Provided herein are methods, compositions, and kits for the detection of immune cell clonotypes and immune cell analytes within a biological sample.

Provided herein are compounds, methods, and compositions for use in determining the cellular origin of circulating cell-free DNA.

Provided herein are compounds, methods, and compositions for use in determining the cellular origin of circulating cell-free DNA.

Methods for human identification using polymorphisms in the Penta E short tandem repeat locus are significant in preventing allelic drop out. An exemplary method encompasses (a) contacting a first primer to a nucleic acid sample to be analyzed, (b) contacting a second primer to the nucleic acid sample, and (c) subjecting the nucleic acid sample, the first primer, and the second primer to an amplification reaction, and thereby forming an amplification product. The first primer, the second primer, or both the first and second primers can be labeled with a non-nucleic-acid label. Additionally, or alternatively, the amplification product can include an adenosine at position 14 from the 5′ end of SEQ ID NO:1, a thymidine at position 21 from the 5′ end of SEQ ID NO:2, or both an adenine at position 14 and a thymidine at position 21 from the 5′ end of SEQ ID NO:3.

Methods for human identification using polymorphisms in the Penta E short tandem repeat locus are significant in preventing allelic drop out. An exemplary method encompasses (a) contacting a first primer to a nucleic acid sample to be analyzed, (b) contacting a second primer to the nucleic acid sample, and (c) subjecting the nucleic acid sample, the first primer, and the second primer to an amplification reaction, and thereby forming an amplification product. The first primer, the second primer, or both the first and second primers can be labeled with a non-nucleic-acid label. Additionally, or alternatively, the amplification product can include an adenosine at position 14 from the 5′ end of SEQ ID NO:1, a thymidine at position 21 from the 5′ end of SEQ ID NO:2, or both an adenine at position 14 and a thymidine at position 21 from the 5′ end of SEQ ID NO:3.

Provided herein are methods for detecting a Ewing sarcoma breakpoint region 1 (EWSR1) fusion gene encoding a neoantigen (e.g., in a patient sample), as well as methods of prognosis and treatment related thereto, in some embodiments, the methods further comprise administering a cancer immunotherapy. In some embodiments, the EWSR1 fusion gene is a fusion gene between EWSR1 and WT1, Fill, ERG, FEV, NR4A3, ATF1, CREB1, CREM, CREB3L/CREB3L2, PA7Z1, NFATC2, KLFI5, C11orf93, ZNF444, PBX1, DDIT3, or TFCP2 that encodes a neoantigen.

Provided herein are methods for detecting a Ewing sarcoma breakpoint region 1 (EWSR1) fusion gene encoding a neoantigen (e.g., in a patient sample), as well as methods of prognosis and treatment related thereto, in some embodiments, the methods further comprise administering a cancer immunotherapy. In some embodiments, the EWSR1 fusion gene is a fusion gene between EWSR1 and WT1, Fill, ERG, FEV, NR4A3, ATF1, CREB1, CREM, CREB3L/CREB3L2, PA7Z1, NFATC2, KLFI5, C11orf93, ZNF444, PBX1, DDIT3, or TFCP2 that encodes a neoantigen.

An object of the present invention is to provide a method of producing a pluripotent stem cell capable of differentiating into a specific cell. According to the present invention, there is provided a method for producing a pluripotent stem cell capable of differentiating into a specific cell, the method including (i) a step of measuring, in a pluripotent stem cell as a sample, a phenotype associated with induction of epithelial-mesenchymal transition before differentiation induction; and (ii) a step of acquiring a pluripotent stem cell capable of differentiating into a specific cell using the measured phenotype as an indicator. According to the present invention, there are further provided a method of selecting a pluripotent stem cell capable of differentiating into a specific cell; a pluripotent stem cell capable of differentiating into a specific cell; a production method of a differentiated cell; a differentiated cell; and a method for quality evaluation of a pluripotent stem cell.

An object of the present invention is to provide a method of producing a pluripotent stem cell capable of differentiating into a specific cell. According to the present invention, there is provided a method for producing a pluripotent stem cell capable of differentiating into a specific cell, the method including (i) a step of measuring, in a pluripotent stem cell as a sample, a phenotype associated with induction of epithelial-mesenchymal transition before differentiation induction; and (ii) a step of acquiring a pluripotent stem cell capable of differentiating into a specific cell using the measured phenotype as an indicator. According to the present invention, there are further provided a method of selecting a pluripotent stem cell capable of differentiating into a specific cell; a pluripotent stem cell capable of differentiating into a specific cell; a production method of a differentiated cell; a differentiated cell; and a method for quality evaluation of a pluripotent stem cell.

The present disclosure provides methods for determining the status of an allograft within a transplant recipient from genotypic data measured from a mixed sample of DNA comprising DNA from both the transplant recipient and from the donor. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.