Obviousness

Obviousness Analysis under 35 U.S.C. § 103 for US Patent 10947589

This analysis identifies combinations of prior art references that would render the claims of US patent 10947589 obvious to a person having ordinary skill in the art (PHOSITA) at the time of the invention (priority date October 22, 2010). The core problem addressed by US10947589 is obtaining accurate genomic copy number information unaffected by amplification distortion, particularly in the context of high-throughput sequencing of genomic DNA prepared by methods like whole genome amplification (WGA).

The primary independent method claim of US10947589, as outlined in the "Summary of the Invention," describes a process comprising:
a) obtaining segments of genomic material;
b) tagging the segments with substantially unique tags to generate tagged nucleic acid molecules;
c) subjecting the tagged nucleic acid molecules to amplification by polymerase chain reaction (PCR);
d) generating tag associated sequence reads by sequencing the PCR product;
e) assigning each tagged nucleic acid molecule to a location on a genome by mapping the subsequence corresponding to the genomic segment; and
f) counting the number of tagged nucleic acid molecules having a different tag that have been assigned to the same location on the genome, thereby obtaining genomic copy number information unaffected by amplification distortion.

The patent's background explicitly acknowledges the "endemic problem" of "amplification distortion" in WGA methods, leading to "non-uniform amplification of the genome," and highlights a "need for a method that allows for copy number determination free of distortions caused by amplification steps" (Description, Background of the Invention). This establishes a clear motivation for a PHOSITA to seek solutions that overcome amplification bias in genomic analysis.

Combination 1: U.S. Pat. No. 7,537,897 in view of general knowledge in the art

References:

• U.S. Pat. No. 7,537,897 (2009)
• General knowledge of high-throughput sequencing and genomic analysis techniques (e.g., WGA, CGH).

Teachings of U.S. Pat. No. 7,537,897:
U.S. Pat. No. 7,537,897 describes "methods for molecular counting by labeling molecules of an input sample with unique oligonucleotide tags and subsequently amplifying and counting the number of different tags".

Obviousness Rationale:
A PHOSITA, aware of the documented problems of amplification distortion in genomic copy number determination using methods like WGA (as detailed in the background of US10947589), would be motivated to employ existing techniques designed to overcome such distortions. U.S. Pat. No. 7,537,897 directly teaches the core mechanism for this solution:

• Step (b) tagging segments: The patent teaches "labeling molecules of an input sample with unique oligonucleotide tags". An "input sample" would naturally include "segments of the genomic material."
• Step (c) amplification: The patent explicitly includes "subsequently amplifying" the tagged molecules.
• Step (f) counting different tags: The patent teaches "counting the number of different tags". This directly corresponds to the inventive step of counting distinct tags to mitigate amplification distortion.

The remaining steps, (a) obtaining segments of genomic material, (d) generating tag associated sequence reads by sequencing, and (e) assigning tagged molecules to genomic locations by mapping reads, represent routine or well-known techniques in molecular biology and bioinformatics by the priority date. For example, methods for obtaining genomic segments (e.g., restriction endonuclease digestion, mechanical shearing) were standard (Description, Definitions). High-throughput sequencing (step d) and mapping reads to a genome (step e) were common practices in genomics for analyzing amplified DNA. The patent itself notes, "High throughput sequencers are in effect single molecule sequencers... sequencing is also counting" (Description, Definitions).

The application of "molecular counting" (as taught by US 7,537,897) to "genomic copy number information" to achieve results "unaffected by amplification distortion" would be a logical and straightforward extension for a PHOSITA. The inherent purpose of "molecular counting" in the prior art is to quantify the original number of molecules despite subsequent amplification, which directly addresses the problem of amplification distortion identified by US10947589.

Combination 2: Miner et al. (2004) in view of general knowledge in the art

References:

• Miner et al. (2004)
• General knowledge of high-throughput sequencing and genomic analysis techniques.

Teachings of Miner et al. (2004):
Miner et al. describes "a method of molecular barcoding to label template DNA prior to PCR amplification, and report that the method allows for the identification of contaminant and redundant sequences by counting only distinctly tagged sequences".

Obviousness Rationale:
Similar to the rationale for U.S. Pat. No. 7,537,897, a PHOSITA facing the recognized challenge of amplification distortion in genomic copy number analysis would look for methods to discern original molecules from amplification duplicates. Miner et al. provides a clear solution:

• Step (b) tagging segments: Miner et al. teach "molecular barcoding to label template DNA prior to PCR amplification". "Template DNA" would include "segments of the genomic material."
• Step (c) amplification: The method is applied "prior to PCR amplification" and thus implicitly involves subsequent PCR amplification.
• Step (f) counting different tags: Miner et al. explicitly state that the method allows "counting only distinctly tagged sequences" to identify "redundant sequences". A PHOSITA would readily understand that identifying and filtering "redundant sequences" by counting "distinctly tagged sequences" is the direct mechanism to correct for amplification distortion.

Again, steps (a), (d), and (e) are routine and conventional steps in genomic analysis that a PHOSITA would apply. The motivation would be to apply Miner et al.'s method of correcting for redundancy/amplification bias to the specific problem of obtaining accurate genomic copy number, a known and significant challenge in the field at the time.

Conclusion

Both U.S. Pat. No. 7,537,897 and Miner et al. (2004) provide substantial teachings that would render the core method claims of US10947589 obvious. They clearly describe the critical inventive steps of tagging nucleic acid molecules with unique tags before amplification, subjecting them to PCR, and then counting the number of different tags to obtain accurate molecular counts, thereby overcoming amplification distortion. A PHOSITA would have been motivated to apply these known molecular counting techniques to the widely recognized problem of obtaining accurate genomic copy number information, which suffered from amplification bias in prior methods like WGA. While US10947589 criticizes the efficiency of ligation-based tagging in some prior art, the broad claims of US10947589 regarding the act of "tagging" itself do not exclude these methods, and alternative tagging methods (such as those preferred by US10947589, like terminal transferase or nick-ligation) would have been obvious alternatives or improvements to a PHOSITA seeking to implement pre-amplification tagging.