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 Objections
Claim 14 is objected to for being dependent on claim 10 which has been cancelled. Examiner has assumed that claim 14 is dependent on claim 11 as both recite a “gene sequencer.”
Claim 15 is objected to for being dependent on claim 13. Claim 15 recites a “gene sequencer” however this is not present in claim 13. Examiner has assumed that claim 15 is dependent on claim 14 rather than claim 13.
Claim 16 is objected to for being dependent on claim 13. Claim 16 recites a “gene sequencer” however this is not present in claim 13. Examiner has assumed that claim 16 is dependent on claim 14 rather than claim 13.
Claim 17 is objected to for being dependent on claim 14. Claim 17 recites a “preset value” however this is not present in claim 14. Examiner has assumed that claim 17 is dependent on claim 15 rather than claim 14.
Claim 18 is objected to for being dependent on claim 11. Claim 18 recites a “computer-readable storage medium” however this is not present in claim 11. Examiner has assumed that claim 18 is dependent on claim 12 rather than claim 11.
Claim 19 is objected to for being dependent on claim 17. Claim 19 recites a “computer-readable storage medium” however this is not present in claim 17. Examiner has assumed that claim 19 is dependent on claim 18 rather than claim 17.
Claim 20 is objected to for being dependent on claim 17. Claim 20 recites a “computer-readable storage medium” however this is not present in claim 17. Examiner has assumed that claim 20 is dependent on claim 18 rather than claim 17.
Claim 21 is objected to for being dependent on claim 18. Claim 21 recites a “preset value” however this is not present in claim 18. Examiner has assumed that claim 21 is dependent on claim 19 rather than claim 18.
Claim 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:
A person shall be entitled to a patent unless –
(a)(2) 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, 9, 11, and 12 are rejected under U.S.C. 102 (a)(2) as being anticipated in view of US20200302297 (hereinafter referred to as Jaganathan)
Regarding claim 1, Jaganathan teaches a base calling method with one embodiment being referred to as a neural-network based base caller, comprising the following steps: acquiring a first image of a biochip in a red light channel and a second image of the biochip in a green light channel [See paragraph 0214 of Jaganathan which discloses that a red and green channel is used for base calling. See additionally 0692 and 0693 which states that analyte arrays (also called microarrays or biochips) are used in the disclosed, method and system];
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performing base grouping according to the first image and the second image, and preliminarily identifying the base type of each group [See Fig 1 where in the deep learning embodiment clusters are primarily identified after image data is received and 0349 where clusters create an intensity pattern that can be associated with a base, See also 0215 where the intensity of the bases are determined from the green and red image];
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adjusting the brightness value of the first image and the brightness value of the second image according to the base types of all the groups [see paragraph 0332 where the intensity of the image is adjusted based on base types];
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performing normalization processing on the first image according to a maximum brightness value and a minimum brightness value of the first image, and performing normalization processing on the second image according to a maximum brightness value and a minimum brightness value of the second image [see paragraph 0586 where the data is normalized so that the 5% of pixels have an intensity values less than zero, and 5% have an intensity value greater than one];
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performing base grouping according to the normalized first image and the normalized second image, and identifying the base type [see 0349 above where the intensity pattern is used to identify a base, see also 0215 where the preprocessing (indicating that this step occurs before the final base calling step) includes the data normalizer].
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Claim 11 and 12 are similarly analyzed to claim 1.
Regarding claim 9, Jaganathan teaches the base calling method according to claim 1, wherein following the step of performing base grouping according to the normalized first image and the normalized second image, and identifying the base type of each group again [see fig 1 above where the bases are grouped again after processing through the neural network] and performing clustering analysis on each group according to the re-identified base type of each group to obtain the final base type of each group [See paragraph 0203 where the neural network based base caller to performs a final base call using clustering analysis].
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Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim 2, 4, 14, 16, 18, and 20 are rejected under U.S.C. 103 as being obvious over Jaganathan in view of Illumina system overview documentation (hereinafter referred to as reference 1) in further view of US20220051407 (hereinafter refer to as Garcia).
Regarding claim 2, Jaganthan teaches a method of base calling using the red and green light intensity data and using graphed cluster centers to determine a base type [See 0203 above], but does not explicitly state calculating a two dimensional histogram, with the axes corresponding to brightness, or determining the radius and angle according to the central position, and identifying the base type accordingly.
Reference 1 teaches calculating a two-dimensional histogram according to the first image and the second image [see fig 23 page 79 of reference 1 where a graph is created according to the red and green image].
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wherein the axes of the two-dimensional histogram respectively correspond to the brightness value of the first image and the brightness value of the second image [see above fig 23 where the x axis is red color image intensity and the y axis is the green color image intensity]; determining independent regions in the two-dimensional histogram to obtain the base grouping result, wherein each independent region corresponds to a certain group [See figure 23 above where the clusters of data points are sorted in to groups of the base pairs, A G T and C, clustered around a central location];
Reference 1 does not teach using the radius and angle to identify the base type. Garcia does teach determining the radius and angle of each group [See paragraph 0175 where the histogram uses the radius and angle to visualize the data in a histogram];
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preliminarily identifying the base type of each group according to its radius and angle [See 0175 above where the radius and angle are used as the steps to perform base calling].
Therefore, it would have been obvious to one with ordinary skill in the art before the effective filing date to combine the base calling method of Jaganathan with the data visualization step of reference 1 to visualize the "intensities for each cluster are extracted from the red and green images and compared against each other, which results in four distinct populations. Each population corresponds to a base" (see page 79 of Reference 1). This combination allows for the base calling method to be more accurately map the different intensities associated with each base. Additionally, Garcia uses the radius and the angle to obtain cross talk coefficients (0175 above) which prevents misidentification of signals to improve accuracy.
Claim 14 and 18 are similarly analyzed to claim 2.
Regarding claim 4, Jaganathan, Garcia, and Reference 1 teach the method of claim 2, wherein the step of performing base grouping according to the normalized first image and the normalized second image, and identifying the base type of each group again specifically comprises: determining whether a first base is comprised among the base types of all the groups [see figure 23 from reference 1 above where individual bases types could be determined the group of bases]; wherein the radius of the group corresponding to the first base is less than a preset value [see 0053 of Garcia where the radius in the clustering operation is set to a preset value of 0.5 for a pre-selected signal (corresponding to a single base type). And 0148 where only the signals in the cluster are processed];
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if yes, calculating the radius of each point in the two-dimensional histogram, and determining the point with a radius less than the preset value as belonging to the group corresponding to the first base [See 0055 of Garcia where spots inside a certain radius are assigned to a base (as indicated by spots being disregarded if already previously assigned in a first radius is step i)];
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identifying the base types of the other groups; if no, directly identifying the base types of the other groups [see paragraph 0055 of Garcia step b where there is a preliminary base call for each spot].
Claim 16 and 20 are similarly analyzed to claim 4.
Allowable Subject Matter
Claims 3, 5-8, 13, 15, 17, 19, and 21 are objected to as being dependent upon a rejected base claim, but would be allowable if the dependencies are fixed, and the claims are rewritten in independent form including all the limitations of the base claim and any intervening claims.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ANUSHA KASHYAPA whose telephone number is (571)272-8766. The examiner can normally be reached Monday-Friday 8am-5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Chan Park can be reached at (571) 272-7409. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ANUSHA KASHYAPA/Examiner, Art Unit 2669 /CHAN S PARK/Supervisory Patent Examiner, Art Unit 2669
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