Prior art

Most Relevant Prior Art for US Patent 12234510

Based on the patent text and search results, the following prior art references are most relevant to US Patent 12234510. The patent itself explicitly discusses these references in its background, highlighting their relevance to the problem it aims to solve (amplification distortion) and noting their limitations.

1. Miner et al. (2004)

• Full Citation: Miner, B. E., Stöger, R. J., Burden, A. F., Laird, C. D., & Hansen, R. S. (2004). Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR. Nucleic Acids Research, 32(17), e135.
• Publication/Filing Date: September 30, 2004 (publication date).
• Brief Description: This paper describes a method of "molecular barcoding to label template DNA prior to PCR amplification". The method "allows for the identification of contaminant and redundant sequences by counting only distinctly tagged sequences" to accurately capture genomic template diversity. The authors used molecular 'batch-stamps' to label each genomic template with a sample ID and analysis date. This method is useful when template DNA is limited.
• Potential Anticipated Claims (under 35 U.S.C. § 102):
  • Method for obtaining genomic copy number information (Claim 1 from the abstract/summary): Miner et al. explicitly teaches labeling template DNA with individual sequence tags (molecular barcoding) prior to PCR amplification to identify "redundant sequences" and count "distinctly tagged sequences" to capture genomic template diversity. This directly anticipates the core steps of segmenting, tagging with unique tags, PCR amplification, sequencing (to generate tag associated sequence reads), mapping, and counting distinct tags to address redundancy (amplification distortion) for genomic material. The patent acknowledges Miner et al. for allowing "identification of contaminant and redundant sequences by counting only distinctly tagged sequences".
  • Composition of matter derived from genomic material (first and second versions): If the method of producing tagged nucleic acid molecules is anticipated, then the resulting composition itself would also be anticipated.

2. U.S. Pat. No. 7,537,897

• Full Citation: U.S. Patent No. 7,537,897 B2 to Brenner et al., titled "Molecular counting."
• Publication/Filing Date: May 26, 2009 (issue date). The patent claims priority from several earlier U.S. applications, with the earliest being Ser. No. 60/761,578 filed January 23, 2006.
• Brief Description: This patent describes "methods and compositions for counting molecules in a sample, wherein each molecule is labeled with a unique oligonucleotide tag." It focuses on amplifying and identifying these tags rather than the molecules themselves, essentially converting the problem of counting molecules into counting tags. The patent also mentions labeling by sampling, where conjugates are formed between molecules to be counted and oligonucleotide tags from a large repertoire.
• Potential Anticipated Claims (under 35 U.S.C. § 102):
  • Method for obtaining genomic copy number information (Claim 1 from the abstract/summary): U.S. Pat. No. 7,537,897 directly teaches "molecular counting by labeling molecules of an input sample with unique oligonucleotide tags and subsequently amplifying and counting the number of different tags". This anticipates the fundamental approach of tagging and counting distinct tags to obtain quantitative information, which in the context of US12234510, is used to correct for amplification distortion to get copy number. The patent itself identifies this reference as describing methods for molecular counting by labeling molecules with unique tags and counting different tags.
  • Method for obtaining mRNA copy number information (both versions): The principle of molecular counting by tagging and counting distinct tags can be directly applied to cDNA derived from mRNA transcripts.
  • Method for obtaining DNA methylation information: The core principle of unique tagging and counting distinct tags, as described in US'897, could be applied to pre-separated methylated/unmethylated fractions.
  • Composition of matter derived from genomic material (both versions) and mRNA transcripts (both versions): If the methods for producing the tagged nucleic acid molecules are anticipated, the resulting compositions are also anticipated.
  • Kit for determining nucleic acid copy number information: The concept of using unique oligonucleotide tags for molecular counting, as taught by US'897, implies the need for such tags and associated reagents in a kit.

Other Relevant Prior Art Mentioned in US12234510's Background:

While the following are highly relevant and contribute to an obviousness argument, Miner et al. and US'897 are most direct in anticipating the "counting different tags" aspect for addressing redundancy/amplification distortion.

• McCloskey et al. (2007):

  • Full Citation: McCloskey, N., Hunt, J., Beavil, R. L., Jutton, M. R., Grundy, G. J., Girardi, E., ... & Gould, H. J. (2007). Soluble CD23 monomers inhibit and oligomers stimulate IgE synthesis in human B cells. Journal of Biological Chemistry, 282(33), 24083-24091.
  • Publication/Filing Date: August 17, 2007 (publication date).
  • Brief Description: The patent notes that McCloskey et al. describe a method of "molecular encoding which does not use ligation but instead uses template specific primers to barcode template DNA molecules prior to PCR amplification". However, it also points out the limitation that "such a method requires that template specific primers be made for each species of template DNA molecule studied."
  • Potential Anticipated Claims: This reference shows molecular encoding prior to PCR amplification but uses template-specific primers, which differs from the "substantially unique tags" that are not template-specific in US12234510's broadest claims. While not directly anticipating the varietal counting of non-template-specific tags, it is relevant for pre-amplification barcoding.

• Parameswaran et al. (2007) and U.S. Pat. No. 7,622,281:

  • Full Citation: Parameswaran, P., Jalili, R., Tao, L., Shokralla, S., Gharizadeh, B., ... & Scherer, R. J. (2007). A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Research, 35(19), e130. U.S. Pat. No. 7,622,281 appears to be a miscitation in the patent text as no such patent relating to molecular barcoding or sequencing by this number was found in public search results. However, Parameswaran et al. (2007) is a valid and highly relevant reference.
  • Publication/Filing Date: October 11, 2007 (publication date for Parameswaran et al.).
  • Brief Description (for Parameswaran et al.): This work describes a "high-information-content barcoding approach in which each sample is associated with two uniquely designed, 10-nucleotide barcodes." It allows for pooling and sequencing of DNA from independent samples and subsequent bioinformatics segregation of the output, maximizing sequencing space and multiplexing capabilities. The purpose is for identifying the source of nucleic acid molecules and high-throughput sequencing of multiple samples.
  • Potential Anticipated Claims: Parameswaran et al. clearly teaches the use of unique barcodes for sample identification and multiplexing during sequencing. This is highly relevant to the "sample tag" embodiments of US12234510. While its primary stated purpose in the patent's background is not to correct for amplification distortion to obtain copy number information unaffected by it, it introduces the concept of unique sample tags for high-throughput analysis.

It is important to note that the provided patent's "Obviousness" section already thoroughly details how Miner et al. (2004) and U.S. Pat. No. 7,537,897, individually or in combination with standard techniques, would render the claims of US12234510 obvious. This prior art analysis aligns with and reinforces that previous assessment.