeller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In reMerck & Co., Inc., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Where a rejection of a claim is based on two or more references, a reply that is limited to what a subset of the applied references teaches or fails to teach, or that fails to address the combined teaching of the applied references may be considered to be an argument that attacks the reference(s) individually. Where an applicant’s reply establishes that each of the applied references fails to teach a limitation and addresses the combined teachings and/or suggestions of the applied prior art, the reply as a whole does not attack the references individually as the phrase is used in Keller and reliance on Keller would not be appropriate. This is because “[T]he test for obviousness is what the combined teachings of the references would have suggested to [a PHOSITA].” In re Mouttet, 686 F.3d 1322, 1333, 103 USPQ2d 1219, 1226 (Fed. Cir. 2012).
In this instant case, the rejection is based on a combination of teachings from three references:
HALLE, which teaches a method of prenatally identifying a genomic alteration in a locus copy number, by analyzing fetal cells in blood obtained from a pregnant woman (entire document, [0030], [0180] for example);
RAYBUCK, which teaches a selective cell lysis technique for reducing maternal DNA contamination and improving the purity of fetal DNA (entire document, page 7-14 for example); and
Bonetta, which teaches Solexa sequencing as a powerful tool for genome analysis (page 407, left-hand col).
Therefore, this argument approach is not sufficient in responding to the grounds of rection based on combined teaching of the art.
3: Applicant argues that the combined teachings of HALLE, RAYBUCK and Bonetta would lead to inoperability, because Bonetta teaches analysis of mRNA.
Applicant further argues that Bonetta, which teaches Solexa sequencing, is "exclusively focused on mRNA expression analysis" and that the "Office has not pointed to any disclosure in Bonetta that would instruct or motivate someone to modify the mRNA expression analysis methods described in Bonetta and instead focus on genomic DNA analysis, as recited in Halle" and Bonetta lacks "reasonable expectation of success in using Solexa for the analysis of genomic DNA as opposed to the analysis of mRNA expression". (Remarks, page 4)
Applicant argues:
"combining the teachings of Bonetta with Halle and Raybuck in an attempt to arrive at the claimed method would render the method of Halle inoperable and therefore unsatisfactory for its intended purpose (MPEP 2143.01 (V)-(VI)). The intended purpose of Halle is to analyze isolated DNA from cells for bi sulphite-based methylation detection. Raybuck describes methods of obtaining nuclei from target nucleated cells, but isolation of nuclei inherently involves washing away the cytosolic components and thus would remove mRNA from the isolated nuclei. If one were to adopt Bonetta's methods of focusing on mRNA from cytosol in some combination of the methods of Halle and Raybuck, as the Office alleges, the nuclei would not be isolated and instead might contaminate the mRNA to be analyzed. Thus, the purpose of Halle and Raybuck, would be frustrated, because genomic DNA could not necessarily be found in the cytosol. In addition, neither Bonetta, nor any one of the other cited references, describes that mRNA expression analysis could be used for analyzing aneuploidy in enriched fetal cells." (Id.)
This argument is not persuasive.
First, applicant appears to misread the rejection. The rejection does not rely on the workflow for analyzing messenger RNA taught in Bonetta. Rather, the rejection is based on the combined teachings of:
(1) a prenatal fetal DNA analysis method, taught by HALLE, which already teaches sequencing (e.g. [0240]) but does not explicitly teach Solexa sequencing;
(2) a selective lysis method for improved fetal DNA purity, taught by RAYBUCK, and
(3) Solexa sequencing platform, taught by Bonetta.
The combination is supported by factual findings and a reasoned rationale, as set forth in the rejection and reproduced below:
"It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the combined teachings of HALLE and RAYBUCK, to use Solexa sequencing for genome analysis, as taught by Bonetta, in identifying fetal genome alternations. Because all three references are in the overlapping field of genome analysis. HALLE already teaches sequencing, and Bonetta's teaching of Solexa sequencing provides an improved, specific sequencing method for genome analysis. This combination represents the predictable use of a known element (Solexa sequencing) according to a known method (performing genome analysis using sequencing) to yield predictable results (See MPEP §2143).
The person of ordinary skill would have had a reasonable expectation of success in combining these teachings because the teachings in the references are technically compatible. Solexa sequencing, as described in Bonetta, is identified as advanced sequencing approach based on amplifying DNA templates on a chip (sequencing by synthesis). Thus, a person of ordinary skill in the art would have reasonably expected Solexa sequencing to be applicable for sequencing any amplifiable DNA, including the DNA amplicons in HALLE.
The result of this combination would have yielded the predictable result of an improved molecular method for prenatally identifying genomic alternations in fetal cells, via effective isolation of fetal cell nuclei and analyze them using Solexa sequencing.
The skilled artisan would have been motivated to combine the teachings, to leverage the several advantages offered by Solexa sequencing, such as high throughput, cost-effectiveness, competitive performance, and capability to both profile known genes and discover unknown ones, as suggested by Bonetta, all of which are desirable improvements in prenatal diagnostic applications." (Non-Final Office Action, page 10-11)
Nowhere does the rejection rely on or propose analyzing messenger RNA.
Accordingly, Applicant's argument does not specifically address why either the findings of fact or the legal conclusion of obviousness is allegedly in error. Thus, this argument in response to the 103 rejections do not comply with 37 CFR 1.111(b) and MPEP § 714.02. However, Applicant’s reply is considered to be a bona fide attempt at a response and is being accepted as a complete response.
Second, this argument fails for assuming an unreasonably low level of background knowledge, creativity, and common sense, inconsistent with the knowledge of a person of ordinary skill in the art. The argument presumes that a skilled artisan, despite knowing the intended purpose in HALLE and RAYBUCK is to obtain and analyze fetal DNA, would be misled by the mRNA sample type in Bonetta and fail to recognize the applicability of Solexa sequencing to DNA. Thus, this argument fails to take into account the background knowledge, creativity, and common sense of the person of ordinary skill (See MPEP §2143.01). A person of ordinary skill is also a person of ordinary creativity, not an automaton, and in many cases will be able to fit teachings of multiple patents together like pieces of a puzzle (See MPEP § 2141.03). Given this creativity the ability to fit teachings of multiple references together like the pieces of a puzzle, one of ordinary skill in the art would be able to combine the teachings in such a way that it would not render the prior art inoperable for their intended purpose, as there are more ways than those proposed by Applicant to combine the references.
A person of ordinary skill in the art would understand that sequencing-by-synthesis methods such as Solexa sequencing are applicable for analyzing both RNA and DNA, and would have had a reasonable expectation of success in applying Solexa sequencing to DNA samples.
This is further supported by reference cited in Applicant's own remarks, filed on February 28, 2025, "[t]o support the fact that those of skill in this field understood the Solexa sequencing platform as of the earliest effective filing date of the present application (June 14, 2006)." (Remarks filed on 02/28/2025, page 5-6)
Zhou et al. 1, cited in the Applicant's remarks, describes the working principle of Solexa (Illumina) sequencing and explicitly teaches that the input for Solexa sequencing is DNA:
"The Illumina (Solexa) Genome Analyzer The Solexa sequencing platform was commercialized in 2006. The working principle (Fig. 2) is sequencing-by synthesis chemistry. Input DNA is fragmented by hydrodynamic shearing to generate < 800 bp fragments. The fragments are blunt ended and phosphorylated, and a single ‘A’ nucleotide is added to the 3¢-ends of the fragments. Then DNA fragments are ligated at both ends to adapters that have a single-base ‘T’ overhang. After denaturation, DNA fragments are immobilized at one end on a solid support-flow cell. The surface of the flow cell is coated densely with the adapters and the complementary adapters. Each single stranded fragment that is immobilized at one end on the surface creates a ‘bridge’ structure by hybridizing with its free end to the complementary adapter on the surface of the flow cell. The adapters on the surface also act as primers for the following PCR amplification. Adding mixtures containing the PCR amplification reagents to the flow cell surface, the DNA fragments are amplified by “bridge PCR” (Adessi, 2000; Fedurco et al., 2006). After several PCR cycles, about 1000 copies of single-stranded DNA fragments are created on the surface, forming a surface-bound colony (the cluster). The reaction mixture for the sequencing chemistry and DNA synthesis is supplied onto the surface, which contains four reversible terminator nucleotides, each labeled with a different fluorescent dye. After incorporation into the DNA strand, the terminator nucleotide as well as its position on the support surface are detected and identified via its fluorescent dye by the CCD camera. The terminator group at the 3¢-end of the base and the fluorescent dye are then removed from the base and the synthesis cycle is repeated. This series of steps continues for a specific number of cycles, as determined by user-defined instrument settings. A base calling algorithm assigns sequences and associated quality values to each read and a quality checking pipeline evaluates the Illumina data from each run, removing poor-quality sequences." (Zhou, page 524, left-hand col)
In view of the foregoing, Applicant's arguments are not found persuasive to overcome the prior art rejections under 35 USC 103. Therefore, the rejections are properly maintained in this Office Action.
Priority
Regarding claim 102 and its dependent claims, the earliest priority is 06/14/2007 because the priority document (11/763,426) filed that date is the first to disclose "Solexa sequencing".
Claim Interpretation -- Maintained
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
For the purpose of applying prior art, claim 102 recites the term "Solexa2 sequencing."
The application's disclosure does not provide any definition for the term "Solexa sequencing." However, Applicant's remarks filed on February 28, 2025 provides the following:
"While applicant maintains that the Office's interpretation of "ultra-deep sequencing" as meaning "any sequence analysis approach for nucleic acids" is clearly overbroad, this issue is moot in light of the present amendment to claim 102 to replace the term "ultra-deep sequencing" with the term "Solexa sequencing," which is known to those of skill in this field as a next generation sequencing platform developed by Solexa, and then by Illumina, which acquired Solexa in a stock-for-stock merger after a definitive merger agreement was signed on November 13, 2006.
To support the fact that those of skill in this field understood the Solexa sequencing platform as of the earliest effective filing date of the present application (June 14, 2006), applicant is submitting herewith copies of three articles that describe this type of sequencing and its use in 2006. For one thing, "[b]y March 2005, Solexa was a publicly traded company on NASDAQ." In addition, "Solexa started shipping its first machines in mid-2006 to some of the major genome centers" (The Solexa Story, Bio-IT World (September 24, 2010)(Exhibit A).
In addition, Reuter et al., "High-Throughput Sequencing Technologies," Mol Cell, 58(4):586-597 (May 21, 2015)(Exhibit B), is a review article that states on page 2: "Illumina/Solexa released the Genome Analyzer II in 2006, and advances in Illumina' s technology over the intervening years have largely set the pace for the tremendous gains in output and reductions in cost (Figure 1 )." Figure 1 in this article shows that the first Solexa/Illumina instruments launched in 2006 (red circle).
Another example is Zhou et al., "The next-generation sequencing technology and application," Protein and Cell, 1(6):520-0536 (June 2010)(Exhibit C), which states that "The Solexa sequencing platform was commercialized in 2006" (page 524). This reference also provides a detailed summary of the working principle of the Solexa platform sequencing method (on page 524 and in Fig. 2).
Given this evidence, applicant submits that those of skill in the field of sequencing nucleic acids, when reading the present application, as of the 2006 filing date, would have been aware of the Solexa sequencing methods and systems, and thus claim 102, which has been amended to recite "Solexa sequencing," should be properly interpreted to mean a specific type of high throughout sequencing by synthesis sequencing method." (Remarks, page 5-6)
Applicant's remarks have been fully considered.
Zhou et al., cited in the Applicant's remarks above, describes the working principle of Solexa (Illumina) sequencing as sequencing-by synthesis. Accordingly, under BRI, the term "Solexa sequencing" is understood as sequencing-by-synthesis technology, such as those sequencing technologies developed and provided by Solexa and Illumina.
For the purpose of applying prior art, claim 112 recites the term "binning," which is not defined in the applicant's disclosure. The specification provides the following description:
"[0041] …Binning may comprise distribution of enriched cells across wells in a plate (such as a 96 or 384 well plate), microencapsulation of cells in droplets that are separated in an emulsion, or by introduction of cells into microarrays of nanofluidic bins.”
“[0075] Enriched target cells (e.g., fnRBC) may be "binned" prior to further analysis of the enriched cells (Figures 24 and 25). Binning is any process which results in the reduction of complexity and/or total cell number of the enriched cell output. Binning may be performed by any method known in the art or described herein. One method of binning is by serial dilution. Such dilution may be carried out using any appropriate platform (e.g., PCR wells, microtiter plates) and appropriate buffers. Other methods include nanofluidic systems which can separate samples into droplets ( e.g., Bio Trove, Raindance, Fluidigm). Such nanofluidic systems may result in the presence of a single cell present in a nanodroplet."
Thus, in light of the specification and under BRI, the term "binning" is interpreted as "any process which results in the reduction of complexity and/or total cell number," such as serial dilution or using nanofluidic systems to divide a sample into smaller portions.
For the purpose of applying prior art, claim 113 recites the term "nanofluidic system", which is not defined in the applicant's disclosure. Paragraph [0075] of the specification provides the only description for this term:
“[0075] … Other methods include nanofluidic systems which can separate samples into droplets ( e.g., Bio Trove, Raindance, Fluidigm). Such nanofluidic systems may result in the presence of a single cell present in a nanodroplet."
Thus, in light of the specification and under BRI, the term "nanofluidic system" is interpreted as any system that can separate samples into droplets.
Claim Rejections - 35 USC § 103 – Maintained
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 102-109 and 116-121 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over HALLE (US20050282213A1 - Methods and kits useful for detecting an alteration in a locus copy number; Published 2005-12-22), in view of
RAYBUCK (WO1998026284A1 - Selective lysis of cells; Published 1998-06-18) and
Bonetta (Bonetta, L. Gene expression: one size does not fit all. Nat Methods 3, 401–408 (2006). doi.org/10.1038/nmeth0506-401; Published May, 2006), as evidenced by
Yamanishi (Yamanishi et al. (2002). Enrichment of rare fetal cells from maternal peripheral blood. Expert Review of Molecular Diagnostics, 2(4), 303).
A) HALLE teaches a method of prenatally identifying a genomic alteration in a locus copy number, by analyzing fetal cells in blood obtained from a pregnant woman (entire document, [0030], [0180] for example).
Regarding claim 102, HALLE teaches a method comprising: obtaining a mixed sample comprising fetal and maternal cells ([0180] blood obtained from pregnant woman);
enriching the mixed sample for fetal cells to produce an enriched sample comprising fetal cells and maternal cells ([0179]-[0181], [0021]); amplifying genomes to produce amplified nucleic acids ([0202], [0208]; [0217]; [0055]; [0057]); and analyzing the amplified nucleic acids for aneuploidy (claim 2; [0018]) using sequencing ([0148], genomic sequencing; [0207]; [0240]).
However, while HALLE teaches performing sequencing to analyze amplified PCR products (e.g. [0240]), it does not specifically teach using Solexa sequencing.
Further, HALLE does not specifically teach lysing fetal cells in the enriched sample and separating nuclei of the fetal cells from other cells and cell components in the enriched sample to produce isolated fetal nuclei.
B) RAYBUCK teaches a method of selective lysis of the plasma membrane of fetal cells to generate intact fetal cell nuclei, whilst leaving maternal nucleated blood cells intact, thereby separating the fetal cell nuclei from any contaminating intact cells and cell debris (entire document, page 7 for example).
Regarding claim 102, RAYBUCK teaches lysing fetal cells in the enriched sample (page 14, lines 18-22) and separating nuclei of the fetal cells from other cells and cell components in the enriched sample to produce isolated fetal nuclei (page 14, lines 27-30 to page 15, lines1-9).
RAYBUCK further teaches its selective lysis technique is useful in prenatal testing for genetic disorders, by providing a safe, simple, rapid and non-invasive means to obtain fetal cell nuclei for diagnosis, with the special advantage of economically and technically efficient:
"The present lysis method permits the selective liberation of foetal cell nuclei from samples containing both foetal and maternal blood cells including, but not limited to, the situation when the foetal cell is present as a rare cell such as in maternal peripheral blood. The invention thus provides a method of generating foetal cell nuclei from such mixed maternal/foetal cell samples with minimal contamination from maternal cell nuclei. The lysis method of the present invention is useful in prenatal diagnosis for foetal abnormalities such as genetic disorders (e.g. β-globin mutations or cystic fibrosis) or chromosomal disorders such as Klinefelter syndrome or aneuploidies (e.g. Down's syndrome). For prenatal screening to be commercially feasible and to allow its availability to every pregnant woman (not just those considered at risk of foetal abnormality), it must be economically and technically efficient. Each stage must be safe and simple and easy to use. There is also a need for rapid sample processing to allow early clinical decisions. The method of the present invention provides a safe, simple, rapid and non-invasive means to obtain foetal cell nuclei for diagnosis. The method has the advantage over prior art methods that the diagnosis can be carried out on samples (such as maternal peripheral blood) in which the foetal cell population is a very small fraction of the total cell count without the requirement for cell enrichment methods. The method has the additional advantage that specialised reagents (such as monoclonal antibodies or density gradients), or expensive instrumentation (such as a flow cytometer) are not required. It is envisaged that the present method can be used as the first stage of a diagnostic method in its own right, or as an aid to early prenatal diagnosis prior to confirmation by standard invasive methods. It is envisaged that the method of the present invention could form part of a kit for sample preparation for diagnostic analysis and may contain a combination of reagents for performing the lysis step, nuclei isolation and analysis." (RAYBUCK, pages 13-14)
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the method taught by HALLE with the selective lysis technique of RAYBUCK because both references are in the same field of prenatal genetic testing. A skilled artisan, aiming to improve methods for fetal cell analysis, would likely encounter both references in their search.
The person of ordinary skill would have had a reasonable expectation of success in combining these teachings because RAYBUCK provides a specific technique for improving the purity of fetal cell DNA by isolating fetal nuclei with reduced contamination from maternal cells -- a known issue in the methods described by HALLE (see [0014][0021[[0174][0178]). RAYBUCK provides a detailed approach to selective lysis, which is technically compatible with the method taught by HALLE. This integration would have predictably yielded a cleaner sample with increased fetal DNA purity for subsequent DNA analysis, crucial for accurate and reliable prenatal diagnosis.
The skilled artisan would have been motivated to combine these teachings to further minimize DNA contamination from maternal cells and achieve economic and technical efficiencies in effective prenatal testing, as suggested by RAYBUCK.
C) The combined teachings of HALLE and RAYBUCK does not teach Solexa sequencing. While HALLE teaches performing sequencing to analyze amplified PCR products (e.g. [0240]), it does not specifically teach using Solexa sequencing.
Bonetta provides a technical overview on molecular biology technologies for gene expression analysis, including Solexa sequencing (entire document).
Regarding claim 102, Bonetta teaches Solexa sequencing as a powerful tool for genome analysis (page 407, left-hand col).
Bonetta further suggests several advantages of Solexa sequencing, such as high throughput, cost-effectiveness, competitive performance, and capability to both profile known genes and discover unknown ones:
"Solexa has developed an alternative, powerful platform through its Genome Analysis System, which will be commercially available to researchers by mid-2006. After constructing a library of 20-base-long cDNA tags corresponding to each expressed transcript, millions of individual DNA molecules are linked, using short oligonucleotide adapters, to the surface of a glass flow cell. Each molecule then undergoes a solid-phase amplification procedure that creates a cluster of DNA molecules each with identical DNA tags. The DNA molecules in each cluster are simultaneously sequenced by Solexa's Sequencing-by-Synthesis chemistry, which uses proprietary fluorescently labeled modified nucleotides. The sequence information is then used to identify the corresponding transcripts and genes, and determine their abundance. “You can use our system for both profiling known genes and discovering unknown ones,” says Gary P. Schroth, director for expression applications research and development. “Solexa's new technology will allow researchers to interrogate up to 5,000,000 tags per sample for a few hundred dollars—costs that are a fraction of those of MPSS and SAGE, and on par with those of hybridization arrays.”" (page 407)
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the combined teachings of HALLE and RAYBUCK, to use Solexa sequencing for genome analysis, as taught by Bonetta, in identifying fetal genome alternations. Because all three references are in the overlapping field of genome analysis. HALLE already teaches sequencing, and Bonetta's teaching of Solexa sequencing provides an improved, specific sequencing method for genome analysis. This combination represents the predictable use of a known element (Solexa sequencing) according to a known method (performing genome analysis using sequencing) to yield predictable results (See MPEP §2143).
The person of ordinary skill would have had a reasonable expectation of success in combining these teachings because the teachings in the references are technically compatible. Solexa sequencing, as described in Bonetta, is identified as advanced sequencing approach based on amplifying DNA templates on a chip (sequencing by synthesis). Thus, a person of ordinary skill in the art would have reasonably expected Solexa sequencing to be applicable for sequencing any amplifiable DNA, including the DNA amplicons in HALLE.
The result of this combination would have yielded the predictable result of an improved molecular method for prenatally identifying genomic alternations in fetal cells, via effective isolation of fetal cell nuclei and analyze them using Solexa sequencing.
The skilled artisan would have been motivated to combine the teachings, to leverage the several advantages offered by Solexa sequencing, such as high throughput, cost-effectiveness, competitive performance, and capability to both profile known genes and discover unknown ones, as suggested by Bonetta, all of which are desirable improvements in prenatal diagnostic applications.
D) All limitations in claims 103-109, and 116-121 are taught by the combined teachings of HALLE, RAYBUCK and Bonetta.
Regarding claim 103, HALLE teaches analyzing for fetal aneuploidy, wherein the fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of one or more chromosomes ([0163]).
Regarding claim 104, HALLE teaches fetal aneuploidy of a chromosome selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y ([0163]).
Regarding claim 105, HALLE teaches fetal aneuploidy comprises trisomy or monosomy ([0163]).
Regarding claim 106, HALLE teaches fetal aneuploidy comprises trisomy, and wherein the trisomy comprises trisomy 13, trisomy 18, or trisomy 21 ([0163]).
Regarding claim 107, HALLE teaches fetal aneuploidy comprises monosomy X and the chromosome suspected of being aneuploid comprises chromosome X([0163]) .
Regarding claim 108, HALLE teaches the fetal aneuploidy comprises XXY ([0244]-[0245]).
Regarding claim 109, HALLE teaches sequencing produces partial genome sequences for analysis ([0238]-[0240], partial genome sequenced downstream of specific amplification of an exon; [0207]).
Regarding claims 116-118, while HALLE does not explicitly disclose ranges of the specific ratios of fetal cells to maternal cells in an enriching step, it inherently does so. In the field of fetal cell analysis, such as prenatal genetic testing, which is in the context of the invention, there is an inherent drive to increase the ratio of fetal cells to maternal cells, so the cells can be analyzed. This is evidenced by Yamanishi (entire document, for examples abstract, lines1-5; page 306, right-hand col, lines 1-3). Therefore, a person of ordinary skill in the art would understand HALLE's teaching to inherently disclose the claimed ratios.
Regarding claim 119, RAYBUCK teaches mixed sample is obtained from whole blood (page 8, lines23-24; page 9, lines7-10).
Regarding claim 120, HALLE teaches contacting the mixed sample with particles coupled to antibodies that selectively bind to fetal cells ([0176]).
Regarding claim 121, HALLE teaches magnetic particles by teaching using kits for enriching fetal cells from maternal blood, from AVIVA Biosciences Corporation ([0181]). The AVIVA Biosciences Corporation kits for enriching fetal cells from maternal blood use magnetic beads coated with antibodies, as evidenced by Yamanishi et al (page 307, right-hand col, lines 15-21).
Claim 111 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over
HALLE, in view of RAYBUCK and Bonetta, as applied to claim 102 above and further in view of FEJGIN (US20060040305A1- Non-invasive prenatal genetic diagnosis using transcervical cells; Published on 2006-02-23).
A) The combined teachings of HALLE RAYBUCK and Bonetta are recited above and applied as for base claim 102.
Regarding claim 111, although each of HALLE, RAYBUCK, and Bonetta teach amplifying genomes (HALLE, ([0202], [0208]; [0217]; [0055]; [0057])(RAYBUCK, page 16, lines 8-13) (Bonetta, page 407), they do not specifically teach amplifying whole genomes.
B) FEJGIN teaches a method of non-invasive prenatal diagnosis for the identification of chromosomal and/or DNA abnormalities (entire document).
Regarding claim 111, FEJGIN teaches performing whole genome amplification of fetal cells ([0265]), and whole genome amplification method is well known in the art ([0230]lines8-14).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply the whole genome amplification approach of FEJGIN to the combined teaching of HALLE, RAYBUCK, and Bonetta, because the references overlap in the field of prenatal testing, specifically concerning genome amplification. Such combination utilizes well-known technique of whole genome amplification to yield predictable results. Specifically, applying the well-known whole genome amplification technique of FEJGIN to the isolated fetal nuclei from the combined teaching of HALLE, RAYBUCK, and Bonetta would have yielded the predictable result of a more comprehensive genome analysis, thus enhancing the detection capabilities for prenatal testing.
Therefore, it would have been obvious to combine the teachings of HALLE, RAYBUCK, and Bonetta with whole genome amplification taught by FEJGIN, representing a predictable use of prior art element according to a known method to yield predictable results (See MPEP §2143).
Claims 112-113 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over HALLE, in view of RAYBUCK, and Bonetta as applied to claim 102 above and further in view of TERSTAPPEN (US6623983B1 - Apparatus and methods for capture and analysis of particulate entities; Published 2003-09-23).
A) The teachings of HALLE, RAYBUCK, and Bonetta are recited above and applied as for base claim 102.
Regarding claims 112-113, although HALLE, RAYBUCK, and Bonetta do not specifically teach use of a nanofluidic system that separates samples into droplets, prior to cell lysis. HALLE teaches enriching fetal cells using flow cytometry ([0021][0177]). RAYBUCK teaches processing fetal cells by prior to the step of lysing fetal cells (page 10, lines27-29, cell samples are aliquoted prior to lysing).
B) TERSTAPPEN teaches a method of collecting cells of interest such as fetal cells within maternal circulation (col7, lines21-30).
Regarding claims 112-113, TERSTAPPEN teaches use of a nanofluidic system (col 5, lines21-26, droplet sorter in flow cytometry) that separates samples into droplets (col 5, lines21-26).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to substitute the general flow cytometry approach used in the combined teaching of HALLE, RAYBUCK, and Bonetta with the droplet sorter flow cytometry from TERSTAPPEN for fetal cell enrichment, because these references overlap in the field of fetal cell analysis from blood. This substitution is a predictable use of a known technique within the same category-- flow cytometry-- with no unexpected change in function or result. Since both HALLE and TERSTAPPEN teach flow cytometry for cell isolation, replacing one with the other would not change the fundamental operation but would utilize a variant of the same technology, yielding the same predictable result of cell enrichment.
Therefore, it would have been obvious to integrate the droplet sorter flow cytometry system of TERSTAPPEN into the fetal cell analysis method taught by the combined teaching of HALLE, RAYBUCK, and Bonetta. This rationale aligns with the principle of KSR for a simple substitution of one known element for another to obtain predictable results, see MPEP 2141.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
1 Zhou et al. The next-generation sequencing technology and application. Protein Cell. 2010 Jun;1(6):520-36. doi: 10.1007/s13238-010-0065-3. Epub 2010 Jul 7. PMID: 21204006; PMCID: PMC4875313.
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