Obviousness — US Patent 12234510

Obviousness Analysis of US Patent 12234510 Under 35 U.S.C. § 103

This analysis assesses the obviousness of US patent 12234510, titled "Varietal counting of nucleic acids for obtaining genomic copy number information," under 35 U.S.C. § 103, by considering combinations of prior art references identified within the patent itself and publicly known techniques.

The core of US12234510's independent claims (e.g., Claim 1, the abstract's method) involves obtaining segments of nucleic acid material (genomic DNA or cDNA), tagging these segments with substantially unique tags, amplifying them via PCR, sequencing the products, mapping the sequences to a reference genome or cDNA library, and critically, counting the number of tagged nucleic acid molecules having a different tag that have been assigned to the same location on the genome/library, to obtain copy number information "unaffected by amplification distortion."

The patent's background explicitly identifies "amplification distortion" (non-uniform amplification of template nucleic acid molecules) in Whole Genome Amplification (WGA) methods as a significant problem. The inventive solution presented is the "varietal counting" approach, where each input molecule is uniquely tagged before amplification, and subsequent counting relies on the number of distinct tags observed at a location, rather than the total number of reads, thereby correcting for amplification bias.

Combinations of Prior Art Rendering Claims Obvious

1. Combination of Miner et al. (2004) with standard WGA/PCR and sequencing techniques:

Miner et al. (2004): This reference is cited in the patent and described as a method of "molecular barcoding to label template DNA prior to PCR amplification," which "allows for the identification of contaminant and redundant sequences by counting only distinctly tagged sequences". "Redundant sequences" are a direct result of amplification distortion.
Standard WGA/PCR and Sequencing Techniques: These are widely known molecular biology techniques for amplifying and analyzing genomic material. The patent's background describes WGA as a common method for obtaining genomic copy number information, albeit with the problem of over-sampling and non-uniform amplification. The ability to sequence amplified DNA and map reads to a genome is also standard practice, as acknowledged by the patent, which states that "High throughput sequencers are in effect single molecule sequencers" and "sequencing is also counting".
Motivation to Combine: A person having ordinary skill in the art (POSITA), when confronted with the acknowledged problem of amplification distortion in WGA/PCR methods for obtaining genomic copy number information, would naturally seek solutions to distinguish original molecules from their amplified copies. Miner et al. directly provides such a solution by teaching pre-amplification molecular barcoding and the subsequent counting of distinctly tagged sequences to identify and account for "redundant sequences". The explicit purpose of Miner et al.'s method is to address the very issue of amplification redundancy that US12234510 aims to overcome. Therefore, a POSITA would be strongly motivated to combine Miner et al.'s approach of tagging and distinct tag counting with standard WGA/PCR and sequencing workflows to achieve genomic copy number information unaffected by amplification distortion. This combination directly leads to all steps of Claim 1 of US12234510, including obtaining segments, tagging with unique tags, PCR amplification, sequencing, mapping, and the crucial step of counting distinct tags to correct for amplification bias. The patent itself effectively concedes this point by detailing Miner et al.'s disclosure and acknowledging its utility in identifying redundant sequences.

2. Combination of U.S. Pat. No. 7,537,897 with standard WGA/PCR and sequencing techniques:

U.S. Pat. No. 7,537,897: The patent acknowledges this prior art as describing "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".
Standard WGA/PCR and Sequencing Techniques: As discussed above, these are well-established methods for genomic analysis.
Motivation to Combine: Similar to the motivation for combining with Miner et al., U.S. Pat. No. 7,537,897 explicitly teaches the labeling of input molecules with unique tags, followed by amplification and counting the number of different tags for "molecular counting". This provides a direct and explicit mechanism to differentiate original molecules from amplified copies. A POSITA seeking to accurately determine genomic copy number using WGA/PCR (known to introduce amplification distortion) would find it obvious to apply the teachings of U.S. Pat. No. 7,537,897 (pre-amplification unique tagging and counting distinct tags) to mitigate these known distortions. The result would be a method for obtaining genomic copy number information unaffected by amplification distortion, encompassing all the steps outlined in Claim 1 of US12234510.

Obviousness of Other Claims

mRNA Copy Number Methods (e.g., methods related to mRNA transcripts): Extending a method proven for DNA to cDNA (which is DNA derived from RNA) is a routine adaptation in molecular biology, especially when addressing an analogous problem like amplification distortion in cDNA libraries. The core concept of varietal counting remains the same.
DNA Methylation Information Method: This method adds a separation step for hemi-methylated and unmethylated molecules. However, the techniques for separating methylated DNA (e.g., methylation sensitive restriction enzymes, antibodies, methyl-C binding proteins) are known in the art. Applying the already obvious varietal counting method to these separated fractions would be an obvious way to obtain methylation information corrected for amplification bias.
Compositions of Matter: If the methods for producing the tagged nucleic acid molecules are obvious, then the resulting compositions of matter, which are products of these obvious processes, would also be obvious.
Kits: The kits typically comprise a terminal transferase and substantially unique primers. The patent itself notes that tagging can be achieved through various methods, including terminal transferase, and considers ligation to be "inefficient" while terminal transferase (TTase) is a "robust enzyme from which high efficiency is expected". Terminal transferase is a known enzyme for adding polynucleotide tails. Substantially unique primers incorporating tags are taught by Miner et al. or U.S. Pat. No. 7,537,897. Therefore, combining these known components into a kit for implementing the obvious varietal counting methods would be an obvious commercial embodiment for a POSITA.

Conclusion

The foundational concept of tagging individual input nucleic acid molecules before amplification and then counting the distinct tags to correct for amplification-induced redundancy and obtain accurate quantitative information (i.e., "molecular counting" or identifying "redundant sequences") was already present in the prior art, specifically in Miner et al. (2004) and U.S. Pat. No. 7,537,897. The patent US12234510 applies this known principle to the specific context of obtaining genomic or mRNA copy number information and methylation status, addressing the well-known problem of amplification distortion in WGA and PCR. The various methods of tagging described (e.g., ligation, terminal transferase) are also known techniques in molecular biology. Consequently, a person having ordinary skill in the art would have been motivated to combine these existing teachings and techniques to predictably achieve the claimed benefits, rendering the independent claims of US12234510 obvious under 35 U.S.C. § 103.