Methods and compositions for preparing extracellular vesicle nucleic acids that preserve spatial-proximity information and applications thereof

Abstract

The technology relates in part to methods and compositions for preparing extracellular vesicle nucleic acids that preserve spatial-proximity information and applications thereof.

Description

[0001]AMG-1022 METHODS AND COMPOSITIONS FOR PREPARING EXTRACELLULAR VESICLE NUCLEIC ACIDS THAT PRESERVE SPATIAL-PROXIMITY INFORMATION AND APPLICATIONS THEREOF Cross Reference to Related Applications This application claims the benefit under 35 U.S.C. § 119(e) of U.S. provisional application number 63 / 514,335, filed July 18, 2023 and U.S. provisional application number 63 / 509,519, filed June 21, 2023, each which is herein incorporated by reference in its entirety. Field The technology relates in part to methods and compositions for preparing extracellular vesicle nucleic acids that preserve spatial-proximity information and applications thereof. Background Extracellular vesicles (EVs) are membrane-enclosed structures that are released from all cells in the body. EVs vary in size, biogenesis, membrane composition, cargo and function. While it remains challenging to separate EV subpopulations, unusually large (1–10 ^m diameter) EVs (L-EVs), referred to as large oncosomes (LO), have successfully been isolated from tumor cells with high migratory and invasive abilities (Vagner T, Spinelli C, Minciacchi VR, Balaj L, Zandian M, Conley A, Zijlstra A, Freeman MR, Demichelis F, De S, Posadas EM, Tanaka H, Di Vizio D. Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma. J Extracell Vesicles.2018 Aug 7;7(1):1505403. doi: 10.1080 / 20013078.2018.1505403. PMID: 30108686; PMCID: PMC6084494). For example, LOs have been identified in tumor tissue and plasma of patients with prostate cancer (PCa) but not in cancer-free individuals and their abundance increases in patients with metastatic castration- resistant prostate cancer (mCRPC). EV cargo is sensitive to disease-induced cellular changes. Consequently, tumor cell- specific EVs are emerging as a potent source of cancer biomarkers because they carry bioactive molecules (proteins, lipids and RNA) that reflect the malignant behavior of the cells they originate from. Some studies have also reported the presence of double stranded genomic DNA (gDNA) in diverse types of EVs. Results from one of the first studies on DNA in EVs demonstrated that different EV populations (apoptotic bodies, microvesicles and exosomes) harbor either TP53 or PTEN mutations, suggesting specific EV types might package different parts of the genome. EVs can also carry mitochondrial DNA, retrotransposons and oncogenes (i.e., c-Myc). Additional studies indicated that the release of small EVs (S-EVs) containing gDNA is driven by specific oncogenes, which are functionally transferred to target cells via EVs. Later reports discovered that exosomes (Exo) contain entire genomes with large fragments of dsDNA AMG-1022 and carry mutations of parental tumor cells. These data suggest diagnostic and prognostic value for EV DNA. Liquid biopsies offer minimally invasive and practical clinical tools. Advancements in sequencing technologies have enabled the analysis of the genomic landscape of cancer using circulating cell-free DNA (cfDNA) and circulating tumor cells (CTCs). Furthermore, liquid biopsies may overcome the limitation of tissue biopsies to capture the tumor heterogeneity and the dynamic evolution of cancer genomes. cfDNA has been used for non-invasive screening of chromosomal alterations in the circulation. However, CTCs are rare in most cancer types and cfDNA is fragmented (~160 bp). Moreover, cfDNA in early stage PCa and during treatment response might underrepresent the cancer genome, i.e. the levels of tumor DNA are lower, thus limiting the sensitivity of standard DNA analyses for detection of tumor-specific genomic alterations. However, the prior art has only shown the extracellular vesicle DNA is high molecular weight and chromatinized (see, e.g. Vagner et al., cited above). In addition, it doesn’t provide any indication on whether individual EVs contain 1 or more chromatinized molecules / aggregates; or any info on whether the 1 or more chromatinized molecule / aggregate are all derived from the same chromosome or different chromosomes, or if from within the same chromosome whether from the same or both homologs of that chromosome. It doesn’t provide any indication whether the 3D structure of chromatin is preserved. What is unknown is whether the 3D chromatin structure is completely or partially destroyed (i.e. the spatial proximity relationship between nucleic acids, such as the DNA-DNA interactions that were in place before the secretion into EVs is either partially or completely lost, resulting in chromatin interactions that are different than the parent cell or entirely non-existent). For example, 3D chromatin structure could become partially or entirely destroyed during the process of being secreted or after being secreted while in EVs but before being harvested for measurement and analysis of spatial proximity relationships (e.g. crosslinking and proximity ligation). However, Applicants have made the discovery that the DNA present in extracellular vesicles contains chromatin with 3D structure present. This observation supports the use of technologies that preserve and / or measure spatial proximity information of nucleic acids in EVs in numerous applications further discussed herein. Summary Provided in certain aspects are methods for preparing nucleic acid from an extracellular vesicle including the step of contacting an extracellular vesicle with one or more agents that preserve spatial-proximity relationships in the nucleic acid of the extracellular vesicle. AMG-1022 Brief Description of the Drawings The drawings illustrate certain implementations of the technology and are not limiting. For clarity and ease of illustration, the drawings are not made to scale and, in some instances, various aspects may be shown exaggerated or enlarged to facilitate an understanding of particular implementations. FIG.1 shows a schematic of the method used in an example of an embodiment of the invention. FIGs.2A-2D show chr11 HiC interaction maps and a Pearson Correlation (PC) matrix of an example of an embodiment of the invention. FIG.3 shows a first principal component eigenvector of an example of an embodiment of the invention. FIG.4 depicts a zoomed in HiC heatmap showing the approx. locus coordinates: Chr8:103,500,000-110,000,000 an example of an embodiment of the invention. FIGs.5A-5B show genome-wide HiC maps of an example of an embodiment of the invention. FIGs.6A-6B show zoomed in HiC heatmaps of exemplary inter-chr translocation between chr3 and chr10 of an example of an embodiment of the invention. FIGs.7A-7B show “genome scan plots” representing a virtual Capture-HiC analysis targeting the CACNB2 gene in an example of an embodiment of the invention. FIGs.8A-8B show “genome scan plots” representing a virtual Capture-HiC analysis targeting the CAMTA1 gene in an example of an embodiment of the invention. FIGs.9A-9B show “genome scan plots” representing a virtual Capture-HiC analysis targeting the PTEN gene in an example of an embodiment of the invention. FIGs.10A-10B show “genome scan plots” representing a virtual Capture-HiC analysis targeting the BCR gene in an example of an embodiment of the invention. FIGs.11A-11B show “genome scan plots” representing a virtual Capture-HiC analysis in K562 cells in an example of an embodiment of the invention. Detailed Description Preparation and analysis of enriched nucleic acid Provided in certain aspects is a method for nucleic acid enrichment, the method including: subjecting target nucleic acid from a nucleic acid sample to nucleic acid cleavage conditions in which nucleic acid fragments are generated; subjecting the target nucleic acid fragments to linking conditions in which proximity ligated nucleic acid molecules are generated; contacting the proximity ligated nucleic acid molecules with a composition comprising a plurality of oligonucleotide probes described herein under hybridization conditions in which hybridization AMG-1022 complexes comprising proximity ligated nucleic acid hybridized to oligonucleotide probes are generated; isolating the complexes; and analyzing nucleic acid in the complexes. The terms nucleic acid(s), nucleic acid molecule(s), nucleic acid fragment(s), target nucleic acid(s), nucleic acid template(s), template nucleic acid(s), nucleic acid target(s), target nucleic acid(s), polynucleotide(s), polynucleotide fragment(s), target polynucleotide(s), polynucleotide target(s), and the like may be used interchangeably throughout the disclosure. The terms refer to nucleic acids of any composition from, such as DNA (e.g., complementary DNA (cDNA; synthesized from any RNA or DNA of interest), genomic DNA (gDNA), genomic DNA fragments, mitochondrial DNA (mtDNA), recombinant DNA (e.g., plasmid DNA), and the like), RNA (e.g., message RNA (mRNA), small interfering RNA (siRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), microRNA, transacting small interfering RNA (ta-siRNA), natural small interfering RNA (nat-siRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), long non-coding RNA (lncRNA), non-coding RNA (ncRNA), transfer-messenger RNA (tmRNA), precursor messenger RNA (pre-mRNA), small Cajal body-specific RNA (scaRNA), piwi- interacting RNA (piRNA), endoribonuclease-prepared siRNA (esiRNA), small temporal RNA (stRNA), signal recognition RNA, telomere RNA, RNA highly expressed by a fetus or placenta, and the like), and / or DNA or RNA analogs (e.g., containing base analogs, sugar analogs and / or a non-native backbone and the like), RNA / DNA hybrids and polyamide nucleic acids (PNAs), all of which can be in single- or double-stranded form, and unless otherwise limited, can encompass known analogs of natural nucleotides that can function in a similar manner as naturally occurring nucleotides. A nucleic acid may be, or may be from, a plasmid, phage, virus, bacterium, autonomously replicating sequence (ARS), mitochondria, centromere, artificial chromosome, chromosome, or other nucleic acid able to replicate or be replicated in vitro or in a host cell, a cell, a cell nucleus or cytoplasm of a cell in certain embodiments. A template nucleic acid in some embodiments can be from a single chromosome (e.g., a nucleic acid sample may be from one chromosome of a sample obtained from a diploid organism). Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, single nucleotide polymorphisms (SNPs), and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and / or deoxyinosine residues. The term nucleic acid is used interchangeably with locus, gene, cDNA, and mRNA encoded by a gene. The term also may include, as equivalents, derivatives, variants and AMG-1022 analogs of RNA or DNA synthesized from nucleotide analogs, single-stranded ("sense" or "antisense," "plus" strand or "minus" strand, "forward" reading frame or "reverse" reading frame) and double-stranded polynucleotides. The term "gene" refers to a section of DNA involved in producing a polypeptide chain; and generally includes regions preceding and following the coding region (leader and trailer) involved in the transcription / translation of the gene product and the regulation of the transcription / translation, as well as intervening sequences (introns) between individual coding regions (exons). A nucleotide or base generally refers to the purine and pyrimidine molecular units of nucleic acid (e.g., adenine (A), thymine (T), guanine (G), and cytosine (C)). For RNA, the base thymine is replaced with uracil (U). Nucleic acid length or size may be expressed as a number of bases. Target nucleic acids may be any nucleic acids of interest. Nucleic acids may be polymers of any length composed of deoxyribonucleotides (i.e., DNA bases), ribonucleotides (i.e., RNA bases), or combinations thereof, e.g., 10 bases or longer, 20 bases or longer, 50 bases or longer, 100 bases or longer, 200 bases or longer, 300 bases or longer, 400 bases or longer, 500 bases or longer, 1000 bases or longer, 2000 bases or longer, 3000 bases or longer, 4000 bases or longer, 5000 bases or longer. In certain aspects, nucleic acids are polymers composed of deoxyribonucleotides (i.e., DNA bases), ribonucleotides (i.e., RNA bases), or combinations thereof, e.g., 10 bases or less, 20 bases or less, 50 bases or less, 100 bases or less, 200 bases or less, 300 bases or less, 400 bases or less, 500 bases or less, 1000 bases or less, 2000 bases or less, 3000 bases or less, 4000 bases or less, or 5000 bases or less. Nucleic acid may be single-stranded or double-stranded. Single-stranded DNA (ssDNA), for example, can be generated by denaturing double-stranded DNA by heating or by treatment with alkali, for example. Accordingly, in some embodiments, ssDNA is derived from double- stranded DNA (dsDNA). Nucleic acid (e.g., genomic DNA, nucleic acid targets, oligonucleotides, probes, primers) may be described herein as being complementary to another nucleic acid, having a complementarity region, being capable of hybridizing to another nucleic acid, or having a hybridization region. The terms “complementary” or “complementarity” or “hybridization” generally refer to a nucleotide sequence that base-pairs by non-covalent bonds to a region of a nucleic acid. In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T), and guanine (G) pairs with cytosine (C) in DNA. In RNA, thymine (T) is replaced by uracil (U). As such, A is complementary to T and G is complementary to C. In RNA, A is complementary to U and vice versa. In a DNA-RNA duplex, A (in a DNA strand) is complementary to U (in an RNA strand). Typically, “complementary” or “complementarity” or “capable of hybridizing” refer to a nucleotide sequence that is at least partially complementary. These terms may also encompass duplexes that are fully complementary such that every nucleotide in one strand is complementary or hybridizes to every nucleotide in the other strand in corresponding positions. In certain instances, a nucleotide sequence may be partially AMG-1022 complementary to a target, in which not all nucleotides are complementary to every nucleotide in the target nucleic acid in all the corresponding positions. The percent identity of two nucleotide sequences can be determined by aligning the sequences for optimal comparison purposes. When the total number of positions is different between the two nucleotide sequences, gaps may be introduced in the sequence of one or both sequences for optimal alignment. The nucleotides at corresponding positions are then compared, and the percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity= # of identical positions / total # of positions×100). When a position in one sequence is occupied by the same nucleotide as the corresponding position in the other sequence, then the molecules are identical at that position. In certain instances, extra or missing bases within a sequence are expressed as gaps in an alignment and may or may not be factored into a percent identity calculation. For example, a percent identity calculation may include a number of mismatches and gaps or may include a number of mismatches only. As used herein, the phrase “hybridizing” or grammatical variations thereof, refers to binding of a first nucleic acid molecule to a second nucleic acid molecule under low, medium or high stringency conditions, or under nucleic acid synthesis conditions. Hybridizing can include instances where a first nucleic acid molecule binds to a second nucleic acid molecule, where the first and second nucleic acid molecules are complementary. As used herein, “specifically hybridizes” refers to preferential hybridization under nucleic acid synthesis conditions of a primer, oligonucleotide, or probe, to a nucleic acid molecule having a sequence complementary to the primer, oligonucleotide, or probe compared to hybridization to a nucleic acid molecule not having a complementary sequence. For example, specific hybridization includes the hybridization of a primer, oligonucleotide, or probe to a target nucleic acid sequence that is complementary to the primer, oligonucleotide, or probe. Primer, oligonucleotide, or probe sequences and length can affect hybridization to target nucleic acid sequences. Depending on the degree of mismatch between the primer, oligonucleotide, or probe and target nucleic acid, low, medium or high stringency conditions may be used to effect primer / target, oligonucleotide / target, or probe / target annealing. As used herein, the term “stringent conditions” refers to conditions for hybridization and washing. Methods for hybridization reaction temperature condition optimization are known, and can be found, e.g., in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y., 6.3.1-6.3.6 (1989). Aqueous and non-aqueous methods are described in the aforementioned reference and either can be used. Non-limiting examples of stringent hybridization conditions include, for example, hybridization in 6X sodium chloride / sodium citrate (SSC) at about 45ºC, followed by one or more washes in 0.2X SSC, 0.1% SDS at 50ºC. Another example of stringent hybridization conditions includes hybridization in 6X sodium chloride / sodium citrate (SSC) at about 45ºC, followed by one or more washes in 0.2X SSC, 0.1% SDS at 55ºC. A further AMG-1022 example of stringent hybridization conditions includes hybridization in 6X sodium chloride / sodium citrate (SSC) at about 45ºC, followed by one or more washes in 0.2X SSC, 0.1% SDS at 60ºC. Often, stringent hybridization conditions are hybridization in 6X sodium chloride / sodium citrate (SSC) at about 45ºC, followed by one or more washes in 0.2X SSC, 0.1% SDS at 65ºC. More often, stringency conditions can include 0.5 M sodium phosphate, 7% SDS at 65ºC, followed by one or more washes at 0.2X SSC, 1% SDS at 65ºC. Stringent hybridization temperatures also can be altered (generally, lowered) with the addition of certain organic solvents, such as formamide for example. Organic solvents such as formamide can reduce the thermal stability of double-stranded polynucleotides, so that hybridization can be performed at lower temperatures, while still maintaining stringent conditions and extending the useful life of heat labile nucleic acids. In some embodiments, target nucleic acids comprise degraded DNA. Degraded DNA may be referred to as low-quality DNA or highly degraded DNA. Degraded DNA may be highly fragmented and may include damage such as base analogs and abasic sites subject to miscoding lesions and / or intermolecular crosslinking. For example, sequencing errors resulting from deamination of cytosine residues may be present in certain sequences obtained from degraded DNA (e.g., miscoding of C to T and G to A). Nucleic acid may be derived from one or more sources (e.g., a biological sample described herein) by methods known in the art. Any suitable method can be used for isolating, extracting and / or purifying DNA from a biological sample (e.g., from blood or a blood product, tissue, tumor), non-limiting examples of which include methods of DNA preparation, various commercially available reagents or kits, such as DNeasy®, RNeasy®, QIAprep®, QIAquick®, and QIAamp®(e.g., QIAamp®Circulating Nucleic Acid Kit, QiaAmp®DNA Mini Kit or QiaAmp®DNA Blood Mini Kit) nucleic acid isolation / purification kits by Qiagen, Inc. (Germantown, Md); GenomicPrep™ Blood DNA Isolation Kit (Promega, Madison, Wis.); GFX™ Genomic Blood DNA Purification Kit (Amersham, Piscataway, N.J.); DNAzol®, ChargeSwitch®, Purelink®, GeneCatcher®nucleic acid isolation / purification kits by Life Technologies, Inc. (Carlsbad, CA); NucleoMag®, NucleoSpin®, and NucleoBond®nucleic acid isolation / purification kits by Clontech Laboratories, Inc. (Mountain View, CA); the like or combinations thereof. In certain aspects, nucleic acid is isolated from a fixed biological sample, e.g., formalin-fixed, paraffin-embedded (FFPE) tissue. Genomic DNA from FFPE tissue may be isolated using commercially available kits – such as the AllPrep®DNA / RNA FFPE kit by Qiagen, Inc. (Germantown, Md), the RecoverAll®Total Nucleic Acid Isolation kit for FFPE by Life Technologies, Inc. (Carlsbad, CA), and the NucleoSpin®FFPE kits by Clontech Laboratories, Inc. (Mountain View, CA). In some embodiments, nucleic acid is extracted from EVs using a lysis procedure. Lysis procedures and reagents are known in the art and may generally be performed by chemical (e.g., detergent, hypotonic solutions, enzymatic procedures, and the like, or combination thereof), physical (e.g., French press, sonication, and the like), or electrolytic lysis methods. Any AMG-1022 suitable lysis procedure can be utilized. For example, chemical methods generally employ lysing agents to disrupt EVs and extract the nucleic acids from the EVs, followed by treatment with chaotropic salts. Physical methods such as freeze / thaw followed by grinding, the use of cell presses and the like also are useful. In some instances, a high salt and / or an alkaline lysis procedure may be utilized. In some instances, a lysis procedure may include a lysis step with EDTA / Proteinase K, a binding buffer step with high amounts of salts (e.g., guanidinium chloride (GuHCl), sodium acetate) and isopropanol, and binding DNA in this solution to silica-based column. Nucleic acids can be present in and obtained from blood (e.g., from the blood of a human subject). Non-limiting examples of sources for EVs are blood, blood plasma, blood serum and urine. In certain aspects, EVs are obtained from a body fluid sample chosen from whole blood, blood plasma, blood serum, amniotic fluid, saliva, urine, pleural effusion, bronchial lavage, bronchial aspirates, breast milk, colostrum, tears, seminal fluid, peritoneal fluid, pleural effusion, and stool. As used herein, the term “obtain” includes obtaining a sample of EVs or nucleic acids derived from EVs directly (e.g., collecting a sample, e.g., a test sample) or obtaining a sample from another who has collected a sample. EVs may be a product of cellular secretion and / or nucleic acid release (e.g., DNA release). Extracellular nucleic acid may be a product of any form of cell death, for example. In some instances, EVs are a product of any form of type I or type II cell death, including mitotic, oncotic, toxic, ischemic, and the like and combinations thereof. Without being limited by theory, EVs may be a product of cell apoptosis and cell breakdown. In some instances, EVs are a product of cell necrosis, necropoptosis, oncosis, entosis, pyrotosis, and the like and combinations thereof. In some embodiments, sample nucleic acid from a test subject is nucleic acids derived from EVs. In some embodiments, nucleic acids are derived from EVs from blood plasma or blood serum from a test subject. In some aspects, nucleic acids derived from EVs are degraded. In certain aspects, nucleic acids derived from EVs comprise cancer nucleic acid (e.g., cancer DNA). In certain aspects, nucleic acids are derived from EVs comprising tumor nucleic acid (e.g., tumor DNA). Nucleic acid derived from EVs can include different nucleic acid species, and therefore is referred to herein as "heterogeneous" in certain embodiments. For example, blood serum or plasma from a person having a tumor or cancer can include EVs with nucleic acid from tumor cells or cancer cells (e.g., neoplasia) and nucleic acid from non-tumor cells or non-cancer cells. In some instances, cancer nucleic acid and / or tumor nucleic acid sometimes is about 5% to about 50% of the overall nucleic acid (e.g., about 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, or 49% of the total nucleic acid is cancer, or tumor nucleic acid). Nucleic acid may be provided for conducting methods described herein with or without processing of the sample(s) containing the nucleic acid. In some embodiments, nucleic acid is provided for conducting methods described herein after processing of the sample(s) containing AMG-1022 the nucleic acid. For example, a nucleic acid can be extracted, isolated, purified, partially purified or amplified from the sample(s). The term “isolated” as used herein refers to nucleic acid removed from its original environment (e.g., the natural environment if it is naturally occurring, or a host cell if expressed exogenously), and thus is altered by human intervention (e.g., "by the hand of man") from its original environment. The term “isolated nucleic acid” as used herein can refer to a nucleic acid removed from a subject (e.g., a human subject). An isolated nucleic acid can be provided with fewer non-nucleic acid components (e.g., protein, lipid) than the amount of components present in a source sample. A composition comprising isolated nucleic acid can be about 50% to greater than 99% free of non-nucleic acid components. A composition comprising isolated nucleic acid can be about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater than 99% free of non-nucleic acid components. The term “purified” as used herein can refer to a nucleic acid provided that contains fewer non-nucleic acid components (e.g., protein, lipid, carbohydrate) than the amount of non-nucleic acid components present prior to subjecting the nucleic acid to a purification procedure. A composition comprising purified nucleic acid may be about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater than 99% free of other non-nucleic acid components. The term “purified” as used herein can refer to a nucleic acid provided that contains fewer nucleic acid species than in the sample source from which the nucleic acid is derived. A composition comprising purified nucleic acid may be about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater than 99% free of other nucleic acid species. In certain examples, small fragments of nucleic acid (e.g., 30 to 500 bp fragments) can be purified, or partially purified, from a mixture comprising nucleic acid fragments of different lengths. In certain examples, nucleosomes comprising smaller fragments of nucleic acid can be purified from a mixture of larger nucleosome complexes comprising larger fragments of nucleic acid. In certain examples, larger nucleosome complexes comprising larger fragments of nucleic acid can be purified from nucleosomes comprising smaller fragments of nucleic acid. In certain examples, cancer cell nucleic acid can be purified from a mixture comprising cancer cell and non-cancer cell nucleic acid. In certain examples, nucleosomes comprising small fragments of cancer cell nucleic acid can be purified from a mixture of larger nucleosome complexes comprising larger fragments of non-cancer nucleic acid. In some embodiments, nucleic acid is provided for conducting methods described herein without prior processing of the sample(s) containing the nucleic acid. For example, nucleic acid may be analyzed directly from a sample without prior extraction, purification, partial purification, and / or amplification. In certain instances, cleavage conditions include contacting the sample nucleic acid with an endonuclease, such as a restriction endonuclease, and sometimes the restriction endonuclease cleaves the sample nucleic acid at ^GATC and G^ANTC, where “^” represents the cut site. In certain instances, sample nucleic acid is contacted with two or more restriction AMG-1022 enzyme types. In certain implementations, linking conditions comprise contacting the nucleic acid fragments with a ligase under conditions in which ends of fragments in proximity are joined. Methodology for preparing proximity ligated nucleic acid is known in the art, and non-limiting examples of such methodology are referred to as Hi-C, 3C, 4C, ChiA-PET and variants thereof (e.g., capture Hi-C), as described additionally herein. In certain instances, oligonucleotide probes include a capture agent, and the complexes are isolated by contacting the complexes with a solid phase comprising a capture agent counterpart that specifically binds to the capture agent under binding conditions. A solid phase sometimes is a plurality of beads, such as magnetic or SEPHAROSE (TM) beads for example. In certain implementations, (i) a capture agent is selected from biotin, avidin and streptavidin, and (ii) the capture agent counterpart is a molecule that specifically binds to the capture agent and independently is selected from biotin, avidin and streptavidin. Hybridization complexes can be isolated by contacting the complexes with a solid phase that includes a capture agent counterpart under conditions in which the capture agent counterpart of the solid phase specifically binds to a capture agent associated with the oligonucleotide probes of the hybridization complexes, and separating the complexes bound to the solid phase from complexes not bound to the solid phase. Any suitable method for carrying out proximity ligation may be used. For example, a Hi- C method typically includes the following steps: (1) digesting the DNA of a chromatin sample with a restriction enzyme (or more broadly, fragmenting), where a non-limiting example of a chromatin sample is chromatin obtained from solubilized and decompacted FFPE (formalin- fixed paraffin embedded) tissue; (2) labelling the digested ends by filling in the 5’-overhangs, such as with biotinylated nucleotides; and (3) ligating the spatially proximal fragmented ends, thus preserving spatial-proximity information of the nucleic acids. Once spatial-proximal contiguity information is preserved, further steps in a HiC method may include: purifying and enriching biotin–labelled ligation junction fragments, preparing a library from the enriched fragments and sequencing the library. Another example of a proximity ligation method may include the following steps: (1) digestion of a chromatin sample with a restriction enzyme (or fragmentation), where a non-limiting example of a chromatin sample is chromatin obtained from solubilized and decompacted FFPE (formalin-fixed paraffin embedded) tissue; (2) blunting the digested or fragmented ends or omission of the blunting procedure; and (3) ligating the spatially proximal ends, thus preserving spatial-proximal contiguity information. Once spatial-proximal contiguity information is preserved, further steps can include: size selection and affinity purification to purify and enrich ligated fragments, which represent ligation junction fragments, preparing a library from the enriched fragments and sequencing the library. In some embodiments, proximity ligated nucleic acid molecules are generated in situ (i.e., within a nucleus). For methods that include Capture HiC, a further step is included where ligation AMG-1022 products containing certain nucleic acid sequences are enriched using one or more capture probes (see e.g., International Patent Application Publication No. WO 2014 / 168575). A capture probe generally includes a short sequence of nucleotides or oligonucleotide (e.g., 10-500 bases in length) capable of hybridizing to another nucleotide sequence. In some embodiments, a capture probe includes a label, e.g., a label for selectively purifying specific nucleic acid sequences of interest. Labels are discussed herein and can include, for example, a biotin or digoxigenin label. Processes that include preparing hybridization complexes comprising proximity ligated nucleic acid hybridized to oligonucleotide probes and then isolating the complexes can enrich the relative abundance of polynucleotides in sample nucleic acid complementary to the oligonucleotide probe polynucleotides, which are referred to as “target polynucleotides” herein. As oligonucleotide probes described herein include polynucleotides complementary to oncogene introns, exons, promoters, and external regions, such probes are useful for enriching oncogene polynucleotides in a sample. A subset of hybridization complexes containing proximity ligated nucleic acid hybridized to probes described herein typically is enriched for oncogene target polynucleotides. Target polynucleotides (e.g., oncogene oligonucleotides) generally are enriched in a subset of hybridization complexes containing proximity ligated nucleic acid hybridized, or that was hybridized, to the probes, relative to all proximity ligated nucleic acid prepared from a nucleic acid sample. Stated another way, the abundance (e.g., percentage) of target polynucleotides (e.g., oncogene polynucleotides) generally is greater in the subset of hybridization complexes containing proximity ligated nucleic acid hybridized, or that was hybridized, to the probes, relative to the abundance of target polynucleotides (e.g., percentage) in all proximity ligated nucleic acid prepared from a nucleic acid sample. Target nucleic acid sometimes is modified as part of a nucleic acid analysis process. A target nucleic acid can be modified to include an identifier (e.g., a tag, an indexing tag), a capture sequence, a label, an adapter, a restriction enzyme site, a promoter, an enhancer, an origin of replication, a stem loop, a complimentary sequence (e.g., a primer binding site, an annealing site), a suitable integration site (e.g., a transposon, a viral integration site), a modified nucleotide, a unique molecular identifier (UMI), the like or combinations thereof. In some embodiments, a nucleic acid or isolated nucleic acid comprises one or more adapters (e.g., sequencing adapters, also known as sequencing adapter oligonucleotides). Sequencing adapters may comprise sequences complementary to flow-cell anchors, and sometimes are utilized to immobilize a nucleic acid to a solid support, such as the inside surface of a flow cell, for example. Adapters and other polynucleotide components described typically are not associated with the nucleic acid in vivo and thereby do not naturally occur with the nucleic acid. In certain instances, analyzing the nucleic acid in the complexes includes sequencing the proximity ligated nucleic acid of the isolated complexes. Target nucleic acid sometimes is modified as part of a sequencing process. In certain implementations, non-naturally occurring AMG-1022 oligonucleotides that facilitate sequencing, known as “sequencing adapter oligonucleotides,” are joined to proximity ligated nucleic acid in the oligonucleotide probe-isolated proximity ligated nucleic acid, thereby forming adapter-modified nucleic acid. Adapter-modified nucleic acid is optionally amplified by an amplification process known in the art, and the adapter-modified nucleic acid (or amplified adapter-modified nucleic acid) is then subjected to sequencing conditions to identify the polynucleotide sequence of proximity ligated nucleic acid. Additional aspects of nucleic acid analytical methodology are described herein. Analysis of nucleic acid from a sample can identify one or more structural variants in the nucleic acid relative to nucleic acid from a reference genome or from another sample in certain instances. Various types of structural variants that can be identified are described herein. Samples Provided herein are methods and compositions for processing and / or analyzing nucleic acid. Nucleic acid utilized in methods and compositions described herein may be isolated from a sample obtained from a subject (e.g., a test subject). A subject can be any living or non-living organism, including but not limited to a human and a non-human animal. Any human or non- human animal can be selected, and may include, for example, mammal, reptile, avian, amphibian, fish, ungulate, ruminant, bovine (e.g., cattle), equine (e.g., horse), caprine and ovine (e.g., sheep, goat), swine (e.g., pig), camelid (e.g., camel, llama, alpaca), monkey, ape (e.g., gorilla, chimpanzee), ursid (e.g., bear), poultry, dog, cat, mouse, rat, fish, dolphin, whale and shark. In some embodiments, a subject is a human. A subject may be a male or female. A subject may be any age (e.g., an embryo, a fetus, an infant, a child, an adult). A subject may be a cancer patient, a patient suspected of having cancer, a patient in remission, a patient with a family history of cancer, and / or a subject obtaining a cancer screen. In some embodiments, a subject is an adult patient. In some embodiments, a subject is a pediatric patient. A nucleic acid sample may be isolated or obtained from any type of suitable biological specimen or sample (e.g., a test sample). A nucleic acid sample may be isolated or obtained from a single cell, a plurality of cells (e.g., cultured cells), cell culture media, conditioned media, a tissue, an organ, or an organism. In some embodiments, a nucleic acid sample is isolated or obtained from a cell(s), tissue, organ, and / or the like of an animal (e.g., an animal subject). In some instances, a nucleic acid sample may be obtained as part of a diagnostic analysis. A sample or test sample may be any specimen that is isolated or obtained from a subject or part thereof (e.g., a human subject, a cancer patient, a tumor). Non-limiting examples of specimens include fluid or tissue from a subject, including, without limitation, blood or a blood product (e.g., serum, plasma, or the like), umbilical cord blood, chorionic villi, amniotic fluid, cerebrospinal fluid, spinal fluid, lavage fluid (e.g., bronchoalveolar, gastric, peritoneal, ductal, ear, arthroscopic), biopsy sample (e.g., from pre-implantation embryo; cancer biopsy), celocentesis sample, cells (blood cells, placental cells, embryo or fetal cells, fetal nucleated AMG-1022 cells or fetal cellular remnants, normal cells, abnormal cells (e.g., cancer cells)) or parts thereof (e.g., mitochondrial, nucleus, extracts, or the like), washings of female reproductive tract, urine, feces, sputum, saliva, nasal mucous, prostate fluid, lavage, semen, lymphatic fluid, bile, tears, sweat, breast milk, breast fluid, the like or combinations thereof. In some embodiments, a biological sample is a cervical swab from a subject. A fluid or tissue sample from which nucleic acid is extracted may be acellular (e.g., cell-free). In some embodiments, a fluid or tissue sample may contain cellular elements or cellular remnants. In some embodiments, cancer cells may be included in the sample. A sample can be a liquid sample. A liquid sample can comprise extracellular nucleic acid (e.g., circulating cell-free DNA). Examples of liquid samples include, but are not limited to, blood or a blood product (e.g., serum, plasma, or the like), urine, cerebrospinal fluid, saliva, sputum, biopsy sample (e.g., liquid biopsy for the detection of cancer), a liquid sample described above, the like or combinations thereof. In certain embodiments, a sample is a liquid biopsy, which generally refers to an assessment of a liquid sample from a subject for the presence, absence, progression or remission of a disease (e.g., cancer). A liquid biopsy can be used in conjunction with, or as an alternative to, a solid biopsy (e.g., tumor biopsy). In certain instances, extracellular nucleic acid is analyzed in a liquid biopsy. In some embodiments, a biological sample may be blood, plasma or serum. The term “blood” encompasses whole blood, blood product or any fraction of blood, such as serum, plasma, buffy coat, or the like as conventionally defined. Blood or fractions thereof often comprise nucleosomes. Nucleosomes comprise nucleic acids and are sometimes cell-free or intracellular. Blood also comprises buffy coats. Buffy coats are sometimes isolated by utilizing a ficoll gradient. Buffy coats can comprise white blood cells (e.g., leukocytes, T-cells, B-cells, platelets, and the like). Blood plasma refers to the fraction of whole blood resulting from centrifugation of blood treated with anticoagulants. Blood serum refers to the watery portion of fluid remaining after a blood sample has coagulated. Fluid or tissue samples often are collected in accordance with standard protocols hospitals or clinics generally follow. For blood, an appropriate amount of peripheral blood (e.g., between 3 to 40 milliliters, between 5 to 50 milliliters) often is collected and can be stored according to standard procedures prior to or after preparation. An analysis of nucleic acid found in a subject’s blood may be performed using, e.g., whole blood, serum, or plasma. An analysis of tumor or cancer DNA found in a patient’s blood, for example, may be performed using, e.g., whole blood, serum, or plasma. Methods for preparing serum or plasma from blood obtained from a subject (e.g., patient; cancer patient) are known. For example, a subject’s blood (e.g., patient’s blood; cancer patient’s blood) can be placed in a tube containing EDTA or a specialized commercial product such as Cell-Free DNA BCT (Streck, Omaha, NE) or Vacutainer SST (Becton Dickinson, Franklin Lakes, N.J.) to prevent blood clotting, and plasma can then be obtained from whole blood through AMG-1022 centrifugation. Serum may be obtained with or without centrifugation-following blood clotting. If centrifugation is used then it is typically, though not exclusively, conducted at an appropriate speed, e.g., 1,500-3,000 times g. Plasma or serum may be subjected to additional centrifugation steps before being transferred to a fresh tube for nucleic acid extraction. In addition to the acellular portion of the whole blood, nucleic acid may also be recovered from the cellular fraction, enriched in the buffy coat portion, which can be obtained following centrifugation of a whole blood sample from the subject and removal of the plasma. A sample may be a tumor nucleic acid sample (i.e., a nucleic acid sample isolated from a tumor). The term “tumor” generally refers to neoplastic cell growth and proliferation, whether malignant or benign, and may include pre-cancerous and cancerous cells and tissues. The terms “cancer” and “cancerous” generally refer to the physiological condition in mammals that is typically characterized by unregulated cell growth / proliferation. In some embodiments, a sample is a blood sample, or a urine sample. In some embodiments, a sample comprises formalin-fixed, paraffin-embedded (FFPE) tissue. In some embodiments, a sample comprises frozen tissue. In some embodiments, a sample comprises EVs derived from peripheral blood. In some embodiments, a sample comprises EVs derived from blood obtained from bone marrow. In some embodiments, a sample comprises EVs obtained from urine. In some embodiments, a sample comprises nucleic acids derived from EVs. In some embodiments, a sample comprises EVs originating from a tumor cell. In some embodiments, a sample comprises an EV or nucleic acid originating from a solid tumor. In some embodiments, a sample comprises an EV or nucleic acid originating from a blood tumor. Nucleic acid analysis methodology Non-limiting examples of processes for analyzing nucleic acid include amplification (e.g., polymerase chain reaction (PCR)), whole genome sequencing, targeted enrichment followed by sequencing, microarray, and fluorescence in situ hybridization (FISH), methods that preserves spatial-proximity information in the nucleic acids, and methods that generate proximity ligated nucleic acid molecules. In some embodiments, a nucleic acid analysis comprises nucleic acid amplification. For example, nucleic acids may be amplified under amplification conditions. The term “amplified” or “amplification” or “amplification conditions” generally refer to subjecting a target nucleic acid in a sample to a process that linearly or exponentially generates amplicon nucleic acids having the same or substantially the same nucleotide sequence as the target nucleic acid, or part thereof. In certain embodiments, the term “amplified” or “amplification” or “amplification conditions” refers to a method that comprises a polymerase chain reaction (PCR). Detecting a structural variant (SV) described herein using amplification (e.g., PCR) may include use of a primer(s) designed to hybridize to a region upstream (e.g., 5’) of one or more SV breakpoints, and / or hybridize to a region downstream (e.g., 3’) of one or more SV breakpoints, hybridize to a region AMG-1022 adjacent to one or more SV breakpoints, and / or hybridize to a region spanning one or more SV breakpoints. Examples of PCR primers useful for identifying a structural variant are provided herein. In some embodiments, a nucleic acid analysis comprises fluorescence in situ hybridization (FISH). Fluorescence in situ hybridization (FISH) is a technique that uses fluorescent probes that bind to a nucleic acid sequence(s) with a high degree of sequence complementarity. In certain configurations, fluorescence microscopy may be used to observe where the fluorescent probe(s) is / are bound to a chromosome. Detecting a structural variant (SV) described herein using fluorescence in situ hybridization (FISH) may include use of probes designed to hybridize to a region upstream (e.g., 5’) of one or more SV breakpoints and hybridize to a region downstream (e.g., 3’) of one or more SV breakpoints, hybridize to a region adjacent to one or more SV breakpoints, and / or hybridize to a region spanning one or more SV breakpoints. Examples of FISH techniques include ‘break-apart’ FISH techniques, dual fusion FISH techniques, and others known in the art. Examples of probes useful for identifying a structural variant are provided herein. In some embodiments, a nucleic acid analysis comprises a microarray (e.g., a DNA microarray, DNA chip, biochip). A DNA microarray is a collection of DNA probes attached to a solid surface. Probes can be short sections of a gene or other genomic DNA element that can hybridize to target nucleic acids in a sample (e.g., under high-stringency conditions). Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine presence, absence, and / or relative abundance of target nucleic acid sequences in the sample. Detecting a structural variant (SV) described herein using DNA microarrays may include use of array probes designed to hybridize to a region upstream (e.g., 5’) of one or more SV breakpoints, hybridize to a region downstream (e.g., 3’) of one or more SV breakpoints, hybridize to a region adjacent to one or more SV breakpoints, and / or hybridize to a region spanning one or more SV breakpoints. Examples of array probes useful for identifying a structural variant are provided herein. In some embodiments, a nucleic acid analysis comprises sequencing (e.g., genome- wide sequencing, targeted sequencing). For targeted sequencing, a target nucleic acid may be amplified (e.g., by PCR with primers specific to universal adaptor sequences and enriched using a probe-based approach, where one or more probes hybridize to a target nucleic acid prior to sequencing, or enriched using other methods involving linear or exponential amplification techniques with at least one primer specific to the target (e.g. anchored multiplex PCR (AMP)), or enriched using Cas9-mediated approaches, such as Cas9-guided adapter ligation, as described in Gilpatrick, T. et al., Targeted nanopore sequencing with Cas9-guided adapter ligation, Nature Biotechnology, volume 38, pages 433–438 (2020). Nucleic acid may be sequenced using any suitable sequencing platform including a Sanger sequencing platform, a high throughput or massively parallel sequencing (next generation sequencing (NGS)) platform, AMG-1022 or the like, such as, for example, a sequencing platform provided by Illumina®(e.g., NovaSeq, HiSeq™, MiSeq™ and / or Genome Analyzer™ sequencing systems); Oxford Nanopore™ Technologies (e.g., MinION sequencing system) or other nanopore sequencing platforms, Ion Torrent™ (e.g., Ion PGM™ and / or Ion Proton™ sequencing systems); Pacific Biosciences (e.g., PACBIO Sequel, Revio, or Onso sequencing systems); Life Technologies™ (e.g., SOLiD sequencing system); Roche (e.g., 454 GS FLX+ and / or GS Junior sequencing systems), Element AVITI™ system, Singular G4 system, Ultima Genomics UG100™ ; or any other suitable sequencing platform. In some embodiments, the sequencing process is a highly multiplexed sequencing process. In certain instances, a full or substantially full sequence is obtained and sometimes a partial sequence is obtained. Nucleic acid sequencing generally produces a collection of sequence reads. As used herein, “reads” (e.g., “a read,” “a sequence read”) are short sequences of nucleotides produced by any sequencing process described herein or known in the art. Reads can be generated from one end of nucleic acid fragments (single-end reads), and sometimes are generated from both ends of nucleic acid fragments (e.g., paired-end reads, double-end reads). In some embodiments, a sequencing process generates short sequencing reads or “short reads.” In some embodiments, the nominal, average, mean or absolute length of short reads sometimes is about 10 continuous nucleotides to about 250 or more contiguous nucleotides. In some embodiments, the nominal, average, mean or absolute length of short reads sometimes is about 50 continuous nucleotides to about 150 or more contiguous nucleotides. In some embodiments, a nucleic acid analysis comprises a method that preserves spatial-proximal relationships and / or spatial-proximal contiguity information (see e.g., International PCT Application Publication No. WO2019 / 104034; International PCT Application Publication No. WO2020 / 106776; International PCT Application Publication No. WO2020236851; Kempfer, R., & Pombo, A. (2019). Methods for mapping 3D chromosome architecture. Nature Reviews Genetics. doi:10.1038 / s41576-019-0195-2; and Schmitt, Anthony D.; Hu, Ming; Ren, Bing (2016). Genome-wide mapping and analysis of chromosome architecture. Nature Reviews Molecular Cell Biology. doi:10.1038 / nrm.2016.104; each of which is incorporated by reference in its entirety, to the extent permitted by law). Methods that preserve spatial-proximity relationships and / or spatial-proximal contiguity information generally refer to methods that capture and preserve the native spatial conformation exhibited by nucleic acids when associated with proteins as in chromatin and / or as part of a nuclear matrix. Spatial- proximal contiguity information can be preserved by proximity ligation, by solid substrate- mediated proximity capture (SSPC), by compartmentalization with or without a solid substrate or by use of a Tn5 tetramer. Methods that preserve spatial-proximal contiguity information may be based on proximity ligation or may be based on a different principle where spatial proximity is inferred. Methods based on proximity ligation may include, for example, 3C, 4C, 5C, Hi-C, TCC, GCC, TLA, PLAC-seq, HiChIP, ChIA-PET, Capture-C, Capture-HiC, single-cell HiC, sciHiC, AMG-1022 single-cell 3C, single-cell methyl-3C, DNAase HiC, Micro-C, Tiled-C, and Low-C. Methods where spatial proximity is inferred based on a principle other than proximity ligation may include, for example, SPRITE, scSPRITE, Genome Architecture Mapping (GAM), ChIA-Drop, imaging- based approaches using labeled probes and visualization of probe-bound DNA (e.g. FISH and derivative techniques based on the principles of visualizing the relative localization of fluorescent probe-bound nucleic acids), and may also include sequencing of an imaged sample (e.g. in situ Genome Sequencing (IGS)). In some embodiments, a nucleic acid analysis comprises generating proximity ligated nucleic acid molecules (e.g., using a method described herein). In some embodiments, a nucleic acid analysis comprises sequencing the proximity ligated nucleic acid molecules, e.g., by a suitable sequencing process known in the art or described herein. In some embodiments, a nucleic acid analysis comprises a method for preparing nucleic acids from particular types of samples that preserves spatial-proximity information in the sequence of the nucleic acids. Nucleic acid molecules that preserve spatial-proximity information can be fragmented and sequenced using short-read sequencing methods (e.g., Illumina, nucleic acid fragments of lengths approximately 500 bp) or intact molecules that preserve spatial-proximity information can be sequenced using long-read sequencing (e.g., Oxford Nanopore, PacBio, or others, nucleic acid fragments of lengths approximately 5kbp or greater). Nucleic acid molecules that preserve spatial-proximity information can be fragmented and sequenced using synthetic long-read sequencing methods (e.g. Illumina Complete Long Reads, Universal Sequencing Technology TELL-seq, and MGI stLFR). In certain embodiments, a sample can be a fixed sample that is embedded in a material such as paraffin (wax). In some embodiments, a sample can be a formalin fixed sample. In certain embodiments, a sample is formalin-fixed paraffin-embedded (FFPE) sample. In some embodiments, a formalin-fixed paraffin-embedded sample can be a tissue sample or a cell culture sample. In some embodiments, a tissue sample has been excised from a patient and can be diseased or damaged. In some embodiments, a tissue sample is not known to be diseased or damaged. In certain embodiments, a formalin-fixed paraffin-embedded sample can be a formalin-fixed paraffin-embedded section, block, scroll or slide. In certain embodiments, a sample can be a deeply formalin-fixed sample, as described below. In certain embodiments, a formalin-fixed paraffin-embedded sample is provided on a solid surface and a method of preparing nucleic acid that preserves spatial-proximal contiguity information is performed on the solid surface. In some embodiments, a solid surface is a pathology slide. In some embodiments, additional downstream reactions are also performed on the solid surface. Those of skill in the art are familiar with methods that can be substituted for steps requiring centrifugation and that achieve a comparable result but are performed on a solid surface. AMG-1022 In some embodiments, methods that preserve spatial-proximal contiguity information comprise methods that generate proximity ligated nucleic acid molecules (e.g., using proximity ligation). A proximity ligation method is one in which natively occurring spatially proximal nucleic acid molecules are captured by ligation to generate ligated products. Proximity ligation methods generally capture spatial-proximity information in the form of ligation products, whereby a ligation junction is formed between two natively spatially proximal nucleic acids. Once the ligation products are formed, the spatial-proximal contiguity information is detected, such as using next generation sequencing, whereby one or more ligation junctions (either from an entire ligation product or fragment of a ligation product) are sequenced (as described herein). With this sequence information, one is informed that the nucleic acid molecules from a given ligation product (or ligation junction) are natively spatially proximal nucleic acids. In some embodiments, reagents that generate proximity ligated nucleic acid molecules can include a restriction endonuclease, a DNA polymerase, a plurality of nucleotides comprising at least one biotinylated nucleotide, and a ligase. In certain embodiments, two or more restriction endonucleases are used. Any suitable method for carrying out proximity ligation may be used, as described herein. Structural variants Provided herein are methods for detecting the presence or absence of a structural variant in a sample. In certain aspects, provided is a method for detecting the presence or absence of a structural variant in a sample, the method comprising analyzing sample nucleic acid from a subject, wherein the analyzing comprises: generating proximity ligated nucleic acid molecules; contacting the proximity ligated nucleic acid molecules with one or more oligonucleotide probes described herein, thereby generating enriched proximity ligated nucleic acid molecules; sequencing the enriched proximity ligated nucleic acid molecules, thereby generating sequences of the sample nucleic acid; and determining the presence or absence of a structural variant in the sample nucleic acid from the sequences. In certain instances, the method includes comparing sequences of the sample nucleic acid to sequences of a reference genome to determine the presence or absence of a structural variant. A structural variant may be referred to as a structural variation and / or a chromosomal rearrangement. A structural variant may comprise one or more of a translocation, inversion, insertion, deletion, and duplication. In some embodiments, a structural variant comprises a microduplication and / or a microdeletion. In some embodiments, a structural variant comprises a fusion (e.g., a gene fusion where a portion of a first gene is inserted into a portion of a second gene). Any type of structural variant, whether it be translocation, inversion, insertion, deletion, and / or duplication as described below, can be of any length, and in some embodiments, is about 1 base or base pair (bp) to about 250 megabases (Mb) in length. In some embodiments, a structural variation is about 1 base or base pair (bp) to about 50,000 kilobases (kb) in length (e.g., about 10 bp, 50 bp, 100 bp, 500 bp, 1 kb, 5 kb, 10kb, 50 kb, 100 kb, 500 kb, 1000 kb, AMG-1022 5000 kb or 10,000 kb in length). A structural variant may be intra-chromosomal (rearrangement of genomic material within a chromosome) or inter-chromosomal (rearrangement of genomic material between two or more chromosomes). A structural variant may comprise a translocation. A translocation is a genetic event that results in a rearrangement of chromosomal material. Translocations may include reciprocal translocations and Robertsonian translocations. A reciprocal translocation is a chromosome abnormality caused by exchange of parts between non-homologous chromosomes - two detached fragments of two different chromosomes are switched. A Robertsonian translocation occurs when two non-homologous chromosomes become attached, meaning that given two healthy pairs of chromosomes, one of each pair sticks and blends together homogeneously. A gene fusion may be created when a translocation joins two genes that are normally separate. Translocations may be balanced (i.e., in an even exchange of material with no genetic information extra or missing, sometimes with full functionality) or unbalanced (i.e., where the exchange of chromosome material is unequal resulting in extra or missing genes or fragments thereof). A structural variant may comprise an inversion. An inversion is a chromosome rearrangement in which a segment of a chromosome is reversed end-to-end. An inversion may occur when a single chromosome undergoes breakage and rearrangement within itself. Inversions may be of two types: paracentric and pericentric. Paracentric inversions do not include the centromere, and both breaks occur in one arm of the chromosome. Pericentric inversions include the centromere, and there is a break point in each arm. A structural variant may comprise an insertion. An insertion may be the addition of one or more nucleotide base pairs into a nucleic acid sequence. An insertion may be a microinsertion (generally a submicroscopic insertion of any length ranging from 1 base to about 10 megabases (e.g., about 1 megabase to about 3 megabases)). In certain embodiments, an insertion comprises the addition of a segment of a chromosome into a genome, chromosome, or segment thereof. In certain embodiments an insertion comprises the addition of an allele, a gene, an intron, an exon, any non-coding region, any coding region, segment thereof or combination thereof into a genome or segment thereof. In certain embodiments an insertion comprises the addition (e.g., insertion) of nucleic acid of unknown origin into a genome, chromosome, or segment thereof. In certain embodiments an insertion comprises the addition (e.g., insertion) of a single base. A structural variant may comprise a deletion. In certain embodiments, a deletion is a genetic aberration in which a part of a chromosome or a sequence of DNA is missing. A deletion can, in certain embodiments, result in the loss of genetic material. In embodiments, a deletion can be translocated to another portion of the genome (balanced translocation or unbalanced translocation), such as on the same chromosome (same arm of the chromosome or other arm of the chromosome) or on a different chromosome. Any number of nucleotides can AMG-1022 be deleted. A deletion can comprise the deletion of one or more entire chromosomes, a segment of a chromosome, an allele, a gene, an intron, an exon, any non-coding region, any coding region, a segment thereof or combination thereof. A deletion can comprise a microdeletion (generally a submicroscopic deletion of any length ranging from 1 base to about 10 megabases (e.g., about 1 megabase to about 3 megabases)). A deletion can comprise the deletion of a single base. A structural variant may comprise a duplication. In certain embodiments, a duplication is a genetic aberration in which a part of a chromosome or a sequence of DNA is copied and inserted back into the genome. In certain embodiments, a duplication is any duplication of a region of DNA. In some embodiments, a duplication is a nucleic acid sequence that is repeated, often in tandem, within a genome or chromosome. In some embodiments a duplication can comprise a copy of one or more entire chromosomes, a segment of a chromosome, an allele, a gene, an intron, an exon, any non-coding region, any coding region, segment thereof or combination thereof. A duplication can comprise a microduplication (generally a submicroscopic duplication of any length ranging from 1 base to about 10 megabases (e.g., about 1 megabase to about 3 megabases)). A duplication sometimes comprises one or more copies of a duplicated nucleic acid. A duplication may be characterized as a genetic region repeated one or more times (e.g., repeated 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 times). Duplications can range from small regions (thousands of base pairs) to whole chromosomes in some instances. Duplications may occur as the result of an error in homologous recombination or due to a retrotransposon event. A structural variant may include a plurality of chromosomal rearrangements (e.g., translocations, inversions, insertions, deletions, duplications). For example, a structural variant may include a plurality of intra-chromosomal rearrangements. In certain instances, a structural variant may include a plurality of inter-chromosomal rearrangements. In certain instances, a structural variant may include a plurality of intra-chromosomal rearrangements and inter- chromosomal rearrangements. A structural variant may be defined according to one or more breakpoints. A breakpoint generally refers to a genomic position (i.e., genomic coordinate) where a structural variant occurs (e.g., translocation, inversion, insertion, deletion, or duplication). A breakpoint may refer to a genomic position where an ectopic portion of genomic material is inserted (e.g., a recipient site for an insertion or a translocation). A breakpoint may refer to a genomic position where a portion of genomic material is deleted (e.g., a donor site for an insertion or a translocation). A breakpoint may refer to a pair of genomic positions (i.e., genomic coordinates) that have become flanking (i.e., adjacent) to one another as a result of a structural variant (e.g., translocation, inversion, insertion, deletion, or duplication). A breakpoint may be defined in terms of a position or positions in a reference genome. A breakpoint may be defined in terms of a position or positions in a human reference genome (e.g., HG38 human reference genome). Generally, genomic positions discussed herein are in reference to an HG38 human reference AMG-1022 genome, and corresponding and / or equivalent positions in any other human reference genome are contemplated herein. A breakpoint may be defined in terms mapping to a position or positions in a reference genome. A breakpoint may be defined in terms of mapping to a position or positions in a human reference genome (e.g., HG38 human reference genome). A breakpoint may map to a position in a reference genome when a nucleic acid sequence located upstream, downstream, or spanning the breakpoint aligns with a corresponding sequence in a reference genome. Any suitable mapping method (e.g., process, algorithm, program, software, module, the like or combination thereof) can be used and certain aspects of mapping processes are described hereafter. Mapping a nucleic acid sequence may comprise mapping one or more nucleic acid sequence reads (e.g., sequence information from a fragment whose physical genomic position is unknown), which can be performed in a number of ways, and often comprises alignment of the obtained sequence reads with a matching sequence in a reference genome. In such alignments, sequence reads generally are aligned to a reference sequence and those that align are designated as being "mapped", "a mapped sequence read" or “a mapped read”. The terms “aligned”, “alignment”, or “aligning” generally refer to two or more nucleic acid sequences that can be identified as a match (e.g., 100% identity) or partial match. Alignments can be done manually or by a computer (e.g., a software, program, module, or algorithm), non- limiting examples of which include the Efficient Local Alignment of Nucleotide Data (ELAND) computer program distributed as part of the Illumina Genomics Analysis pipeline. Alignment of a sequence read can be a 100% sequence match. In some cases, an alignment is less than a 100% sequence match (e.g., non-perfect match, partial match, partial alignment). In some embodiments an alignment is about a 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 79%, 78%, 77%, 76% or 75% match. In some embodiments, an alignment comprises a mismatch (i.e., a base not correctly paired with its canonical Watson-Crick base partner (e.g., A or T incorrectly paired with C or G). In some embodiments, an alignment comprises 1, 2, 3, 4 or 5 mismatches. Two or more sequences can be aligned using either strand. In certain embodiments a nucleic acid sequence is aligned with the reverse complement of another nucleic acid sequence. In certain instances, extra or missing bases within a sequence are expressed as gaps in an alignment and may or may not be factored into a percent identity calculation. For example, a percent identity calculation may include a number of mismatches and gaps or may include a number of mismatches only. Various computational methods can be used to map and / or align sequence reads to a reference genome. Non-limiting examples of computer algorithms that can be used to align sequences include, without limitation, BLAST, BLITZ, BWA, FASTA, BOWTIE 1, BOWTIE 2, ELAND, MAQ, PROBEMATCH, SOAP or SEQMAP, or variations thereof or combinations AMG-1022 thereof. In some embodiments, sequence reads can be aligned with reference sequences and / or sequences in a reference genome. In some embodiments, the sequence reads can be found and / or aligned with sequences in nucleic acid databases known in the art including, for example, GenBank, dbEST, dbSTS, EMBL (European Molecular Biology Laboratory) and DDBJ (DNA Databank of Japan). BLAST or similar tools can be used to search the identified sequences against a sequence database. A structural variant may be defined in terms of a receiving site and a donor site. A receiving site may be referred to as a first partner or “partner 1” and a donor site may be referred to as a second partner or “partner 2.” In some embodiments, a structural variant may be defined in terms of comprising an ectopic portion of genomic DNA (i.e., a portion of genomic DNA at a receiving site from a different region of a chromosome or from a different chromosome). The ectopic portion may be referred to as a donor portion. In some embodiments, a structural variant may comprise an ectopic portion of genomic DNA (i.e., a portion of genomic DNA at a receiving site from a different region of a chromosome or from a different chromosome). The ectopic portion may be referred to as a donor portion. If the ectopic portion (donor portion) is from the same chromosome as the structural variant, the ectopic portion may be from a location outside of the position ranges provided herein for certain structural variants. The ectopic portion may comprise genomic DNA from a genomic coordinate window provided herein, or part thereof. The ectopic portion may comprise genomic DNA from a genomic coordinate window provided herein, or part thereof, and may further comprise genomic DNA from a region outside of a genomic coordinate window provided herein. In some embodiments, an ectopic portion of genomic DNA is characterized by its location (e.g., observed location for a given sample or samples) at a receiving site (e.g., at a structural variant site). In some embodiments, an ectopic portion is characterized by its location (e.g., observed location for a given sample samples) relative to a coding region of a gene and / or oncogene. A coding region of a gene and / or oncogene generally refers to a part of the gene and / or oncogene that is transcribed and translated into protein (i.e., the sum total of its exons). In some embodiments, an ectopic portion is within a coding region of a gene and / or oncogene. In some embodiments, an ectopic portion is not within a coding region of a gene and / or oncogene. For example, an ectopic portion may be located in an intronic region, an intergenic region, or within another gene. In some embodiments, an ectopic portion is located at a position in proximity to a coding region for a gene and / or oncogene. The term “in proximity” may refer to spatial proximity and / or linear proximity. In some embodiments, a structural variant may comprise extrachromosomal DNA (ecDNA) (see e.g. Dong et al., Extrachromosomal DNA (ecDNA) in cancer: mechanisms, functions, and clinical implications, Front. Oncol.(2023) 13: 1194405). Spatial proximity generally refers to 3-dimensional chromatin proximity, which may be assessed according to a method that preserves spatial-proximity relationships, such as a AMG-1022 method described herein or any suitable method known in the art. An ectopic portion may be located at a position in spatial proximity to a coding region for a gene and / or oncogene when an ectopic portion and a gene and / or oncogene (or a fragment thereof) are ligated in a proximity ligation assay or are bound by a common solid phase in a solid substrate-mediated proximity capture (SSPC) assay, for example. Linear proximity generally refers to a linear base-pair distance, which may be assessed according to mapped distances in a reference genome, for example. Linear proximity distance may be provided as a distance between a 5’ or 3’ end of an ectopic portion and a 5’ or 3’ end of a gene and / or exon. An ectopic portion may be located at a position in linear proximity to a coding region of a gene and / or oncogene when the ectopic portion is within about 1,000 base pairs, about 2,000 base pairs, about 3,000 base pairs, about 4,000 base pairs, about 5,000 base pairs, about 10,000 base pairs, about 20,000 base pairs, about 30,000 base pairs, about 40,000 base pairs, about 50,000 base pairs, about 60,000 base pairs, about 70,000 base pairs, about 80,000 base pairs, about 90,000 base pairs, about 100,000 base pairs, about 200,000 base pairs, about 300,000 base pairs, about 400,000 base pairs, about 500,000 base pairs, about 600,000 base pairs, about 700,000 base pairs, about 800,000 base pairs, about 900,000 base pairs, or about 1,000,000 base pairs of a coding region of a gene and / or oncogene. A structural variant may be associated with one or more genes. For example, a structural variant may be associated with one or more oncogenes. An oncogene is a gene that, when altered, is associated with cancer. Genetic alterations, also described herein as cancer- associated nucleic acids, may include mutations, structural variants (e.g. translocations), copy number variations, insertions / deletions, single nucleotide variants (SNVs), chromothripsis. and the like and combinations thereof. Any of these genetic alterations and / or combinations thereof can be detected in embodiments of the invention described herein. As used herein, the term structural variant is used to describe any genetic alteration, unless context dictates otherwise. Genetic alterations may be located within a gene and / or oncogene (i.e., intragenic) or outside of / adjacent to a gene and / or oncogene (i.e., intergenic, extragenic). For structural variants, the terms “outside of” and “adjacent to,” as used herein in reference to a structural variant being outside of or adjacent to a gene generally means that a breakpoint of a structural variant is not within the gene. The structural variant can contain the gene, such as an inversion of the gene, an insertion of the gene, a duplication of the gene, or the like, or can contain a portion of the gene. In certain aspects, the structural variant may not include the gene, i.e., the structural variant does not contain the gene, insertion, inversion, duplication or any portion thereof. In certain instances, alterations may be located within a different gene. Alterations may be located in a portion of genomic DNA that is proximal to a gene and / or oncogene (e.g., within a certain linear proximity and / or within a certain spatial proximity). Alterations may affect expression of a gene and / or oncogene (e.g., increased expression, decreased expression, no expression, constitutive expression). Alterations may affect the function of a protein encoded by AMG-1022 a gene and / or oncogene (e.g., increased function, decreased function, loss-of-function, gain-of- function, constitutive function, change in function). In some embodiments, a structural variant and / or breakpoint of a structural variant is within a gene (e.g., within an intron and / or exon of a gene (e.g., an oncogene)). In some embodiments, a structural variant and / or breakpoint of a structural variant is outside of a gene (e.g., within an external region). In some embodiments, a structural variant and / or breakpoint of a structural variant is adjacent to a gene (e.g., within an external region). Thus, in some embodiments, a structural variant and / or a breakpoint for a structural variant is not within a gene (e.g., an oncogene). In certain instances, a structural variant and / or breakpoint of a structural variant (e.g., an intergenic structural variant) may be defined in terms of linear distance to a gene (e.g., an oncogene). Linear distance may be measured from the 5’ end of a gene and / or a 3’ end of a gene. In some embodiments, a structural variant and / or a breakpoint for a structural variant may be located at least about 1 kb to about 700 kb from the 5’ end or 3’ end of a gene. For example, a structural variant and / or a breakpoint for a structural variant may be located at least about 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 10 kb, 20 kb, 30 kb, 40 kb, 50 kb, 60 kb, 70 kb, 80 kb, 90 kb, 100 kb, 200 kb, 300 kb, 400 kb, 500 kb, 600 kb, or 700 kb from the 5’ end or 3’ end of a gene. Kits Provided in certain embodiments are kits. A kit may include any components and compositions described herein (e.g., oligonucleotide probes, nucleic acids, primers, vectors, enzymes) useful for performing any of the methods described herein, in any suitable combination. Kits may further include any reagents, buffers, or other components useful for carrying out any of the methods described herein. A kit sometimes includes one or more isolated enzymes. In certain instances, a kit can include one or more isolated restriction enzymes suitable for cleaving sample nucleic acid into target sample nucleic acid fragments. A kit sometimes includes an isolated ligase suitable for ligating cleaved sample nucleic acid fragments that are in proximity to one another after cleavage. In certain implementations, a kit includes an isolated polymerase, such as a polymerase useful for conducting an amplification process. A kit sometimes includes one or more oligonucleotide primers useful for conducting an amplification process, and sometimes includes one or more adapter oligonucleotides useful for conducting a sequencing process. Certain enzymes (e.g., isolated enzymes) typically are not associated with polynucleotides of oligonucleotide probes and / or sample nucleic acid in vivo and do not naturally occur together. A kit in certain implementations includes a solid phase comprising a capture agent suitable for specifically binding to a capture agent counterpart incorporated in oligonucleotide probes and thereby suitable for capturing, isolating, purifying and / or enriching probe hybridization complexes. A solid phase sometimes is a plurality of beads. In certain AMG-1022 implementations, a capture agent is selected from biotin, avidin and streptavidin, and the capture agent counterpart is a molecule that specifically binds to the capture agent and independently is selected from biotin, avidin and streptavidin. A kit in certain implementations will have reagents that enable any of the methods described herein to analyze nucleic acids of EVs, such as, but not limited to FISH, HiC, optical mapping and the like. Components of a kit may be present in separate containers, or multiple components may be present in a single container. Suitable containers include a single tube (e.g., vial), one or more wells of a plate (e.g., a 96-well plate, a 384-well plate, and the like), and the like. Kits may also comprise instructions for performing one or more methods described herein and / or a description of one or more components described herein. For example, a kit may include instructions for using oligonucleotide probes and other components described herein. Instructions and / or descriptions may be in printed form and may be included in a kit insert. In some embodiments, instructions and / or descriptions are provided as an electronic storage data file present on a suitable computer readable storage medium, e.g., portable flash drive, DVD, CD-ROM, diskette, and the like. A kit also may include a written description of an internet location that provides such instructions or descriptions. Table 1 Table 1 lists all the disclosures involving technology for preserving spatial-proximity information and applications thereof that are hereby incorporated in their entirety into the current application. AMG-1022 AMG-1022 Certain Implementations Following are non-limiting examples of certain implementations of the technology. ----RESERVED----- Example The example(s) set forth below illustrates certain implementations and does not limit the technology. Example 1: L-EVs isolation: A variety of L-EVs isolation methods may be compatible. The ones we used were based on differential centrifugation, but other commercial reagents such as density gradient mediums AMG-1022 (e.g. Stem Cell Technologies OPTIPREP (TM)), isolation kits, instruments, and methods may be compatible on their own, or in combination with differential centrifugation. The L-EVs isolation method used was to isolate “large extracellular vesicles”, because Vagner et al. showed that the DNA in L-EVs was long (high molecular weight), double stranded, and chromatinized. Although the L-EVs may be the ideal population for those reasons, and because cancer cells may preferentially secrete L-EVs, it is noted that S-EVs or other types of DNA-containing vesicles secreted by cells are also contemplated by the invention. Any technique for preserving spatial-proximity information can be used. Including, but not limited to, any methods disclosed in the disclosures of Table 1. Including in some embodiments, in vitro chromatin assembly such as that disclosed in WO2023091592A1, WO2022147129A1, WO2017070123A1, WO2016019360A1, WO2016134034A1, WO2017147279A1, WO2019094636A1, WO2017197300A1, WO2016154540A1, WO2019152543A1, WO2018195091A1, WO2020264185A1, the disclosures of which are hereby incorporated in their entirety. Including, in some embodiments, a nucleic acid analysis comprises a method that preserves spatial-proximal relationships and / or spatial proximal contiguity information (see e.g., International PCT Application Publication No. WO2019 / 104034; International PCT Application Publication No. WO2020 / 106776; International PCT Application Publication No. WO2020236851; Kempfer, R., & Pombo, A. (2019). Methods for mapping 3D chromosome architecture. Nature Reviews Genetics. doi:10.1038 / s41576-019-0195-2; and Schmitt, Anthony D.; Hu, Ming; Ren, Bing (2016). Genome-wide mapping and analysis of chromosome architecture. Nature Reviews Molecular Cell Biology. doi:10.1038 / nrm.2016.104; each of which is incorporated by reference in its entirety, to the extent permitted by law). Methods that preserve spatial-proximal relationships and / or spatial proximal contiguity information generally refer to methods that capture and preserve the native spatial conformation exhibited by nucleic acids when associated with proteins as in chromatin and / or as part of a nuclear matrix. Spatial-proximal contiguity information can be preserved by proximity ligation, by solid substrate-mediated proximity capture (SSPC), by compartmentalization with or without a solid substrate or by use of a Tn5 tetramer. Methods that preserve spatial-proximal contiguity information may be based on proximity ligation or may be based on a different principle where spatial proximity is inferred. Methods based on proximity ligation may include, for example, 3C, 4C, 5C, Hi-C, TCC, GCC, TLA, PLAC-seq, HiChIP, ChIA-PET, Capture-C, Capture-HiC, single- cell HiC, sciHiC, single-cell 3C, single-cell methyl-3C, DNAase HiC, Micro-C, Tiled-C, and Low- C. Methods where spatial proximity is inferred based on a principle other than proximity ligation may include, for example, SPRITE, scSPRITE, Genome Architecture Mapping (GAM), ChIA- Drop, imaging-based approaches using labeled probes and visualization of probe-bound DNA (e.g. FISH and derivative techniques based on the principles of visualizing the relative localization of fluorescent probe-bound nucleic acids), and may also include sequencing of an imaged sample (e.g. in situ Genome Sequencing (IGS)). In some embodiments, a nucleic acid AMG-1022 analysis comprises generating proximity ligated nucleic acid molecules (e.g., using a method described herein). In some embodiments, a nucleic acid analysis comprises sequencing the proximity ligated nucleic acid molecules, e.g., by a suitable sequencing process known in the art or described herein. DNA Sequencing Methodologies that do not preserve spatial-proximity information (on their own): DNA Sequencing Methodologies that do not preserve spatial-proximity information (on their own), including but not limited to Shotgun WGS, Linked-Read WGS and other forms of synthetic long-read sequencing, Mate-pair WGS and similar techniques (Fosmids, BACs), Long- read WGS, and other known or anticipated DNA Sequencing methodologies that do not preserve spatial-proximity information (on their own), either sequenced “in bulk” or with single- cell and / or spatial resolution, either in “genome-wide” or “targeted” format (“targeted” meaning, for example, by using known or anticipated target enrichment methodologies (e.g. probe based enrichment or PCR), or depletion methodologies (e.g. using CRISPR), or other targeted sequencing techniques (e.g. adaptive sampling), and either sequenced on any known or anticipated short or long-read sequencing platform. DNA Sequencing Methodologies that do preserve spatial-proximity information: Proximity Ligation DNA sequencing: Genome-wide proximity ligation sequencing techniques, including but not limited to: 3C- seq, Hi-C, DNAase HiC, Micro-C, Low-C, TCC, GCC, single-cell HiC, sciHiC, single-cell 3C, single-cell methyl-3C and other genome-wide bulk or single-cell and / or spatial derivatives, sequenced on any known or anticipated short or long-read sequencing platforms. Targeted proximity ligation sequencing techniques, including but not limited to 3C- (q)PCR, 4C, 5C, Targeted Locus Amplification, PLAC-seq, HiChIP, ChIA-PET, Capture-C, Capture-HiC, Tiled-C and other genome-wide bulk or single-cell or spatial derivatives, including additional “targeted” techniques (“targeted” meaning, for example, by using known or anticipated target enrichment methodologies (e.g. probe based enrichment or PCR, or protein enrichment), or depletion methodologies (e.g. using CRISPR), or other targeted sequencing techniques (e.g. adaptive sampling), and sequenced on any known or anticipated short or long- read sequencing platforms. Non-proximity Ligation DNA sequencing: Non-proximity ligation sequencing techniques, including but not limited to: SPRITE, scSPRITE, other SPRITE derivatives or related techniques involving barcoding of chromatin aggregates, ChIA-Drop or other droplet-based chromatin aggregate barcoding and sequencing techniques, and Genome Architecture Mapping or related techniques where spatial proximal contiguity is inferred from co-occurrence in cryosections. In addition, it is anticipated that AMG-1022 additional derivatives of the above may be suitable for proximity fusion detection (i.e. finding fusions adjacent to a cancer gene), including “targeted” versions (“targeted” meaning, for example, by using known or anticipated target enrichment methodologies (e.g. probe based enrichment or PCR), or depletion methodologies (e.g. using CRISPR), or other targeted sequencing techniques (e.g. adaptive sampling), and sequenced on any known or anticipated short or long-read sequencing platforms. Imaging Methodologies: Classic DNA FISH analysis, with one probe on either side of a breakpoint, can detect SVs. However, recent derivatives thereof, including but not limited to SeqFISH, MERFISH, and OligoFISSEQ, could also detect SVs. Imaging plus Sequencing Methodologies: In situ Genome Sequencing (IGS), or related techniques that sequence DNA molecules “in situ”, measuring the location in the nucleus of each sequenced DNA molecule. Optical genome mapping PCR – As an example, breakpoint-crossing PCR could be used to SVs, so long as the breakpoint is flanked by PCR primers. Methodologies that infer breakpoints based on genomic coverage – in the absence of identifying a sequence fragment that contains a genomic breakpoint of an SV, techniques may be used to infer structural variant breakpoints based on genomic coverage alone. For example, cytogenic microarrays (e.g. including but not limited to array-based CGH, SNP microarrays, or DNA methylation arrays) can be used to identify copy number gains and losses (i.e. unbalanced chromosomal rearrangements), and the genomic positions where the copy number gain or loss starts / ends can be inferred to be a structural variant breakpoint. While the description here uses microarrays as an example methodology for generating genomic coverage data, it is anticipated that essentially any of the above described sequencing-based methodologies or Optical Genome Mapping, or any technique that reliably quantifies genome coverage could potentially be used to infer breakpoints based on coverage, and potentially enable the detection of SVs in the absence of an analyzed DNA fragment containing a breakpoint. Analysis of spatial-proximity information includes chromatin conformation including all scales of chromatin conformation within EVs, including but not limited to compartments, TADs, loops, and the like. Analysis of spatial proximity information also includes including detection and analysis of structural variants, haplotype phasing, and de novo genome assembly. In some embodiments, a nucleic acid analysis comprises a method for preparing nucleic acids from particular types of samples that preserves spatial-proximity relationships and / or spatial-proximity information in the sequence of the nucleic acids. Nucleic acid molecules that AMG-1022 preserve spatial-proximity information can be fragmented and sequenced using short-read sequencing methods (e.g., Illumina, nucleic acid fragments of lengths approximately 500 bp) or intact molecules that preserve spatial-proximal contiguity information can be sequenced using long-read sequencing (e.g., Illumina, Oxford Nanopore, or others, nucleic acid fragments of lengths approximately 5Kbp or greater). In some embodiments, methods that preserve spatial-proximal contiguity information comprise methods that generate proximity ligated nucleic acid molecules (e.g., using proximity ligation). A proximity ligation method is one in which natively occurring spatially proximal nucleic acid molecules are captured by ligation to generate ligated products. Proximity ligation methods generally capture spatial-proximal contiguity information in the form of ligation products, whereby a ligation junction is formed between two natively spatially proximal nucleic acids. Once the ligation products are formed, the spatial-proximal contiguity information is detected using next generation sequencing, whereby one or more ligation junctions (either from an entire ligation product or fragment of a ligation product) are sequenced (as described herein). With this sequence information, one is informed that the nucleic acid molecules from a given ligation product (or ligation junction) are natively spatially proximal nucleic acids. In some embodiments, reagents that generate proximity ligated nucleic acid molecules can include a restriction endonuclease, a DNA polymerase, a plurality of nucleotides comprising at least one biotinylated nucleotide, and a ligase. In certain embodiments, two or more restriction endonucleases are used. Oligonucleotides Oligonucleotides may be artificially synthesized. Accordingly, certain embodiments are synthetic oligonucleotides. An oligonucleotide generally refers to a nucleic acid (e.g., DNA, RNA) polymer that is distinct from a target nucleic acid (e.g., a target nucleic acid comprising one or more structural variants described herein), and may be referred to as oligos, probes, and / or primers. Oligonucleotides may be short in length (e.g., less than 50 bp, less than 40 bp, less than 30 bp, less than 20 bp, less than 10 bp). In some embodiments, oligonucleotides are between about 10 to about 500 consecutive nucleotides in length. For example, an oligonucleotide may be about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, or 500 consecutive nucleotides in length. Oligonucleotides may be designed to hybridize to a region of a sample nucleic acid that is proximal to, adjacent to, and / or spanning a structural variant described herein, or portion thereof. Oligonucleotides may be designed to hybridize to a region of a sample nucleic acid that comprises a receiving site, a donor site, or a combination of a receiving site and a donor site. Oligonucleotides may include probes and / or primers useful for detecting presence, absence, or amount of a structural variant in a nucleic acid sample. Probes and / or primers may be used in conjunction with any suitable nucleic acid analysis (e.g., a nucleic acid analysis AMG-1022 method described herein). For example, probes and / or primers may be used in an amplification process (e.g., PCR, quantitative PCR), FISH (e.g., labeled FISH probes, labeled FISH probe pairs (e.g., with fluorophore and quencher)), microarray, nucleic acid capture, nucleic acid enrichment, nucleic acid sequencing, and the like. Oligonucleotides may be designed to hybridize to a portion or portions of a genome that is / are proximal to, adjacent to, overlapping, partially overlapping, or spanning a structural variant or portion thereof. Oligonucleotides may include a probe or primer capable of hybridizing to a region of a first breakpoint and a region of a second breakpoint of a structural variant described herein. Accordingly, such probes and primers comprise a first sequence complementary to a receiving site in a structural variant and a second sequence complementary to a donor site in a structural variant. Such probes and primers are useful for detecting the presence, absence, or amount of a structural variant in a sample, for example, by way of hybridizing to the sample nucleic acid when the structural variant is present and not hybridizing to the sample nucleic acid when the structural variant is absent. Examples: Method: L-EVs were isolated according to Vagner et al, J Extracell Vesicles, 2018, with minor modifications to further ensure the Hi-C signal coming from the final exosome Hi-C data was truly coming from the L-EVs. These additional steps involving spiking-in another cell line (K562 human leukemia cells) during L-EV isolation, and an additional 2 centrifugation steps. The steps highlighted in bold below indicate the modifications / additional steps relative to Vagner et al. Briefly, PC-3 prostate cancer cells were grown in cell culture. During cell culture, L-EVs are secreted by cells into the cell culture media. In parallel, K562 cells were grown in cell culture as well, separate from the PC-3 cells. Step 1: At 85% cell confluency, the PC-3 cell culture media (containing the L-EVs) were transferred to a new tube. Step 2: The remaining PC-3 cells were collected and saved for Hi-C. Step 3: 1 million K562 cells were collected and transferred into the tube containing the PC-3 cell culture media (containing the EVs). This effectively “spikes-in” K562 cells into the tube containing the PC-3 L-EVs. Step 4: Cells and other large debris were pelleted by centrifugation (leaving the smaller particles, such as L-EVs, in the supernatant). Step 5: The supernatant (containing the PC-3C L-EVs) was transferred to a new tube. Step 6: The supernatant (containing the PC-3 L-EVs) was centrifuged at 2800g to pellet any additional larger debris / cells (leaving L-EVs in the supernatant). AMG-1022 Step 7: The supernatant (containing the PC-3C L-EVs) was transferred to a new tube, and steps 6-7 was repeated once more. Step 8: The supernatant (containing the PC-3 L-EVs) was centrifuged at 10,000g to pellet the L-EVs. Afterwards, the supernatant was removed and the pellet of L-EVs was crosslinked and subject to Hi-C. Another embodiment of a method in accordance with an embodiment of the invention. 1. Cultured PC-3 Cells to approximately 85% confluency in T-182 cm tissue culture flasks (n=5) in DMEM / F12 + 10% FBS + l-glutamine and pen / strep 2. Condition media for L-EV collection a. Remove serum containing media and culture cells in DMEM / F12 without FBS for 24 hours (5% CO2, 37 degrees, ambient O2). b. Each flask contains 50 ml of serum free media and ~45 million cells. 3. Collect conditioned media from each flask and transfer 50 mL conical tubes (n=5 tubes). a. Spike in 1 million K562 (in 1mL of serum free DMEM / F12) cells into each individual 50 mL conical containing conditioned media from PC3 cells. b. Centrifuge at 300 g for 10 minutes at 4 °C – to remove cells and debris. c. Collect media ensuring not to disturb any pellet (leave 500 µl of media at bottom). 4. Centrifuge media at 2800 g for 10 minutes at 4 °C a. Collect media ensuring not to disturb any pellet (leave 500 µl of media at bottom). b. Check for presence of cells / debris under microscope. If cells are still present, repeat step 4 one more time. 5. Centrifuge media at 10,000 g for 30 minutes at 4 °C for isolation of L-EVs a. Resuspend L-EVs in 1 mL of cold, sterile PBS. b. Combine PBS from all tubes and bring up to 5 ml. 6. Crosslink L-EVs: a. Add 270 µl of 37% formaldehyde (final formaldehyde concentration of 2%) b. Incubate at room temperature for 10 minutes. c. Add 460 µl of 2.5M Glycine and incubate at room temperature for 10 minutes. d. Incubate at 4 °C on ice for an additional 15 minutes. AMG-1022 7. Pellet crosslinked L-EVs at 10,000 g for 30 minutes at 4° C 8. Remove supernatant. 9. Proceed to HiC (such as using commercial kits, such as Arima Genomics Arima-HiC kits). Variations to protocols that preserve spatial-proximity information (HiC) may be amenable, or preferred, for spatial proximity analysis of L-EVs. For example, it is envisioned that the conventional cellular lysis step of proximity ligation protocols may be unnecessary or potentially even detrimental towards the quality of the spatial proximity information obtained from an L-EV sample. As such, the lysis step may be omitted. Also, either in combination with the omission of cellular lysis or in isolation, it is also envisioned that the treatment of the L-EV sample with denaturing detergents during protocols that preserve spatial-proximity information, such as the use of SDS, may be unnecessary or potentially even detrimental towards the quality of the spatial proximity information obtained from an L-EV sample. As such, the steps in protocols that preserve spatial-proximity information involving a treatment with denaturing detergents may be omitted, or reduced in terms of the concentration of detergent, duration of the detergent reaction, temperature of the detergent reaction, or a combination thereof. Moreover, if the utilization of detergents such as SDS are reduced or omitted, the subsequent utilization of an agent to quench the SDS treatment, such as Triton X-100, may also be reduced or omitted. Examples of protocols that preserve spatial- proximity information that do not utilize either SDS or Triton X-100 include but are not limited to Micro-C (Krietenstein et al, Molecular Cell, 2020), and emerging protocols such as Intact HiC using either MNase, DNAse, or restriction enzyme-based chromatin fragmentation (ENCODE consortium). Lastly, either in combination with the modification to lysis and SDS / TritonX-100 treatment, it is also envisioned that additional crosslinking may potentially improve the quality of the spatial proximity information obtained from an L-EV sample. As such, steps in protocols that preserve spatial-proximity information involving crosslinking may happen with a variety of crosslinking agents known in the art, and also combination of crosslinking agents known in the art to either crosslink a sample simultaneously or sequentially. For e.g. the utilization of agents such as formaldehyde in combination (either sequentially or simultaneously) with crosslinking agents such as disuccinimidyl gluterate (DSG) and / or ethylene glycol bis(succinimidyl succinate) (EGS). By way of one non-limiting example, utilization of multiple crosslinkers in the context of bulk cellular proximity ligation analysis are known in the art (Krietenstein et al, Molecular Cell, 2020; Oksuz et al, Nature Methods, 2021). AMG-1022 In some embodiments, cross-linking with one or two crosslinking agents in the spatial- proximity analysis is used. In some embodiments, two crosslinking agents are used sequentially. In addition, certain embodiments of inventive proximity ligation protocols can be performed with no cross-linking agent (see, e.g. Brant et al., Exploiting native forces to capture chromosome conformation in mammalian cell nuclei, Mol. Systs. Biol. (2016) 12(12): 891) or with alternative agents, such as psoralen or azide, to create functional dendrimers (see, e.g. You et al,, Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution, Nat. Biotech. (2021) 39(2): 225-235). Further, additional variations to protocols that preserve spatial-proximity information may be amenable, or preferred, for spatial proximity analysis of L-EVs. For example, it is envisioned that immobilizing the L-EV sample at various steps in the protocol may potentially improve the quality of the spatial proximity information obtained from an L-EV sample. For example, it may be advantageous to immobilize the L-EVs directly onto a solid substrate for the entire or partial protocol that preserves spatial-proximity information, similar to what has been previously described (Ramani et al, Nature Protocols, 2016). When applied to an L-EV sample, it is envisioned that the L-EV membrane would bind to and become immobilized on the surface of a solid substrate, such as a magnetic bead. Such immobilization may be carried out in combination with other protocol variation(s) (e.g. the lysis, SDS / Triton, and crosslinking steps) or in isolation. Similarly, in alternative embodiments, the L-EV membrane could first be lysed during the proximity ligation protocol, and then the L-EV chromatin be immobilized onto the solid substrate during the protocol that preserves spatial-proximity information. Methods that preserve spatial-proximity information to employ such a strategy on cellular sample inputs are known in the art (e.g. Sandoval-Velasco et al, Biorxiv, 2023; Kalhor et al, Nature Biotech, 2011). Additional protocol variations may include methods of digesting DNA that may be adhered to the outer surface of the L-EVs, prior to the analysis of spatial proximity information of the nucleic acids within the L-EVs. The basic steps of the methods shown above are illustrated in FIG.1. FIGs.2A-2D show chr11 HiC interaction maps, prepared at 1Mb resolution for the L-EVs (FIG.2A) and PC-3 cells (FIG.2C). Also shown is a Pearson Collection (PC) matrix of chr11, also prepared at 1Mb resolution for the L-EVs (FIG.2B) and PC-3 cells (FIG.2D). FIG.3 depicts the first principal component eigenvector at 1Mb bin size on chr11 for the L-EVs (middle) and PC-3 cells (bottom). Upward blocks represent a positive eigenvalue and downward blocks represent negative eigenvalue. The top track shows gene position. FIG.4 depicts a zoomed in HiC heatmap showing the approximate locus coordinates: Chr8:103,500,000-110,000,000. The upper right HiC map shows PC-3 HiC interactions across the locus, while reflected on the lower left of the HiC map shows L-EV HiC interactions across AMG-1022 the locus. Black arrows point to the notable loop or contact domains, which appear to be conserved between the PC-3 cells and the L-EVs derived from the PC-3 cells. FIGs.5A-5B show genome-wide HiC maps, depicting the landscape of inter- chromosomal SVs (evidenced by strong inter-chromosomal HiC interaction signal) for PC-3 cells (FIG.5A) and L-EVs (FIG.5B). FIGs.6A-6B show zoomed in HiC heatmaps of exemplary inter-chr translocation between chr3 and chr10 for PC-3 cells (FIG.6A) and L-EVs (FIG.6B). The small black box is the breakpoint call from HiC-Breakfinder. The gene CACNB2 contains a breakpoint. Bin size of HiC map = 10kb, breakpoint call at 1kb, max color red = 3 contacts; black box on the matrix is the SV call. FIGs.7A-7B show “genome scan plots” representing a virtual Capture-HiC analysis targeting the CACNB2 gene in both the PC-3 (FIG.7A) and L-EV samples (FIG.7B). The CACNB2 gene is the same gene containing a breakpoint shown in the HiC heatmap of FIG.6. FIGs.8A-8B show “genome scan plots” representing a virtual Capture-HiC analysis targeting the CAMTA1 gene in both the PC-3 (FIG.8A) and L-EV (FIG.8B) samples. CAMTA1 was found to have a breakpoint from the HiC analysis of PC-3 cells and L-EVs. FIGs.9A-9B show “genome scan plots” representing a virtual Capture-HiC analysis targeting the PTEN gene in both the PC-3 (FIG.9A) and L-EV (FIG.9B) samples. PTEN was found to have a breakpoint from the HiC analysis of PC-3 cells and L-EVs. FIGs.10A-10B show “genome scan plots” representing a virtual Capture-HiC analysis targeting the BCR gene in both the PC-3 (FIG.10A) and L-EV (FIG.10B) samples. BCR is known to have a breakpoint (fused to ABL) in K562 cells but not PC-3 cells and is not observed to be rearranged in PC-3 cells or L-EVs. FIGs.11A-11B show “genome scan plots” representing a virtual Capture-HiC analysis targeting either the CACNB2 (FIG.11B) or BCR (FIG.11A) genes in K562 cells (the cell ‘spiked in’ to the L-EV media before L-EV isolation). BCR is known to have a breakpoint (fused to ABL) in K562 cells but not PC-3 cells. CACNB2 was found to have a breakpoint in PC-3 cells (and the L-EVs) but is not observed to have a rearrangement in K562 cells. Also included in certain embodiments is combining any of the spatial-proximity techniques with other modalities to the analysis, like co-analyzing DNA methylation using techniques such as combining HiC with bisulfite conversion (like the published methyl-HiC), and other combinations of modalities, such as ATAC (chromatin assembly, protein expression and gene expression and the like. An intact HiC protocol can also be used in certain embodiments. AMG-1022 Prophetic Example Based in part on the working example(s) above in cell culture, it is expected that performing a nucleic acid analysis of EV samples derived from a (prospective) patient would result in the discovery of 3D chromosome structure and, therefore, allow for detection or monitoring of a genetic variation in the EV nucleic acid of a (prospective) patient. For example, a blood sample can be drawn from a (prospective) patient using standard techniques. The plasma would be separated from the blood sample and processed further to isolate EVs using first differential centrifugation as described herein and, optionally, using a differential gradient purification and isolation step, such as OPTIPREP™, to further isolate and purify the EVs from the (prospective) patient sample. The purified EVs would then be subjected to any nucleic analysis described herein, alone or in combination. In an embodiment, proximity ligation methods as described herein would be performed on the purified EVs. If the (prospective) patient has cancer, it is presumed that the cancer cells will release EVs reflecting the genetic alteration of the cancer cell into the (prospective) patient‘s blood stream and the nucleic acid analysis done on EVs purified from such a (prospective) patient’s sample would detect genetic alterations, thus alerting the (prospective) patient, healthcare provider or the like to the presence of cancer cell(s) in the (prospective) patient. Such knowledge would allow for the diagnosis, detection, treatment or monitoring of the cancer in a (prospective) patient. One example of treatment would be administering an appropriate dose of a pharmaceutical that is known in the art to, or believed to, ameliorate the negative effects of a genetic alteration of a cancer cell. For one, non-limiting example, administration of p^^^^^^^^^^^^ to ameliorate the effects of a genetic alteration in, or adjacent to, the PD-L1 gene. Applications Applications of spatial-proximity information: Genetic variation detection, including but not limited to structural variants listed in disclosures of Table 1 Combine with other workflows such as disclosed in patent documents in Table 1. Analysis of spatial-proximity information includes chromatin conformation including all scales of chromatin conformation within EVs, including but not limited to compartments, TADs, loops, and the like. Further comments on applications of analyzing spatial proximity information of L-EVs: AMG-1022 Chromatin conformation and genome function and regulation: Since the EVs (for example L-EVs) were released from a parent cell, such as a tumor cell, chromatin conformation analysis of L-EVs may be used to determine the state of 3D chromatin conformation in the parent cell, such as a tumor cell, without measuring the 3D chromatin conformation from the parent cell directly. Therefore, it is envisioned that chromatin conformation biomarkers - such as a specific chromatin interaction or a set of chromatin interactions, can be measured from the L-EVs to detect chromatin conformation biomarkers of the parent cells, such as tumor cells. Along these lines, because it is known that certain 3D chromatin conformations (loops, TADs, compartments, etc) are correlated with underlying gene expression, DNA methylation patterns, and chromatin states, it is anticipated that other genomic, epigenomic, or transcriptomic features can be determined based on the chromatin conformation analysis of the L-EVs. And if the chromatin conformation of the L-EVs reflects that of the parent cell, then it is anticipated that the chromatin conformation analysis of the L-EVs could inform genomic, epigenomic, or transcriptomic features of the parent cells, such as tumor cells. Genome assembly -- Given that the data described herein (HiC analysis of L-EVs) demonstrates that 3D chromatin conformation is present in L-EVs, and given that chromatin conformation data (from for example, HiC) can be used as a source of long-range contiguity to facilitate de novo genome assembly, it is anticipated that proximity ligation analysis of L-EVs could facilitate de novo assembly of the parent cell genome, such as the tumor cell (“cancer genome”). The de novo assembly could be carried out using individual methods, or a combination of methods, the methods of which include: short reads, long-reads, optical maps, linked reads, and spatial proximity data (such as proximity ligation data). Haplotype Phasing – Given that the data described herein (HiC analysis of L-EVs) demonstrates that 3D chromatin conformation is present in L-EVs, and given that chromatin conformation data (from for example, HiC) can be used as a source of long-range contiguity to facilitate haplotype phasing. it is anticipated that proximity ligation analysis of L-EVs could facilitate haplotype phasing of parent cell genome, such as the tumor cell (“cancer genome”). For example, genomic variants could be identified (either from the analysis of the DNA from the L-EVs or from a separate tissue biopsy, and / or from a germline specimen such as blood), and then haplotypes (targeted or whole chromosome) could be generated using the spatial proximity data analysis of the L-EVs. In some embodiments, the haplotyping method will be one disclosed in the documents of Table 1. Other types of analysis and applications mentioned herein, such as chromatin conformation analyses and genome assembly analyses could be carried out in a haplotype resolved fashion, assuming haplotypes were accurately defined from the spatial proximity analysis of the L-EVs. AMG-1022 In some embodiments, the DNA in EVs has high h-cis interaction frequency and low h- trans interaction frequency such as is described in the patent disclosures of Table 1. General applications: In the broadest sense, the application of the technology would apply to any scenario where one can measure an analyte of a parent cell, but without analyzing the parent cell itself, and instead by measuring an analyte secreted from the parent cell into the EVs, which is isolated from blood, tissue or urine or other bodily fluid or any other know type of biological sample. Disease screening, such as cancer screening. Such as prostate cancer screening, for example: prostate cancer screening based on the evidence from here (www.ncbi.nlm.nih.gov / pmc / articles / PMC6084494 / ) that prostate cancer patients secrete EVs. There are several other applications of detecting genomic variants from liquid biopsies, such as measuring response to therapy (such as in the neoadjuvant setting or adjuvant setting), detecting minimal residual disease (such as after surgery), and recurrence monitoring. All of these applications are envisioned from spatial proximity analysis of nucleic acids in EVs. While a main application described herein is to measure the spatial proximity of nucleic acids (e.g. DNA molecules) from cancer cells (and analyze the data in all ways spatial proximity data can be analyzed as relevant to cancer analyses), some embodiments relate to other diseases or other scenarios where this paradigm applies, e.g. in the context of organ transplant, if the organ is rejected by the immune system and the cells are dying, EVs may be secreted for which one could do a spatial proximity analysis on to detect spatial proximity signals of immune rejection. In some embodiments, other disease cells (aside from cancer cells), that are known to secrete EVs. Any of the techniques and applications described herein could apply to research and clinical (e.g. diagnostic) applications. Any of the techniques and applications described herein could apply to human and non- human research and clinical (e.g. diagnostic) applications. For example, cancer diagnostics in dogs, horses, etc. For example, research in mouse, rat, pig, and other commonly used model organisms. * * * The entirety of each patent, patent application, publication and document referenced herein is incorporated by reference. Citation of patents, patent applications, publications and AMG-1022 documents is not an admission that any of the foregoing is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents. Their citation is not an indication of a search for relevant disclosures. All statements regarding the date(s) or contents of the documents is based on available information and is not an admission as to their accuracy or correctness. The technology has been described with reference to specific implementations. The terms and expressions that have been utilized herein to describe the technology are descriptive and not necessarily limiting. Certain modifications made to the disclosed implementations can be considered within the scope of the technology. Certain aspects of the disclosed implementations suitably may be practiced in the presence or absence of certain elements not specifically disclosed herein. Each of the terms “comprising,” “consisting essentially of,” and “consisting of” may be replaced with either of the other two terms. The term “a” or “an” can refer to one of or a plurality of the elements it modifies (e.g., “a reagent” can mean one or more reagents) unless it is contextually clear either one of the elements or more than one of the elements is described. The term “about” as used herein refers to a value within 10% of the underlying parameter (i.e., plus or minus 10%; e.g., a weight of “about 100 grams” can include a weight between 90 grams and 110 grams). Use of the term “about” at the beginning of a listing of values modifies each of the values (e.g., “about 1, 2 and 3” refers to "about 1, about 2 and about 3"). When a listing of values is described, the listing includes all intermediate values and all fractional values thereof (e.g., the listing of values "80%, 85% or 90%" includes the intermediate value 86% and the fractional value 86.4%). When a listing of values is followed by the term "or more," the term "or more" applies to each of the values listed (e.g., the listing of "80%, 90%, 95%, or more" or "80%, 90%, 95% or more" or "80%, 90%, or 95% or more" refers to "80% or more, 90% or more, or 95% or more"). When a listing of values is described, the listing includes all ranges between any two of the values listed (e.g., the listing of "80%, 90% or 95%" includes ranges of "80% to 90%," "80% to 95%" and "90% to 95%"). Certain implementations of the technology are set forth in the claim(s) that follow(s).

Claims

AMG-1022 What is claimed is:

1. A method for preparing nucleic acid from an extracellular vesicle, comprising: contacting an extracellular vesicle with one or more agents that preserve spatial-proximity relationships in the extracellular vesicle nucleic acid.

2. The method of claim 1, wherein the extracellular vesicle is subject derived.

3. The method of claim 2, wherein the subject is suspected of having or has cancer.

4. The method of claim 1, wherein the agents that preserve spatial-proximity relationships in the extracellular vesicle nucleic acid are selected from the group consisting of a restriction endonuclease, a DNA polymerase, a plurality of nucleotides comprising at least one biotinylated nucleotide, and a ligase.

5. A method of treating a subject that has, or is suspected of having, cancer, the method comprising: a) identifying and / or selecting a subject comprising a genetic alteration in the genome of the subject; and b) if the subject has cancer, treating the subject so identified and / or selected with a treatment that ameliorates the effect of the genetic alteration.

6. The method of claim 5, wherein identifying and / or selecting a subject comprising a genetic alteration in the genome of the subject comprises: a) performing a nucleic acid analysis on extracellular vesicle nucleic acid obtained from a subject; and b) detecting whether the genetic alteration is present or absent in the extracellular vesicle nucleic acid according to the analysis in a).

7. The method of claim 6, wherein the nucleic acid analysis preserves spatial-proximity relationships in the extracellular vesicle nucleic acids.

8. The method of claim 7, wherein the nucleic acid analysis comprises proximity ligation.

9. A method for detecting the presence or absence of a genetic alteration in a sample, the method comprising: a) performing a nucleic acid analysis on an extracellular vesicle obtained from a subject; andAMG-1022 b) detecting whether a genetic alteration is present or absent in the extracellular vesicle according to the analysis in (a).

10. The method of claim 9, wherein the nucleic acid analysis preserves spatial-proximity relationships of the extracellular vesicle nucleic acid.

11. The method of claim 10, wherein the nucleic acid analysis comprises proximity ligation.

12. A method for non-invasive monitoring of cancer-associated genetic content in a subject, comprising: a) obtaining at least two samples comprising an extracellular vesicle collected from the subject, wherein the extracellular vesicle comprises nucleic acid; b) performing a nucleic acid analysis on the extracellular vesicle nucleic acid obtained from a subject; and c) detecting whether a genetic alteration is present or absent in the extracellular vesicle nucleic acid according to the analysis in b) and, wherein the two samples collected in a) are collected at least at two different time points.

13. A method for non-invasive monitoring of cancer-associated genetic content in a subject, comprising: a) obtaining at least two samples comprising an extracellular vesicle collected from the subject, wherein the extracellular vesicle comprises nucleic acid and wherein the two samples collected are collected at least at two different time points; b) performing a nucleic acid analysis on the extracellular vesicle nucleic acid obtained from a subject; and c) comparing, at least at two different time points, an amount of cancer-associated nucleic acid in the extracellular vesicle nucleic acid according to the analysis in b).

14. The method of claim 13 wherein the amount of cancer-associated nucleic acid is a relative amount, wherein relative is relativity between the at least two different time points.

15. The method of claim 13 wherein the amount of cancer-associated nucleic acid is a relative amount, wherein relative is relativity between cancer-associated nucleic acid and non-cancer associated nucleic acid.AMG-1022 16. The method of claim 13 wherein the at least two different timepoints are selected from the group consisting of: time points before treatment, time points after treatment, and at least one time point before treatment combined with at least one time point after treatment.

17. The method of claim 16, wherein treatment is selected from the group consisting of surgery, resection, chemotherapy, and drug treatment.

18. The methods of any one of claims 12-17, wherein the nucleic acid analysis preserves spatial-proximity relationships of the extracellular vesicle nucleic acid.

19. The method of any one of claims 12-17, wherein the nucleic acid analysis comprises proximity ligation.

20. The method of claim 12 or claim 13, wherein the minimal residual disease is detected.

Images