The present invention provides a method for integrally detecting nondestructive measurement information and genome-related information of single cells. More specifically, the present invention uses a method including: preparing a plurality of compartments containing single cell or a derivative thereof, a first bead(s), and a second bead(s) per compartment; detecting both nondestructive measurement information of single cell and imaging information of the first bead(s) and associating the nondestructive measurement information of single cell with the imaging information of the first bead(s) before preparation of each compartment or in each compartment; obtaining a hybridized complex; producing an amplified product derived from the hybridized complex; and integrally detecting nondestructive measurement information and genome-related information in single cell.

The present invention provides a method for integrally detecting nondestructive measurement information and genome-related information of single cells. More specifically, the present invention uses a method including: preparing a plurality of compartments containing single cell or a derivative thereof, a first bead(s), and a second bead(s) per compartment; detecting both nondestructive measurement information of single cell and imaging information of the first bead(s) and associating the nondestructive measurement information of single cell with the imaging information of the first bead(s) before preparation of each compartment or in each compartment; obtaining a hybridized complex; producing an amplified product derived from the hybridized complex; and integrally detecting nondestructive measurement information and genome-related information in single cell.

Provided herein are methods of preparing cell-free DNA (cfDNA) for sequencing such that variant allele frequencies are maintained. Also provided are sequencing libraries prepared according to such methods. In addition, methods are provided for analyzing sequencing reads to determine variant allele frequencies. These methods may be used for diagnosing and/or evaluating cancer patients.

Provided herein are methods of preparing cell-free DNA (cfDNA) for sequencing such that variant allele frequencies are maintained. Also provided are sequencing libraries prepared according to such methods. In addition, methods are provided for analyzing sequencing reads to determine variant allele frequencies. These methods may be used for diagnosing and/or evaluating cancer patients.

A nucleic acid amplification method using a solid-phase carrier according to the present invention comprises: capturing a target nucleic acid comprising mRNA on a solid-phase carrier; carrying out complementary-strand synthesis on the solid phase; carrying out exonuclease treatment to degrade and remove unreacted target- capturing nucleic acid on the solid phase; and then carrying out mRNA degradation and homopolymer addition by TdT reaction in the presence of a chain-terminating nucleotide triphosphate. According to the method of the present invention, cDNA can be stably and highly efficiently amplified even from a small amount of sample even in cases where the ratio of the amount of enzyme to the DNA substrate on the solid phase is excessive, where the reaction time is excessive, and/or where reagents show lot-to-lot variation. Further, the amplification method of the present invention can broaden the range of applications of techniques in which analysis using a specific-binding molecule labeled with an oligonucleic acid such as a DNA-labeled antibody and analysis of transcripts are carried out simultaneously.

A nucleic acid amplification method using a solid-phase carrier according to the present invention comprises: capturing a target nucleic acid comprising mRNA on a solid-phase carrier; carrying out complementary-strand synthesis on the solid phase; carrying out exonuclease treatment to degrade and remove unreacted target- capturing nucleic acid on the solid phase; and then carrying out mRNA degradation and homopolymer addition by TdT reaction in the presence of a chain-terminating nucleotide triphosphate. According to the method of the present invention, cDNA can be stably and highly efficiently amplified even from a small amount of sample even in cases where the ratio of the amount of enzyme to the DNA substrate on the solid phase is excessive, where the reaction time is excessive, and/or where reagents show lot-to-lot variation. Further, the amplification method of the present invention can broaden the range of applications of techniques in which analysis using a specific-binding molecule labeled with an oligonucleic acid such as a DNA-labeled antibody and analysis of transcripts are carried out simultaneously.

Disclosed herein include methods and compositions for selectively amplifying and/or extending nucleic acid target molecules in a sample. The methods and compositions can, for example, reduce the amplification and/or extension of undesirable nucleic acid species in the sample, and/or allow selective removal of undesirable nucleic acid species in the sample.

Disclosed herein include methods and compositions for selectively amplifying and/or extending nucleic acid target molecules in a sample. The methods and compositions can, for example, reduce the amplification and/or extension of undesirable nucleic acid species in the sample, and/or allow selective removal of undesirable nucleic acid species in the sample.

A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.