Abstract: The technology relates in part to compositions that include oligonucleotide probes useful for enriching nucleic acid preparation products for analysis, kits and related methods. Described herein are compositions comprising: a plurality of oligonucleotide probes capable of hybridizing to target nucleic acid fragments of cancer gene exons, introns, and untranslated regions surrounding cancer genes resulting from nucleic acid restriction enzyme cleavage of a nucleic acid sample, for use in capture-C technologies and methods associated therewith.

Abstract: In certain aspects, the technology relates to methods of selecting and/or treating subjects having cancer, where the subjects are identified as having at least one genetic structural variant associated with, or adjacent to, the PTPRD gene, the CD274 gene and/or the CD273, wherein the subject having cancer for potential responsiveness to treatment with a PTPRD-targeted therapeutic and/or an immune checkpoint blockade.

Abstract: The technology relates in part to a method and compositions for comprehensive genomic profiling.

Abstract: The technology relates in part to compositions that include oligonucleotide probes useful for enriching nucleic acid preparation products for analysis, kits and related methods. The technology further relates in part to Chromosome conformation capture (3C) and similar technologies. The technology further relates in part to kits, compositions, and methods involving oligonucleotide probes capable of interacting with cancer genes.

Abstract: The technology relates in part to methods and compositions for detecting oncogenic structural variants.

Abstract: Provided herein are methods and compositions for preparing nucleic acids in samples that preserve spatial-proximal contiguity information. Samples include, but are not limited to, formalin-fixed paraffin-embedded (FFPE) samples, deeply formalin-fixed samples and samples that comprise protein:cfDNA complexes.

Abstract: Provided herein are methods for detecting the presence or absence of a chromosome rearrangement in a formalin-fixed paraffin embedded (FFPE) sample with no detectable genomic variant associated with cancer. In certain embodiments, the methods include selecting a sample and performing a nucleic acid analysis on the selected sample and detecting whether a chromosome rearrangement is present or absent in the selected sample according to the nucleic acid analysis. In preferred embodiments, the nucleic acid analysis is a method that preserves spatial-proximal contiguity information.

Abstract: The technology relates in part to methods and compositions for detecting oncogenic structural variants.

Abstract: The technology relates in part to methods of selecting for and/or treating subjects having cancer, where the subjects are identified as having at least one genetic structural variant that renders them suitable candidates for a treatment method that includes the administration of at least one inhibitor of a PD-1 pathway and/or an inhibitor of the interaction of the PD-1 receptor with PD-L1 and/or PD-L2.

Abstract: The technology relates in part to methods and compositions for detecting oncogenic structural variants.

Abstract: The technology relates in part to methods of selecting for and/or treating subjects having cancer, where the subjects are identified as having at least one genetic structural variant that renders them suitable candidates for a treatment method that includes the administration of at least one homologous recombination deficient direct therapy, such as an inhibitor of a polyadenosine diphosphate-ribose polymerase (PARP) enzyme.

Abstract: The present disclosure relates to methods to deconvolute a mixture sample of genetic material from different origins or sources. The disclosed methods can be used in various applications, including, the non-invasive determination of a fetal genome, a fetal -ome (e.g. exome). or other targeted fetal locus from cell-free nucleic acids in maternal plasma or other body fluids; the determination of cancer-associated mutations from cell-free nucleic acids in a body fluid sample that contains a mixture of nucleic acids from normal cells and tumor cells; and quantification of donor cell contamination using a body fluid from a transplantation recipient to monitor and/or predict the outcome of a transplantation procedure.

Abstract: Provided herein are methods and compositions for preparing nucleic acid templates wherein spatial-proximal and molecular contiguity of target nucleic acids is preserved, and the sequencing data obtained therefrom is used, but not limited to, identification of genomic variants, determination of contiguity information to inform assemblies of target nucleic acids de novo including deconvolution of haplotype phase information, and analyses of conformation and topology of target nucleic acids.

Abstract: The present disclosure relates to methods to deconvolute a mixture sample of genetic material from different origins or sources. The disclosed methods can be used in various applications, including, the non-invasive determination of a fetal genome, a fetal -ome (e.g. exome). or other targeted fetal locus from cell-free nucleic acids in maternal plasma or other body fluids; the determination of cancer-associated mutations from cell-free nucleic acids in a body fluid sample that contains a mixture of nucleic acids from normal cells and tumor cells; and quantification of donor cell contamination using a body fluid from a transplantation recipient to monitor and/or predict the outcome of a transplantation procedure.

Abstract: Provided herein are methods and compositions for preparing nucleic acid templates wherein spatial-proximal and molecular contiguity of target nucleic acids is preserved, and the sequencing data obtained therefrom is used, but not limited to, identification of genomic variants, determination of contiguity information to inform assemblies of target nucleic acids de novo including deconvolution of haplotype phase information, and analyses of conformation and topology of target nucleic acids.

Abstract: Provided herein are methods and compositions for preparing nucleic acids in samples that preserve spatial-proximal contiguity information. Samples include, but are not limited to, formalin-fixed paraffin-embedded (FFPE) samples, deeply formalin-fixed samples and samples that comprise protein:cfDNA complexes.