A method of sequencing nucleic acids is provided using sequencing by ligation and/or sequencing by hybridization.

A method of sequencing nucleic acids is provided using sequencing by ligation and/or sequencing by hybridization.

The invention relates to a method for the detection of a target nucleotide sequence in a sample based on an oligonucleotide ligation assay wherein probes are used that contain (a combination of) sequence-based identifiers that can identify the sample and the target sequence (i.e. locus and/or allele combination) wherein after the ligation step, the ligated probes, or after amplification, the amplified ligated probes, are restricted using restriction enzymes to cut of part of the probes and continue with those parts (identifiers and target sequence) that contain the relevant information in the sequencing step.

The invention relates to a method for the detection of a target nucleotide sequence in a sample based on an oligonucleotide ligation assay wherein probes are used that contain (a combination of) sequence-based identifiers that can identify the sample and the target sequence (i.e. locus and/or allele combination) wherein after the ligation step, the ligated probes, or after amplification, the amplified ligated probes, are restricted using restriction enzymes to cut of part of the probes and continue with those parts (identifiers and target sequence) that contain the relevant information in the sequencing step.

This disclosure provides, inter alia, a probe system probe system for analyzing a nucleic acid sample. In some embodiments, the probe system may comprise: a set of identifier oligonucleotides of sequence B, a set of splint oligonucleotides of formula X-A-B-Z, wherein sequence A is complementary to a genomic fragment and sequence B is complementary to at least one member of the set of identifier oligonucleotides, and one or more probe sequences comprising X and Z. Each splint oligonucleotide is capable of hybridizing to the probe sequences, a member of the set of identifier oligonucleotides and a genomic fragment, thereby producing a ligatable complex of formula X-A-B-Z. The probe system can be used to identify a chromosome aneuploidy in cell free DNA, for example.

This disclosure provides, inter alia, a probe system probe system for analyzing a nucleic acid sample. In some embodiments, the probe system may comprise: a set of identifier oligonucleotides of sequence B, a set of splint oligonucleotides of formula X-A-B-Z, wherein sequence A is complementary to a genomic fragment and sequence B is complementary to at least one member of the set of identifier oligonucleotides, and one or more probe sequences comprising X and Z. Each splint oligonucleotide is capable of hybridizing to the probe sequences, a member of the set of identifier oligonucleotides and a genomic fragment, thereby producing a ligatable complex of formula X-A-B-Z. The probe system can be used to identify a chromosome aneuploidy in cell free DNA, for example.

This application relates to methods for ligating oligonucleotides having complementarity to a target nucleic acid, and amplifying the ligated oligonucleotides, where ligation and amplification occur in the same reaction mixture.

This application relates to methods for ligating oligonucleotides having complementarity to a target nucleic acid, and amplifying the ligated oligonucleotides, where ligation and amplification occur in the same reaction mixture.

Multiplexed methods of detecting an analyte in a sample using two or more padlock probes each specific to a different target sequence are described. The target sequence is either part of an analyte or indicative of the presence of an analyte in the sample. Each padlock probe includes an analyte-specific reporter sequence, and either a restriction cleavage site located 3 of the analyte-specific reporter sequence, and/or a first amplification primer binding site for an amplification reaction. Where the padlock probe includes a restriction cleavage site, cleavage at the restriction cleavage site occurs 3 of the analyte-specific reporter sequence. Where the padlock probe includes a first amplification primer binding site for the further amplification reaction, it does not contain a second amplification primer binding site 5 of the analyte-specific reporter sequence. Panels of probes and kits for the same are also described.

Multiplexed methods of detecting an analyte in a sample using two or more padlock probes each specific to a different target sequence are described. The target sequence is either part of an analyte or indicative of the presence of an analyte in the sample. Each padlock probe includes an analyte-specific reporter sequence, and either a restriction cleavage site located 3 of the analyte-specific reporter sequence, and/or a first amplification primer binding site for an amplification reaction. Where the padlock probe includes a restriction cleavage site, cleavage at the restriction cleavage site occurs 3 of the analyte-specific reporter sequence. Where the padlock probe includes a first amplification primer binding site for the further amplification reaction, it does not contain a second amplification primer binding site 5 of the analyte-specific reporter sequence. Panels of probes and kits for the same are also described.