PATENT CLAIM ANALYSIS

Application Number: 16053118
Application Type: Utility
Filing Date: 2018-08
Publication Date: 2019-02
Patent Classification: ["506", "004000"]

Abstract:
The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.

Claim (Index 34):
A method for detecting and measuring carry-over over contamination in a sample, comprising:\n (a) attaching sequence tags to cancer genes in a sample obtained from an individual to form tag-nucleic acid conjugates, wherein at least one of the cancer genes or copies thereof has a different sequence tag attached, and wherein the cancer genes from the sample are characteristic of a cancer of the individual, wherein the attaching comprises:\n (i) combining in a reaction mixture under primer extension conditions a first set of primers with the sample, wherein each primer of the first set comprises sequence complementary to a cancer gene, a 5\u2032-non-complementary end containing a first primer binding site and a sequence tag disposed between the sequence complementary to the cancer gene and the first primer binding site, wherein the sequence complementary to a cancer gene of each primer from the first set anneals to a different cancer gene at a first predetermined location and is extended to form a first extension product; and \n (ii) adding to the reaction mixture under primer extension conditions a second set of primers, wherein each primer of the second set has sequence complementary to a cancer gene, wherein the sequence complementary to the cancer gene anneals to the first extension product at a second predetermined location, and wherein each primer of the second set is extended to form a second extension product, wherein each second extension product comprises a first primer binding site, sequence tag, and cancer gene sequence; \n (b) amplifying the tag-nucleic acid conjugates; (c) sequencing the amplified tag-nucleic acid conjugates to generate sequence reads for each of the amplified tag-nucleic acid conjugates, wherein each of the sequence reads has an error rate, and wherein each of the sequence reads comprises a tag sequence and a cancer gene sequence; (d) comparing the sequence reads for each of the amplified tag-nucleic acid conjugates to separately determined tag sequences from other samples; and (e) determining the presence, absence and/or level of contamination by the identity of one or more tag sequences with any separately determined tag sequences from the other samples.

Metadata:
- Claim Count in Document: 59.0
- Percentile: 96.0
- Lexical Diversity: 1.58696
- Patent Class: 506.0
- Transitional Phrase Type: open
- Component Type: 1
- Foreign Priority: False
- Related Applications: ['14317087', '15611093', '13835093', '13859210', '14329873']

Analysis Scores:
- 35 USC 101 Eligibility (BERT): 0.4666750190532377
- 35 USC 102 Novelty (BERT): 0.5929813999287306
- Combined Prediction Score: 0.479305657140787
- Mean Citation Score: 416.700184
- Max Citation Score: 522.2295
- Similarity Product: 421.2386435696483

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

Dataset: test