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 .
Status of the Claims
Claims 1-24 are pending. Claims 1-24 are the subject of this NON-FINAL Office Action. This is the first action on the merits.
Claim Interpretation
Par. 0114 of the specification states that the term “about” is meant to encompass variations within 20%, 10%, 5%, or 1% of the specified value. The term “about” will be interpreted under the broadest reasonable interpretation as being within 20% of a specified value.
Claim 1 recites:
“A system for labeling nucleic acid molecules in a sample comprising a set of oligonucleotides comprising a plurality of barcodes, each barcode comprising a stretch of contiguous bases comprising:
(i) a sample barcode comprising a pre-determined number of sample index positions comprising one or more specific nucleotides, wherein the location of sample index positions varies between samples; and
(ii) a molecular barcode comprising molecular index positions comprising a nucleotide that differs from the nucleotides at sample index positions,
wherein sample index positions are interspersed among molecular index positions.”
The limitation “each barcode comprising a stretch of contiguous bases” is interpreted as the barcode, which contains both a sample barcode and a molecular barcode, is a single continuous region which can contain additional bases other than the sample index positions and the molecular index positions. Under the broadest reasonable interpretation, the barcode can be as short as two bases, encompassing a single sample index position and a single molecular index position, or as long as the entire oligonucleotide.
The limitation “index positions” is interpreted in accordance with par. 0040 of the specification, which is a nucleotide position within a barcode that can be used to identify the origin or source of a nucleic acid molecule. The index position is not required to be any particular type of nucleotide.
The limitation “pre-determined number of sample index positions” is interpreted in accordance with par. 0042 of the specification, which states that a particular number of positions can be assigned to a sample index to identify the sample a nucleic acid molecule came from.
Par. 0115 states that the term “nucleic acid” refers to any DNA molecule, RNA molecule, or nucleic acid analogues, and that the term “nucleic acid molecule” is meant to include fragments of nucleic acid molecules as well as any full-length or non-fragmented nucleic acid molecule. Par. 0116 states that the term “nucleotide” includes both individual units of ribonucleic acid and deoxyribonucleic acid as well as nucleoside and nucleotide analogs, modified nucleotides such as labeled nucleotides, and non-naturally occurring analogue structures.
The claim states that the pre-determined number of sample index positions comprise one or more specific nucleotides, and that the molecular barcode comprises molecular index positions comprising a nucleotide that differs from the nucleotides at sample index positions. The claim does not require that sample index positions must comprise the same type of nucleotide.
The claim also does not require that molecular index positions must comprise the same type of nucleotide. The claim states that the molecular barcode comprises molecular index positions comprising “a nucleotide that differs from the nucleotides at sample index positions.” The specification does not define how this difference is to occur. The specification provides examples stating that the type of nucleotide at a molecular index position is different from the type of nucleotide at sample index positions.
Under the broadest reasonable interpretation, this limitation only requires that a single nucleotide is different from a nucleotide at a sample index positions. As the nucleotides can be any type of nucleotide, the different nucleotide encompasses any and all types of nucleotides, including individual units of ribonucleic acid and deoxyribonucleic acid as well as nucleoside and nucleotide analogs, modified nucleotides such as labeled nucleotides, and non-naturally occurring analogue structures.
Regarding the limitation “wherein sample index positions are interspersed among molecular index positions,” under the broadest reasonable interpretation, this encompasses embodiments wherein the sample index positions and the molecular index positions can overlap by a single nucleotide.
Therefore, under the broadest reasonable interpretation, the barcode comprises any stretch of contiguous bases wherein at least one nucleotide designated as a molecular index position is different from a nucleotide designated as a sample index position. The different nucleotide can be any type of nucleotide, including any labeled nucleotide, modified nucleotide, or nucleotide analog. Claim 13 recites the same limitations as claim 1; therefore, the interpretation described above applies to claim 13.
Additionally, the specification appears to indicate that the location of the sample index positions within the barcode is what creates the sample barcode (e.g. Fig. 1). However, claim 1 only requires that the location of sample index positions varies between samples. Under the broadest reasonable interpretation, this encompasses embodiments wherein the location of the sample index positions are different but does not provide information regarding the identity of the sample.
The system of claim 1 and the set of claim 13 require a single sample, and states that the location of sample index positions varies between samples. The claims do not require multiple samples. Therefore, in the system of claim 1 and the set of claim 13, every sample barcode can be in the same location for a given sample.
Regarding claims 9 and 21, under the broadest reasonable interpretation, any given sample index position and any given molecular index position nucleotide can be selected from the list. The claims do not require that every sample index position nucleotide must be the same, and the claims do not require that every molecular index position nucleotide must be the same. The claims encompass the embodiment wherein each sample index position nucleotide can be chosen independently from the other sample index position nucleotides.
Claim Rejections - 35 USC § 112
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 1-24 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.
Regarding claim 1 and 13, it is unclear what the scope of the claim is.
Claim 1 and claim 13 recite “a pre-determined number of sample index positions comprising one or more specific nucleotides.” It is unclear whether every sample index position of a sample barcode has the same type of nucleotide, or whether every sample index position of a sample barcode can comprise a different nucleotide which is specifically chosen (e.g. so that the all sample index positions correspond to a given sequence). Similarly, it is unclear whether every molecular index position comprises the same nucleotide as the other molecular index positions, or whether the nucleotides used can vary in relation to a particular sample index position.
Claim 1 and claim 13 do not place any limitations of the identities of the nucleotides beyond the molecular index positions comprising a nucleotide that differs from the nucleotides at sample index positions. The claims therefore encompass any possible sequence comprising any possible nucleotides, and encompass any form of a barcode so long as it provides information about the identity of the nucleic acid. The claims do not describe what information in the sample barcode is used to provide information about the sample or what information in the molecular barcode is used to provide information about the molecule.
Claim 5 and 17 recites the limitation “wherein the sample barcode comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 sample index positions, or a combination thereof. It is unclear how the sample barcode can comprise a combination of a number of sample index positions. It is unclear whether a combination of the numbers refers to the sum of two or more sample index positions (e.g. a combination of 2 and 20 results in 22 sample index positions), or whether the combination refers to a different limitation.
Claim 9 and 21 allows for each individual sample index nucleotide to be chosen independently. It is unclear how each individual sample index nucleotide correlates to each molecular index position. It is unclear if these are specific sets of nucleotides (e.g. there is one molecular index position for each sample index position), or if there are specific correlations between the sample index positions and the molecular index positions (e.g. if the sample index position in location 1 is the nucleotide “A”, then the molecular index positions in locations 2-4 are C, G, and/or T), or if there is some other method of choosing which sample index position corresponds to which molecular index position.
If each sample index position nucleotide is chosen independently of the others, which then according to claim 9 and claim 21 dictates what the molecular index position nucleotide can be, it is not clear whether this fulfills the limitation of claims 1 and 13 that the molecular barcode comprises molecular index positions comprising a nucleotide that differs from the nucleotides at sample index positions.
For example, if a single nucleotide at a given sample index position is “A,” and a single nucleotide at a given molecular index position is “T,” and the remainder molecular index position nucleotides are chosen randomly without regard to the sample index position nucleotides, it is unclear whether this fulfills the limitation that the molecular index positions comprise a nucleotide that differs from the nucleotides at sample index positions.
The example described in par. 0126 and Fig. 1 shows that all of the sample index positions are comprised of the same type of nucleotide (e.g. “A”), while the molecular index positions are comprised of any other type of nucleotide excluding “A” (e.g. C, G, and/or T). Furthermore, par. 0120 and 0150 indicates that the molecular barcodes can be random, and thus the specification does not require that the molecular barcode nucleotides must be specifically chosen. However, the claims encompass any and all combinations of nucleotides.
In view of claims 9 and 21, it is unclear what the full scope of the independent claims is. It is unclear whether every sample index position nucleotide is chosen independently of each other, and if so, how the molecular index position nucleotides are chosen in relation to the sample index position nucleotides, or whether every sample index position nucleotide is the same type or types of nucleotides and every molecular index position nucleotide is excluded from being that type. The specification provides examples indicating that every sample index position is identified by the same type or types of nucleotide, and the molecular index position nucleotides can be any type of nucleotide beyond the ones chosen for the sample index position nucleotides, but does not provide a definition which would require this and is not described in the claims.
Finally, it is unclear from the claims whether the barcode comprising a sample barcode and molecular barcode are referring to barcodes as the commonly-known in the art barcodes where a given sequence provides information about the sample and molecule, whether the sample barcode and the molecular barcode are referring to a particular spatial arrangement which creates a pattern corresponding to a particular barcode where the nucleotides are merely used as a label for type of barcode it corresponds to (e.g. all “A” correspond to a sample barcode and all “T” correspond to a molecular barcode in a given region), or whether these barcodes are a combination of both sequence-based and location-based labeling.
Regarding claim 10 and 22, it is unclear what is meant by “additional index barcodes comprising index positions.” It is not clear how an index barcode can comprise a position, or whether the index positions are required to be comprised of an additional nucleotide or nucleotide sequence.
Additionally, it is unclear whether these index positions or index position nucleotides are chosen in a similar manner to the molecular index position nucleotides (e.g. so that each of the sample index position nucleotides, molecular index position nucleotides, and additional index position nucleotides are comprised of unique and/or distinct types of nucleotides), or if the index position nucleotides are chosen independently of the sample index position nucleotides and the molecular index position nucleotides.
Regarding claim 12 and 24, it is unclear what is meant by “non-barcode positions comprising sites for hybridization, sites for sequence primer binding, sites for amplification, or any combination thereof.” It is unclear whether this is stating that the oligonucleotide can comprise additional regions outside of the barcode comprising sample index and molecular index positions, or whether the barcode positions and non-barcode positions are interspersed.
Claim Rejections - 35 USC § 102
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 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.
Claim(s) 1-8, 9-20, and 22-24 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tori et al. (WO 2018/089550 A1; cited on the IDS filed on 07/08/2025).
Regarding claims 1 and 13, Tori teaches a BUMI (Barcode and UMI) tag which is made up a series of interspersed barcode (sample index position) and unique molecular identifiers (molecular index position) bases (pg. 38, lines 3-16).
Regarding claims 2 and 14, Tori teaches that the number of barcode bases in a BUMI tag may vary, and the pattern and ratio of barcode and UMI bases can also be varied (pg. 38, lines 17-31).
Regarding claims 3-4 and 15-16, Tori teaches that the length of a given BUMI tag may vary, ranging in some instances from 5 to 25 nts, wherein specific lengths of interest include 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, and 16 nts (pg. 38, lines 13-16).
Regarding claims 5-8 and 17-20, Tori teaches that the number of barcode bases may vary, ranging in some instances from 1 to 20 nts, and the number of UMI bases may vary, ranging in some instances from 1 to 20 nts and provides an example of a minimum 10 base BUMI tag comprising at least 4 barcode bases and 6 UMI bases (pg. 38, lines 16-31).
Regarding claims 10-11 and claim 22-23, Tori the inclusion of barcode sequences such as a source barcode sequence or a cell barcode sequence (pg. 32, lines 3-22; pg. 80, clauses 16-22).
Regarding claims 12 and 24, Tori teaches additional sites such as hybridization domains and primer binding domains (pg. 5, lines 28-31; pg. 6, lines 1-4; pg. 59, lines 2-7).
Claim(s) 1, 9, 13, and 21 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wiley (US 2015/0072344 A1; cited on the IDS filed 07/08/2025).
Regarding claim 1 and 13, Wiley teaches a BUMI (Barcode and UMI) tag which is comprised of a series of interspersed barcode (sample index position) and unique molecular identifiers (molecular index position) bases (Abstract; par. 0009).
Regarding claims 9 and 21, Wiley provides an example of a barcode with the sequence GTCCAT (Fig. 1; Table 1). As the UMI can be any of these nucleotides, it would necessarily result in one of the barcode (sample index position) nucleotides differing from one of the UMI (molecular index position) nucleotides.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Randi L Beil whose telephone number is (571)272-1147. The examiner can normally be reached M-F 8:00 am - 5:00 pm.
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/R.L.B./Examiner, Art Unit 1684
/AARON A PRIEST/Primary Examiner, Art Unit 1681