阅读说明：本技术 通过染色体相互作用遗传调节免疫响应 (Genetic modulation of immune responses through chromosomal interactions ) 是由 亚历山大·埃科利特切夫 阿鲁尔·塞尔瓦姆·拉马达斯 伊万·亨特 于 2018-11-02 设计创作，主要内容包括：一种用于分析与免疫响应相关的染色体区域和相互作用的方法。(A method for analyzing chromosomal regions and interactions associated with immune responses.)

1.A method for detecting a chromosomal state representative of a subgroup in a population, comprising determining the presence or absence of a chromosomal interaction associated with the chromosomal state within a defined region of a genome, wherein the subgroup is associated with a state of an immune-responsive individual; and is

-wherein the chromosomal interactions are optionally determined by a method of determining which chromosomal interactions are associated with chromosomal states corresponding to an immune response subgroup of the population, comprising contacting a first set of nucleic acids from a subgroup having a different chromosomal state with a second set of index nucleic acids, and allowing hybridization of complementary sequences, wherein the nucleic acids of the first and second sets of nucleic acids represent a ligation product comprising sequences from two chromosomal regions clustered together in a chromosomal interaction, and wherein the hybridization pattern between the first and second sets of nucleic acids allows determination of which chromosomal interactions are specific for an immune response subgroup; and is

-wherein the chromosomal interactions are:

(i) present in any one of the regions or genes listed in table 1; and/or

(ii) Corresponding to any of the chromosomal interactions represented by any of the probes shown in Table 1, and/or

(iii) (iii) is present in a region comprising or flanking the 4,000 bases of (i) or (ii);

or

a) Present in any one of the regions or genes listed in table 13; and/or

b) Corresponding to any of the chromosomal interactions represented by any of the probes shown in Table 13, and/or

c) Is present in a region comprising or flanking 4,000 bases of (a) or (b);

or

(α) is present in any one of the regions or genes listed in Table 16, and/or

(β) corresponds to any of the chromosomal interactions represented by any of the probes shown in Table 16, and/or

(. gamma.) is present in a region of 4,000 bases comprising or flanking (α) or (β).

2. The method of claim 1, wherein the specific combination of chromosomal interactions is typed as:

(i) contains all chromosomal interactions represented by the probes in table 1; and/or

(ii) Comprising at least 10, 50, 100, 150, 200, or 300 chromosomal interactions represented by probes in table 1; and/or

(iii) Are present together in at least 10, 50, 100, 150 or 200 regions or genes listed in table 1; and/or

(iv) Wherein at least 10, 50, 100, 150, 200, or 300 chromosomal interactions that are present in a region that comprises or is flanked by 4,000 bases of the chromosomal interactions represented by the probes in Table 1 are typed.

3. The method of claim 1, wherein the specific combination of chromosomal interactions is typed as:

(i) contains all chromosomal interactions represented by the probes in table 13; and/or

(ii) Comprising at least 10, 50, 100, 150, 200, or 300 chromosomal interactions represented by probes in table 13; and/or

(iii) Are present together in at least 10, 50, 100, 150 or 200 regions or genes listed in table 13; and/or

(iv) Wherein at least 10, 50, 100, 150, 200, or 300 chromosomal interactions that are present in a region that comprises or is flanked by 4,000 bases of the chromosomal interactions represented by the probes in Table 13 are typed.

4. The method of claim 1, wherein the specific combination of chromosomal interactions is typed as:

(i) contains all chromosomal interactions represented by the probes in table 16; and/or

(ii) Comprising at least 10, 20, 30, or 40 chromosome interactions represented by the probes in table 16; and/or

(iii) Are present together in at least 10, 20, 30 or 40 regions or genes listed in table 16; and/or

(iv) Wherein at least 10, 20, 30, or 40 chromosomal interactions that are present in a region that comprises or flanks 4,000 bases of the chromosomal interactions represented by the probes in Table 16 are typed.

5. The method of any one of the preceding claims, wherein the chromosome interaction:

typing in a sample from an individual, and/or

-typing by detecting the presence or absence of a DNA loop at the site of said chromosomal interaction, and/or

Typing by detecting the presence or absence of distal regions of chromosomes clustered together in chromosome conformation, and/or

-typing by detecting the presence of linked nucleic acids, which are produced during said typing and whose sequence comprises two regions each corresponding to a chromosomal region that is clustered together in said chromosomal interaction, wherein the detection of said linked nucleic acids is preferably performed by using:

(i) a probe having at least 70% identity to any particular probe sequence mentioned in table 1, and/or (ii) a primer pair having at least 70% identity to any primer pair in table 4; or

(a) A probe having at least 70% identity to any particular probe sequence mentioned in table 13, and/or (b) a primer pair having at least 70% identity to any primer pair in table 13, or

(α) a probe that is at least 70% identical to any of the specific probe sequences mentioned in table 16, and/or (β) a primer pair that is at least 70% identical to any of the primer pairs in table 17.

6. The method of any preceding claim, wherein:

-the second set of nucleic acids is from a larger group of individuals than the first set of nucleic acids; and/or

-the first set of nucleic acids is from at least 8 individuals; and/or

-the first group of nucleic acids is from at least 4 individuals of a first subgroup and at least 4 individuals of a second subgroup, the second subgroup preferably being non-overlapping with the first subgroup; and/or

-performing the method to select an individual for medical treatment; and/or

-the immune response is a response to immunotherapy or immune checkpoint therapy; and/or

The immune response is a response to cancer immunotherapy, and/or

-performing the method to determine an immune response at one or more defined time points, wherein optionally at least one of the time points is during the course of a treatment.

7. The method of any preceding claim, wherein:

-the second set of nucleic acids represents an unselected set; and/or

-wherein the second set of nucleic acids is bound to the array at defined positions; and/or

-wherein the second set of nucleic acids represents chromosomal interactions in at least 100 different genes; and/or

-wherein the second set of nucleic acids comprises at least 1,000 different nucleic acids representing at least 1,000 different chromosomal interactions; and/or

-wherein the first set of nucleic acids and the second set of nucleic acids comprise at least 100 nucleic acids of 10 to 100 nucleotide bases in length.

8. The method according to any one of the preceding claims, wherein the first set of nucleic acids is obtainable in a method comprising the steps of: -

(i) Cross-linking regions of chromosomes that cluster together in a chromosomal interaction;

(ii) subjecting the cross-linked region to cleavage, optionally by restriction digestion with an enzyme; and

(iii) ligating the cross-linked cleaved DNA ends to form the first set of nucleic acids (in particular comprising ligated DNA).

9. The method of any one of the preceding claims:

-wherein at least 10 to 200 different chromosomal interactions are typed, preferably in 10 to 200 different regions or genes; and optionally

(a) Typing between 50 and 100 different chromosomal interactions, each of said chromosomal interactions being located in a different gene and/or a different region as defined in table 1; or

(b) Typing between 50 and 100 different chromosomal interactions, each of which is located in a different gene and/or a different region defined in table 13; or

(c) Typing from 20 to 40 different chromosomal interactions, each of which is located in a different gene and/or a different region defined in table 16;

and/or

-performing the method to select whether the individual receives immunotherapy, wherein the immunotherapy preferably comprises small molecule immunotherapy, antibody immunotherapy or cellular immunotherapy.

10. The method of any one of the preceding claims, wherein the defined region of the genome:

(i) comprises a Single Nucleotide Polymorphism (SNP); and/or

(ii) Expressing micro rna (mirna); and/or

(iii) Expression of non-coding rna (ncrna); and/or

(iv) Expressing a nucleic acid sequence encoding at least 10 contiguous amino acid residues; and/or

(v) An expression regulatory element; and/or

(vii) Comprising a CTCF binding site.

11. The method of any one of the preceding claims, performed to identify or design a therapeutic agent for immunotherapy;

-wherein preferably the method is used to detect whether a candidate agent is capable of causing a change in chromosomal status associated with different levels of immune response;

-wherein the chromosomal interaction is represented by any probe in table 1; and/or

-the chromosomal interaction is present in any region or gene listed in table 1;

and wherein, optionally:

-the chromosomal interactions are determined by the method for determining which chromosomal interactions are related to the chromosomal status as defined in claim 1, and/or

Monitoring changes in chromosomal interactions using (i) probes having at least 70% identity to any of the probe sequences mentioned in table 1, and/or (ii) primer pairs having at least 70% identity to any of the primer pairs in table 4.

12. The method of any one of the preceding claims, performed to identify or design a therapeutic agent for immunotherapy;

-wherein preferably the method is used to detect whether a candidate agent is capable of causing a change in chromosomal status associated with different levels of immune response;

-wherein the chromosomal interaction is represented by any probe in table 13; and/or

-the chromosomal interaction is present in any region or gene listed in table 13;

and wherein, optionally:

-the chromosomal interactions are determined by the method for determining which chromosomal interactions are related to the chromosomal status as defined in claim 1, and/or

Monitoring changes in chromosomal interactions using (i) probes having at least 70% identity to any of the probe sequences mentioned in table 13, and/or (ii) primer pairs having at least 70% identity to any of the primer pairs in table 13.

13. The method of any one of the preceding claims, performed to identify or design a therapeutic agent for immunotherapy;

-wherein preferably the method is used to detect whether a candidate agent is capable of causing a change in chromosomal status associated with different levels of immune response;

-wherein the chromosomal interaction is represented by any probe in table 16; and/or

-the chromosomal interaction is present in any region or gene listed in table 16;

and wherein, optionally:

-the chromosomal interactions are determined by the method for determining which chromosomal interactions are related to the chromosomal status as defined in claim 1, and/or

Monitoring changes in chromosomal interactions using (i) probes having at least 70% identity to any of the probe sequences mentioned in table 16, and/or (ii) primer pairs having at least 70% identity to any of the primer pairs in table 17.

14. The method of claim 11, 12 or 13, comprising selecting a target based on the detection of chromosomal interactions, and preferably screening modulators of the target to determine a therapeutic agent for immunotherapy, wherein the target is optionally a protein.

15. A therapeutic agent for use in a method of immunotherapy of an individual determined to be in need thereof by the method of any one of claims 1 to 10.

16. The method of any one of claims 1 to 14 or therapeutic agent for use according to claim 15, wherein typing or detecting comprises specific detection of the ligation products by quantitative PCR (qpcr) using primers capable of amplifying the ligation products and probes that bind to the ligation sites during the PCR reaction, wherein the probes comprise sequences complementary to sequences from each of the chromosomal regions that are clustered together in the chromosomal interaction, wherein preferably the probes comprise:

an oligonucleotide that specifically binds to the ligation product, and/or

A fluorophore covalently linked to the 5' terminus of the oligonucleotide, and/or

A quencher covalently linked to the 3' terminus of the oligonucleotide, and

optionally, optionally

The fluorophore is selected from the group consisting of HEX, Texas Red, and FAM; and/or

The probe comprises a nucleic acid sequence of 10 to 40 nucleotide bases in length, preferably 20 to 30 nucleotide bases in length.

Technical Field

The present invention relates to detecting chromosomal interactions.

Background

The disease process is complex and results cannot be predicted using available methods. In particular, it is difficult to predict a patient's response to a particular therapy.

Disclosure of Invention

Specific chromosomes at a locus due to modulation of epigenetic control settings associated with pathology or therapyThe presence or absence of a conformational signature (CCS). CCS have a mild off-rate and when representing a particular phenotype or pathology they will only change to a new phenotype with physiological signal transduction or due to external intervention. Furthermore, the measurements of these events are binary, and thus the reads are in sharp contrast to the continuous reads of different levels of DNA methylation, histone modification and most non-coding RNAs. Continuous readings used by most molecular biomarkers to date present challenges to data analysis because the magnitude of variation of a particular biomarker varies greatly from patient to patient, which presents a problem with classification statistics when they are used to stratify patient populations. These categorical statistics are more amenable to the use of biomarkers that do not have amplitude and provide only a binary score of "yes or no" phenotypic differences, suggesting chromosome conformation (EpiSwitch)^TM) Biomarkers are an excellent source of potential diagnostic, prognostic, and predictive biomarkers.

The present inventors have identified (identify) genomic regions with chromosomal interactions that are associated with immune response (immunoresponsiveness, immune response capacity) using a method that allows identification of subgroups in a population. It has been discovered that the identified regions, genes and specific chromosomal interactions from two independent studies using different therapies to treat two different conditions determine the patient's general immune response, including modulation of cell surface signaling pathways and modulation of T cell activation by immune response. The inventors' work allows tracking of changes in immune response, for example during disease or treatment.

Accordingly, the present invention provides a method for detecting a chromosomal state representative of a subgroup in a population, comprising determining the presence or absence of a chromosomal interaction associated with the chromosomal state within a defined region of a genome, wherein the subgroup is associated with a state of an immune-responsive individual (immunoresponsive induced virtual); and is

-wherein the chromosomal interactions are optionally identified by a method of determining which chromosomal interactions are associated with chromosomal states corresponding to immune response subgroups of a population, the method comprising contacting a first set of nucleic acids from subgroups having different chromosomal states with a second set of index nucleic acids, and allowing the complementary sequences to hybridise, wherein the nucleic acids in the first and second sets of nucleic acids represent a ligation product comprising sequences from two chromosomal regions clustered together in a chromosomal interaction, and wherein the hybridisation pattern between the first and second sets of nucleic acids allows determining which chromosomal interactions are specific for an immune response subgroup; and is

-wherein the chromosomes interact:

(i) present in any one of the regions or genes listed in table 1; and/or

(ii) Corresponding to any of the chromosomal interactions represented by any of the probes shown in Table 1, and/or

(iii) Is present in a region comprising or flanked by (flank), 4,000 bases of (i) or (ii).

The invention also provides a method for detecting a chromosomal state representative of a subgroup in a population, comprising determining the presence or absence of a chromosomal interaction associated with the chromosomal state within a defined region of a genome, wherein the subgroup is associated with a state of an immune-responsive individual; and is

-wherein the chromosomal interactions are optionally identified by a method of determining which chromosomal interactions are associated with chromosomal states corresponding to immune response subgroups of a population, the method comprising contacting a first set of nucleic acids from subgroups having different chromosomal states with a second set of index nucleic acids, and allowing the complementary sequences to hybridise, wherein the nucleic acids of the first and second sets of nucleic acids represent a ligation product comprising sequences from two chromosomal regions that are clustered together in a chromosomal interaction, and wherein the hybridisation pattern between the first and second sets of nucleic acids allows determining which chromosomal interactions are specific for an immune response subgroup; and is

-wherein the chromosomes interact:

a) is present in any one of the regions or genes listed in table 13; and/or

b) Corresponding to any of the chromosomal interactions represented by any of the probes shown in Table 13, and/or

c) Is present in a region comprising or flanking 4,000 bases of (a) or (b).

The invention further provides a method for detecting a chromosomal state representative of a subgroup in a population, comprising determining the presence or absence of a chromosomal interaction associated with the chromosomal state within a defined region of a genome, wherein the subgroup is associated with a state of an immune-responsive individual; and is

-wherein the chromosomal interactions are optionally identified by a method of determining which chromosomal interactions are associated with chromosomal states corresponding to an immune response subgroup of the population, comprising contacting a first set of nucleic acids from a subgroup having a different chromosomal state with a second set of index nucleic acids, and allowing hybridization of the complementary sequences, wherein the nucleic acids in the first and second sets of nucleic acids represent a ligation product comprising sequences from two chromosomal regions that are clustered together in a chromosomal interaction, and wherein the hybridization pattern between the first and second sets of nucleic acids allows determination of which chromosomal interactions are specific for the immune response subgroup; and is

-wherein the chromosomes interact:

(α) is present in any of the regions or genes listed in Table 16, and/or

(β) corresponds to any of the chromosomal interactions represented by any of the probes shown in Table 16, and/or

(. gamma.) is present in a region of 4,000 bases comprising or flanking (α) or (β).

Detailed Description

Aspects of the invention

The present invention relates to a set of epigenetic markers involved in the regulation of the immune system, in particular through cell surface signaling pathways and T cell activation.

The invention also includes monitoring the state of the immune system to determine its responsiveness to a particular therapy. This means that the patient can be provided with the appropriate therapy and it can be determined whether the patient has retained or lost the 'responder' status. Thus, in one embodiment, the present invention provides a 'real-time' continuous readout of 'responder' status, allowing personalized treatment of patients, accurately reflecting the needs of the patient.

Immune responsiveness

The immune responsiveness may thus be responsive to immunotherapy.immunotherapy may modulate, block or stimulate immune checkpoints, and thus may target or modulate PD-L1, PD-L2 or CT L A4 or any other immune checkpoint molecule disclosed herein, and thus may be immune checkpoint therapy.

In one embodiment, the immune responsiveness is responsiveness to a PD-1 inhibitor or a PD-L1 inhibitor, including responsiveness to an antibody specific for PD-1 or PD-L1 PD-1 is a 'programmed cell death protein' and PD-L1 is a 'programmed death ligand 1'.

Cancer is generally any cancer mentioned herein, and is, for example, melanoma, lung cancer, non-small cell lung cancer (NSC L C), diffuse large B-cell lymphoma, liver cancer, hepatocellular carcinoma, prostate cancer, breast cancer, leukemia, acute myeloid leukemia, pancreatic cancer, thyroid cancer, nasal cancer, brain cancer, bladder cancer, cervical cancer, non-Hodgkin's lymphoma, ovarian cancer, large bowel cancer, or renal cancer.

The term 'antibody' includes all fragments and derivatives of the antibody that retain the ability to bind to an antigen target, such as single chain scFV or Fab.

As will be discussed later, the immune responsiveness to any of the therapies, cells, or drugs mentioned herein can be determined. In some embodiments, any of the therapies, cells, or drugs mentioned herein can be administered to an individual for which an immune response has been determined.

Method of the invention

The method of the present invention comprises a typing system for detecting chromosomal interactions associated with immune responses. Such typing may use the EpiSwitch referred to herein based on chromosomal cross-linking regions clustered together in chromosomal interactions^TMThe system, allowing the chromosomal DNA to be cleaved, and then ligating the nucleic acids present in the crosslinking entity to derive a ligated nucleic acid having sequences from the two regions forming the chromosomal interaction. Detection of such linked nucleic acids allows determination of the presence or absence of specific chromosomal interactions.

Chromosomal interactions can be identified using the methods described above, wherein first and second populations of nucleic acids are used. EpiSwitch may also be used^TMTechniques generate these nucleic acids.

Epigenetic interactions relevant to the present invention

As used herein, the terms 'epigenetic' and 'chromosomal' interaction generally refer to interactions between distal end regions of chromosomes that are dynamic and change, form or disrupt depending on the state of the chromosomal region.

In particular methods of the invention, chromosomal interactions are typically detected by first generating a linked nucleic acid comprising sequences from two regions of a chromosome that are part of the interaction. In such a process, the regions may be cross-linked by any suitable means. In a preferred embodiment, the interaction is cross-linked using formaldehyde, but may also be cross-linked by any aldehyde or D-biotin-e-aminocaproic acid-N-hydroxysuccinimide ester or digoxigenin-3-O-methylcarbonyl-e-aminocaproic acid-N-hydroxysuccinimide ester. Paraformaldehyde can crosslink DNA strands 4 angstroms apart. Preferably, the chromosomes interact on the same chromosome, and optionally are 2 to 10 angstroms apart.

Chromosomal interactions may reflect the state of a chromosomal region, e.g., whether transcribed or repressed in response to a change in physiological conditions. It has been found that the herein defined chromosome interactions specific for a subgroup are stable, thus providing a reliable method for measuring differences between two subgroups.

Furthermore, chromosomal interactions specific for a feature, such as immune responsiveness, for example, will typically occur early in a biological process as compared to other epigenetic markers, such as methylation or binding changes to histones. Thus, the method of the invention enables detection of early stages of a biological process. This allows early intervention (e.g. therapy) and thus may be more effective. Chromosomal interactions also reflect the current state of an individual and can therefore be used to assess changes in immune responses. Furthermore, there was little change in the relevant chromosomal interactions between individuals within the same subgroup. It is very useful to detect chromosomal interactions, with up to 50 possible interactions per gene, so that the method of the invention can interrogate 500,000 different interactions.

Preferred marker sets

Herein, the term 'marker' or 'biomarker' refers to a specific chromosomal interaction that can be detected (typed) in the present invention. Specific markers are disclosed herein, any of which may be used in the present invention. Additional marker sets may be used, for example in combinations or numbers disclosed herein. Specific markers disclosed in the tables herein are preferred, and markers present in the genes and regions mentioned in the tables herein are preferred. These may be typed by any suitable method, such as the PCR-based or probe-based methods disclosed herein, including qPCR methods. Markers are defined herein by position or by probe and/or primer sequences.

Location and cause of epigenetic interactions

Epigenetic chromosomal interactions may overlap and include regions of the chromosome shown to encode related or undescribed genes, but may equally well be in intergenic regions. It should also be noted that the present inventors have found that epigenetic interactions of all regions are equally important in determining chromosomal locus (loci) status. These interactions are not necessarily in the coding region of a particular gene located at a locus, but may be in intergenic regions.

The chromosomal interactions detected in the present invention may be due to changes in underlying DNA sequences, environmental factors, DNA methylation, non-coding antisense RNA transcripts, non-mutagenic carcinogens, histone modification, chromatin remodeling, and specific local DNA interactions. Changes that lead to chromosomal interactions may be caused by changes in the underlying nucleic acid sequence, which itself does not directly affect the gene product or the pattern of gene expression. Such changes may be, for example, SNPs inside and/or outside the gene, gene fusions and/or deletions of intergenic DNA, microrna (microrna) and non-coding RNA. For example, about 20% of SNPs are known to be located in non-coding regions, and thus the above method is also useful in non-coding cases. In one embodiment, the regions that are clustered together to form interacting chromosomes are less than 5kb, 3kb, 1kb, 500 base pairs or 200 base pairs apart on the same chromosome.

Preferably, the detected chromosomal interactions are within any of the genes mentioned in table 1. However, it may also be upstream or downstream of the gene, e.g., up to 50,000, up to 30,000, up to 20,000, up to 10,000 or up to 5000 bases upstream or downstream from the gene or coding sequence.

Preferably, the detected chromosomal interactions are within any of the genes mentioned in table 13. However, it may also be upstream or downstream of the gene, e.g., up to 50,000, up to 30,000, up to 20,000, up to 10,000 or up to 5000 bases upstream or downstream from the gene or coding sequence.

Preferably, the detected chromosomal interactions are within any of the genes mentioned in table 16. However, it may also be upstream or downstream of the gene, e.g., up to 50,000, up to 30,000, up to 20,000, up to 10,000 or up to 5000 bases upstream or downstream from the gene or coding sequence.

Subgroups, time points and personalized treatments

The object of the present invention is to determine the level of immune response. This may be at one or more defined points in time, for example at least 1, 2, 5, 8 or 10 different points in time. The duration of time between at least 1, 2, 5 or 8 time points may be at least 5, 10, 20, 50, 80 or 100 days. Usually at least 1, 2 or 5 time points are before the start of the treatment and/or at least 1, 2 or 5 time points are after the start of the treatment.

As used herein, "subgroup" preferably refers to a subgroup of a population (a subgroup in a population), more preferably a subgroup of a population of a particular animal, e.g., a particular eukaryote or mammal (e.g., a human, a non-human primate, or a rodent, e.g., a mouse or a mouse). Most preferably, "subgroup" refers to a subgroup in the human population.

The invention includes specific subgroups within the detection and treatment populations. The inventors have found that chromosome interactions differ between subsets (e.g., at least two subsets) of a given population. Identifying these differences would enable the physician to classify the patient as part of a subset of the population described in the present method. Thus, the present invention provides a method for physicians to personalize their medications based on their epigenetic chromosomal interactions.

In one embodiment, the invention relates to testing whether an individual is a 'responder' once one is found to be a 'responder', a relevant treatment may be administered, typically a treatment against an immune checkpoint molecule (e.g. PD-1, PD-L1 or CT L a 4).

Generation of ligated nucleic acids

Certain embodiments of the invention utilize ligated nucleic acids, particularly ligated DNA. These contain sequences from two regions that come together in a chromosomal interaction and thus provide information about the interaction. EpiSwitch as described herein^TMMethods use the generation of such linked nucleic acids to detect chromosomal interactions.

Thus, the method of the invention may comprise the step of generating a ligated nucleic acid (e.g.DNA) by (including a method comprising) the steps of:

(i) preferably in vitro, cross-linking epigenetic chromosomal interactions present at a chromosomal locus;

(ii) optionally isolating the cross-linked DNA from the chromosomal locus;

(iii) subjecting the cross-linked DNA to cleavage, e.g. restriction digestion by an enzyme that cleaves at least once (in particular an enzyme that cleaves at least once within the chromosomal locus);

(iv) ligating the cross-linked sheared DNA ends (particularly to form a DNA loop); and (v) optionally identifying the presence of said ligated DNA and/or said DNA loop, in particular using techniques such as PCR (polymerase chain reaction) to identify the presence of specific chromosomal interactions.

For any of the embodiments mentioned herein, these steps may be performed to detect chromosomal interactions. The steps may also be performed to produce the first and/or second set of nucleic acids referred to herein.

PCR (polymerase chain reaction) can be used to detect or identify the ligated nucleic acids, e.g., the size of the PCR product produced can indicate the presence of a specific chromosomal interaction, and thus can be used to identify the status of a locus. In preferred embodiments, at least 1, 2 or 3 of the primers or primer pairs shown in table 4 are used in the PCR reaction. In other embodiments, at least 1, 2, or 3 of the primers or primer pairs shown in table 13 are used in a PCR reaction. In other embodiments, the PCR reaction uses at least 1, 2, or 3 primers or primer pairs shown in table 17. One skilled in the art will appreciate a number of restriction enzymes that can be used to cleave DNA within a chromosomal locus of interest. It will be apparent that the particular enzyme used will depend on the locus under study and the sequence of the DNA located therein. A non-limiting example of a restriction enzyme that can be used to cleave DNA according to the invention is TaqI.

Such as EpiSwitch^TMTechnical solution and other embodiments

EpiSwitch^TMThe technique also involves the use of microarrays of EpiSwitch^TMMarker data detects phenotype-specific epigenetic chromosome conformation signatures. Embodiments utilizing linked nucleic acids in the manner described herein, e.g., EpiSwitch^TMThere are several advantages. They have a lower level of random noise, for example because nucleic acid sequences from a first set of nucleic acids of the invention hybridize or do not hybridize to a second set of nucleic acids. This provides a binary result, allowing complex mechanisms to be measured at the epigenetic level in a relatively simple manner. EpiSwitch^TMThe technique also has fast processing time and low cost. In one embodiment, the treatment time is 3 hours to 6 hours.

Samples and sample processing

The method of the invention will generally be carried out on a sample. The sample may be obtained at a defined time point, for example at any time point defined herein. The sample typically contains DNA from an individual. It will typically comprise cells. In one embodiment, the sample is obtained by minimally invasive means, and may be, for example, a blood sample. DNA may be extracted and cleaved with standard restriction enzymes. This allows a predetermination of which chromosome conformations are retained, and EpiSwitch can be used^TMAnd (5) platform detection. Since chromosomal interactions are synchronized between tissue and blood (including horizontal transfer), blood samples can be used to detect chromosomal interactions in tissues, such as those associated with disease. For certain conditions, such as cancer, the use of blood is advantageous because genetic noise caused by mutations can affect chromosome interaction 'signals' in the relevant tissues.

Properties of nucleic acids of the invention

The present invention relates to certain nucleic acids, for example, ligated nucleic acids described herein as used or produced in the methods of the invention. These may be the same as or any of the properties of the first and second nucleic acids mentioned herein. The nucleic acids of the invention typically comprise two parts, each part comprising a sequence from one of two regions of a chromosome that are clustered together in a chromosome interaction. Typically, each portion is at least 8, 10, 15, 20, 30 or 40 nucleotides in length, for example 10 to 40 nucleotides in length. Preferred nucleic acids comprise sequences from any of the genes mentioned in any of the tables. Generally, preferred nucleic acids comprise the specific probe sequences mentioned in table 1; or fragments and/or homologues of such sequences. Preferred nucleic acids may comprise the specific probe sequences mentioned in table 13; or fragments and/or homologues of such sequences. Preferred nucleic acids may comprise the specific probe sequences mentioned in table 16; or fragments and/or homologues of such sequences.

Preferably, the nucleic acid is DNA. It is understood that where specific sequences are provided, the invention may be used with complementary sequences as desired in particular embodiments. Preferably, the nucleic acid is DNA. It is understood that where specific sequences are provided, the invention may be used with complementary sequences as desired in particular embodiments.

The primers shown in Table 4 can also be used in the invention described herein. In one embodiment, the primers used comprise any of the following: the sequences shown in Table 4; or a fragment and/or homologue of any of the sequences shown in table 4. The primers shown in Table 13 can also be used in the invention described herein. In one embodiment, the primers used comprise any of the following: the sequences shown in table 13; or a fragment and/or homologue of any of the sequences shown in table 13. Primers shown in Table 17 can also be used in the invention described herein. In one embodiment, the primers used comprise any one of the following: the sequences shown in table 17; or a fragment and/or homologue of any of the sequences shown in table 17.

Second set of nucleic acid-index sequences

The second set of nucleic acid sequences functions as a set of index sequences and is essentially a set of nucleic acid sequences suitable for identifying subgroup-specific sequences. They may represent 'background' chromosome interactions and may or may not be selected in some way. They are usually a subset of all possible chromosomal interactions.

The second set of nucleic acids may be obtained by any suitable method. They may be calculated or may be based on chromosomal interactions in the individual. They generally represent a larger population than the first group of nucleic acids. In a particular embodiment, the second set of nucleic acids represents all possible epigenetic chromosomal interactions in a particular genome. In another specific embodiment, the second set of nucleic acids represents a substantial portion of all possible epigenetic chromosomal interactions present in the population described herein. In a particular embodiment, the second set of nucleic acids represents at least 50% or at least 80% of the epigenetic chromosome interactions in at least 20, 50, 100 or 500 genes, e.g., from 20 to 100 or from 50 to 500 genes.

The second set of nucleic acids typically represents at least 100 possible epigenetic chromosomal interactions that modify, modulate or in any way mediate a phenotype in the population. The second set of nucleic acids may represent chromosomal interactions that affect a disease state (typically associated with diagnosis or prognosis) in a species. The second set of nucleic acids typically comprises sequences representing epigenetic interactions related and unrelated to the immune response subgroup.

In a particular embodiment, the second set of nucleic acids is derived at least in part from naturally occurring sequences in a population, and is typically obtained by in silico methods. The nucleic acid may further comprise a single or multiple mutation compared to the corresponding part of the nucleic acid as present in the naturally occurring nucleic acid. Mutations include deletions, substitutions and/or additions of one or more nucleotide base pairs. In a particular embodiment, the second set of nucleic acids may comprise sequences representing homologues and/or orthologues having at least 70% sequence identity with a corresponding part of the nucleic acids present in the naturally occurring species. In another specific embodiment, at least 80% sequence identity or at least 90% sequence identity to a corresponding portion of a nucleic acid present in a naturally occurring species is provided.

Properties of the second group of nucleic acids

In a particular embodiment, there are at least 100 different nucleic acid sequences in the second set of nucleic acids, preferably at least 1000, 2000 or 5000 different nucleic acid sequences, with up to 100,000, 1,000,000 or 10,000,000 different nucleic acid sequences. A typical number may be 100 to 1,000,000, for example 1,000 to 100,000 different nucleic acid sequences. All or at least 90% or at least 50% or these will correspond to different chromosomal interactions.

In a particular embodiment, the second set of nucleic acids represents chromosomal interactions in at least 20 different loci or genes, preferably at least 40 different loci or genes, more preferably at least 100, at least 500, at least 1000, or at least 5000 different loci or genes, e.g., 100 to 10,000 different loci or genes. The second set of nucleic acids is of a length suitable for use in their specific hybridization to the first set of nucleic acids according to Watson-Crick (Watson Crick) base pairing to identify chromosome interactions specific to the subset. Typically, the second set of nucleic acids will comprise two portions that correspond in sequence to two chromosomal regions that are brought together in a chromosomal interaction. The second set of nucleic acids typically comprises nucleic acid sequences of at least 10, preferably 20, and still preferably 30 bases (nucleotides) in length. In another embodiment, the nucleic acid sequence may be at most 500, preferably at most 100, and still preferably at most 50 base pairs in length. In a preferred embodiment, the second set of nucleic acids comprises nucleic acid sequences of 17 to 25 base pairs. In one embodiment, at least 100, 80% or 50% of the second set of nucleic acid sequences have a length as described above. Preferably, the different nucleic acids do not have any overlapping sequences, e.g., at least 100%, 90%, 80%, or 50% of the nucleic acids do not have identical sequences over at least 5 contiguous nucleotides.

Assuming that the second set of nucleic acids serves as an 'index', the same set of second nucleic acids may be used with a different set of first nucleic acids representing subgroups with different characteristics, i.e. the second set of nucleic acids may represent a 'universal' set of nucleic acids that may be used to identify chromosomal interactions associated with different characteristics.

First group of nucleic acids

The first set of nucleic acids is typically from a subset associated with an immune response. The first nucleic acid may have any of the characteristics and properties of the second set of nucleic acids mentioned herein. The first set of nucleic acids is typically derived from a nucleic acid that has been treated and processed as described herein (particularly EpiSwitch)^TMCross-linking and cutting steps). Typically, the first set of nucleic acids represents all or at least 80% or 50% of the chromosomal interactions present in a sample taken from an individual.

Typically, the first set of nucleic acids represents chromosomal interactions across a smaller population of loci or genes represented by the second set of nucleic acids than the second set of nucleic acids, i.e., the second set of nucleic acids represents a background or indexed set of interactions in a defined set of loci or genes.

Nucleic acid libraries

Any type of population of nucleic acids referred to herein may be present in the form of a library comprising at least 200, at least 500, at least 1000, at least 5000, or at least 10000 different nucleic acids of that type, for example 'first' or 'second' nucleic acids. Such libraries may be in the form of binding to an array.

Hybridization of

The present invention requires a means to allow hybridization of all or part of complementary nucleic acid sequences from the first set of nucleic acids and the second set of nucleic acids. In one embodiment, all of the first set of nucleic acids are contacted with all of the second set of nucleic acids in a single assay, i.e., in a single hybridization step. However, any suitable assay may be used.

Labeled nucleic acids and hybridization patterns

The nucleic acids mentioned herein may preferably be labelled with a separate label, such as a fluorophore (fluorescent molecule) or a radiolabel, which facilitates detection of successful hybridisation. Some markers can be detected under UV light. Hybridization patterns, e.g., on an array as described herein, represent differences in epigenetic chromosomal interactions between two subgroups, thereby providing a means to compare epigenetic chromosomal interactions and determine which epigenetic chromosomal interactions are specific for a subgroup in the population of the invention.

The term 'hybridization pattern' broadly encompasses the presence and absence of hybridization between the first and second sets of nucleic acids, i.e., which specific nucleic acids in the first set hybridize to which specific nucleic acids in the second set, and thus is not limited to any particular assay or technique, or requires a surface or array having a detectable 'pattern'.

Selecting subgroups with specific characteristics

The present invention provides a method comprising detecting the presence or absence of a chromosomal interaction, typically between 5 and 20 or between 5 and 500 such interactions, preferably between 20 and 300 or between 50 and 100 interactions, to determine the presence or absence of a characteristic associated with an immune response in an individual. Preferably, the chromosomal interaction is a chromosomal interaction in any of the genes mentioned herein. In one embodiment, the genotyped chromosomal interactions are those represented by the nucleic acids in table 1. In another embodiment, the chromosomal interaction is a chromosomal interaction as set forth in table 13. In another embodiment, the chromosomal interaction is a chromosomal interaction as set forth in table 16. The column in the table labeled 'loop detected' shows which subset (i.e., responder or non-responder) was detected for each probe.

Individuals to be tested

Examples of the species from which the subject being tested is derived are described herein. In addition, the individual to be tested in the method of the invention may be selected in some way. The subject may be susceptible to any of the conditions described herein and/or may require any of the therapies mentioned therein. The subject may be receiving any of the therapies mentioned herein.

In one embodiment, the individuals tested lack response to treatment and are tested to find out if they are 'pseudo-progressors' who will respond to treatment in the second phase of the disease despite not responding in the early stages.

Preferred gene regions, loci, genes and chromosomal interactions

Preferred gene regions, loci, genes and chromosomal interactions are mentioned in the tables (e.g., table 1) for all aspects of the invention. Typically in the methods of the invention, the chromosomal interaction is detected from at least 1, 2, 10, 50, 100, 150, 200 or 300 of the relevant genes listed in table 1. Preferably, the presence or absence of at least 1, 2, 10, 50, 100, 150, 200, or 300 relevant specific chromosomal interactions represented by the probe sequences in table 1 is detected. Chromosomal interactions may be upstream or downstream of any of the genes mentioned herein, e.g., 50kb upstream or 20kb downstream, e.g., from the coding sequence.

In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 1.a are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 1.b are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 1.c are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 1.d are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 1.e are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 1.f are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 1.g are typed.

Typically, at least 5, 10, 15, 20, 30, 40, or 70 chromosomes interact from any gene or region disclosed in the tables herein or in portions of the tables disclosed herein. Typically, the chromosomal interactions that are typed are present in at least 20, 50, 100, 200, 300 or all of the genes mentioned in table 2. Typically, the chromosomal interactions that are typed are present in at least 10, 20, 50, 70 or all of the genes mentioned in table 3.

Preferred gene regions, loci, genes and chromosomal interactions are mentioned in table 13 for all aspects of the invention. Typically, in the methods of the invention, the chromosomal interactions are detected from at least 1, 2, 10, 50, 100, 150, 200, or 300 relevant genes listed in table 13. Preferably, the presence or absence of at least 1, 2, 10, 50, 100, 150, 200, or 300 relevant specific chromosomal interactions represented by the probe sequences in table 13 is detected. Chromosomal interactions may be upstream or downstream of any of the genes mentioned herein, e.g., 50kb upstream or 20kb downstream, e.g., from the coding sequence.

In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 13.a are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 13.b are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 13.c are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 13.d are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 13.e are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 13.f are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 13.g are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 13.h are typed. In one embodiment, at least 5, 10, 15, 20 or all of the chromosomal interactions in table 13.i are typed.

Typically, at least 5, 10, 15, 20, 30, 40, or 70 chromosomes interact from any gene or region disclosed in the tables herein or in portions of the tables disclosed herein. Typically, the genotypic chromosomal interactions are present in at least 20, 50, 100, 200, 300 or all of the genes mentioned in table 13. Typically, the genotypic chromosomal interactions are present in at least 10, 20, 50, 70 or all of the genes mentioned in table 13.

Preferred gene regions, loci, genes and chromosomal interactions are mentioned in table 16 for all aspects of the invention. Typically, in the methods of the invention, the chromosomal interactions are detected from at least 1, 2, 10, 20, 30, or 40 of the relevant genes listed in table 16. Preferably, the presence or absence of at least 1, 2, 10, 20, 30, or 40 relevant specific chromosomal interactions represented by the probe sequences in table 16 is detected. Chromosomal interactions may be upstream or downstream of any of the genes mentioned herein, e.g., 50kb upstream or 20kb downstream, e.g., from the coding sequence.

In one embodiment, at least 5, 10 or 15 or all of the chromosomal interactions in table 18 are typed.

Typically, at least 5, 10, 15, 20, 30, 40, or 70 chromosomal interactions are typed from any gene or region disclosed in the tables herein or in portions of the tables disclosed herein. Typically, the genotypic chromosomal interactions are present in at least 20, 50, 100, 200, 300 or all of the genes mentioned in table 13. Typically, the genotypic chromosomal interactions are present in at least 10, 20, 50, 70 or all of the genes mentioned in table 13.

In one embodiment, at least 5, 10, 15, 20, 30, 40 or 70 different chromosomal interactions are typed from the chromosomal interactions defined in any of tables 1, 13 and 16. In another embodiment, at least 50%, 80%, or all of the typed chromosomal interactions are from tables 1, 13, and 16.

In one embodiment, the locus (including the genes and/or locations where chromosomal interactions are detected) may comprise a CTCF binding site. This is any sequence capable of binding to the transcription repressor CTCF. The sequence may consist of or comprise the sequence CCCTC, which may be present in 1, 2 or 3 copies at the locus. The CTCF binding site sequence may comprise the sequence CCGCGNGGNGGCAG (in IUPAC notation). The CTCF binding site may be located within at least 100, 500, 1000, or 4000 bases of chromosomal interaction, or may be located within any of the chromosomal regions shown in table 1. The CTCF binding site may be located within at least 100, 500, 1000, or 4000 bases of chromosomal interaction, or may be located within any of the chromosomal regions shown in table 13.

In one embodiment, the detected chromosomal interaction is present in any of the gene regions shown in table 13. In the case where the ligated nucleic acid is detected in this method, the sequence shown by any of the probe sequences in Table 13 can be detected.

Thus, sequences from two regions of the probe (i.e., from two sites of chromosomal interaction) can generally be detected. In a preferred embodiment, the probes used in the method comprise or consist of a sequence that is identical to or complementary to a probe shown in any table. In some embodiments, the probes used comprise sequences homologous to any of the probe sequences shown in the table.

Tables provided herein

Table 1 shows probes (Episwitch) representing chromosomal interactions associated with immune responses^TMMarkers) data and genetic data. The sequences shown for the probe sequences can be used to detect ligation products generated from two sites of the gene regions that are clustered together in a chromosomal interaction, i.e., the probe will comprise a sequence that is complementary to the sequence in the ligation product. The first two sets of start-end positions show the probe positions and the last two sets of start-end positions show the relevant 4kb region. The following information is provided in the probe data sheet:

-HyperG _ Stats: parameter discovery for significant EpiSwitch in loci based on hyper-geometric enrichment^TMP-value of probability of number of markers

Total Probe Count Total (Probe Count Total): EpiSwitch tested at the locus^TMTotal number of conformations

Significant Probe Count Sig (Probe Count Sig, Probe Count signal): EpiSwitch found statistically significant at the locus^TMNumber of conformations

-FDR HyperG: multiple test (non-immune response (Fimmensuissive) discovery rate) corrected hyper-geometric p-value

Significant percentage (Percent Sig): relative to inNumber of markers tested at the locus, significance EpiSwitch^TMPercentage of marker

-logFC: base 2 logarithm (FC) of the epigenetic ratio

-AveExpr: average log2 expression of probes across all arrays and channels

-T: moderated t statistic

-p-value: original p value

-adj.p value: adjusted p-value or q-value

B-B statistic (singles (logs) or B) is the log odd number of differential gene expression (log-odds, log probability).

-FC-non-log-fold change

FC _ 1-non-log multiple change centered at zero

L S-binary value associated with the FC _1 value set to-1 if the FC _1 value is below-1.1 and set to 1 if the FC _1 value is above 1.1.

Table 1 shows the genes found to exhibit the relevant chromosomal interactions. The other tables show similar data. P-values in the loci table and HyperG _ Stats (finding significant EpiSwitch in loci based on parameters for hypergeometric enrichment)^TMP-value of probability of the number of markers) is the same column L S shows the presence or absence of an interaction associated with a particular responder state.

The probe was designed 30bp from the Taq1 site. In the case of PCR, PCR primers are usually designed to detect the ligation product, but their positions from the Taq1 site will vary.

The position of the probe is as follows:

30 bases upstream of TaqI site on starting 1-fragment 1

End of TaqI restriction site on 1-fragment 1

TaqI restriction site on Start 2-fragment 2

End of 30 bases downstream of TaqI site on 2-fragment 2

4kb sequence position:

4000 bases upstream of TaqI site on starting 1-fragment 1

End of TaqI restriction site on 1-fragment 1

TaqI restriction site on Start 2-fragment 2

Ending 4000 bases downstream of TaqI site on 2-fragment 2

The G L MNET values are related to the process of fitting the entire lasso or elastic net regularization (λ set to 0.5 (elastic net)).

Tables 1 and 4 relate to the detection of immune responses. Table 2 shows the overlap between the two studies performed and table 3 shows the overlap with interferon gamma-associated markers. The invention can be practiced using the markers disclosed/represented in any table. Other tables, including tables 13 and 1, may be interpreted in a similar manner as described above for table 1.

Preferred embodiments of sample preparation and chromosome interaction detection

Methods of preparing samples and detecting chromosome conformation are described herein. Optimized (non-conventional) versions of these methods may be used, for example, as described in this section.

Typically, the sample will contain at least 2x10⁵And (4) cells. The sample may contain up to 5x10⁵And (4) cells. In one embodiment, the sample will contain 2x10⁵To 5.5x10⁵And (4) cells.

Described herein are cross-linking of epigenetic chromosomal interactions that occur at a chromosomal locus. This may be done before cell lysis occurs. Cell lysis may be carried out for 3 to 7 minutes, for example 4 to 6 or about 5 minutes. In some embodiments, cell lysis is performed for at least 5 minutes and less than 10 minutes.

Digestion of DNA with restriction enzymes is described herein. Typically, DNA is limited to a time period of about 10 to 30 minutes (e.g., about 20 minutes) at about 55 ℃ to about 70 ℃ (e.g., about 65 ℃).

Preferably, frequent cutting restriction enzymes are used, which produce fragments of ligated DNA with average fragment sizes up to 4000 base pairs. Optionally, the restriction enzyme produces fragments of ligated DNA having an average fragment size of about 200 to 300 base pairs, for example about 256 base pairs. In one embodiment, a typical fragment size is 200 base pairs to 4,000 base pairs, e.g., 400 to 2,000 or 500 to 1,000 base pairs.

In one embodiment of the EpiSwitch method, no DNA precipitation step is performed between the DNA restriction digestion step and the DNA ligation step.

DNA ligation is described herein. Typically, DNA ligation is performed for 5 to 30 minutes, e.g., about 10 minutes.

The proteins in the sample may be enzymatically digested, for example using a protease, optionally proteinase K. The protein may be subjected to enzymatic digestion for a period of about 30 minutes to 1 hour, for example about 45 minutes. In one embodiment, there is no cross-linking reversal or phenolic DNA extraction step after protein digestion, e.g., proteinase K digestion.

In one embodiment, PCR detection is capable of detecting a single copy of the ligated nucleic acid, preferably in a binary read out of the presence/absence of the ligated nucleic acid.

FIG. 25 shows a preferred method of detecting chromosomal interactions.

Methods and uses of the invention

The method of the invention can be described in different ways. It may be described as a method of preparing a linked nucleic acid comprising (i) cross-linking in vitro chromosomal regions that have been brought together in a chromosomal interaction; (ii) subjecting the cross-linked DNA to cleavage or restriction digest cleavage; and (iii) ligating the cross-linked cleaved DNA ends to form a ligated nucleic acid, wherein detection of the ligated nucleic acid can be used to determine the chromosomal status at the locus, and wherein preferably:

the locus may be any locus, region or gene mentioned in table 1, and/or

-wherein the chromosomal interaction may be any chromosomal interaction mentioned herein or any chromosomal interaction corresponding to any of the probes disclosed in table 1, and/or

-wherein the ligation product may have or comprise (i) a sequence identical or homologous to any of the probe sequences disclosed in table 1; or (ii) a sequence complementary to (ii).

The method of the invention may be described as a method for detecting chromosome states representative of different subgroups in a population, comprising determining the presence or absence of a chromosome interaction within a defined epigenetically active region of a genome, wherein preferably:

-the subgroups are defined by the presence or absence of an immune response, and/or

The chromosomal status may be at any of the loci, regions or genes mentioned in table 1; and/or

The chromosomal interaction may be any chromosomal interaction mentioned in table 1 or corresponding to any probe disclosed in the table.

The method of the invention may be described as a method of preparing a linked nucleic acid comprising (i) cross-linking in vitro chromosomal regions that have been brought together in a chromosomal interaction; (ii) subjecting the cross-linked DNA to cleavage or restriction digest cleavage; and (iii) ligating the cross-linked cleaved DNA ends to form a ligated nucleic acid, wherein detection of the ligated nucleic acid can be used to determine the chromosomal status at the locus, and wherein preferably:

the locus may be any locus, region or gene mentioned in table 13, and/or

-wherein the chromosomal interaction may be any chromosomal interaction mentioned herein or corresponding to any of the probes disclosed in table 13, and/or

-wherein the ligation product may have or comprise (i) a sequence identical or homologous to any of the probe sequences disclosed in table 13; or (ii) a sequence complementary to (ii).

The method of the invention may be described as a method for detecting chromosome states representative of different subgroups in a population, comprising determining the presence or absence of a chromosome interaction within a defined epigenetically active region of the genome, wherein preferably:

-the subgroups are defined by the presence or absence of an immune response, and/or

The chromosomal status may be at any locus, region or gene mentioned in table 13; and/or

The chromosomal interaction may be any chromosomal interaction mentioned in table 13 or corresponding to any probe disclosed in the table.

The method of the invention may be described as a method of preparing a linked nucleic acid comprising (i) cross-linking in vitro chromosomal regions that have been brought together in a chromosomal interaction; (ii) subjecting the cross-linked DNA to cleavage or restriction digest cleavage; and (iii) ligating the crosslinked cleaved DNA ends to form a ligated nucleic acid, wherein detection of the ligated nucleic acid can be used to determine the chromosomal status at the locus, and wherein preferably:

the locus may be any locus, region or gene mentioned in table 16, and/or

-wherein the chromosomal interaction may be any chromosomal interaction mentioned herein or corresponding to any of the probes disclosed in table 16, and/or

-wherein the ligation product may have or comprise (i) a sequence identical or homologous to any of the probe sequences disclosed in table 16; or (ii) a sequence complementary to (ii).

The method of the invention may be described as a method for detecting chromosome states representative of different subgroups in a population, comprising determining the presence or absence of a chromosome interaction within a defined epigenetically active region of a genome, wherein preferably:

-the subgroups are defined by the presence or absence of an immune response, and/or

The chromosomal status may be at any locus, region or gene mentioned in table 16; and/or

The chromosomal interaction may be any chromosomal interaction mentioned in table 16 or corresponding to any probe disclosed in the table.

The present invention encompasses detecting chromosomal interactions at any of the loci, genes, or regions mentioned in table 1. The invention includes the use of the nucleic acids and probes mentioned herein for detecting chromosomal interactions, preferably in at least 1, 5, 10, 50, 100, 200, 250, 300 different loci or genes, e.g. the use of at least 1, 5, 10, 50, 100, 200, 250, 300 such nucleic acids or probes for detecting chromosomal interactions. The invention encompasses the detection of chromosomal interactions using any of the primers or primer pairs listed in table 4 or using variants of these primers as described herein (sequences comprising primer sequences or fragments and/or homologues comprising primer sequences).

The present invention includes detecting chromosomal interactions at any of the loci, genes, or regions mentioned in table 13. The invention includes the use of the nucleic acids and probes mentioned herein for detecting chromosomal interactions, preferably in at least 1, 5, 10, 50, 100, 200, 250, 300 different loci or genes, e.g. the use of at least 1, 5, 10, 50, 100, 200, 250, 300 such nucleic acids or probes for detecting chromosomal interactions. The invention encompasses the detection of chromosomal interactions using any of the primers or primer pairs listed in table 13 or using variants of these primers (sequences comprising primer sequences or fragments and/or homologues comprising primer sequences) as described herein.

The present invention includes detecting chromosomal interactions at any of the loci, genes, or regions mentioned in table 16. The invention includes the use of the nucleic acids and probes mentioned herein for detecting chromosomal interactions, preferably in at least 1, 5, 10, 50, 100, 200, 250, 300 different loci or genes, e.g. the use of at least 1, 5, 10, 50, 100, 200, 250, 300 such nucleic acids or probes for detecting chromosomal interactions. The invention encompasses the detection of chromosomal interactions using any of the primers or primer pairs listed in table 17 or using variants of these primers (sequences comprising primer sequences or fragments and/or homologues comprising primer sequences) as described herein.

When analyzing whether a chromosomal interaction occurs 'within' a defined gene, region or location, both parts of the chromosome that are together in the interaction are within the defined gene, region or location, or in some embodiments, only a part of the chromosome is within the defined gene, region or location.

Use of the methods of the invention for identifying novel treatments

Knowledge of chromosomal interactions can be used to identify new therapies for a disease condition. The present invention provides methods and uses of the chromosomal interactions defined herein for identifying or designing new therapeutic agents, e.g., those associated with immunotherapy.

Homologues

Homologs of polynucleotide/nucleic acid (e.g., DNA) sequences are contemplated herein. Such homologues typically have at least 70% homology, preferably at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 98% or at least 99% homology, for example over a region of at least 10, 15, 20, 30, 100 or more contiguous nucleotides, or across a nucleic acid portion from a region of the chromosome involved in the chromosomal interaction. Homology can be calculated based on nucleotide identity (sometimes referred to as "hard homology").

Thus, in particular embodiments, homologs of a polynucleotide/nucleic acid (e.g., DNA) sequence are referred to herein by reference to percent sequence identity. Typically, such homologues have a sequence identity of at least 70%, preferably at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 98% or at least 99%, for example over a region of at least 10, 15, 20, 30, 100 or more contiguous nucleotides, or across a nucleic acid portion from a region of the chromosome involved in the chromosomal interaction.

For example, the UWGCG Package provides the BESTFIT program, which can be used to calculate homology and/or% sequence identity (e.g., using its default settings) (Devereux et al (1984) Nucleic Acids Research 12, p 387-395.) the PI L EUP and B L AST algorithms can be used to calculate homology and/or% sequence identity and/or aligned sequences (e.g., identifying equivalent or corresponding sequences (typically using their default settings)), e.g., as described in Altschul S.F. (1993) J Mol Evol36:290 Evol 300; Altschul, S, F et al (1990) J Mol Biol 215: 403-10.

Software for performing B L AST analysis is publicly available through the National Center for biotechnology information, this algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W that match or satisfy some positive-valued threshold score T when aligned with words of the same length in database sequences in the query sequence, referred to as neighborhood word score thresholds (Altschul et al, supra.) these initial neighborhood word hits act as seeds that initiate searches to find HSPs containing them.

B L AST algorithms perform a statistical analysis of the similarity between two sequences, see, e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA90: 5873-5787. B L AST algorithms provide a measure of similarity which is the minimum sum probability (P (N)) that provides an indication of the probability that a match between two polynucleotide sequences will occur by chance.

Homologous sequences typically differ by 1, 2, 3, 4 or more bases, for example less than 10, 15 or 20 bases (which may be a substitution, deletion or insertion of a nucleotide). These changes can be measured over any of the regions described above relative to when calculating homology and/or% sequence identity.

For example, homology of a 'pair of primers' can be calculated by treating two sequences as one sequence (as if the two sequences were joined together) for subsequent comparison with another primer pair, which in turn is treated as a single sequence.

Array of cells

The second set of nucleic acids may be bound to the array, and in one embodiment there are at least 15,000, 45,000, 100,000 or 250,000 different second nucleic acids bound to the array, which preferably represents at least 300, 900, 2000 or 5000 loci. In one embodiment, one, or more, or all of the different second populations of nucleic acids bind to more than one different region of the array, and are in fact repeated on the array, allowing for error detection. The array may be based on the AgilentSurePrint G3 Custom CGH microarray platform. The detection of binding of the first nucleic acid to the array may be performed by a two-color system.

Therapeutic agents (to which responsiveness is determined or selected based on testing according to the invention)

Therapeutic agents are mentioned herein. The invention provides such agents for use in the prevention or treatment of disease conditions in certain individuals, such as those identified by the methods of the invention. This may comprise administering to an individual in need of treatment a therapeutically effective amount of an agent. The present invention provides the use of an agent in the manufacture of a medicament for the prevention or treatment of a condition in a certain individual.

The formulation of the medicament will depend on the nature of the medicament. The agent will be provided in the form of a pharmaceutical composition comprising the agent and a pharmaceutically acceptable carrier or diluent. Suitable carriers and diluents include isotonic saline solutions, for example phosphate buffered saline. Typical oral dosage compositions include tablets, capsules, liquid solutions and liquid suspensions. The medicament may be formulated for parenteral, intravenous, intramuscular, subcutaneous, transdermal or oral administration.

The dosage of the medicament may be determined according to various parameters, in particular according to the substance used; the age, weight, and condition of the individual being treated; the route of administration; and the required protocol. The physician will be able to determine the route of administration and the dosage required for any particular agent. However, suitable doses may be in the range of 0.1 to 100mg/kg body weight, such as 1 to 40mg/kg body weight, for example 1 to 3 times daily.

In one embodiment, the invention includes detecting responsiveness to a therapeutic agent (e.g., any of the therapeutic agents mentioned herein). This may be done before the start of the treatment and/or during the treatment.

The therapy may be a monotherapy or a combination therapy, for example an immune checkpoint modulator (inhibitor) using PD-1 and or its ligand PD-L the therapy may be a combination of anti-PD-1 or anti-PD-L with another drug (yipimema/ipilimumab) or small molecule that targets a checkpoint such as CT L a4 the PD-1 inhibitor may be pembrolizumab (Keytruda) or nivolumab (optivo), the modulator or therapeutic of PD-L may be altuzumab (tecentiq)), avilamab (bavenysian), doluzumab (infinibizi), CA-170, yiprimumab, tremelimumab, pembrolizumab, pimlizumab, BMS935559, gvax2 323280, 3894736, MSB 063946, MDX 6559, BMS 6580.

The therapy may comprise administration of an agent that targets and/or modulates the interferon gamma or JAK-START pathway.

The therapeutic agent may be any such agent disclosed in any table herein (e.g., table 9, 10, or 11), or may target any 'target' disclosed herein, including any protein disclosed herein in any table (including table 1, 13, or 16). It is to be understood that any agents disclosed in combination are also to be considered disclosed for administration alone.

Forms of matter mentioned herein

Any of the substances mentioned herein, such as nucleic acids or therapeutic agents, may be in purified or isolated form. They may be in a form different from that found in nature, for example, they may be present in combination with other substances with which they do not occur in nature. Nucleic acids (including portions of sequences defined herein) can have sequences that differ from those found in nature, e.g., having at least 1, 2, 3, 4, or more nucleotide changes in the sequences described in the homology section. The nucleic acid may have a heterologous sequence at the 5 'or 3' end. Nucleic acids may be chemically different from those found in nature, e.g., they may be modified in some way, but preferably still capable of Watson-Crick base pairing. Where appropriate, the nucleic acid will be provided in double-stranded or single-stranded form. The present invention provides all of the specific nucleic acid sequences referred to herein in either single-or double-stranded form, and thus includes complementary strands to any of the disclosed sequences.

The invention provides a kit for performing any of the methods of the invention, comprising detecting chromosomal interactions associated with an immune response. Such kits may include specific binding agents capable of detecting the relevant chromosomal interactions, such as reagents capable of detecting the ligated nucleic acids produced by the methods of the invention. Preferred reagents present in the kit include probes, or primer pairs, capable of hybridizing to the ligated nucleic acids, e.g., primer pairs capable of amplifying the ligated nucleic acids in a PCR reaction, as described herein.

The present invention provides a device capable of detecting relevant chromosomal interactions. The device preferably comprises any specific binding agent, probe or primer pair capable of detecting a chromosomal interaction, such as any such agent, probe or primer pair described herein.

Detection method

In one embodiment, the quantitative detection of a linker sequence associated with a chromosomal interaction is performed using a probe that is detectable after activation during a PCR reaction, wherein the linker sequence comprises sequences from two chromosomal regions that come together during the epigenetic chromosomal interaction, wherein the method comprises contacting the linker sequence with the probe during the PCR reaction, and detecting the extent of activation of the probe, and wherein the probe binds to the linker site. The methods generally allow the detection of specific interactions in a MIQE compliant manner using dual labeled fluorogenic hydrolysis probes.

The probes are typically labeled with a detectable label having an inactive and active state so as to be detectable only upon activation. The degree of activation will be related to the degree of template (ligation product) present in the PCR reaction. Detection may be performed during all or part of the PCR process, for example, during at least 50% or 80% of the PCR cycles.

In one embodiment, the fluorophore is attached to the 5 'terminus of the oligonucleotide and the quencher is covalently attached to the 3' terminus of the oligonucleotide the fluorophore that can be used in the methods of the invention includes FAM, TET, JOE, subunit horse Yellow (Yakima Yellow), HEX, cyanine 3, ATTO 550, TAMRA, ROX, Texas Red (TexasRed), cyanine 3.5, L C610, L C640, ATTO 647N, cyanine 5, cyanine 5.5, and ATTO 680 the quencher that can be used with an appropriate fluorophore includes TAM, BHQ1, DAB, Eclip, BHQ2, and BBQ650, optionally wherein the fluorophore is selected from the group consisting of HEX, Texas Red and FAM preferred combinations of the fluorophore and the quencher include BHQ1 and BHQ 2.

Use of probes in qPCR assays

The hydrolysis probes of the invention are typically optimized for temperature gradients with concentration-matched negative controls. Preferably, a single-step PCR reaction is optimized. More preferably, a standard curve is calculated. The advantage of using specific probes bound across the junction of the linker sequences is that specificity for the linker sequences can be achieved without the use of nested PCR methods. The methods described herein allow for accurate and precise quantification of low copy number targets. The target linker sequence may be purified prior to temperature gradient optimization, e.g., gel purification. The target junction sequence can be sequenced. Preferably, about 10ng or 5 to 15ng, or 10 to 20ng, or 10 to 50ng, or 10 to 200ng of template DNA is used for the PCR reaction. The forward and reverse primers are designed such that one primer binds to a sequence of one of the chromosomal regions represented in the linker DNA sequence and the other primer binds to the other chromosomal region represented in the linker DNA sequence, e.g., by being complementary to the sequence.

Selection of ligated DNA targets

The invention includes selecting primers and probes for use in the PCR methods defined herein, including selecting primers based on the ability to bind and amplify a ligated sequence, and selecting probe sequences based on the characteristics of the target sequence to be bound, particularly the curvature of the target sequence.

Probes are typically designed/selected to bind to a linker sequence, which is a juxtaposed restriction fragment spanning the restriction site. In one embodiment of the invention, the predicted curvature of possible junction sequences associated with a particular chromosomal interaction is calculated, for example using a particular algorithm as referenced herein. The curvature may be expressed in degrees per helical turn, for example 10.5 ° per helical turn. The linker sequence is selected for targeting wherein the linker sequence has a curvature propensity peak fraction of at least 5 ° per helix turn, typically at least 10 °, 15 ° or 20 ° per helix turn, for example 5 ° to 20 ° per helix turn. Preferably, the curvature propensity score is calculated per helical turn for at least 20, 50, 100, 200 or 400 bases, e.g., 20 to 400 bases upstream and/or downstream of the ligation site. Thus, in one embodiment, the target sequence in the ligation product has any of these levels of curvature. The target sequence may also be selected based on the lowest thermodynamic structure free energy.

Specific embodiments

In one embodiment, only the intrachromosomal interactions are typed/detected, and no extrachromosomal interactions (between different chromosomes) are typed/detected.

In particular embodiments, certain chromosomal interactions are not typed, such as any of the specific interactions mentioned herein (e.g., as defined by any of the probes or primer pairs mentioned herein). In some embodiments, chromosomal interaction typing is not performed in any of the genes mentioned herein (e.g., any of the genes mentioned in the figures, including any or all of the genes mentioned in figures 2 and 4).

In one embodiment, the chromosomal interactions represented by any or all of the probes or primers in tables 5-7 are not typed. In another embodiment, the chromosomal interactions present in any or all of the genes listed in tables 5-7 are not typed. In a further embodiment, the chromosomal interactions present in any or all of the regions listed in tables 5-7 are not typed.

In one embodiment, the immune response is not associated with antibody therapy. In another embodiment, the immune response is not associated with an anti-PD-1 therapy (e.g., anti-PD-1 therapy for melanoma). In another embodiment, the immune response is not associated with treatment with one or more of the following: hematologic cancer, leukemia, prostate cancer, breast cancer, diffuse large B-cell lymphoma.

Screening method

The invention provides a method of determining which chromosomal interactions are associated with chromosomal states corresponding to an immune response subgroup of a population, comprising contacting a first set of nucleic acids from a subgroup having a different chromosomal state with a second set of index nucleic acids, and allowing hybridization of complementary sequences, wherein the nucleic acids in the first and second sets of nucleic acids represent a ligation product comprising sequences from two chromosomal regions that are clustered together in a chromosomal interaction, and wherein the hybridization pattern between the first and second sets of nucleic acids allows determination of which chromosomal interactions are specific for the immune response subgroup. Subgroups may be any specific subgroup defined herein, for example with reference to a particular condition or therapy.

Publication (S)

The contents of all publications mentioned herein are incorporated by reference into this specification and can be used to further define features relevant to the present invention.

Watch (A)

Table 1 shows the final set of markers used to test immune responsiveness.

Table 2 shows shared markers between anti-PD-1 and anti-PD-L1 studies.

Table 3 shows the markers overlapping the interferon gamma activated ORF.

Table 4 shows primer pairs that can be used to detect markers associated with immune responses.

Tables 5 to 7 show markers, genes, and regions that are not included in certain embodiments.

Table 8 shows immune checkpoint molecules.

Table 9 provides examples of cancer therapies.

Tables 10 and 11 show combination therapy and monotherapy in certain embodiments of the invention. In some embodiments, these are therapies that test for responsiveness. In other embodiments, these therapies are administered to a patient according to the test results of the present invention.

Table 12 provides a description of the genes relevant to the present invention.

Table 13 shows another set of markers used to test immune responsiveness.

Tables 14 and 15 describe genes related to embodiments of the present invention.

Tables 16 to 18 show markers for testing immune responsiveness.

Modes for carrying out the invention

Paragraph a. a method for detecting a chromosomal state representative of a subgroup in a population, comprising determining the presence or absence of a chromosomal interaction associated with the chromosomal state within a defined region of a genome, wherein the subgroup is associated with a state of an immune-responsive individual; and is

-wherein the chromosomal interactions are optionally determined by a method of determining which chromosomal interactions are associated with chromosomal states corresponding to an immune response subgroup of the population, comprising contacting a first set of nucleic acids from a subgroup having a different chromosomal state with a second set of index nucleic acids, and allowing hybridization of the complementary sequences, wherein the nucleic acids in the first and second sets of nucleic acids represent a ligation product comprising sequences from two chromosomal regions that are clustered together in a chromosomal interaction, and wherein the hybridization pattern between the first and second sets of nucleic acids allows determining which chromosomal interactions are specific for the immune response subgroup; and is

-wherein the chromosomal interactions are:

(i) present in any one of the regions or genes listed in table 1; and/or

(ii) Corresponding to any of the chromosomal interactions represented by any of the probes shown in Table 1, and/or

(iii) (iii) is present in a region comprising or flanking the 4,000 bases of (i) or (ii);

or

a) Present in any one of the regions or genes listed in table 13; and/or

b) Corresponding to any of the chromosomal interactions represented by any of the probes shown in Table 13, and/or

c) Is present in a region comprising or flanking 4,000 bases of (a) or (b).

Paragraph b. the method according to paragraph a, wherein the specific combination of chromosomal interactions is typed as:

(i) contains all chromosomal interactions represented by the probes in table 1; and/or

(ii) Comprising at least 10, 50, 100, 150, 200, or 300 chromosomal interactions represented by probes in table 1; and/or

(iii) Together in at least 10, 50, 100, 150, or 200 regions or genes listed in table 1; and/or

(iv) Wherein at least 10, 50, 100, 150, 200, or 300 chromosomal interactions that are present in a region that comprises or is flanked by 4,000 bases of the chromosomal interactions represented by the probes in Table 1 are typed.

Paragraph c. the method according to paragraph a, wherein the specific combination of chromosomal interactions is typed as:

(i) contains all chromosomal interactions represented by the probes in table 13; and/or

(ii) Comprising at least 10, 50, 100, 150, 200, or 300 chromosomal interactions represented by probes in table 13; and/or

(iii) Are present together in at least 10, 50, 100, 150 or 200 regions or genes listed in table 13; and/or

(iv) Wherein at least 10, 50, 100, 150, 200, or 300 chromosomal interactions that are present in a region that comprises or is flanked by 4,000 bases of the chromosomal interactions represented by the probes in Table 13 are typed.

D. A method according to any one of the preceding paragraphs, wherein the chromosome interactions are:

typing in a sample from an individual, and/or

Typing by detecting the presence or absence of a DNA loop at the site of chromosomal interaction, and/or

Typing by detecting the presence or absence of distal regions of chromosomes clustered together in chromosome conformation, and/or

-typing by detecting the presence of linked nucleic acids, which are produced during said typing and whose sequence comprises two regions each corresponding to a chromosomal region that are clustered together in a chromosomal interaction, wherein detection of linked nucleic acids is preferably performed by using:

(i) a probe having at least 70% identity to any particular probe sequence mentioned in table 1, and/or (ii) a primer pair having at least 70% identity to any primer pair in table 4; or

(a) A probe having at least 70% identity to any particular probe sequence mentioned in table 13, and/or (b) a primer pair having at least 70% identity to any primer pair in table 13.

E. The method according to any of the preceding paragraphs, wherein:

-the second set of nucleic acids is from a larger group of individuals than the first set of nucleic acids; and/or

-the first set of nucleic acids is from at least 8 individuals; and/or

-the first group of nucleic acids is from at least 4 individuals of the first subgroup and at least 4 individuals of a second subgroup, which preferably does not overlap with the first subgroup; and/or

-performing the method to select an individual for medical treatment; and/or

-the immune response is a response to immunotherapy or immune checkpoint therapy; and/or

The immune response is a response to cancer immunotherapy, and/or

-performing the method to determine an immune response at one or more defined time points, wherein optionally at least one time point is during the course of the treatment.

F. The method according to any of the preceding paragraphs, wherein:

-the second set of nucleic acids represents the unselected set; and/or

-wherein the second set of nucleic acids is bound to the array at defined positions; and/or

-wherein the second set of nucleic acids represents chromosomal interactions in at least 100 different genes; and/or

-wherein the second set of nucleic acids comprises at least 1,000 different nucleic acids representing at least 1,000 different chromosomal interactions; and/or

-wherein the first set of nucleic acids and the second set of nucleic acids comprise at least 100 nucleic acids of 10 to 100 nucleotide bases in length.

G. A method according to any one of the preceding paragraphs, wherein the first set of nucleic acids is obtainable in a method comprising the steps of: -

(i) Cross-linking regions of chromosomes that cluster together in a chromosomal interaction;

(ii) subjecting the cross-linked region to cleavage, optionally by restriction digestion with an enzyme; and

(iii) ligating the cross-linked cleaved DNA ends to form a first set of nucleic acids (in particular comprising ligated DNA).

H. A method according to any of the preceding paragraphs:

-wherein at least 10 to 200 different chromosomal interactions are typed, preferably in 10 to 200 different regions or genes; and optionally (a) typing from 50 to 100 different chromosomal interactions, each located in a different gene and/or a different region as defined in table 1; or (b) between 50 and 100 different chromosomal interactions, each located in a different gene and/or in a different region as defined in table 13, have been typed;

and/or

-it is performed to select whether the individual is to receive immunotherapy, wherein the immunotherapy preferably comprises small molecule immunotherapy, antibody immunotherapy or cellular immunotherapy.

I. A method according to any of the preceding paragraphs, wherein the defined region of the genome:

(i) comprises a Single Nucleotide Polymorphism (SNP); and/or

(ii) Expressing micro rna (mirna); and/or

(iii) Expression of non-coding rna (ncrna); and/or

(iv) Expressing a nucleic acid sequence encoding at least 10 contiguous amino acid residues; and/or

(v) An expression regulatory element; and/or

(vii) Comprising a CTCF binding site.

J. A method according to any one of the preceding paragraphs, performed to identify or design a therapeutic agent for immunotherapy;

-wherein preferably the method is used to detect whether a candidate agent is capable of causing a change in chromosomal status associated with different levels of immune response;

-wherein the chromosomal interaction is represented by any probe in table 1; and/or

-chromosomal interactions are present in any region or gene listed in table 1;

and wherein, optionally:

-the chromosomal interactions are determined by the method for determining which chromosomal interactions are related to the chromosomal status as defined in claim 1, and/or

Monitoring changes in chromosomal interactions using (i) probes having at least 70% identity to any of the probe sequences mentioned in table 1, and/or (ii) primer pairs having at least 70% identity to any of the primer pairs in table 4.

K. A method according to any one of the preceding paragraphs, performed to identify or design a therapeutic agent for immunotherapy;

-wherein preferably the method is used to detect whether a candidate agent is capable of causing a change in chromosomal status associated with different levels of immune response;

-wherein the chromosomal interaction is represented by any probe in table 13; and/or

-chromosomal interactions are present in any region or gene listed in table 13;

and wherein, optionally:

-the chromosomal interactions are determined by the method for determining which chromosomal interactions are related to the chromosomal status as defined in claim 1, and/or

Monitoring changes in chromosomal interactions using (i) probes having at least 70% identity to any of the probe sequences mentioned in table 13, and/or (ii) primer pairs having at least 70% identity to any of the primer pairs in table 13.

L, the method according to paragraph J or K, comprising selecting a target based on detection of chromosomal interactions, and preferably screening for modulators of the target to determine a therapeutic agent for immunotherapy, wherein the target is optionally a protein.

A therapeutic agent for use in a method of immunotherapy of an individual determined to be in need of the therapeutic agent by a method according to any one of paragraphs a to I.

N. the method according to any of paragraphs a to K or the therapeutic agent for use according to paragraph M, wherein typing or detecting comprises specifically detecting the ligation products by quantitative PCR (qpcr) using primers capable of amplifying the ligation products and probes that bind to the ligation sites during the PCR reaction, wherein the probes comprise sequences that are complementary to sequences from each of the chromosomal regions that have clustered together in a chromosomal interaction, wherein preferably the probes comprise:

an oligonucleotide that specifically binds to the ligation product, and/or

A fluorophore covalently linked to the 5' terminus of the oligonucleotide, and/or

A quencher covalently linked to the 3' terminus of the oligonucleotide, and

optionally, the step of (a) is carried out,

the fluorophore is selected from the group consisting of HEX, Texas Red, and FAM; and/or

The probe comprises a nucleic acid sequence of 10 to 40 nucleotide bases in length, preferably 20 to 30 nucleotide bases in length.

Description of the preferred embodiments

EpiSwitch^TMPlatform technology detects epigenetic regulatory signatures of regulatory changes between normal and abnormal conditions at a locus. EpiSwitch^TMThe platform determines and monitors the basic epigenetic level of gene regulation associated with the regulatory high order structure of the human chromosome (also known as chromosome conformation signature). Chromosome signature is a unique primary step in the gene deregulation cascade. They are high-order biomarkers with a series of unique advantages over biomarker platforms that utilize late-stage epigenetic and gene expression biomarkers (e.g., DNA methylation and RNA profiling).

EpiSwitch^TMArray assay

Customized EpiSwitch^TMThe array screening platform has 4 unique chromosome conformations with densities of 15K, 45K, 100K and 250K, each chimeric fragment is repeated 4 times on the array, resulting in effective densities of 60K, 180K, 400K and 1 million, respectively.

Custom designed EpiSwitch^TMArray of cells

15K EpiSwitch^TMArrays can screen whole genomes, including with EpiSwitch^TMBiomarker discovery techniques query about 300 loci. EpiSwitch^TMThe array is constructed based on an Agilent SurePrint G3 customized CGH microarray platform; this technique provided 4 densities, 60K, 180K, 400K and 1 million probes. Since each EpiSwitch^TMProbes appear in quadruplicate, so the density of each array is reduced to 15K, 45K, 100K and 250K, allowing statistical evaluation of reproducibility. Potential EpiSwitch for each genetic locus query^TMThe average number of markers was 50; thus, the number of loci that can be investigated is 300, 900, 2000 and 5000.

EpiSwitch^TMCustom array piping

EpiSwitch^TMThe array is a two-color system, with a set of samples at EpiSwitch^TMThe library was labeled in Cy5 after generation, while the other samples to be compared/analyzed (control) were labeled in Cy 3. The array was scanned using an Agilent SureScan scanner and the resulting features were extracted using Agilent feature extraction software. Then use EpiSwitch in R^TMProcessing of arrays Using Standard bicolour packs in Bioconductor in R: L imma.standardization of arrays Using L immaNormalization of the in-array function was done and compared to the Agilent positive control and EpiSwitch on the chip^TMFiltering the data based on Agilent flag calls, removing Agilent control probes, and averaging technical replicate probes for analysis using L imma<1.1 or>1.1 and passing p<0.1FDR p-value, Coefficient of Variation (CV)<Further screening was performed on 30% of the probes. To reduce probe set, multifactorial analysis was further performed using the FactorMineR software package in R.

Note that L IMMA is a linear model and empirical Bayesian procedure for assessing differential expression in microarray experiments L IMMA is an R software package for analyzing gene expression data generated by microarrays or RNA-Seq.

The probe pool was initially selected based on the adjusted p-value and final sorting was performed based on FC and CV < 30% (arbitrary cut-off) parameters. Further analysis and a final list are derived based on only the first two parameters (adj.p-value; FC).

Statistical pipeline

Using EpiSwitch in R^TMAnalysis software Package Process EpiSwitch^TMScreening the array to select high value EpiSwitch^TMMarker to translate to EpiSwitch^TMOn a PCR platform.

Step 1

Probes were selected based on the corrected p-value (false discovery rate, FDR), which is the product of the modified linear regression model. Probes below the p-value < 0.1 were selected and then further reduced by the Epigenetic Ratio (ER), which had to be < -1.1 or >1.1, in order to be selected for further analysis. The final filtration is the Coefficient of Variation (CV), which must be below 0.3.

Step 2

The top 40 markers were selected from the statistical list based on their ER to be selected as markers for PCR translation. The first 20 markers with the highest negative ER burden and the first 20 markers with the highest positive ER burden form a list.

Step 3

The markers (probes of statistical significance) obtained from step 1 form the basis for enrichment analysis using hyper-geometric enrichment (HE). This analysis enables the reduction of markers from the list of important probes and the formation of a translation to EpiSwitch together with the markers from step 2^TMList of probes on PCR platform.

HE processes the statistical probes to determine which genetic locations have abundant statistically significant probes, indicating which genetic locations are pivotal in epigenetic differences.

The most significantly enriched loci based on corrected p-values were selected to generate a probe list. Genetic positions below the p-value of 0.3 or 0.2 were selected. Statistical probes mapped to these genetic positions were formed with the markers from step 2 for EpiSwitch^TMHigh value markers for PCR translation.

Array design and processing

Array design

1. The genetic loci were processed using SII software (currently v3.2) to:

a. extraction of genomic sequences (Gene sequences with 50kb upstream and 20kb downstream) at these specific genetic loci

b. Defining the probability of sequences in this region participating in CCs

c. Cleavage of sequences using specific REs

d. Determining which restriction fragments are likely to interact in a particular direction

e. The possibility of different CCs interacting together is ranked.

2. Determining array size and thus the number of available probe positions (x)

3. The x/4 interactions were extracted.

4. For each interaction, a sequence of 30bp to the restriction site of part 1 and a sequence of 30bp to the restriction site of part 2 are defined. Check if those regions are repeated, if not, exclude and take the next interaction in the list. Two 30bp ligations were made to define a probe.

5. A list of x/4 probes plus defined control probes was created and replicated 4 times to create a list to be created on the array.

6. The probe list was uploaded to the Agilent Sure design website to customize the CGH array.

7. Agilent custom CGH arrays were designed using a probe set.

Array processing

1. Using EpiSwitch^TMThe samples were processed for template production by Standard Operating Procedures (SOP).

2. Clean up was done by ethanol precipitation in an array processing laboratory.

3. Samples were processed according to the Agilent SureTag complete DNA labeling kit-this kit is based on CGH of Agilent oligonucleotide arrays for genomic DNA analysis enzymatic labeling of blood, cells or tissues.

4. Scanning was performed using an Agilent C scanner, using Agilent feature extraction software.

EpiSwitchTM

The EpiSwitchTM biomarker signature shows high robustness, sensitivity and specificity in the stratification of complex disease phenotypes. The technology utilizes the latest breakthrough in epigenetic science, monitors and evaluates the information of the chromosome conformation signature as an epigenetic biomarker and is very similar. Current research methods developed in academic settings require 3 to 7 days to biochemically process cellular material in order to detect CCS. Those programs have limited sensitivity and repeatability; and cannot be switched from EpiSwitch at the design stage^TMThe targeted insight provided by the analysis software package benefits.

EpiSwitch^TMArray computer marker determination

By EpiSwitch^TMArrays CCS locus assessments on the genome were performed directly on clinical samples from the test population to determine all relevant hierarchical lead biomarkers. EpiSwitch^TMArray platforms are used for marker determination due to their high throughput capability, as well as their ability to rapidly screen a large number of loci. The array used was an Agilent custom CGH array that allowed querying of targets determined by computer softwareAnd (5) a material.

EpiSwitch^TMPCR

Then, pass EpiSwitch^TMVerification by EpiSwitch or DNA sequencer (i.e., Roche 454, Nanopore MinION, etc.)^TMArray-determined potential markers. Selection of the top PCR marker with statistical significance and showing the best reproducibility to further reduce to the final EpiSwitch^TMSignature set and verified in separate sample cohorts. EpiSwitch^TMPCR can be performed by a trained technician following established standardized protocol protocols. All protocols and manufacturing of reagents are performed according to ISO 13485 and 9001 certification to ensure quality of work and the ability to transport protocols. EpiSwitch^TMPCR and EpiSwitch^TMThe array biomarker platform is compatible with whole blood and cell line analysis. The test is sensitive enough to detect very low copy number abnormalities using small amounts of blood.