DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application is being examined under the pre-AIA first to invent provisions.
Election/Restrictions
2. Applicant’s election without traverse of Group III (including claims 8-9, as well as newly added claims 10-13) in the reply filed on 7/28/2026 is acknowledged.
For the election of species requirement, applicant has elected the following species of chromosomal region: Hs8 (start position 8304215 and end position 8351172, as determined by human genome build 37). However, upon further consideration, the election of species requirement has been withdrawn.
3. Claims 1-13 are pending in the application. Claims 1-7 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 8-13 are currently under examination.
Specification
4. The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see paragraph [0112] of the specification as filed). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
5. The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Claim Rejections - 35 USC § 112
6. 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.
7. Claims 8-13 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 pre-AIA the applicant regards as the invention.
(1). Claim 8 recites “data obtained in step (1)” in line 5 (emphasis provided). However, there is no “step (1)” mentioned in the text prior to the recitation “data obtained in step (1)”. Furthermore, since claim 8 is drawn to a “system” (i.e., a product which is defined by structural features) rather than a method, it is unclear how such a claimed “system” could comprise any method step.
Claims 9-13, each of which depends from claim 8, are also rejected for the same reason(s) as discussed above.
In the interest of compact prosecution and for purposes of current examination, “data obtained in step (1)” as recited in line 5 of claim 8 is being interpreted as “data obtained from the sample analyzer”.
(2). Claim 9, which depends from claim 8, recites “the result of the correlating step” in line 2 (emphasis provided). Since the claimed system is defined by structural features and does not comprise any method step, it is not clear what is meant by the recitation “the correlating step”.
In the interest of compact prosecution and for purposes of current examination, “the result of the correlating step” as recited in line 2 of claim 9 is being interpreted as “the result of the correlating [[step]] from the computer system”.
Claim Rejections - 35 USC § 102
8. The following is a quotation of the appropriate paragraphs of pre-AIA 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) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
(e) the invention was described in (1) an application for patent, published under section 122(b), by another filed in the United States before the invention by the applicant for patent or (2) a patent granted on an application for patent by another filed in the United States before the invention by the applicant for patent, except that an international application filed under the treaty defined in section 351(a) shall have the effects for purposes of this subsection of an application filed in the United States only if the international application designated the United States and was published under Article 21(2) of such treaty in the English language.
9. Claims 8-9, 11 and 13 are rejected under pre-AIA 35 U.S.C. 102(a) and 102(e) as being anticipated by Shih et al. (WO 2009/051842 A2), as evidenced by the product flyer for ABI PRISM 7000 Sequence Detection System (ABI PRISM 7000 Sequence Detection System, Applied Biosystems, 2010).
Regarding claims 8 and 11
Shih et al. teach, throughout the whole document, a system (e.g., ABI PRISM 7000 Sequence Detection System as used in Example I (see page 18, line 16 – page 19, line 2), as well as Example IV (see page 23, lines 25-27: “The same experimental approach used in Example II, including the methods, reagents and primers provided in Example I, will be used to measure DNA copy number and length integrity in cell-free DNA in plasma, serum, effusion, urine and/or sputum samples.”). As evidenced by the product flyer for ABI PRISM 7000 Sequence Detection System, ABI PRISM 7000 Sequence Detection System is a real-time PCR system comprising a PCR machine and a computer system, wherein the computer system automatically receives and analyzes data obtained from the PCR machine.) for analyzing circulating cell-free DNA, comprising: a sample analyzer (e.g., the PCR machine comprised in ABI PRISM 7000 Sequence Detection System) for determining the presence or absence or the amount of a circulating cell-free DNA having a nucleotide sequence of at least 25 nucleotides falling within any chromosomal region (i.e., the PCR machine is capable of determining the presence or absence or the amount of any DNA sequence segment falling within any chromosomal region with properly designed PCR primers. See page 8, lines 9-22; page 11, lines 16-23; paragraph bridging pages 23-24); a computer system (e.g., the computer system comprised in ABI PRISM 7000 Sequence Detection System) for automatically receiving and analyzing data obtained from the sample analyzer (as evidenced by the product flyer for ABI PRISM 7000 Sequence Detection System and as discussed above), and for correlating the presence of, or an increased amount of, said circulating cell-free DNA with a diagnosis of breast cancer (e.g., since the presence of, or an increased amount (or copy number) of, certain circulating cell-free DNA is associated with a diagnosis of cancer such as breast cancer (see Examples I-V), the presence of, or an increased amount (or copy number) of, such circulating cell-free DNA as shown in the computer system (comprised in ABI PRISM 7000 Sequence Detection System) would inherently/naturally correlate with the diagnosis of cancer such as breast cancer.).
Regarding claims 9 and 13
The system according to Shih et al., further comprising a display module (e.g., the computer monitor or display screen of the computer system comprised in ABI PRISM 7000 Sequence Detection System) displaying the result (i.e., diagnosis of cancer such as breast cancer) of the correlating from the computer system (i.e., as discussed above, the presence of, or an increased amount (or copy number) of, the circulating cell-free DNA as shown in the computer system directly translates to (or points to) a diagnosis of cancer such as breast cancer), wherein the display module is a display screen (see the product flyer for ABI PRISM 7000 Sequence Detection System).
10. Claims 8-10 and 13 are rejected under pre-AIA 35 U.S.C. 102(b) as being anticipated by Beck et al. (Clin. Chem. 2009, 55(4):730-738, published online 1/30/2009), as evidenced by the Operator’s Manual for GS FLX genome sequencer system (Genome Sequencer FLX Operator’s Manual, Roche Diagnostics, October 2008).
Regarding claims 8 and 10
Beck et al. teach, throughout the whole document, a system (e.g., GS FLX genome sequencer system (see page 731, column 2, paragraph 2). As evidenced by the Operator’s Manual for GS FLX genome sequencer system, GS FLX genome sequencer system comprises a sequencer (i.e., sequencing machine) and a computer system/subsystem (see page 19), wherein the computer system/subsystem automatically receives and analyzes data obtained from the sequencer (see the whole document).) for analyzing circulating cell-free DNA, comprising: a sample analyzer (e.g., the sequencer or sequencing machine comprised in the GS FLX genome sequencer system) for determining the presence or absence or the amount of a circulating cell-free DNA having a nucleotide sequence of at least 25 nucleotides falling within any chromosomal region (i.e., since the GS FLX genome sequencer is designed for whole genome sequencing (see page 731, column 2, paragraph 2), it is capable of determining the presence or absence or the amount of any DNA sequence segment falling within any chromosomal region. Furthermore, each of chromosomal regions as recited in claim 8 would inherently be assayed for its presence or absence via pyrosequencing of the cell-free DNA isolated from serum using the GenomePlex® Single Cell Whole Genome Amplification Kit (Sigma-Aldrich) followed by BLAST analysis to the human reference genome (see page 731, column 2, paragraphs 2-4.).); a computer system (e.g., the computer system/subsystem comprised in the GS FLX genome sequencer system) for automatically receiving and analyzing data obtained from the sample analyzer (as evidenced by the Operator’s Manual for GS FLX genome sequencer system and as discussed above), and for correlating the presence of, or an increased amount of, said circulating cell-free DNA with a diagnosis of breast cancer (e.g., since the presence of, or an increased amount of, certain circulating cell-free DNA is associated with a diagnosis of cancer (which would include breast cancer) or other disease (see page 730, column 2, last full paragraph; page 737, column 2, paragraph 1), the presence of, or an increased amount of, such circulating cell-free DNA as shown in the computer system (comprised in the GS FLX genome sequencer system) would inherently/naturally correlate with the diagnosis of such cancer or other disease.)
Regarding claims 9 and 13
The system according to Beck et al., further comprising a display module (e.g., LCD monitor. See page 19 of the Operator’s Manual for GS FLX genome sequencer system) displaying the result of the correlating from the computer system (i.e., as discussed above, the presence of, or an increased amount of, the circulating cell-free DNA as shown in the display module directly translates to (or points to) a diagnosis), wherein the display module (e.g., LCD monitor) is a display screen (see page 19 of the Operator’s Manual for GS FLX genome sequencer system).
11. Claims 8-9 and 12-13 are rejected under pre-AIA 35 U.S.C. 102(b) as being anticipated by Kang et al. (US 2007/0048742 A1).
Regarding claims 8 and 12
Kang et al. teach, throughout the whole document, a method of diagnosing a disease or cancer caused by chromosome abnormality (see Abstract; paragraphs [0002] and [0143]), comprising: preparing a genomic DNA microarray/chip, wherein the genomic DNA microarray/chip can include genomic DNA fragments which are corresponding to the whole genome of the organism to be detected for chromosome abnormality (see paragraphs [0007], [0031]-[0038], [0079] and [0176]); determining, in a blood sample (see paragraph [0155] and claim 37) from a patient, the presence or absence or the amount of a circulating cell-free DNA of at least 25 nucleotides falling within any target chromosomal region(s) (see paragraphs [0038], [0040]-[0063] and [0146]-[0172]); and correlating the presence of, or an increased amount of, said circulating cell-free DNA with a diagnosis of the disease or cancer caused by chromosome abnormality (see paragraphs [0013], [0059]-[0063], [0079] and [0167]-[0177]).
Along with the method, Kang et al. also teach a system (e.g., a “microarray chip analyzer” system (see paragraph [0284]) comprising a “microarray chip analyzer” and a “PC” [i.e., personal computer] (see paragraphs [0287]-[0293])), that is used in the method, for analyzing circulating cell-free DNA, comprising: a sample analyzer (e.g., the “microarray chip analyzer” which is a microarray instrument) for determining the presence or absence or the amount of a circulating cell-free DNA having a nucleotide sequence of at least 25 nucleotides falling within any chromosomal region (i.e., the “microarray chip analyzer” can be used to analyze any DNA microarray. Furthermore, the DNA microarray/chip used in the method of Kang et al. can include genomic DNA fragments which are corresponding to the whole genome of the organism to be detected for chromosome abnormality (see paragraphs [0007], [0031]-[0038], [0079] and [0176]), thus it is capable of determining the presence or absence or the amount of any DNA sequence segment falling within any chromosomal region. In addition, Kang et al. specifically teach the chromosomal region as set forth in line 26 of Table 2 (i.e., Hs19 with start position at 4176228 and end position at 4211314) of the instant application (see Table 2 at page 20, chromosomal region No. 1169, which encompasses the chromosomal region as set forth in line 26 of Table 2 of the instant application) and the chromosomal region as set forth in line 12 of Table 6 (i.e., Hs6 with start position at 170477988 and end position at 170480867) of the instant application (see Table 2 at page 11, chromosomal region No. 520, which encompasses the chromosomal region as set forth in line 12 of Table 6 of the instant application).); a computer system (e.g., the “PC” [i.e., personal computer] comprised in the “microarray chip analyzer” system) for automatically receiving and analyzing data obtained from the sample analyzer (see paragraphs [0287]-[0298]), and for correlating the presence of, or an increased amount of, said circulating cell-free DNA with a diagnosis of breast cancer (e.g., since the presence of, or an increased amount of, certain circulating cell-free DNA directly correlates to a diagnosis of the disease or cancer (which would include breast cancer) caused by chromosome abnormality (see Abstract; paragraphs [0002] and [0143]), the presence of, or an increased amount of, such circulating cell-free DNA as shown in the computer system would inherently/naturally correlate with the diagnosis of such disease or cancer.).
Regarding claims 9 and 13
The system according to Kang et al., further comprising a display module (e.g., 1280x1024 display system. See paragraph [0293]) displaying the result of the correlating from the computer system (i.e., as discussed above, the presence of, or an increased amount of, the circulating cell-free DNA as shown in the display module directly translates to (or points to) a diagnosis), wherein the display module (e.g., 1280x1024 display system) is a display screen (see paragraph [0293]).
Conclusion
12. No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAIJIANG ZHANG whose telephone number is (571)272-5207. The examiner can normally be reached Monday - Friday, 8:30 am - 5 pm.
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/KAIJIANG ZHANG/Primary Examiner, Art Unit 1684
