The present disclosure relates to methods and compositions involving HCR reactions that involve initiators that are split into two or more parts. Effective HCR is dependent upon two or more of these split initiators being brought into proximity (e.g., via binding events mediated by a target) such that a full initiator is formed that is capable of triggering HCR signal amplification.

The present invention relates to a method of detecting specific nucleic acid sequences and a device for performing the method therein. The specific nucleic acid may be prepared from a subject-specimen or from an environmental specimen and the method is performed in isothermal conditions.

The present invention relates to a method of detecting specific nucleic acid sequences and a device for performing the method therein. The specific nucleic acid may be prepared from a subject-specimen or from an environmental specimen and the method is performed in isothermal conditions.

This disclosure provides methods and kits useful in analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications, and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The method is based on the hybridization of amplified fragments obtained from the sample, e.g., using molecular inversion probes (MIP) to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP.

This disclosure provides methods and kits useful in analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications, and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The method is based on the hybridization of amplified fragments obtained from the sample, e.g., using molecular inversion probes (MIP) to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP.

The present disclosure relates to compositions, methods, and kits for generating capture probes on a substrate for identifying the location of analytes in a biological sample. In particular, disclosed is a method of generating a spatial array comprising: (a) providing a substrate comprising a plurality of acceptor oligonucleotides, wherein an acceptor oligonucleotide of the plurality of acceptor oligonucleotides comprises a spatial barcode and a first ligation handle, and wherein the 5′ end of the acceptor oligonucleotide is attached to the substrate; (b) providing a plurality of universal splint oligonucleotides, wherein a universal splint oligonucleotide of the plurality of universal splint oligonucleotides comprises a sequence complementary to the first ligation handle and a sequence complementary to a second ligation handle present in a donor oligonucleotide of a plurality of donor oligonucleotides; and (c) ligating the donor oligonucleotide comprising a capture domain to the 3′ end of the acceptor oligonucleotide to generate a capture probe, wherein the universal splint oligonucleotide is hybridized to the first ligation handle and the second ligation handle, thereby generating a spatial array.

The present disclosure relates to compositions, methods, and kits for generating capture probes on a substrate for identifying the location of analytes in a biological sample. In particular, disclosed is a method of generating a spatial array comprising: (a) providing a substrate comprising a plurality of acceptor oligonucleotides, wherein an acceptor oligonucleotide of the plurality of acceptor oligonucleotides comprises a spatial barcode and a first ligation handle, and wherein the 5′ end of the acceptor oligonucleotide is attached to the substrate; (b) providing a plurality of universal splint oligonucleotides, wherein a universal splint oligonucleotide of the plurality of universal splint oligonucleotides comprises a sequence complementary to the first ligation handle and a sequence complementary to a second ligation handle present in a donor oligonucleotide of a plurality of donor oligonucleotides; and (c) ligating the donor oligonucleotide comprising a capture domain to the 3′ end of the acceptor oligonucleotide to generate a capture probe, wherein the universal splint oligonucleotide is hybridized to the first ligation handle and the second ligation handle, thereby generating a spatial array.

Techniques are provided for generating an array-specific range of Tm values to be used for calling a sample in a given array positive or negative for a target nucleic acid sequence. A sample well in an array is provided with a control sample containing a control nucleic acid sequence. The control sample is amplified by thermal cycling the sample well. A Tm value for the control sample is identified and compared to an expected Tm value for the control nucleic acid sequence to calculate a relationship between the identified control Tm value and the expected control Tm value. By applying this relationship to an expected Tm value for a target nucleic acid sequence, an array-specific range of Tm values for the target nucleic acid sequence is generated and can be used for calling an experimental sample in the same array positive or negative for the target nucleic acid sequence.

Techniques are provided for generating an array-specific range of Tm values to be used for calling a sample in a given array positive or negative for a target nucleic acid sequence. A sample well in an array is provided with a control sample containing a control nucleic acid sequence. The control sample is amplified by thermal cycling the sample well. A Tm value for the control sample is identified and compared to an expected Tm value for the control nucleic acid sequence to calculate a relationship between the identified control Tm value and the expected control Tm value. By applying this relationship to an expected Tm value for a target nucleic acid sequence, an array-specific range of Tm values for the target nucleic acid sequence is generated and can be used for calling an experimental sample in the same array positive or negative for the target nucleic acid sequence.

The present invention provides a nucleic acid amplification based method for detecting a hypervirulent Clostridium difficile strain in a biological sample. The present invention is based on the use of oligonucleotide primers and probes specific to negative and positive markers in hypervirulent Clostridium difficile genome.