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 .
DETAILED ACTION
Status of the Claims
Claims 1-13, 16-23 and 25-31 are pending and the subject of this NON-FINAL Office Action.
New Grounds of Rejection - 35 USC § 112- Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(B) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-13, 16-23 and 25-31 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
The metes and bounds of the claims are so unclear and confusing that the Office cannot determine if the instant claims are patentable because it would require the Office to speculate as to the metes and bounds of the instant claims. See MPEP § 2173.06 (“Second, where there is a great deal of confusion and uncertainty as to the proper interpretation of the limitations of a claim, it would not be proper to reject such a claim on the basis of prior art. As stated in In re Steele, 305 F.2d 859, 134 USPQ 292 (CCPA 1962), a rejection under 35 U.S.C. 103 should not be based on considerable speculation about the meaning of terms employed in a claim or assumptions that must be made as to the scope of the claims.”).
Specifically, at step (d), it is unclear what is required by “coupling the first probe oligonucleotide and the second probe oligonucleotide, thereby generating a ligation product.” Coupling two probes does not necessarily lead to ligation. For example, two probes can hybridize, or interact via streptavidin and biotin, or other interactions. Merely stating that this “thereby” generates ligation product fails to provide any clarity or meaning to merely coupling probes. In other words, it is not clear if Applicants mean that coupling includes hybridization, affinity interactions or other interactions, or if this coupling is a ligation step.
Moreover, the first and second probes hybridize to a single mRNA, yet also hybridize to two separately-located and separately-barcoded capture probes on an array, which is also confusing. The claims require
providing an array comprising a first plurality of capture probes, wherein a first capture probe of the first plurality of capture probes comprises: (i) a first spatial barcode and (ii) a first capture domain, and wherein the first capture probe is attached to a substrate; and a second plurality of capture probes, wherein a second capture probe of the second plurality of capture probes comprises: (iii) a second spatial barcode and (iv) a second capture domain, wherein the plurality of second capture probes is attached at a different location on the substrate from the first plurality of capture probes, and wherein the first spatial barcode and the second spatial barcode are different.
In other words, the capture probes are attached to an array, and each is at a different location on the array with different spatial barcodes, each spatial barcode identifying a single location (e.g. x1, y1). If these capture probes are later hybridized to the single mRNA (through the two probe oligos on the mRNA that have the two capture probe sequences on their ends), then this would yield a confusing situation. That is, now a single mRNA would have two different spatial barcodes, yielding the inability to spatially identify the mRNA because each spatial barcode identifies a single location.
In sum, the claimed spatial barcoding of the mRNA in a tissue is confusing due to the non-limiting, yet confusing “thereby” ligation clause; and the capture probes-probe oligos configuration.
In contrast, as best the Examiner can determine, Applicants may intend to claim the technique shown in Figures 15-17, which shows the following:
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To summarize the basic outline, this method uses two probe hybridized to a single mRNA, each probe with tails that include capture probe hybridizing sequences. As explained in the description of Figure 15,
FIG. 15B shows an exemplary high-density barcoding pattern where each box represents a feature (e.g., as described herein). For example, the same spatial barcode e.g., BC-L-01 can be used across the first row in combination with a different BC—R spatial barcode (e.g., BC—R-01; BC—R-02; BC—R-03; BC—R-04; etc.). Similarly, the same spatial barcode e.g., BC—R-01 can be used down the first column in combination with a different BC-L spatial barcode (e.g., BC-L-01; BC-L-02; BC-L-03; BC-L04; etc.). FIG. 15C shows an exemplary high-density barcoding pattern where each box represents a feature, however, only a single barcode is used per feature. When the capture probes are released diffusion of the barcodes occurs and they can hybridize to the capture probe binding domains of the ligation product.
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In other words, one barcode identifies a row, the other identifies a column (e.g. BC-L-01= x1, BC-R-01= y1, etc.). This is a different invention from a single-location barcode. Thus, applying prior art would require conjecture as to the scope of Applicants’ claims.
New Grounds of Rejections - 35 USC § 102
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:
Novelty; Prior Art.—A person shall be entitled to a patent unless—
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; or
the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention..
Claims 1-13, 16-23 and 25-31 are rejected under 35 U.S.C. § 102(a)(2) as being anticipated by BAVA (US20210262018).
As best the Examiner can determine, Applicants intend to claim the technique shown in Figures 15-17, which shows the following:
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To summarize the basic outline, this method uses two probe hybridized to a single mRNA, each probe with tails that include capture probe hybridizing sequences. As explained in the description of Figure 15,
FIG. 15B shows an exemplary high-density barcoding pattern where each box represents a feature (e.g., as described herein). For example, the same spatial barcode e.g., BC-L-01 can be used across the first row in combination with a different BC—R spatial barcode (e.g., BC—R-01; BC—R-02; BC—R-03; BC—R-04; etc.). Similarly, the same spatial barcode e.g., BC—R-01 can be used down the first column in combination with a different BC-L spatial barcode (e.g., BC-L-01; BC-L-02; BC-L-03; BC-L04; etc.). FIG. 15C shows an exemplary high-density barcoding pattern where each box represents a feature, however, only a single barcode is used per feature. When the capture probes are released diffusion of the barcodes occurs and they can hybridize to the capture probe binding domains of the ligation product.
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In other words, one barcode identifies a row, the other identifies a column (e.g. BC-L-01= x1, BC-R-01= y1, etc.).
As to claims 1-13, 16-23 and 25-31, BAVA teaches a method of spatially barcoding a target nucleic acid in a biological sample, the method comprising: (a) providing an array comprising a first plurality of capture probes, wherein a first capture probe of the first plurality of capture probes comprises: (i) a first spatial barcode and (ii) a first capture domain, and wherein the first capture probe is attached to a substrate; and a second plurality of capture probes, wherein a second capture probe of the second plurality of capture probes comprises: (iii) a second spatial barcode and (iv) a second capture domain, wherein the plurality of second capture probes is attached at a different location on the substrate from the first plurality of capture probes, and wherein the first spatial barcode and the second spatial barcode are different and on barcode identifies a row, the other a column (Figs. 12 & 17; paras. 01291, 1296, 0309ff); (b) permeabilizing the tissue section (“Alternatively, the sample may be permeabilized and fixed/crosslinked to restrict mobility of one or more target analytes, while allowing spatially-barcoded capture probes to migrate towards and/or into or onto the sample”; para. 0261, for example); (c) hybridizing a first probe oligonucleotide and a second probe oligonucleotide to the target mRNA, wherein the first probe oligonucleotide and the second probe oligonucleotide each comprise from 2 to 500 nucleotides in length, wherein the first probe oligonucleotide and the second probe oligonucleotide each comprise a sequence that is complementary to a first sequence and a second sequence of the target mRNA, respectively, and wherein the first probe oligonucleotide further comprises a first capture probe binding domain on its tail and the second probe oligonucleotide further comprises a second capture probe binding domain on its tail (Fig. 13); (d) ligating the first probe oligonucleotide and the second probe oligonucleotide (Fig. 13); (e) releasing the first capture probe and optionally, the second capture probe from the substrate (“In any of the preceding embodiments, the method can comprise releasing the plurality of capture agents from the substrate (or the first substrate) or from the second substrate, and/or delivering or driving the released plurality of capture agents towards and/or into or onto the biological sample”; paras. 0027, 0411-12); and (f) after step (e), hybridizing (i) the first capture domain of the released first capture probe to the first capture probe binding domain of the ligation product, and optionally, (ii) the, (ii) the second capture domain of the second capture probe to the second capture probe binding domain of the ligation product, thereby spatially barcoding the target nucleic acid in the biological sample (Asbtract; Figs. 1-2); and (g) determining (i) the sequence of the ligation product of the spatially barcoded product, or a complement thereof, (ii) the sequence of the first spatial barcode, or a complement thereof, and optionally, (iii) the sequence of the second spatial barcode, or a complement thereof, and using the determined sequences of (i), (ii), and optionally, (iii) to determine the location of the target mRNA in the tissue section (id.) The spatial barcodes identify columns and rows (see e.g. Fig. 17, para. 0427).
Prior Art
The following prior art teaches spatial barcoding using x/y or column/row barcodes on capture probes, along with oligos that are ligated on target nucleic acids and later attached to the capture probes: US20110245111; US 20170016063; US 20220220544; US 20240287587; US 20230304074.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Aaron Priest whose telephone number is (571)270-1095. The examiner can normally be reached 8am-6pm.
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/AARON A PRIEST/Primary Examiner, Art Unit 1681
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