The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.

The present invention relates to extraction of a signal for a target nucleic acid sequence from signals for two target nucleic acid sequences in a sample. The present invention can contribute to dramatic improvement in methods for detecting target nucleic acid sequences using different detection temperatures and reference values. The present invention using an amended reference value as well as an initial reference value can lead to increasing the detection accuracy in methods for detecting target nucleic acid sequences using different detection temperatures and reference values.

The present invention relates to extraction of a signal for a target nucleic acid sequence from signals for two target nucleic acid sequences in a sample. The present invention can contribute to dramatic improvement in methods for detecting target nucleic acid sequences using different detection temperatures and reference values. The present invention using an amended reference value as well as an initial reference value can lead to increasing the detection accuracy in methods for detecting target nucleic acid sequences using different detection temperatures and reference values.

In order to induce aging while cutting the costs associated with adding cytokines at different aging stages, in a system for aging induction including a first culture chamber for perfusing, with a culture medium, a subject of aging-induction, the subject of aging-induction being derived from a living organism; a second culture chamber for perfusing, with a culture medium, a secretor that secretes a cytokine; and a control device for aging induction including a detection unit, a memory unit and a control unit, a protocol for aging induction defining a procedure of aging induction is stored, and in the control unit, an aging state of the subject of aging-induction is detected with a detection unit, and based on the protocol for aging induction, a flow rate at which the culture medium containing the cytokine secreted by the secretor is supplied to the subject of aging-induction is controlled according to the aging state of the subject of aging-induction.

In order to induce aging while cutting the costs associated with adding cytokines at different aging stages, in a system for aging induction including a first culture chamber for perfusing, with a culture medium, a subject of aging-induction, the subject of aging-induction being derived from a living organism; a second culture chamber for perfusing, with a culture medium, a secretor that secretes a cytokine; and a control device for aging induction including a detection unit, a memory unit and a control unit, a protocol for aging induction defining a procedure of aging induction is stored, and in the control unit, an aging state of the subject of aging-induction is detected with a detection unit, and based on the protocol for aging induction, a flow rate at which the culture medium containing the cytokine secreted by the secretor is supplied to the subject of aging-induction is controlled according to the aging state of the subject of aging-induction.

An analytics system uses metagenomics to generate predictions indicating performance of biological or physical samples. In an embodiment, a method includes determining sequence data of a soil sample. The method further includes determining a plurality of features of the soil sample using the sequence data. The plurality of features is determined based at least in part on a measure of a first microbe detected in the soil sample and a different measure of a second microbe detected in the soil sample. The method further includes inputting the plurality of features to a model trained using measures of the first microbe and the second microbe detected in a plurality of soil samples. The method further includes generating, by the model using the plurality of features, a prediction of physical attribute of a plant grown in the soil sample.

An analytics system uses metagenomics to generate predictions indicating performance of biological or physical samples. In an embodiment, a method includes determining sequence data of a soil sample. The method further includes determining a plurality of features of the soil sample using the sequence data. The plurality of features is determined based at least in part on a measure of a first microbe detected in the soil sample and a different measure of a second microbe detected in the soil sample. The method further includes inputting the plurality of features to a model trained using measures of the first microbe and the second microbe detected in a plurality of soil samples. The method further includes generating, by the model using the plurality of features, a prediction of physical attribute of a plant grown in the soil sample.

The present disclosure relates to detecting microsatellite indels in cancer patients and those at high risk for cancer, and is useful for early detection of specific types of cancer and early onset of relapse. More particularly, the present disclosure relates to compositions, methods, and kits for classifying and treating neoplasia and tumors with microsatellite instability. The instant classifier identifies preferred therapeutic options, including combination therapies, for MSI tumor or cancer, and is particularly useful for patient stratification so that patients who would be treatable by immunotherapy drugs may be identified at a very low cost.

The present disclosure relates to detecting microsatellite indels in cancer patients and those at high risk for cancer, and is useful for early detection of specific types of cancer and early onset of relapse. More particularly, the present disclosure relates to compositions, methods, and kits for classifying and treating neoplasia and tumors with microsatellite instability. The instant classifier identifies preferred therapeutic options, including combination therapies, for MSI tumor or cancer, and is particularly useful for patient stratification so that patients who would be treatable by immunotherapy drugs may be identified at a very low cost.

The present disclosure is directed to enabling search and extraction of data stored in DNA with optimized data structures and functions. Accordingly, systems and methods are provided herein for performing certain functions on data stored in nucleic acid molecules. The present disclosure covers at least the following areas of interest: (1) data structures to provide efficient access and search of information stored in nucleic acid molecules, (2) accurate and quick reading of information stored in nucleic acid molecules, (3) targeted approaches to accessing subsets of information stored in nucleic acid molecules, (4) a rank function that determines a count of particular bit or symbol value in a set of information stored in nucleic acid molecules, (5) functions including counting, locating, and extracting occurrences of a specific pattern in a message of information stored in nucleic acid molecules, and (6) an if-then-else operation to sort data stored in nucleic acid molecules.