PATENT CLAIM ANALYSIS

Application Number: 16120072
Application Type: Utility
Filing Date: 2018-08
Publication Date: 2018-12
Patent Classification: ["435", "006120"]

Abstract:
Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand. This method uniquely capitalizes on the redundant information stored in double-stranded DNA, thus overcoming technical limitations of prior methods utilizing data from only one of the two strands.

Claim (Index 37):
A method for sequencing nucleic acid molecules from a sample using unique molecular identifiers (UMIs), wherein each unique molecular identifier (UMI) is an oligonucleotide sequence that can be used to identify an individual molecule of a double-stranded DNA fragment in the sample, comprising:\n (a) applying adapters to both ends of double-stranded DNA fragments in the sample to obtain DNA-adapter products, wherein the adapters each comprise a double-stranded hybridized region, a single-stranded 5\u2032 arm, a single-stranded 3\u2032 arm, and an adapter-specific UMI on one strand or each strand of the adapter, the adapter-specific UMI being selected from a plurality of adapter-specific UMIs, and wherein each double-stranded DNA fragment in the sample comprises a fragment-specific UMI on one strand or each strand of the double-stranded DNA fragment; (b) amplifying both strands of the DNA-adapter products to obtain a plurality of amplified nucleic acid products; (c) sequencing the plurality of amplified nucleic acid products, thereby obtaining a plurality of reads each comprising an adapter-specific UMI sequence corresponding to an adapter-specific UMI on an adapter and a fragment-specific sequence corresponding to a fragment-specific UMI on a double-stranded DNA fragment in the sample; (d) identifying a plurality of adapter-specific UMI sequences for the plurality of reads; (e) identifying a plurality of fragment-specific UMI sequences for the plurality of reads; and (f) determining sequences of the double-stranded DNA fragments in the sample using the plurality of reads obtained in (c), the plurality of adapter-specific UMI sequences identified in (d), and the plurality of fragment-specific UMI sequence identified in (e).

Metadata:
- Claim Count in Document: 77.0
- Percentile: 96.0
- Lexical Diversity: 1.51639
- Patent Class: 435.0
- Transitional Phrase Type: open
- Component Type: 1
- Foreign Priority: False
- Related Applications: ['16120019', '16120091', '15660785', '14386800', '15867031']

Analysis Scores:
- 35 USC 101 Eligibility (BERT): 0.6990838182667743
- 35 USC 102 Novelty (BERT): 0.6493703642876728
- Combined Prediction Score: 0.6941124728688641
- Mean Citation Score: 643.059952
- Max Citation Score: 740.9465299999997
- Similarity Product: 573.1918060793648

Labels:
- Claim Label 101: 1
- Claim Label 102: 0
- Claim Label 103: 1
- Claim Label 112: 1
- Combined Label: 0
- Label 101 Adjusted: 1

Dataset: test