Abstract: The scChIA-Drop method is a microfluidics-based dual-indexing strategy for single-cell and single-molecule chromatin interaction analysis.

Abstract: The invention described herein provides reagents (e.g., kits), compositions, and methods for carrying out an unbiased genome-wide strategy to identify the functional targets for all ncRNAs.

Abstract: The invention, in part, relates to ChIA-Drop methods, which comprise methods of drop-based sequencing.

Abstract: The present invention provides a method for next generation chromatin interaction assays based on the single molecule protein-detection and DNA-sequencing platform at the single molecule and single nucleus single molecule levels. The present invention has the advantages of single molecule resolution in single nuclei and the elimination of proximity ligation and PCR amplification steps. The present invention provides revolutionary biological insights in the organization of the 3D genome and its modulation.

Abstract: The invention, in part, relates to ChIA-Drop methods, which comprise methods of drop-based sequencing.

Abstract: The invention described herein provides reagents (e.g., kits), compositions, and methods for carrying out an unbiased genome-wide strategy to identify the functional targets for all ncRNAs.

Abstract: The invention described herein provides methods and systems for comprehensive genomic analysis that enables the detection of a broad range of genomic variations, including single nucleotide polymorphisms (SNPs), small insertions or deletions (indels), Tandem Base Mutations (TBM), copy number variations (CNVs), structural variations (SVs), and combination thereof, in a single assay. The invention can be used, for example, to analyze the complicated underlying genomic defects in diseases and conditions such as Autism spectrum disorders (ASD), cancers, Alzheimer's disease, and other neurological disorders.

Abstract: The invention described herein provides reagents (e.g., kits), compositions, and methods for carrying out an unbiased genome-wide strategy to identify the functional targets for all ncRNAs.

Abstract: The present invention relates to a method for determining or making of a prognosis if a patient has cancer or is at an increased risk of having cancer, the method comprising testing for the presence of one or more cancer-associated fusion genes, or proteins derived thereof, in a sample obtained from a patient. More specifically, the present invention relates to fusion genes CLEC16A-EMP2, SNX2-PRDM6, MLL3-PRKAG2, DUS2L-PSKH1 and CLDN18-ARHGAP26 in gastric cancer. Use of the method and a kit when used in the method are also provided.

Abstract: The invention described herein provides reagents (e.g., kits), compositions, and methods for carrying out an unbiased genome-wide strategy to identify the functional targets for all ncRNAs.

Abstract: A transcript mapping method according to an embodiment of the invention is described hereinafter and combines short tag based (SAGE and MPSS) efficiency with the accuracy of full-length cDNA (flcDNA) for comprehensive characterization of transcriptomes. This method is also referred to as Gene Identification Signature (GIS) analysis. In this method, the 5? and 3? ends of full-length cDNA clones are initially extracted into a ditag structure, with the ditag concatemers of the ditag being subsequently sequenced in an efficient manner, and finally mapped to the genome for defining the gene structure. As a GIS ditag represents the 5? and 3? ends of a transcript, it is more informative than SAGE and MPSS tags. Segment lengths between 5? and 3? tag pairs are obtainable including orientation, ordering and chromosome family for efficient transcript mapping and gene location identification.

Abstract: We describe a polymorphic variant of a BIM {BCL2L11) gene which comprises, in 5? to 3? order, the nucleotide sequence set out in SEQ ID NO: 5 followed immediately by the nucleotide sequence set out in SEQ ID NO: 7. The BIM polymorphic variant may be characterised by lacking the nucleotide sequence set out in SEQ ID NO: 6. It may be used to detect BCR-ABL-independent TKI-resistance (resistance to treatment with tyrosine kinase inhibitors) for chronic myelogenous leukaemia, c-KIT/PDGFR-independent TKI-resistance for gastrointestinal stromal tumours (GIST), EGFR-independent TKI-resistance for non-small cell lung cancer (NSCLC) or JAK2-independent TKI-resistance for a myeloproliferative disorder, in an individual comprising such a polymorphism.

Abstract: There is provided a method and system for processing and/or mapping ditag nucleotide sequence(s) to a genome, the ditag sequence comprising the 5? terminal tag and the 3? terminal tag of a nucleic acid molecule or fragment thereof or genomic fragment. The method of processing comprises preparing a database or file comprising at least one ditag sequence. The method of mapping comprises preparing a database or file of ditag(s), and mapping the ditag sequence(s) to the genome, comprising matching the 5? and the 3? terminal tags of the ditag sequence to at least a portion of the genome.

Abstract: The present invention provides at least one isolated linear composite nucleic acid molecule comprising at least one first tag from at least one first nucleic acid molecule and at least one second tag from at least one second nucleic acid molecule, wherein the first and second nucleic acids interact in a nucleic acid mixture; and wherein the first and second tags are from different nucleic acid molecules. The invention also provides a method of producing at least one isolated linear composite nucleic acid and to a method of detecting and/or identifying nucleic acid interactions.

Abstract: We describe a method of providing an indication of an instance of expression of a gene, the method comprising the steps of: (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic acid with the first nucleic acid cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.

Abstract: An isolated oligonucleotide comprising at least one ditag, wherein the ditag comprises two joined first and second sequence tags, wherein the first tag comprises the 5?-terminus sequence and the second tag comprises the 3?-terminus sequence of a nucleic acid molecule or a fragment thereof. The ditag analysis is useful for gene discovery and genome mapping.

Abstract: A method of providing an indication of an instance of expression of a gene is described herein, the method which may comprise the steps of: (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic acid with the first nucleic acid cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.

Abstract: A transcript mapping method according to an embodiment of the invention is described hereinafter and combines short tag based (SAGE and MPSS) efficiency with the accuracy of full-length cDNA (flcDNA) for comprehensive characterization of transcriptomes. This method is also referred to as Gene Identification Signature (GIS) analysis. In this method, the 5? and 3? ends of full-length cDNA clones are initially extracted into a ditag structure, with the ditag concatemers of the ditag being subsequently sequenced in an efficient manner, and finally mapped to the genome for defining the gene structure. As a GIS ditag represents the 5? and 3? ends of a transcript, it is more informative than SAGE and MPSS tags. Segment lengths between 5? and 3? tag pairs are obtainable including orientation, ordering and chromosome family for efficient transcript mapping and gene location identification.

Abstract: The present invention provides an isolated oligonucleotide and a method using the isolated oligonucleotide to detect and/or identify at least two polynucleotides from a nucleic acid-protein complex. The oligonucleotide comprises at least one first tag and at least one second tag, wherein the first and second tags are obtained from a nucleic acid-protein complex.

Abstract: A transcript mapping method according to an embodiment of the invention is described hereinafter and combines short tag based (SAGE and MPSS) efficiency with the accuracy of full-length cDNA (flcDNA) for comprehensive characterization of transcriptomes. This method is also referred to as Gene Identification Signature (GIS) analysis. In this method, 5? and 3? terminal tags are obtained from a transcript and the terminal tags are for identifying 5? and 3? sites located on a genome sequence. Further, occurring segments and thus feasible gene locations are identified along the genome sequence after the 5? and 3? sites are identified. A data structure is also generated for indexing the genome sequence so that the terminal tags can be mapped to the genome sequence.