PATENT CLAIM ANALYSIS

Application Number: 16389680
Application Type: Utility
Filing Date: 2019-04
Publication Date: 2019-10
Patent Classification: ["506", "002000"]

Abstract:
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Claim (Index 56):
A method for detecting somatic genetic variants in cell-free deoxyribonucleic acid (cfDNA) molecules from a blood sample for cancer testing in a human subject, the method comprising:\n (a) contacting between 1 nanogram (ng) to 100 ng of cfDNA molecules derived from the blood sample with at least an 80\u00d7 molar excess of adapters relative to the plurality of cfDNA molecules to attach at least 20% of the cfDNA molecules to a respective pair of adapters from among the adapters, said adapters comprising a set of molecular barcodes comprising from 5 to 100 different molecular barcodes having respective molecular barcode sequences,\n wherein the respective pair of adapters comprises a first adapter having a molecular barcode sequence from among the set of molecular barcodes that is attached to a first end of a cfDNA molecule from among the cfDNA molecules and a second adapter having a molecular barcode sequence from among the set of molecular barcodes that is attached to a second end of the cfDNA molecule, \n wherein at least some of the tagged parent polynucleotides have an identical pair of molecular barcode sequences with respect to one another, and \n wherein the molecular barcode sequences are from 5-20 base pairs in length; \n (b) amplifying a plurality of the tagged parent polynucleotides to produce progeny polynucleotides; (c) selectively enriching the progeny polynucleotides for target regions associated with cancer to produce enriched progeny polynucleotides; (d) sequencing at least a subset of the enriched progeny polynucleotides to produce sequencing reads; (e) aligning mappable portions of a plurality of the sequencing reads to one or more reference sequences to produce mapped sequence reads; (f) grouping a plurality of the mapped sequence reads into families based on sequence information of the molecular barcode sequences and the beginning and end regions of the mappable portions of the mapped sequence reads; and (g) detecting, from among the families, the presence or absence of one or more somatic genetic variants comprising a single nucleotide variation (SNV), an insertion or deletion (indel), a copy number variation (CNV), or a gene fusion.

Metadata:
- Claim Count in Document: 89.0
- Percentile: 100.0
- Lexical Diversity: 1.84286
- Patent Class: 506.0
- Transitional Phrase Type: open
- Component Type: 1
- Foreign Priority: False
- Related Applications: ['16283635', '16277712', '16283629', '15076565', '15492659']

Analysis Scores:
- 35 USC 101 Eligibility (BERT): 0.6714684690152147
- 35 USC 102 Novelty (BERT): 0.6260617670005109
- Combined Prediction Score: 0.6669277988137443
- Mean Citation Score: 619.082214
- Max Citation Score: 646.71344
- Similarity Product: 549.9138229506111

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

Dataset: test