Abstract: The invention relates to a kit of parts for detecting one or more polymorphisms in a plurality of target nucleotide sequences in a plurality of samples, wherein the kit of parts comprises (i) a first probe and a second probe, wherein the first probe comprises a first target specific section and a first tag section that is non-complementary to the target nucleotide sequence and that comprises a first universal primer binding site, wherein the second probe comprises a second target specific section and a second tag section that is non-complementary to the target nucleotide sequence; and (ii) a first primer and optionally a second primer wherein the first primer comprises a sample-specific identifier sequence and wherein the first primer can hybridize to the first universal primer binding site.

Abstract: The current invention pertains to a method for sequencing of a target nucleic acid fragment from a nucleic acid sample, comprising the steps of cleaving the nucleic acid sample with a first and a second RNA guided or DNA guided endonuclease complex, preferably a first and a second gRNA-CAS complex, thereby generating the target nucleic acid fragment and at least one non-target nucleic acid fragment. The generated fragments are subsequently contacted with an exonuclease, wherein the exonuclease digests only the non-target nucleic acid fragments. Subsequently said target nucleic acid fragment is sequenced using nanopore selective sequencing. The invention further pertains to the use of the enriched target nucleic acid fragments for nanopore selective sequencing the target nucleic acid fragment.

Abstract: The invention pertains to a method for labelling a target nucleic acid fragment using a combination of a site-specific nuclease and a reverse transcriptase. The labelling results in the addition of a specific nucleotide sequence to at least one free 3?-end of the target nucleic acid fragment. The invention further relates to a method for determining the sequence of the target nucleic acid fragment as well as construct and kit for use in the method of the invention.

Abstract: The current invention pertains to adapters comprising a protelomerase recognition sequence, preferably a TeIN protelomerase recognition sequence. The adapters of the invention can be used for the preparation of a nucleic acid molecule library. The invention also relates to a method for producing a nucleic acid molecule library using one or more adapters comprising a protelomerase recognition sequence. The adapters may be contacted with a protelomerase to cleave and close the ends of the adapters. Said closed adapters are e.g. protected against exonuclease treatment. The method of the invention further concerns an amplification method and a sequencing method using adapters having a protelomerase recognition sequence.

Abstract: The current invention pertains to a method for the enrichment of a target nucleic acid fragment from a nucleic acid sample, comprising the steps of cleaving the nucleic acid sample with a first and a second RNA guided or DNA guided endonuclease complex, preferably a first and a second gRNA-CAS complex, thereby generating the target nucleic acid fragment and at least one non-target nucleic acid fragment. The generated fragments are subsequently contacted with an exonuclease, wherein the exonuclease digests only the non-target nucleic acid fragments. The invention further pertains to the use of the enriched target nucleic acid fragments for preparing an adapter ligated target nucleic acid fragment and for sequencing the target nucleic acid fragment.

Abstract: The current invention pertains to a reliable method for determining the relative frequency of a sequence variant of interest in a nucleic acid sample derived from at least one polyploid cell, wherein the method uses a UMI to correct for any amplification biases. The invention further pertains to the use of a UMI for accurately determining the relative frequency of a sequence variant of interest in a nucleic acid sample derived from at least one polyploid cell.

Abstract: The invention relates to a kit of parts for detecting one or more polymorphisms in a plurality of target nucleotide sequences in a plurality of samples, wherein the kit of parts comprises (i) a first probe and a second probe, wherein the first probe comprises a first target specific section and a first tag section that is non-complementary to the target nucleotide sequence and that comprises a first universal primer binding site, wherein the second probe comprises a second target specific section and a second tag section that is non-complementary to the target nucleotide sequence; and (ii) a first primer and optionally a second primer wherein the first primer comprises a sample-specific identifier sequence and wherein the first primer can hybridize to the first universal primer binding site.

Abstract: The invention concerns a method for the production of oligonucleotides. The method of the invention uses a combination of amplification, restriction and affinity purification to produce high quality oligonucleotides. The invention further pertains to a nucleic acid precursor for use in the method of the invention, a solid support comprising said nucleic acid precursor and a kit for use in the method of the invention.

Abstract: The invention relates to a kit of parts for detecting one or more polymorphisms in a plurality of target nucleotide sequences in a plurality of samples, wherein the kit of parts comprises (i) a first probe and a second probe, wherein the first probe comprises a first target specific section and a first tag section that is non-complementary to the target nucleotide sequence and that comprises a first universal primer binding site, wherein the second probe comprises a second target specific section and a second tag section that is non-complementary to the target nucleotide sequence; and (ii) a first primer and optionally a second primer wherein the first primer comprises a sample-specific identifier sequence and wherein the first primer can hybridize to the first universal primer binding site.

Abstract: The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3? end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker.

Abstract: 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.

Abstract: 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.

Abstract: The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3? end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker.

Abstract: The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3? end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker.

Abstract: 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.

Abstract: 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.

Abstract: The method of the present invention now provides a technique for generating sequence information from nucleic acid samples based on knowledge from part(s) of the nucleotide sequence. The knowledge of the partial sequence may include knowledge about the presence of restriction sites. The knowledge of the partial sequence can be used to generate adaptor-ligated or nucleotide-elongated fragments. From the combination of information on the ligated adaptor and the Known Nucleotide Sequence Section, probes can be designed. The probes can be used in the provision of circularized fragments that can be sequenced. Combining the known and determined sequences adds sequence information to the already existing sequence information and complements the available genomic sequence information.

Abstract: The method of the present invention now provides a technique for generating sequence information from nucleic acid samples based on knowledge from part(s) of the nucleotide sequence. The knowledge of the partial sequence may include knowledge about the presence of restriction sites. The knowledge of the partial sequence can be used to generate adaptor ligated or nucleotide-elongated fragments. From the combination of information on the ligated adaptor and the Known Nucleotide Sequence Section, probes can be designed. The probes can be used in the provision of circularised fragments that can be sequenced. Combining the known and determined sequences adds sequence information to the already existing sequence information and complements the available genomic sequence information.

Abstract: Method for de novo whole genome sequencing based on a (sequence-based) physical map of a DNA sample clone bank based on end-sequencing tagged adapter-ligated restriction fragments, in combination with sequencing adapter-ligated restriction fragments of the DNA sample wherein the recognition sequence of the restriction enzyme used in the generation of the physical map is identical to at least part of the recognition sequence of the restriction enzyme used in the generation of the DNA sample.

Abstract: The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3? end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker.