US 12234510

US Patent 12234510B2: Concise Summary

Title: Varietal counting of nucleic acids for obtaining genomic copy number information

Assignee: Cold Spring Harbor Laboratory

Inventors: James Hicks, Nicholas Navin, Jennifer Troge, Zihua Wang, Michael Wigler

Filing Date: 2019-02-07

Issue Date: 2025-02-25

Abstract: A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to polymerase chain reaction (PCR) amplification, generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules assigned to the same location on the genome having a different tag, thereby obtaining genomic copy number information unaffected by amplification distortion.

Independent Claims Overview:

The patent includes several independent claims outlining methods and compositions related to obtaining genomic or mRNA copy number information, as well as kits for doing so.

• Method for obtaining genomic copy number information (Claim 1, also present in Abstract): This claim describes a method to get genomic copy number data without errors from amplification. It involves breaking genomic material into segments, attaching unique tags to these segments (one tag per segment) to create "tagged nucleic acid molecules," amplifying these tagged molecules using PCR, and then sequencing them to get "tag associated sequence reads." Each tagged molecule is then mapped to a specific location on the genome. Finally, the number of distinct tagged nucleic acid molecules (identified by their different tags) at the same genomic location is counted to determine copy number.
• Method for obtaining mRNA copy number information (Claim related to mRNA transcripts, first version): This method focuses on mRNA copy number. It starts by converting mRNA transcripts into cDNA, then optionally segmenting the cDNA. These cDNA (or segments) are tagged with substantially unique tags to form tagged nucleic acid molecules. Similar to the genomic method, these are amplified by PCR, sequenced, mapped to a cDNA library, and finally, the number of different tagged molecules at each location on the cDNA library is counted to get mRNA copy number information.
• Method for obtaining mRNA copy number information (Claim related to mRNA transcripts, second version): This alternative method for mRNA copy number involves generating tagged nucleic acid molecules by subjecting mRNA transcripts to a polymerase reaction with primers binding to the polyA tail to create first-order derivative strands. A polynucleotide tail is then added to these strands, followed by another polymerase reaction using primers that bind to this new tail, generating second-order derivative strands. At least one set of these primers (from the first or second polymerase reaction) must be "substantially unique primers" to generate the tagged nucleic acid molecules. The subsequent steps of PCR amplification, sequencing, mapping to a cDNA library, and counting distinct tags are then performed.
• Method for obtaining DNA methylation information: This method provides DNA methylation information. It begins by obtaining segments of genomic material and adding a polynucleotide tail to their ends to create zero-th order derivative strands. These strands are then subjected to a polymerase reaction with "essentially unique primers" that hybridize to the polynucleotide tail, forming tagged nucleic acid molecules. These tagged molecules are then separated into hemi-methylated and unmethylated groups. Each group is amplified by PCR, sequenced, mapped to the genome, and the number of distinct tagged molecules at each genomic location is counted to obtain DNA methylation information.
• Composition of matter derived from genomic material (first version): This claim describes a composition of tagged nucleic acid molecules derived from genomic material, produced by a specific process. The process involves obtaining genomic segments, adding a polynucleotide tail, then performing two polymerase reactions with intervening polynucleotide tail additions. At least one of the polymerase reactions must use "substantially unique primers" to generate the tagged nucleic acid molecules.
• Composition of matter derived from genomic material (second version): This is another composition claim for tagged nucleic acid molecules from genomic material. The production process involves obtaining genomic segments, adding a polynucleotide tail, then a ligation reaction with primers capable of hybridizing to the polynucleotide tail (ligating a primer to the 5' ends). This is followed by a polymerase reaction using different primers that hybridize to the polynucleotide tail and a polymerase with 3'-5' proofreading activity. Again, at least one of the primer sets (from ligation or polymerase reaction) must comprise "substantially unique primers."
• Composition of matter derived from mRNA transcripts (first version): This claim describes a composition of tagged nucleic acid molecules derived from mRNA transcripts. The process involves obtaining cDNA from mRNA, optionally segmenting it, and then tagging the cDNA or segments with substantially unique tags. Each resulting tagged nucleic acid molecule contains one cDNA (or segment) and a tag.
• Composition of matter derived from mRNA transcripts (second version): This composition claim also relates to tagged nucleic acid molecules derived from mRNA transcripts. The process involves obtaining mRNA transcripts, performing a polymerase reaction with primers hybridizing to the polyA tail to get first-order derivative strands, adding a polynucleotide tail, and then a second polymerase reaction with primers hybridizing to the added tail to generate second-order derivative strands. At least one of the primer sets (from the first or second polymerase reaction) must be "substantially unique primers."
• Kit for determining nucleic acid copy number information: This kit comprises a terminal transferase and a plurality of substantially unique primers. These primers contain substantially unique tags and are designed to hybridize to a polynucleotide tail added by the terminal transferase.

CAFC 2026 Dockets:

No specific results were found for US patent 12234510 in the CAFC 2026 dockets. While Google Patents indicates "Family has litigation" and mentions a "US case filed in Delaware District Court" (1:25-cv-00263) and a "PTAB case IPR2025-01353 filed (Not Instituted - Merits)", these specific references were not within the scope of a direct search for "CAFC 2026 dockets 12234510" for the requested date. Therefore, I do not have authoritative information about CAFC activity for this patent in 2026.