Prior art

The USPTO database search for patent number 10947589 confirms the existence of US10947589B2, titled "Varietal counting of nucleic acids for obtaining genomic copy number information," which was granted on March 16, 2021, and is currently active.

Based on the provided patent text for US10947589B2 and the search results, the following are the most relevant prior art references discussed within the patent itself:

Identified Prior Art for US10947589B2

1. U.S. Pat. No. 7,622,281 (Parameswaran et al.)

• Full Citation: U.S. Pat. No. 7,622,281, "Compositions and methods for nucleic acid quantification" to Parameswaran et al., issued November 24, 2009.
• Publication/Filing Date: The patent indicates it was issued on November 24, 2009. The earliest priority date is October 20, 2005.
• Brief Description: This patent describes methods of labeling nucleic acid molecules with barcodes to identify the source of the molecules, enabling high-throughput sequencing of multiple samples.
• Potential Anticipation (35 U.S.C. § 102): US10947589B2 states that methods like this "do not provide genomic information unaffected by amplification distortion." While it may anticipate the general concept of labeling nucleic acids with barcodes for multiplexing (identifying sample source during sequencing), it does not teach the specific "varietal counting" methodology to overcome amplification distortion for accurate genomic copy number determination as claimed in US10947589B2 (e.g., claims 1, 7, 8, 9, 13, 14, 15, 16).

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

• Full Citation: U.S. Pat. No. 7,537,897, "Molecular counting" to Fan et al., issued May 26, 2009.
• Publication/Filing Date: Issued May 26, 2009. Priority dates include January 23, 2006.
• Brief Description: This patent describes methods for molecular counting by labeling input sample molecules with unique oligonucleotide tags, followed by amplification and counting the number of different tags. The problem of counting molecules is converted into counting tags.
• Potential Anticipation (35 U.S.C. § 102): US10947589B2 explicitly notes that U.S. Pat. No. 7,537,897 describes "molecular counting by labeling molecules of an input sample with unique oligonucleotide tags and subsequently amplifying and counting the number of different tags." This directly addresses the "counting different tags" aspect of US10947589B2's claims. However, US10947589B2 distinguishes itself by stating that U.S. Pat. No. 7,537,897 describes labeling by ligation, which "has been found to be an inefficient reaction." Therefore, this patent potentially anticipates the core concept of counting unique tags to infer molecule numbers (relevant to claims 1, 7, 8, 9, which involve counting "different tags"). The novelty of US10947589B2, in this context, would lie in how the tagging is performed to overcome the inefficiency or other limitations of the prior art methods (e.g., using terminal transferase or nick-ligation as described in various embodiments and claims 13, 14, 17 of US10947589B2).

3. Miner et al. (2004)

• Full Citation: Miner, B. E., Stoger, 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: Published online September 30, 2004.
• Brief Description: This publication 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, thereby capturing genomic template diversity.
• Potential Anticipation (35 U.S.C. § 102): Similar to U.S. Pat. No. 7,537,897, Miner et al. (2004) teaches "molecular barcoding to label template DNA prior to PCR amplification" and "counting only distinctly tagged sequences" to address redundancy and contamination, which are aspects of amplification distortion. US10947589B2 explicitly mentions that Miner et al. describes labeling by ligation, which "has been found to be an inefficient reaction." Thus, this reference also potentially anticipates the fundamental idea of using unique tags and counting them to correct for amplification issues (relevant to claims 1, 7, 8, 9). The distinction for US10947589B2 would be in providing more efficient or robust tagging methods.

4. McCloskey et al. (2007)

• Full Citation: McCloskey, M. L., Stöger, R., Hansen, R. S., & Laird, C. D. (2007). Encoding PCR products with batch-stamps and barcodes. Biochemical Genetics, 45(11-12), 761-767.
• Publication/Filing Date: Published online October 23, 2007.
• Brief Description: This publication describes a method of molecular encoding that uses template-specific primers to barcode template DNA molecules prior to PCR amplification, rather than ligation, to address source uncertainty, contamination, biased amplification, and product redundancy.
• Potential Anticipation (35 U.S.C. § 102): McCloskey et al. (2007) is recognized by US10947589B2 for using template-specific primers for barcoding prior to PCR amplification, avoiding ligation. However, US10947589B2 differentiates itself by noting that such a method "requires that template specific primers be made for each species of template DNA molecule studied." This implies that McCloskey et al. potentially anticipates the concept of non-ligation-based tagging prior to PCR to mitigate amplification bias, but it does not anticipate the use of substantially unique tags that are not template-specific for each individual molecule, which is central to US10947589B2's approach for broad copy number determination without prior knowledge of all target sequences (relevant to claims 1, 7, 8, 9, and the compositions and kits of claims 13-17).

5. Eid et al. (2009)

• Full Citation: Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., ... & Turner, S. (2009). Real-time DNA sequencing from single polymerase molecules. Science, 323(5910), 133-138.
• Publication/Filing Date: Published online November 20, 2008, and in print January 2, 2009.
• Brief Description: This publication describes a single-molecule real-time sequencing method where sequencing data is obtained from a DNA polymerase performing uninterrupted template-directed synthesis using distinguishable fluorescently labeled dNTPs.
• Potential Anticipation (35 U.S.C. § 102): US10947589B2 acknowledges Eid et al. as describing single-molecule sequencing but explicitly states that "these methods do not provide genomic information unaffected by amplification distortion." While it describes sequencing single molecules, it does not involve ex vivo tagging and subsequent PCR amplification followed by counting unique tags to correct for amplification distortion introduced during PCR, which is the core problem solved by US10947589B2. Therefore, it likely anticipates the general sequencing aspect (step d in claims 1, 7, 8, 9) but not the preceding tagging, amplification, and distinct tag counting steps for copy number determination.