Methods and systems for genetic analysis
Inventors
West, John • Haudenschild, Christian • Chen, Richard
Assignees
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Publication Number
US-12258628-B2
Publication Date
2025-03-25
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 relates to personalized genetic testing in which a first assay is performed on nucleic acid molecules extracted from at least one biological sample from a subject to produce first nucleic acid sequence data. The biological sample comprises a tumor sample, and the first assay comprises whole genome sequencing using sequencing by synthesis. The sequence data are aligned to a reference genome to extract a set of genetic characteristics, which are aggregated to generate a signature of the subject.
A personalized probe set is obtained for the subject, where the personalized probe set comprises the signature generated from the aggregating step or complements thereof. The personalized probe set is used in a second assay performed on nucleic acid molecules extracted from one or more plasma samples from the subject. The second assay uses a microarray containing the personalized probe set to obtain second nucleic acid sequence data.
Biomedical information of the subject is output based on an analysis comparing results from the first assay with results from the second assay. The described genetic characteristics include variant and typing types derived from the first assay, and the microarray-based second assay is used to detect genetic information in plasma samples for downstream biomedical reporting.
Claims Coverage
The document includes one independent claim. Across that independent claim, the approach combines four core inventive features: a first whole genome sequencing by synthesis assay on tumor-derived nucleic acids, alignment-based extraction and aggregation into a subject signature, generation of a personalized probe set incorporating the signature or complements thereof, and microarray-based second assay on plasma samples followed by comparative analysis outputting biomedical information.
Two-stage personalized genetic testing with first sequencing and second microarray assay
A method for personalized genetic testing comprising performing a first assay on nucleic acid molecules extracted from at least one biological sample from a subject to produce a first set of nucleic acid sequence data, extracting genetic characteristics from the first set of nucleic acid sequence data by aligning to a reference genome, aggregating the genetic characteristics to generate a signature of the subject, obtaining a personalized probe set that comprises the signature or complements thereof, performing a second assay on nucleic acid molecules extracted from one or more plasma samples using a microarray to obtain a second set of nucleic acid sequence data, wherein the microarray comprises the personalized probe set, and outputting biomedical information based on an analysis comparing results from the first assay with results from the second assay.
First assay as whole genome sequencing by synthesis on tumor sample
The method of personalized genetic testing where the at least one biological sample comprises a tumor sample from the subject and the first assay comprises whole genome sequencing, wherein the whole genome sequencing comprises sequencing by synthesis.
Signature-driven personalized probe set
The method wherein a set of one or more genetic characteristics is extracted by aligning the first set of nucleic acid sequence data to a reference genome, the genetic characteristics are aggregated to generate a signature of the subject, and a personalized probe set is obtained for the subject such that the personalized probe set comprises the signature of aggregating step (c) or complements thereof.
Plasma microarray second assay using the personalized probe set
The method wherein a second assay is performed on nucleic acid molecules extracted from one or more plasma samples from the subject using a microarray to obtain a second set of nucleic acid sequence data, wherein the microarray comprises the personalized probe set.
Overall, the claim coverage centers on a sequencing-by-synthesis tumor assay that is aligned to a reference genome to extract genetic characteristics and aggregate them into a subject signature, which is then used to define a personalized microarray probe set for plasma-sample testing, followed by comparative analysis to output biomedical information.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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