DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 2-21 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The issues in this rejection stem from the preliminary amendment of 02/13/2025 made after the filing date (02/12/2024). The issues also stem from the way the term “padlock probe” is used in the claims and the specification.
Claim 2 recites “contacting the biological sample with a spatial array comprising a plurality of capture probes, wherein a capture probe of the plurality comprises…a padlock probe”.
In the specification, the term “padlock probe” is used in two ways.
The first way refers to a molecule not integral to the capture probe, but which interacts with the capture probe such that the padlock probe is transformed into a closed circular molecule, which is then used as a template in a rolling circle amplification reaction. The second way refers to the product of that rolling circle amplification reaction: “…thereby generating a padlock probe sequence with multiple copies of the capture domain.” This process is explained in the specification at page 1, last paragraph through line 8 on page 2. This is a process of creating an extended capture probe containing multiple copies of a spatial barcode and a capture domain, and is illustrated in figure 7, upper panel. Further explanation is given on page 3 (footnotes provided):
“In some instances, the spatial barcode and the capture domain are located between the first docking sequence and the second docking sequence of the capture probe.1 In some instances, the ligated padlock probe further comprises a primer sequence, or a complement thereof, and a spatial domain, or a complement thereof. In some instances, the amplifying comprises rolling circle amplification. In some instances, the padlock probe comprises a 3'OH group, wherein the 3'OH group is a primer for the rolling circle amplification2.
In some instances, the step of hybridizing the padlock probe to the capture probe utilizes a splint oligonucleotide that comprises a sequence complementary to the capture probe and a sequence complementary to the padlock probe3.
In some instances, the ligating step further includes extending the padlock probe via a nucleic acid extension reaction using the capture probe as a template. In some instances, the extending occurs prior to the ligating step.4”
Based on the language of claim 2, and what is disclosed in the specification, there are at least two possible interpretations for “wherein a capture probe of the plurality comprises…a padlock probe” as recited in claim 2.
The capture probe is composed of a “capture probe” and a separate “padlock probe”, such as is illustrated in figure 7:
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However, there is no disclosure in the application as-filed of contacting a sample to such a “capture probe”, where the padlock probe is still present.
At page 33, paragraph 3, the specification reads: “After generating a plurality of padlock probes from the rolling circle amplification steps, in some instances, the biological sample is contacted with the substrate.” The lack of a positive recitation of removing the padlock probes (i.e. the circular padlock probes, not the complementary copies of the padlock probes) prior to contacting the sample with the substrate, however, does not provide written description of such padlock probes being present when the sample is contacted with the substrate.
The specification also reads (page 34, second full paragraph): “In some embodiments, the biological sample is permeabilized contemporaneously with or prior to contacting the biological sample with a padlock probe.” However, in this context, is not clear that the specification is referring to the padlock probe per se, or the complementary copies of the padlock probe incorporated into the capture probe by the rolling circle amplification process.
The specification also reads (page 35, first full paragraph): “After permeabilization, in some instances, the analytes are captured by the capture domains of the padlock probe. In some embodiments, such methods of increasing capture efficiency of a spatial array described herein includes contacting the spatial array with the biological sample and allowing the analyte to interact with the padlock probes.” Again, it is not clear that the specification is referring to the padlock probe per se, or the complementary copies of the padlock probe incorporated into the capture probe by the rolling circle amplification process.
The specification also discloses (page 36, second full paragraph, emphasis provided): “In some embodiments, provided herein are methods for spatially detecting an analyte (e.g., detecting the location of an analyte, e.g., a biological analyte) from a biological sample (e.g., present in a biological sample), the method comprising: (a) optionally staining and/or imaging a biological sample on a substrate; (b) permeabilizing (e.g., providing a solution comprising a permeabilization reagent to) the biological sample on the substrate; (c) contacting the biological sample with an array comprising a plurality of capture probes and padlock probes, wherein the padlock probe captures the biological analyte; and (d) analyzing the captured biological analyte, thereby spatially detecting the biological analyte; wherein the biological sample is fully or partially removed from the substrate.” The specification at page 37, second full paragraph, contains similar language. It is not clear whether the specification is referring to capture probes that comprise the padlock probes (integrally, as complementary copies of padlock probes), or whether the padlock probes are the closed circular molecules such as represented in figure 7:
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The capture probe comprises multiple copies of a sequence complementary to the padlock probe (i.e. a “padlock probe sequence”, as mentioned, e.g., on page 2, line 7 of the specification) integral to the capture probe, as shown, e.g., in figure 9. However, this is not compatible with the additional language in claim 2 indicating that the padlock probe comprises:
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These are features disclosed in the specification to be comprised by the padlock probe itself (prior to ligation), rather than in the product of the rolling circle amplification. Therefore, this interpretation also introduces new matter.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 2-21 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
As noted above in the rejection under 35 USC 112(a), there are at least two possible interpretations for the language “wherein a capture probe of the plurality comprises…a padlock probe”. As noted in MPEP 2173.05(b)(II), “…where the elements of a claim have two or more plausible constructions such that the examiner cannot readily ascertain positional relationship of the elements, the claim may be rendered indefinite. See, e.g., Ex parte Miyazaki, 89 USPQ2d 1207 (Bd. Pat. App. & Inter. 2008) (precedential) and Ex parte Brummer, 12 USPQ2d 1653 (Bd. Pat. App. & Inter. 1989).”
Here, as noted in the rejection under 35 USC 112(a), it cannot be determined whether the language means that the capture probe literally comprises, as an integral element, the padlock probe (i.e. the “padlock probe” is the complementary sequence of the padlock probe used to extend the original capture probe, as illustrated in figure 7), or whether the padlock probe is the padlock probe per se, and is associated with the capture probe via hybridization (also as illustrated in figure 7). Therefore, the claims are indefinite.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SAMUEL C WOOLWINE whose telephone number is (571)272-1144. The examiner can normally be reached 9am-5:30pm.
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/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681
1 See footnote 4.
2 How this would work is unclear. Once ligated, the padlock probe does not comprise a free 3’ end or 3’OH group. Furthermore, the ligated padlock probe serves as a template for the rolling circle amplification, not as a primer. Based on the illustration in figure 7, it is the capture probe which contains the free 3’OH group and serves as a primer for the rolling circle amplification.
3 This alternative is illustrated in the bottom panel of figure 7.
4 In this way, the completed padlock probe incorporates sequences complementary to the spatial barcode and capture domain of the capture probe. When the capture probe is extended by rolling circle amplification using the padlock probe as a template, the extended capture probe will comprise multiple copies of the spatial barcode and capture domain, as illustrated in figure 9 (which does not show the barcodes, but does show the capture domains).
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