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 45):
A method for detecting and measuring carry-over over contamination in a sample, comprising:\n (a) attaching sequence tags to recombined nucleic acids from B-cells and/or T-cells in a sample obtained from an individual to form tag-nucleic acid conjugates, wherein at least one of the recombined nucleic acids from B-cells and/or T-cells or copies thereof has a different sequence tag attached, wherein the attaching comprises:\n (i) combining in a reaction mixture under primer extension conditions a first set of primers with a sample of recombined nucleic acids from B-cells and/or T-cells and/or cell-free DNA, wherein each primer of the first set comprises a receptor-specific portion, a 5\u2032-non-complementary end containing a first primer binding site and a sequence tag disposed between the receptor-specific portion and the first primer binding site, wherein the receptor-specific portion anneals to a different recombined nucleic acid 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 a receptor-specific portion, wherein the receptor-specific portion 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, a sequence tag, and recombined nucleic acid encoding a portion of a T cell receptor chain or a B cell receptor chain; \n (b) amplifying the tag-nucleic acid conjugates; (c) sequencing a sample of the tag-nucleic acid conjugates to provide sequence reads each comprising a tag sequence and a recombined nucleic acid 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): 0.4661866033505102
- 35 USC 102 Novelty (BERT): 0.5941398131464588
- Combined Prediction Score: 0.4789819243301051
- Mean Citation Score: 416.700184
- Max Citation Score: 522.2295
- Similarity Product: 426.606796135068

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