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
1. This Office Action is in response to the application filed on 11/15/2024.
Claims 1-7 are pending.
Priority
2. This application is a Divisional of 17/724,115 (Patent US 12,176,070), which was filed on 04/19/2022, was acknowledged and considered.
Information Disclosure Statement
3. The information disclosure statement (IDS) filed on 04/012025 complies with the provisions of M.P.E.P. 609. The examiner has considered it.
Claim Rejections - 35 USC § 112
4. 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-AlA), 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.
5. Claims 1-7 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AlA), 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-AlA 35 U.S.C. 112, the applicant), regards as the invention.
6. The preamble in independent claim 1 and claim 4 indicate “facilitating rapid genome sequence analysis” and the last paragraph of these claims indicate “generating a merged file from the plurality of files by causing each particular computing nodes of the plurality of computing nodes to write respective data entries from compression blocks within the region of interest of the corresponding file to generate the merged file in parallel”. The Examiner, however, is unsure the merging from multiple files into a single file in parallel increases the processing speed of genome sequence analysis. Further explanation is recommended.
Claims 2-3 and 5-7 are rejected for being dependent on a rejected base claim
Examiner’s Note
7. Preliminary mappings of some pertinent arts:
Rooyen et al, US 9,519,752, [Column 3, lines 48-56 (“sequence fragments, typically from 100-1,000 nucleotides in length, are produced without any indication as to where in the genome they align. Therefore, in order to generate full length chromosomal genomic constructs, these fragments of DNA sequences need to be mapped, aligned, merged, and/or compared to a reference genomic sequence.”)] [Column 16, lines 62-67 through column 17, lines 1-6 (“improved algorithms directed to more efficiently and/or more accurately performing one or more of local realignment, duplicate marking, base quality score recalibration, variant calling, compression, and/or decompression functions are provided”)] [Column 17, lines 7-26 (“a platform of technologies for performing genetic analyses are provided where the platform may include the performance of one or more of: mapping, aligning, sorting, local realignment, duplicate marking, base quality score recalibration, variant calling, compression, and/or decompression functions. In certain instances, the implementation of one or more of these platform functions is for the purpose of performing one or more of determining and/or reconstructing a subject's consensus genomic sequence, comparing a subject's genomic sequence to a referent sequence, e.g., a reference or model genetic sequence, determining the manner in which the subject's genomic DNA differs from a referent, e.g., variant calling, and/or for performing a tertiary analysis on the subject's genomic sequence, such as for genome-wide variation analysis, gene function analysis, protein function analysis, e.g., protein binding analysis, quantitative and/or assembly analysis of genomes and/or transcriptomes, as well as for various diagnostic, and/or a prophylactic and/or therapeutic evaluation analyses”)] [Column 62, lines 16-33 (“it is easily possible for multiple 1's in the registers to merge into common positions, corresponding to multiple of the simultaneous backtraces merging together onto common backtrace paths. Once two or more of the simultaneous backtraces merge together, they remain merged indefinitely, because henceforth they will utilize scoring vector information from the same cell. It has been observed, empirically and for theoretical reasons, that with high probability, all of the simultaneous backtraces merge into a singular backtrace path, in a relatively small number of backtrace steps, which e.g. may be a small multiple, e.g. 8, times the number of scoring cells in the wavefront. For example, with a 64-cell wavefront, with high probability, all backtraces from a given wavefront boundary merge into a single backtrace path within 512 backtrace steps. Alternatively, it is also possible, and not uncommon, for all backtraces to terminate within the number, e.g. 512, of backtrace steps.”)].
McMillen et al, US 20140371109, [Paragraphs 11 and 13 (“Rather, sequence fragments, typically from 100-1,000 nucleotides in length, are produced without any indication as to where in the genome they align. Therefore, in order to generate full length chromosomal genomic constructs, or determine variants with respect to a reference genomic sequence, these fragments of DNA sequences need to be mapped, aligned, merged, and/or compared to a reference genomic sequence”)] [Paragraph 68 (“A typical algorithm useful in performing such a function is a Burrows-Wheeler transform, which is used to map a selection of reads to a reference using a compression formula that compresses repeating sequences of data”)] [Paragraphs 76-77 and 79 (“a platform of technologies for performing genetic analyses are provided where the platform may include the performance of one or more of: mapping, aligning, sorting, local realignment, duplicate marking, base quality score recalibration, variant calling, compression, and/or decompression functions. In certain instances, the implementation of one or more of these platform functions is for the purpose of performing one or more of determining and/or reconstructing a subject's consensus genomic sequence, comparing a subject's genomic sequence to a referent sequence, e.g., a reference or model genetic sequence, determining the manner in which the subject's genomic DNA differs from the reference sequence”)] [Paragraph 119 (“For instance, a tree-like data structure serving as an index of the reference genome may be queried by tracing a path through the tree, corresponding to a subsequence of a read being mapped, that is built up by adding nucleotides to the subsequence, using the added nucleotides to select next links to traverse in the tree, and going as deep as necessary until a unique sequence has been generated. This unique sequence may also be termed a seed, and may represent a branch and/or root of the sequence tree data structure. Alternatively, the tree descent may be terminated before the accumulated subsequence is fully unique, so that a seed may map to multiple locations in the reference genome. Particularly, the tree may be built out for every starting position for the reference genome, then the generated reads may be compared against the branches and/or roots of the tree and these sequences may be walked through the tree to find where in the reference genome the read fits. More particularly, the reads of the FASTQ file may be compared to the branches and roots of the reference tree and once matched therewith the location of the reads in the reference genome may be determined. For example, a sample read may be walked along the tree until a position is reached whereby it is determined that the accumulated subsequence is unique enough so as to identify that the read really does align to a particular position in the reference, such as walking through the tree until a leaf node is reached”)] [Paragraphs 224 and 227 (“the horizontal top boundary may be configured to represent the genomic reference sequence, which may be laid out across the top row of the array according to its base pair composition. Likewise, the vertical boundary may be configured to represent the sequenced and mapped query sequences that have been positioned in order, downwards along the first column, such that their nucleotide sequence order is generally matched to the nucleotide sequence of the reference to which they mapped” and “When the end of a boundary or the end of the array has been reached and/or a computation leading to the highest score for all of the processed cells is determined (e.g., the overall highest score identified) then a backtrace may be performed so as to find the pathway that was taken to achieve that highest score”)] [Paragraph 237 (“From a currently completed alignment boundary, e.g., a particular scored wave front position, backtrace is initiated from all cell positions on the boundary. Such backtrace from all boundary cells may be performed sequentially, or advantageously, especially in a hardware implementation, all the backtraces may be performed together. It is not necessary to extract alignment notations, e.g., CIGAR strings, from these multiple backtraces; only to determine what alignment matrix positions they pass through during the backtrace. In an implementation of simultaneous backtrace from a scoring boundary, a number of 1-bit registers may be utilized, corresponding to the number of alignment cells, initialized e.g., all to `1`s, representing whether any of the backtraces pass through a corresponding position.”)] [Paragraph 238 (“it is easily possible for multiple `1`s in the registers to merge into common positions, corresponding to multiple of the simultaneous backtraces merging together onto common backtrace paths. Once two or more of the simultaneous backtraces merge together, they remain merged indefinitely, because henceforth they will utilize scoring vector information from the same cell. It has been observed, empirically and for theoretical reasons, that with high probability, all of the simultaneous backtraces merge into a singular backtrace path, in a relatively small number of backtrace steps, which e.g. may be a small multiple, e.g. 8, times the number of scoring cells in the wavefront. For example, with a 64-cell wavefront, with high probability, all backtraces from a given wavefront boundary merge into a single backtrace path within 512 backtrace steps. Alternatively, it is also possible, and not uncommon, for all backtraces to terminate within the number, e.g. 512, of backtrace steps.”)].
Pertinent Arts
8. Strathmann, US 20030148313, discloses application of parallel genomic analysis, wherein the detailed implementation comprises: (1) Preparing a library comprising a collection of two or more sample-tagged polynucleotide clones; (2) carrying out a nucleic acid sequencing reaction on the library wherein a first sequencing primer binding site or no sequencing primer binding site is used to generate a plurality of tagged reaction products from the sample-tagged clones in the collection; (3) separating the reaction products according to size; (4) collecting fractions of the separated reaction products; (5) amplifying the products collected in step (4) to generate tagged amplicons; (6) hybridizing the tagged amplicons to an array comprising tag complements; and (7) determining a plurality of polynucleotide sequences of the sample-tagged clones by detecting the hybridizations to deconvolute a plurality of sequence ladders for the sample-tagged clones in the collection.
Patzer, US 20040059721, discloses multiple alignment genome sequence matching, wherein the detailed implementation comprises: (a) providing a first storage vector which is able to store a first series of digital sequence elements, (b) providing a means for shifting the contents of said first storage vector one or more elements, (c) providing a second storage vector which is able to store a second series of digital sequence elements, (d) providing a comparison engine which is operatively connected between said first storage vector and said second storage vector which will: (1) provide a plurality of comparison sets, said comparison sets providing a plurality of equivalence operators, (2) provide a means of testing the bit-wise equivalence of an element from said first storage vector to an element from said second storage vector via said equivalence operators, (3) provide the parallel operation of said comparison sets of said equivalence operators so that the equivalence of a plurality of elements in a plurality of possible alignments between said first storage vector and said second storage is tested, (e) providing a plurality of logical AND operators, each of which can take a plurality of inputs, (f) providing a means for moving the outputs of said equivalence operators in said comparison sets to the inputs of said logical AND operators, (g) whereby the output of said logical AND operator is asserted if an exact match between all elements of the particular alignment tested by the associated comparison set occurs or is not asserted if one or more elements of that alignment does not match, (h) providing a means for triggering the first storage vector to shift its elements by a predetermined amount with respect to the second storage vector, (i) providing a means for triggering the first storage vector to accept additional elements from said first series of digital sequence elements, whereby said first series of digital sequence elements represents the sequence to be searched, and whereby said second series of digital sequence elements represents the query sequence to be matched against the first sequence, and whereby the method can be used to look for exact matches of predetermined length between the search and query sequences by testing the equivalence of multiple elements from multiple alignments in parallel to improve speed over a sequential, element-by-element matching.
Selly, US 20090307218, discloses searching a target DNA or RNA genome in parallel, wherein the detailed implementation comprises: encoding the target sequence as superpositions of wavefunctions, encoding the probe as one or more wavefunctions, and comparing the encoded target with the encoded probe. The encoding of the target may involve applying a transform (e.g., discrete Fourier transform) to the target sequence to obtain the wavefunctions used to form the one or more superposition representations.
Gao et al, US 20110008775, discloses high throughput parallel DNA sequencing, wherein the detailed implementation comprises: a) mixing a plurality of nucleic acid templates and beads comprising oligonucleotides attached to the bead capable of binding the nucleic acid templates to the beads in a first reaction solution comprising reagents necessary to amplify the nucleic acid templates to form an amplification mixture; b) forming a first emulsion from the amplification mixture so as to create a plurality of droplets comprising the nucleic acid templates, beads, and first reaction solution, wherein at least one of the droplets comprises a single nucleic acid template and a single bead encapsulated in the first reaction solution, wherein the droplets are contained in the same vessel; c) amplifying the nucleic acid templates in the droplets to form amplified copies of the nucleic acid templates; d) breaking the first emulsion and washing the beads; e) mixing the nucleic acid templates attached to the beads in a second reaction solution comprising four different deoxynucleoside triphosphates, a processive DNA polymerase, and four different labeled DNA synthesis terminating agents which terminate DNA synthesis at a specific nucleotide base; f) forming an second emulsion to create a plurality of droplets comprising the nucleic acid templates, beads, and second reaction solution, wherein at least one of the droplets comprises DNA templates of a single sequence on a single bead encapsulated in the second reaction solution, wherein the droplets are contained in the same vessel and wherein each termination agent terminates DNA synthesis at a different nucleotide base, thereby forming terminated sequences; g) breaking the second emulsion and washing the beads while retaining the terminated sequences on the beads; h) loading the beads into a plurality of capillaries such that at least one of the capillaries contains a single bead; i) dissociating the terminated sequences from the bead; j) separating the terminated sequences according to their size; and k) detecting the terminated sequences by the labeled synthesis terminating reagents whereby at least a part of the nucleotide base sequence of said DNA molecule can be determined.
Jones, US 20030044784, discloses iterative and regenerative DNA sequence, wherein the detailed implementation comprises: a) digesting said double stranded nucleic acid segment with a restriction enzyme to produce a double stranded molecule having a single stranded overhang sequence corresponding to an enzyme cut site; b) providing an adaptor having a cycle identification tag, a restriction enzyme recognition domain, a sequence identification region, and a detectable label; c) hybridizing said adaptor to said double stranded nucleic acid having said single-stranded overhang sequence to form a ligated molecule; d) identifying said nucleotide n by identifying said ligated molecule; e) amplifying said ligated molecule from step (d) with a primer specific for said cycle identification tag of said adaptor; and f) repeating steps (a) through (d) on said amplified molecule from step (e) to yield the identity of said nucleotide n+x, wherein x is less than or equal to the number of nucleotides between a recognition domain for a restriction enzyme and an enzyme cut site.
Raymond et al, US 20140274731, discloses targeted genomic analysis, wherein the detailed implementation comprises: (a) hybridizing a tagged genomic library with a multifunctional capture probe module complex, wherein the multifunctional capture probe module selectively hybridizes to a specific genomic target region in the genomic library, and wherein the tagged genomic library comprises genomic DNA ligated to a multifunctional adaptor molecule comprising one or more nucleic acid tags, wherein the one or more nucleic acid tags identify a genomic DNA clone; (b) isolating the tagged genomic library-multifunctional capture probe module complex from a); (c) performing 3'-5’ exonuclease enzymatic processing on the isolated tagged genomic library-multifunctional capture probe module complex from b) using an enzyme with 3'-5' exonuclease activity to remove the single stranded 3’ ends; (d) performing PCR on the enzymatically processed complex from c) wherein the tail portion of the multifunctional capture probe molecule is copied in order to generate a hybrid nucleic acid molecule, wherein the hybrid nucleic acid molecule comprises the genomic target region capable of hybridizing to the multifunctional capture probe module and the complement of the multifunctional capture probe module tail sequence; and (e) performing targeted genetic analysis on the hybrid nucleic acid molecule from d).
Wong, US 5935793, discloses parallel polynucleotide sequencing using tagged primers, wherein the detailed implementation comprises: (a) providing a plurality of sample polynucleotide fragments, (b) from said sample fragments, forming a mixture of different length sequencing fragments that are complementary to at least two different sample fragments, wherein (1) each sequencing fragment terminates at a predefined end with a known base or bases, and (2) each sequencing fragment contains an identifier tag sequence which identifies the sample fragment to which the sequencing fragment corresponds and optionally, the terminating base-type of the fragment, wherein said forming includes the steps of (1) inserting said sample polynucleotide fragments into a plurality of identical vectors, to form a mixture of sequencing vectors, (2) isolating a plurality of unique-sequence clones from said sequencing vector mixture, (3) hybridizing to each unique-sequence clone, a tagged primer containing (i) an identifier tag sequence, and (ii) a first primer sequence located on the 3'-side of the tag sequence, to form a primer-vector hybrid, where a different identifier tag sequence is used to identify each unique- sequence clone, (4) performing one or more chain extension reactions on each hybrid to form different-length sequencing fragments each terminating with a known base or bases, and (5) combining the different-length sequencing fragments generated from the hybrids, to form said sequencing fragment mixture, (c) separating said sequencing fragments on the basis of fragment length under conditions effective to resolve fragments differing in length by a single base, to produce a plurality of resolved size-separated fragments, (d) collecting the size-separated fragments in separate aliquots, (ce) amplifying the identifier tag sequences in each aliquot to form multiple copies of oligonucleotides complementary to the identifier tag sequences, and optionally, multiple copies of the identifier tag sequences also, (f) contacting each amplified aliquot with an array of immobilized different-sequence tag probes, each tag probe (1) being capable of hybridizing specifically with one of said identifier tag sequences or a tag sequence complement thereof, and (2) having an addressable location in said array, where said contacting is conducted under conditions effective to provide specific hybridization of the identifier tag sequences, or tag sequence complements, with the corresponding immobilized tag probes, to form a hybridization pattern on said array, (g) from the hybridization pattern formed, determining a nucleotide sequence for at least one sample fragment.
9. Any inquiry concerning this communication or earlier communications from the examiner should be directed to [Hung D. Le], whose telephone number is [571-270-1404]. The examiner can normally be communicated on [Monday to Friday: 9:00 A.M. to 5:00 P.M.].
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Apu Mofiz can be reached on [571-272-4080]. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Hung Le
09/11/2025
/HUNG D LE/Primary Examiner, Art Unit 2161