Methods and systems for genetic analysis
Inventors
Bartha, Gabor T. • Chandratillake, Gemma • Chen, Richard • Garcia, Sarah • Lam, Hugo Yu Kor • Luo, Shujun • Pratt, Mark R. • West, John
Assignees
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Publication Number
US-11976326-B2
Publication Date
2024-05-07
Expiration Date
Abstract
This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.
Core Innovation
The invention analyzes nucleic acid sample(s) of a subject by generating at least a first subset and a second subset of nucleic acid molecules from one or more nucleic acid samples. The first subset is selectively enriched with pulldown probes that selectively enrich for an exome, and the second subset is selectively enriched with pulldown probes that selectively enrich for genomic features selected from known disease traits, known drug traits, and known biomedically interpretable variants.
The genomic features in the second subset include a plurality of polymorphisms based on or extracted from one or more databases and observed in a population of one or more samples. Each enriched subset is subjected to a corresponding assay to yield a first result comprising a first nucleic acid sequence and a second result comprising a second nucleic acid sequence.
With the aid of a computer processor, the method combines the first result and the second result to generate an output comprising a consensus sequence from the first nucleic acid sequence and the second nucleic acid sequence. The invention generates one or more biomedical outputs that include biomedical information of the subject indicative of the output of the consensus sequence.
The biomedical outputs suggest, select, designate, recommend, or otherwise determine a course of treatment and/or prevention of a disease or condition, or recommend modifying or continuing one or more therapies. Where the disease or condition comprises a cancer, the course of treatment or the one or more therapies comprises a cancer vaccine.
Claims Coverage
The independent claims define four main inventive features: dual subset generation with selective pulldown enrichment, separate assays to generate nucleic acid sequences, computer-processor combination into a consensus sequence, and biomedical outputs indicating treatment or prevention, including cancer vaccine use.
Dual selective enrichment for exome and disease-linked genomic features
Generating at least a first subset of nucleic acid molecules selectively enriched with pulldown probes that enrich for an exome, and a second subset selectively enriched with pulldown probes that enrich for genomic features selected from known disease traits, known drug traits, and known biomedically interpretable variants, including a plurality of polymorphisms based on or extracted from one or more databases and observed in a population of one or more samples.
Separate assays to yield sequence results for each subset
Subjecting the first subset of nucleic acid molecules to a first assay to yield a first result comprising a first nucleic acid sequence, and subjecting the second subset of nucleic acid molecules to a second assay to yield a second result comprising a second nucleic acid sequence.
Computer-processor combination into a consensus sequence
Combining, with the aid of a computer processor, the first result and the second result to generate an output comprising a consensus sequence from the first nucleic acid sequence and the second nucleic acid sequence.
Biomedical outputs indicating cancer treatment or prevention
Generating one or more biomedical outputs that include biomedical information of the subject indicative of the output of the consensus sequence, where the biomedical information suggests, selects, designates, recommends, or otherwise determines a course of treatment and/or prevention, or recommends modifying or continuing one or more therapies, and the disease or condition comprises a cancer and the course of treatment or the one or more therapies comprises a cancer vaccine.
Overall, the claims cover a two-subset enrichment workflow, separate assays generating two nucleic acid sequences, consensus-sequence generation via a computer processor, and biomedical outputs that support cancer treatment or prevention, including cancer vaccine recommendations.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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