EP4555103A1 - Certification of animal-derived product(s) based on dna-methylation - Google Patents
Certification of animal-derived product(s) based on dna-methylationInfo
- Publication number
- EP4555103A1 EP4555103A1 EP23738732.9A EP23738732A EP4555103A1 EP 4555103 A1 EP4555103 A1 EP 4555103A1 EP 23738732 A EP23738732 A EP 23738732A EP 4555103 A1 EP4555103 A1 EP 4555103A1
- Authority
- EP
- European Patent Office
- Prior art keywords
- animal
- test
- methylation
- test animal
- product sample
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Pending
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Classifications
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/112—Disease subtyping, staging or classification
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/154—Methylation markers
Definitions
- the present invention relates to a method of determining certification of an unknown animal derived product sample based on specific panels of genes that provide a source for the generation of DNA methylation profiles which are specific for a distinct certification.
- DNA methylation profiling may be used to determine the distinct certification of animal-derived products.
- the distinct certification may include halal, kosher and the like.
- BACKGROUND OF THE INVENTION Sustainable food production is presently considered among the globally most important societal needs. As the value chains of the agriculture and aquaculture industries are highly complex, certificates have been established to reinforce consumer relationships and trust.
- Kosher certification i.e., designation of a food item as Kosher
- Halal certification i.e., designation of a food item as Halal
- Kosher certification i.e., designation of a food item as Kosher
- Halal certification i.e., designation of a food item as Halal
- Judaic ritual slaughter Shechita
- Islamic ritual slaughter Zabihah
- Health, safety and also animal welfare considerations demand that the origins of animal products, and in particular meat products, should be traceable, so that quality assurance audits, and monitoring procedures can be effectively and reliably carried out.
- a customer may be unable to determine a type of animal from which the meat is derived based on visual inspection. This may result in a person who abides by a dietary restriction being hesitant to consume animal products.
- Physical conditions and/or chemical conditions of an animal may be altered based on the way the animal has been slaughtered. For example, it is well known that cortisol levels of animals for which Kosher slaughter or Halal slaughter may be performed may be different from cortisol levels of animals that undergo another means of slaughter.
- different types of meats obtained from different animals may be associated with physical differences and/or chemical differences. For example, proteins from pork meat of a pig may differ from proteins from beef meat of a cow.
- Differences may also exist in relation to different breeds of a particular type of animal, different cuts of meat of a particular animal, or the like. This may limit an effectiveness of comparing an unknown sample of meat to a set of known reference samples of meat.
- DNA methylation patterns of animals contain important information about their rearing conditions. For example, a comparison of genome-wide patterns of methylation and variation at the DNA level revealed that a highly significant proportion of epigenetic variation could be associated with fitness differences and rearing conditions such as captivity in salmon (Le Luyer J et al.2017 PNAS vol 114, no 49). Koop et al. and Rhein et al. also separately confirmed that methylation patterns are maintained postmortem and are consistent regardless of the level of decomposition of the sample.
- the present invention attempts to solve the problems above by providing a method using DNA methylation patterns to distinguish one type of animal derived product from another type of animal derived product and to be able to determine the means of killing or slaughtering the animal from which the animal derived product derives from and thereby certify the product accurately and reliably.
- the present invention is based on the finding that the means of slaughtering an animal, results in stress in the internal environment of the animal and this can permanently change the genome of the animal through epigenetics.
- the capability to adapt to the environment (i.e. means of slaughtering) and maintain the adapted biological pattern depends on epigenetic mechanisms, including DNA methylation.
- the present invention is based on the finding that the method of slaughtering an animal for food consumption may also result in changes in epigenetic mechanisms of the animal, including DNA methylation patterns and these patterns may be passed down to the different products that may derive from the animal.
- the inventors have unexpectedly found that this property can be utilized to identify "epigenetic fingerprints" on the genome that are specific to a method of slaughter of not just one animal but possibly all the animals that undergo the same method of slaughter.
- these ‘epigenetic fingerprints’ may be specific not only for the animal that is slaughtered in a particular way but also for any product that stems from the very animal (an individual).
- the present invention provides means to identify the specific method of slaughter of a particular animal, for example rearing animals also known as livestock and poultry from which an animal-derived product comes from.
- the method according to any aspect of the present invention may be used to determine if an animal-derived product is derived from an animal that has been slaughtered in a particular way or not. More in particular, the method according to any aspect of the present invention may be used to determine if an animal-derived product is derived from an animal that has been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or if the animal has been bled to death.
- the method according to any aspect of the present invention may then be used to accurately and reliably determine the method of slaughter of an animal and then provide and/or confirm the certification of any sample that originates from the animal. Further, the method according to any aspect of the present invention may also be used to identify if any animal-derived product is accurately and reliably certified, particularly where the certification is based on the method of slaughter of the animal.
- a method of certifying a test animal-derived product sample comprising the steps of: (a) determining a test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile obtained from (a) with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death wherein a difference in the test methylation profile of (a) compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid
- a method of certifying a test animal-derived product sample comprising the steps of: (a) determining the methylation status of at least one CpG site within the genomic material obtained from the animal-derived product sample, (b) comparing the methylation status of the CpG site from (a) with that of a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death, wherein a difference in the test methylation status of (a) in the test animal compared to the CpG site in the control animal is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular vein
- a method of certifying a test animal-derived product sample comprising the steps of: (a) determining the test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile determined in (a) with a panel of predetermined reference methylation profiles of the same biological taxon of the test animal from which the product sample derives, wherein each of the predetermined reference methylation profiles is specific for a distinctly certified reference animal that - has been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus; and/or - bled to death; wherein if the test methylation profile is significantly similar to one of the predetermined reference methylation profiles, the test animal derived product sample has the same distinct certification as that of the predetermined
- animal-derived product refers to products that originate from animals.
- test animal-derived product refers to the sample or subject in question that is to undergo the method according to any aspect of the present invention.
- meat and meat products also including fat, flesh, blood, and lesser-known products, such as isinglass and rennet, poultry products (meat and eggs), dairy products (milk and cheese), and non-food products such as fiber (wool, mohair, cashmere, leather and the like).
- Animal-derived products may also include products that can be made using animal products (e.g. fat) such as soap, creams and such.
- the animal-derived product is meat, eggs, blood, brain, sperm, milk and any other tissue or sample that provides genomic DNA.
- the animal-derived product is meat.
- certification of quality refers to a certificate or a confirmation given by designated certification agencies that endorse the quality of a particular animal derived product, including food for use and/or consumption by human beings.
- certification of quality is used interchangeably with the term ‘certification’.
- certifications of distinct food quality may include ‘Haltungsform’, ‘Tiermple’, ‘Ohne Gentechnik’, ‘halal’, ‘kosher’, and other safe labels that confirm that a product sold has been prepared in accordance with specific religious or safety regulations.
- the term ‘certification of food quality’ refers to a certificate or a confirmation given by designated certification agencies that endorse the quality, source or means of slaughter of a particular food for consumption by human beings.
- the certified quality may be a distinct certified food quality, or distinct certification and this may be kosher, non- kosher, halal or non-halal.
- the distinct certified food quality or certification of the sample X may be kosher, non-kosher, halal or non-halal. More in particular, kosher or halal refers to the sample X originating from an animal that was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and/or the oesophagus. Even more in particular, the animal is drained of blood.
- kosher used in combination with food according to any aspect of the present invention refers to food that conforms to Jewish dietary regulations of kashrut (dietary law) or food that may be consumed according to halakha (law).
- Kosher used in relation to meat relates particularly to a manner in which animals are prepared for consumption.
- meat may be considered kosher when the meat comes from animals that have been slaughtered according to Jewish law where the animal is killed by a single cut across the throat to a precise depth, severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and the oesophagus, no higher than the epiglottis and no lower than where cilia begin inside the trachea, causing the animal to bleed to death.
- Such slaughter is to be carried out using a large, razor-sharp knife, which is checked before each slaughter to ensure that it has no irregularities (such as nicks and dents).
- the slaughter is usually also carried out by a shochet or a rabbi.
- Kosher meat usually refers to most meats excluding pig.
- kosher meat may be selected from beef, chicken, lamb, mutton, goat meat and mixtures thereof.
- Kosher meat does not include shellfish, which under Jewish tradition is not permitted for consumption. Although Jewish traditions permit consumption of vertebrate fish, since there is no special method of slaughtering vertebrate fish, all vertebrate fish may be considered kosher. Any food or meat that does not fall within the definition of ‘kosher’ will then be considered as ‘non-kosher’.
- the term ‘halal’ used in combination with food according to any aspect of the present invention refers to food that conforms to Islamic dietary laws and especially meat processed and prepared in accordance with those requirements.
- halal meat usually refers to most meats excluding pig. In particular, halal meat may be selected from beef, chicken, lamb, mutton, goat meat and mixtures thereof.
- test used in conjunction with the term subject and/ or animal in the present disclosure refers to an entity that is subjected to the method according to any aspect of the present invention and is the basis for an analysis application of the present invention.
- An “(individual) test subject”, an “(individual) group of test subjects” or a “test profile” or an ‘test animal derived product’ is therefore a (individual) subject or group of subjects being tested according to the invention or a profile being obtained or generated in this context.
- reference shall denote, mostly predetermined, entities which are used for a comparison with the test entity.
- the term ‘reference animal’ refers to an animal used for comparison or as a control in reference to the ‘test animal’.
- sample and/or ‘test animal-derived product sample’ used in accordance with any aspect of the present invention refers to an entity that may be subject to the method of the present invention.
- a sample may be any (test) animal-derived product that may be subject to the method of the present invention to determine the distinct certification by first determining the DNA methylation profile and then comparing this test methylation profile with a control.
- Blockchain may also be used to make the information easily available for the consumer.
- the method according to any aspect of the present invention may be used to identify an unknown sample (i.e. animal-derived product sample) based on DNA methylation patterns.
- DNA methylation patterns may then be compared with reference DNA methylation patterns to trace the animal-derived product sample back to the slaughterhouse or farmhouse from which the sample originates and then determine whether the unknown sample corresponds to an animal which has been slaughtered according to Kosher, Halal, non-Kosher or non-Halal practices. In this way, a buyer or a consumer of meat can verify that meat being sold as or marketed as being Kosher or Halal is genuine.
- the term “comprising” is to be construed as encompassing both “including” and “consisting of”, both meanings being specifically intended, and hence individually disclosed aspects of the present invention.
- methylation profile refers to the status of a specific methylation site (i.e.
- methylated vs. non-methylated which means a residue or methylation site is methylated or not methylated. Then, based on the methylation status of one or more methylation sites, a methylation profile may be determined. Accordingly, the term "methylation profile” or also “methylation pattern” refers to the relative or absolute concentration of methylated C residues or unmethylated C residues at any particular stretch of residues in the genomic material of a biological sample.
- cytosine (C) residue(s) not typically methylated within a DNA sequence are methylated, it may be referred to as "hypermethylated”; whereas if cytosine (C) residue(s) typically methylated within a DNA sequence are not methylated, it may be referred to as "hypomethylated”.
- cytosine (C) residue(s) within a DNA sequence are methylated as compared to another sequence from a different region or from a different individual (e.g., relative to normal nucleic acid or to the standard nucleic acid of the reference sequence), that sequence is considered hypermethylated compared to the other sequence.
- the cytosine (C) residue(s) within a DNA sequence are not methylated as compared to another sequence from a different region or from a different individual, that sequence is considered hypomethylated compared to the other sequence.
- Measurement of the levels of differential methylation may be done by a variety of ways known to those skilled in the art.
- One method is to measure the methylation level of individual interrogated CpG sites determined by the bisulfite sequencing method, as a non-limiting example.
- the term “hypermethylation” refers to the average methylation state corresponding to an increased presence of 5-mCyt at one or a plurality of CpG dinucleotides within a DNA sequence of a test DNA sample, relative to the amount of 5-mCyt found at corresponding CpG dinucleotides within a normal control DNA sample.
- control refers to an animal derived product not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or not having been bled to death.
- hypermethylation refers to the average methylation state corresponding to a decreased presence of 5-mCyt at one or a plurality of CpG dinucleotides within a DNA sequence of a test DNA sample, relative to the amount of 5-mCyt found at corresponding CpG dinucleotides within a normal control DNA sample.
- control refers to an animal derived product not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or not having been bled to death.
- a “methylated nucleotide” or a “methylated nucleotide base” refers to the presence of a methyl moiety on a nucleotide base, where the methyl moiety is usually not present in a recognized typical nucleotide base.
- cytosine in its usual form does not contain a methyl moiety on its pyrimidine ring, but 5-methylcytosine contains a methyl moiety at position 5 of its pyrimidine ring. Therefore, cytosine in its usual form may not be considered a methylated nucleotide and 5-methylcytosine may be considered a methylated nucleotide.
- thymine may contain a methyl moiety at position 5 of its pyrimidine ring, however, for purposes herein, thymine may not be considered a methylated nucleotide when present in DNA.
- Typical nucleotide bases for DNA are thymine, adenine, cytosine and guanine.
- Typical bases for RNA are uracil, adenine, cytosine and guanine.
- a "methylation site" is the location in the target gene nucleic acid region where methylation has the possibility of occurring.
- a location containing CpG is a methylation site wherein the cytosine may or may not be methylated.
- methylated nucleotide refers to nucleotides that carry a methyl group attached to a position of a nucleotide that is accessible for methylation.
- methylated nucleotides are usually found in nature and to date, methylated cytosine that occurs mostly in the context of the dinucleotide CpG, but also in the context of CpNpG- and CpNpN-sequences may be considered the most common. In principle, other naturally occurring nucleotides may also be methylated but they will not be taken into consideration with regard to any aspect of the present invention.
- a “CpG site” or “methylation site” is a nucleotide within a nucleic acid (DNA or RNA) that is susceptible to methylation either by natural occurring events in vivo or by an event instituted to chemically methylate the nucleotide in vitro.
- a “methylated nucleic acid molecule” refers to a nucleic acid molecule that contains one or more nucleotides that is/are methylated.
- the term ‘epigenetic change’ as used herein refers to a chemical (e.g., methylation) change or protein (e.g., histones) change that takes place to a gene body or a promoter thereof. Through epigenetic changes, environmental factors like. diet, stress and prenatal nutrition can make an imprint on genes passed from one generation to the next.
- bisulfite encompasses any suitable type of bisulfite, such as sodium bisulfite, or another chemical agent that is capable of chemically converting a cytosine (C) to a uracil (U) without chemically modifying a methylated cytosine and therefore can be used to differentially modify a DNA sequence based on the methylation status of the DNA, e.g., U.S. Pat. Pub. US 2010/0112595 (Menchen et al.).
- a reagent that "differentially modifies" methylated or non-methylated DNA encompasses any reagent that modifies methylated and/or unmethylated DNA in a process through which distinguishable products result from methylated and non-methylated DNA, thereby allowing the identification of the DNA methylation status.
- processes may include, but are not limited to, chemical reactions (such as a C to U conversion by bisulfite) and enzymatic treatment (such as cleavage by a methylation-dependent endonuclease).
- an enzyme that preferentially cleaves or digests methylated DNA is one capable of cleaving or digesting a DNA molecule at a much higher efficiency when the DNA is methylated, whereas an enzyme that preferentially cleaves or digests unmethylated DNA exhibits a significantly higher efficiency when the DNA is not methylated.
- any “non-bisulfite-based method” and “non-bisulfite-based quantitative method” are comprised to test for a methylation status at any given methylation site to be tested. Such terms refer to any method for quantifying methylated or non-methylated nucleic acid that does not require the use of bisulfite.
- the terms also refer to methods for preparing a nucleic acid to be quantified that do not require bisulfite treatment.
- non-bisulfite-based methods include, but are not limited to, methods for digesting nucleic acid using one or more methylation sensitive enzymes and methods for separating nucleic acid using agents that bind nucleic acid based on methylation status.
- methyl-sensitive enzymes and "methylation sensitive restriction enzymes” are DNA restriction endonucleases that are dependent on the methylation state of their DNA recognition site for activity. For example, there are methyl-sensitive enzymes that cleave or digest at their DNA recognition sequence only if it is not methylated.
- a “biological sample” in context of the invention may comprise any biological material obtained from the subject or group of subjects that contains genomic material, and may be liquid, solid or both, may be tissue or bone, or a body fluid such as blood, lymph, etc.
- the biological sample useful for the present invention may comprise biological cells or fragments thereof.
- pre-selected methylation sites refers to methylation sites that were selected from genes or regions that showed the highest degree of methylation variation during the training of the method and fulfils certain quality criteria such as a minimum sequencing coverage of ⁇ 5x were considered and for ⁇ 5 qualified CpG sites. Additionally, genes that have an average methylation level ⁇ 0.1 or an average methylation level >0.9 can be excluded due to their limited dynamic range. “Reference methylation profiles” may be defined on the basis of multiple training samples using multivariate statistical methods, such as such as Principal Component analysis or Multi-Dimensional Scaling. In particular, the CpG site according to any aspect of the present invention, particularly in the pre-selected methylation sites is selected from the Table A below:
- the pre-determined reference profile may be used in the context of a control animal, where the control animal has been correctly certified (i.e. where the control animal has neither been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus nor of having been bled to death).
- the control animal may thus have been slaughtered using non-halal and non-kosher means of slaughtering that may be termed the normal means of slaughtering.
- a panel of pre-determined reference profiles for control animals may include profiles from different samples that have been obtained from different parts of control animals (not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus nor of having been bled to death).
- the panel of pre-determined reference profiles may include at least one profile for egg, at least one profile for meat (muscle, tissue, organs etc.), at least one profile for milk and the like.
- Each of these samples may have its own unique pre-determined methylation reference profile that also forms a part of the panel of pre-determined reference profiles
- the pre-determined reference profile may be used in the context of reference animals that may have been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or having been bled to death.
- a panel of pre-determined reference profiles may be prepared for different samples that are from animals that have been confirmed to be slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or having been bled to death.
- the panel of pre-determined reference profiles may include at least one profile for egg, at least one profile for meat (muscle, tissue, organs etc.), at least one profile for milk and the like from animals that have been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or having been bled to death.
- Each of these samples may have its own unique pre-determined methylation reference profile that also forms a part of the panel of pre-determined reference profiles
- the control may a type of meat of the same species or the same animal taxon as the animal-derived product sample or unknown sample which has a known certification.
- the pre-determined reference profile may be obtained from different types of meat with a known certification.
- the control may be chicken meat that is certified ‘halal’.
- the halal chicken meat may be a mix of different parts of the chicken (i.e. breast, thigh, kidney, liver etc.).
- the halal chicken meat may be from one part of a chicken.
- a methylation profile may be obtained to be the pre-determined reference profile (the control) that may be used to determine if the test sample (meat) is halal or non-halal by determining if the methylation profile of the test sample is significantly similar to the pre-determined reference profile.
- the methylation profile of different types of halal meat from one species of animal may be identical.
- the methylation profile of different types of halal meat from different species of animals may also be identical.
- the control may be chicken meat that is certified ‘kosher’.
- the kosher chicken meat may be a mix of different parts of the chicken (i.e. breast, thigh, kidney, liver etc.).
- the kosher chicken meat may be from one part of a chicken.
- a methylation profile may be obtained to be the pre-determined reference profile (the control) that may be used to determine if the test sample (meat) is kosher or non- kosher by determining if the methylation profile of the test sample is significantly similar to the pre- determined reference profile.
- the methylation profile of different types of kosher meat from one species of animal may be identical.
- the methylation profile of different types of kosher meat from different species of animals may also be identical.
- the pre-determined reference profiles may include methylation profiles of different parts of meat (i.e.
- the panel of predetermined reference methylation profiles according to any aspect of the present invention is distinct for different test animal-derived products. That is to say, each predetermined reference methylation profile is distinct for a single animal-derived product .
- the panel of predetermined reference methylation profiles may thus include many different predetermined reference methylation profiles from different parts of an animal or several animals of the same biological taxon as the test animal. There will also be different panels of predetermined reference methylation profiles for different animal taxon, and the relevant panel of predetermined reference methylation profiles unique for an animal taxon will depend on the animal taxon of the test animal.
- the term “significantly similar” in context of the present disclosure, and in particular in context with the comparison of methylation profiles shall mean a similarity observed by statistical means (i.e. by using bioinformatics) and/or also by observation using the eye.
- test profile overlaps with a reference profile that is defined by multiple training samples through multivariate statistical methods, such as Principal Component analysis or Multi-Dimensional Scaling.
- a test profile is significantly similar to the pre- determined reference profile if more than 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99% % of the methylation pattern/ profile overlaps with that of the reference profile.
- a similarity of a test profile to more than one, such as two, three or even all reference profile reduces the significance of the similarity.
- the similarity of the test methylation profile to the reference methylation profile takes into consideration the experimental error that occurs in all methods.
- the animal-derived product sample may be a single type of meat, different types of meat, a single part of a type of meat, different parts of a single type of meat or different parts of different types of meat.
- the sample may be from any biological entity having a DNA genome and DNA genome methylation.
- the methylation site is a CpG site.
- the biological entity may be any animal excluding a pig.
- the animal may be selected from the group consisting of chicken, lamb, camel, cow, goat, sheep, horse, donkey, turkey, duck, goose, quail, rabbit and mule. More in particular, the animal may be selected from the group consisting of cow, sheep, goat, camel, chicken, goose, duck and turkey.
- the term ‘meat’ herein may thus be understood to include chicken, lamb, beef, mutton, goat, camel, chicken, goose, duck, turkey and mixtures thereof.
- the one or more pre-selected methylation sites in (a) are methylation sites associated with tissue specific gene expression, preferably wherein the pre-selected methylation sites are associated with gene expression of one distinct tissue.
- the tissue may be selected from (i) metabolic tissue such as gut tissue, said gut tissue preferably being ileum or jejunum, (ii) muscular tissue, (iii) skin tissue, and (iv) organ tissue, said organ tissue preferably being hepatic and / or pancreatic tissue.
- a method of verifying certification of a test animal-derived product sample that has been certified to derive from a test animal that was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or that was bled to death comprising the steps of: (a) determining a test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile obtained from (a) with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or
- a method for confirming or rejecting an assumed certification of an animal derived product sample comprising - comparison of a test methylation profile obtained from genomic material of the animal derived product sample with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death, wherein a difference in the test methylation profile compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or
- a method of determining if a test animal-derived product sample is obtained from a test animal that has been bled to death or slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus the method comprising: - comparison of a test methylation profile obtained from genomic material of the test animal derived product sample with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death.
- the certification is kosher or halal where the animal is slaughtered by a cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and/or the oesophagus. Additionally, or alternatively, the certification kosher or halal where the animal is drained of blood.
- a certification of a test animal derived product sample certifying that the test animal was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and/or the oesophagus
- the method for determining that the test animal was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and/or the oesophagus comprises the steps of: (a) determining a test methylation profile of one or more pre-selected methylation sites within the genomic material contained in the test animal-derived product sample; and (b) comparing the test methylation profile determined in (a) with a panel of predetermined reference methylation profiles of the same biological taxon of the test animal from which the product sample derives, wherein each of the predetermined reference
- the test animal is drained of blood.
- DNA methylation profiling for determining for certifying of an animal-derived product sample.
- the certification of the animal-derived product sample is kosher or halal where the test animal is slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the test animal is bled to death.
- Figure 1 is the results of Principle Component Analysis (PCA) of 6706643 CpG sites with min coverage 10 in all halal and non-halal samples.
- Figure 2 is the results of Principle Component Analysis (PCA) of 76339 Differentially methylated positions (DMPs) identified.
- PCA Principle Component Analysis
- DMPs Differentially methylated positions
- halal meat examples include Pasar, ZAC Butchery, Hego premium, RedMart and Keesong, whereas non halal meat was purchased from Pasar, Tegel, Farm fresh, Ryan and AW’s in Singapore.
- Genomic DNA was purified from the breast tissue samples using DNeasy Blood & Tissue Kit (Qiagen) and is quantified using PicroGreen or NanoDropTM 2000.
- the genomic DNA (500ng) from breast tissue samples was used to prepare libraries for Whole Genome Bisulfite Sequencing (WGBS). The sequencing of the libraries was performed by a third party on a NovaSeq platform which generated 125GB data per sample with 20X coverage.
- MethylKit generates a 'prcomp' object, which can be used to extract and plot the principal components.
- the use of MethylKit is disclosed in Akalin A, et al. Genome Biol.2012;13(10): R87.
- Principal Component Analysis is a dimensionality-reduction method which can transform large data sets to a few principal components.
- the first few principal components generally retain most of the variation present in the dataset and are useful for emphasizing the grouping structure in the data Principle Component Analysis (PCA) of CpG sites with min coverage 10 in all samples: 6706643 as shown in Figure 1.
- Principal Component Analysis (PCA) of 76339 DMPs identified is shown in Figure 2. Plotting of the first two principal components of the CpGs before and after differential methylation analysis reveal meaningful clustering of the samples. Differentially methylated Positions (DMPs) were able to effectively cluster of the halal and non-halal groups in a meaningful way.
- Table 1.8000 CpG sites of the 76339 significantly differentially methylated Positions (DMPs) are provided.
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Abstract
The present invention relates to a method of certifying a test animal-derived product sample, the method comprising the steps of: (a) determining a test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile obtained from (a) with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or esophagus and/or the control animal is not bled to death wherein a difference in the test methylation profile of (a) compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death and the test animal-derived product is certified so, and wherein the pre-selected methylation sites are CpG sites selected from genes or regions of genomic DNA from the control and test animal that shows the highest degree of methylation variation during the training of the method.
Description
CERTIFICATION OF ANIMAL-DERIVED PRODUCT(S) BASED ON DNA-METHYLATION FIELD OF THE INVENTION The present invention relates to a method of determining certification of an unknown animal derived product sample based on specific panels of genes that provide a source for the generation of DNA methylation profiles which are specific for a distinct certification. In particular, DNA methylation profiling may be used to determine the distinct certification of animal-derived products. The distinct certification may include halal, kosher and the like. BACKGROUND OF THE INVENTION Sustainable food production is presently considered among the globally most important societal needs. As the value chains of the agriculture and aquaculture industries are highly complex, certificates have been established to reinforce consumer relationships and trust. However, certificates are based on audits at specific farms and can be easily tampered by moving livestock from non-certified farms to certified farms. Furthermore, surveillance of sustainable farming practices is imperfect as it is largely limited to audits. This leaves room for fraudulent activities in the industry, so there is an urgent need for a tamper-proof analysis and certification of meat. Further, there are people in the world that abide by dietary restrictions that relate specifically to a tradition or a religion that they follow. For example, some Jewish people eat only foods that have been deemed Kosher in accordance with Jewish law. Similarly, some people from the Muslim religion may desire to eat only foods that have been deemed Halal in accordance with Islamic law. Other people may have other dietary restrictions that relate to other traditions, religions, ethical codes, or the like. Both Kosher certification (i.e., designation of a food item as Kosher) and Halal certification (i.e., designation of a food item as Halal) of food, including meat involve the conformance with specific laws that relate to the slaughter of animals. For example, Judaic ritual slaughter (Shechita) and Islamic ritual slaughter (Zabihah) require an animal to be cut across the neck with a non-serrated blade in a single clean attempt to sever main blood vessels of the animal, and to drain the blood of the animal. Health, safety and also animal welfare considerations demand that the origins of animal products, and in particular meat products, should be traceable, so that quality assurance audits, and monitoring procedures can be effectively and reliably carried out. There is, however, no present means of accurately and reliably tracing the origins of meat. In particular, outside of trusting the labels found on the meat packets and shops, there is no reliable, effective and easy to use method for distinguishing halal meat from non-halal meat and kosher meat from non-kosher meat. That is to say, although meat may be certified as Kosher (i.e., allowed under the Jewish tradition) or Halal (i.e., allowed under the Islamic tradition), buyers may be unable to determine whether the meat was properly slaughtered based on visual inspection. Moreover, when consuming food at a restaurant, customers may be unable to view an inspection label affixed to packaging of meat prior to preparation of the meat. Furthermore, a customer may be unable to determine a type of animal from which the meat is derived based on visual inspection. This may result in a person who abides by a dietary restriction being hesitant to consume animal products.
Physical conditions and/or chemical conditions of an animal may be altered based on the way the animal has been slaughtered. For example, it is well known that cortisol levels of animals for which Kosher slaughter or Halal slaughter may be performed may be different from cortisol levels of animals that undergo another means of slaughter. Also, different types of meats obtained from different animals may be associated with physical differences and/or chemical differences. For example, proteins from pork meat of a pig may differ from proteins from beef meat of a cow. Differences may also exist in relation to different breeds of a particular type of animal, different cuts of meat of a particular animal, or the like. This may limit an effectiveness of comparing an unknown sample of meat to a set of known reference samples of meat. Recent studies have shown that DNA methylation patterns of animals contain important information about their rearing conditions. For example, a comparison of genome-wide patterns of methylation and variation at the DNA level revealed that a highly significant proportion of epigenetic variation could be associated with fitness differences and rearing conditions such as captivity in salmon (Le Luyer J et al.2017 PNAS vol 114, no 49). Koop et al. and Rhein et al. also separately confirmed that methylation patterns are maintained postmortem and are consistent regardless of the level of decomposition of the sample. One of the only aspects that still affects the methylation pattern of the sample would be the DNA integrity and amount of DNA that is found in the sample (Koop et al., 2021 International Journal of Legal Medicine 135:167–173 and Rhein et al., 2015 Frontiers in Genetics 6: 182). In view of the above, there is an urgent need to provide means for identifying and quality controlling the certification of organisms, in particular food and more particularly animal material derived to satisfy the dietary restrictions relating to a tradition, a religion, an ethical code, or the like followed strictly by people. DESCRIPTION OF THE INVENTION The present invention attempts to solve the problems above by providing a method using DNA methylation patterns to distinguish one type of animal derived product from another type of animal derived product and to be able to determine the means of killing or slaughtering the animal from which the animal derived product derives from and thereby certify the product accurately and reliably. The present invention is based on the finding that the means of slaughtering an animal, results in stress in the internal environment of the animal and this can permanently change the genome of the animal through epigenetics. In particular, the capability to adapt to the environment (i.e. means of slaughtering) and maintain the adapted biological pattern depends on epigenetic mechanisms, including DNA methylation. In particular, the present invention is based on the finding that the method of slaughtering an animal for food consumption may also result in changes in epigenetic mechanisms of the animal, including DNA methylation patterns and these patterns may be passed down to the different products that may derive from the animal.
The inventors have unexpectedly found that this property can be utilized to identify "epigenetic fingerprints" on the genome that are specific to a method of slaughter of not just one animal but possibly all the animals that undergo the same method of slaughter. For example, these ‘epigenetic fingerprints’ may be specific not only for the animal that is slaughtered in a particular way but also for any product that stems from the very animal (an individual). Based on these findings, the present invention provides means to identify the specific method of slaughter of a particular animal, for example rearing animals also known as livestock and poultry from which an animal-derived product comes from. In particular, the method according to any aspect of the present invention may be used to determine if an animal-derived product is derived from an animal that has been slaughtered in a particular way or not. More in particular, the method according to any aspect of the present invention may be used to determine if an animal-derived product is derived from an animal that has been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or if the animal has been bled to death. In this way, the method according to any aspect of the present invention may then be used to accurately and reliably determine the method of slaughter of an animal and then provide and/or confirm the certification of any sample that originates from the animal. Further, the method according to any aspect of the present invention may also be used to identify if any animal-derived product is accurately and reliably certified, particularly where the certification is based on the method of slaughter of the animal. According to one aspect of the present invention, there is provided a method of certifying a test animal-derived product sample, the method comprising the steps of: (a) determining a test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile obtained from (a) with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death wherein a difference in the test methylation profile of (a) compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death and the test animal-derived product is certified so; and wherein the pre-selected methylation sites are CpG sites selected from genes or regions of genomic DNA from the control and test animal that shows the highest degree of methylation variation during the training of the method. According to another aspect of the present invention, there is provided a method of certifying a test animal-derived product sample, the method comprising the steps of:
(a) determining the methylation status of at least one CpG site within the genomic material obtained from the animal-derived product sample, (b) comparing the methylation status of the CpG site from (a) with that of a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death, wherein a difference in the test methylation status of (a) in the test animal compared to the CpG site in the control animal is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death and the test animal-derived product is certified so. According to yet another aspect of the present invention, there is provided a method of certifying a test animal-derived product sample, the method comprising the steps of: (a) determining the test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile determined in (a) with a panel of predetermined reference methylation profiles of the same biological taxon of the test animal from which the product sample derives, wherein each of the predetermined reference methylation profiles is specific for a distinctly certified reference animal that - has been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus; and/or - bled to death; wherein if the test methylation profile is significantly similar to one of the predetermined reference methylation profiles, the test animal derived product sample has the same distinct certification as that of the predetermined reference methylation profile and is derived from a test animal that has been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or bled to death and the test animal- derived product is certified so. As used herein, the term ‘animal-derived product’ refers to products that originate from animals. In particular, the term ‘test animal-derived product’ refers to the sample or subject in question that is to undergo the method according to any aspect of the present invention. These products from animals may include meat and meat products, also including fat, flesh, blood, and lesser-known products, such as isinglass and rennet, poultry products (meat and eggs), dairy products (milk and cheese), and non-food products such as fiber (wool, mohair, cashmere, leather and the like). Animal-derived products may also include products that can be made using animal products (e.g. fat) such as soap, creams and such. In one example, the animal-derived product is meat, eggs,
blood, brain, sperm, milk and any other tissue or sample that provides genomic DNA. In particular, the animal-derived product is meat. The term ‘certification of quality’ refers to a certificate or a confirmation given by designated certification agencies that endorse the quality of a particular animal derived product, including food for use and/or consumption by human beings. The term ‘certification of quality’ is used interchangeably with the term ‘certification’. These certifications are usually found on the packaging of the animal-derived product including food to be consumed and are printed by the manufactures of the products. Examples of certifications of distinct food quality may include ‘Haltungsform’, ‘Tierwohl’, ‘Ohne Gentechnik’, ‘halal’, ‘kosher’, and other safe labels that confirm that a product sold has been prepared in accordance with specific religious or safety regulations. Specifically, the term ‘certification of food quality’ refers to a certificate or a confirmation given by designated certification agencies that endorse the quality, source or means of slaughter of a particular food for consumption by human beings. According to any aspect of the present invention, the certified quality may be a distinct certified food quality, or distinct certification and this may be kosher, non- kosher, halal or non-halal. In one example, the distinct certified food quality or certification of the sample X according to any aspect of the present invention may be kosher, non-kosher, halal or non-halal. More in particular, kosher or halal refers to the sample X originating from an animal that was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and/or the oesophagus. Even more in particular, the animal is drained of blood. The term ‘kosher’ used in combination with food according to any aspect of the present invention refers to food that conforms to Jewish dietary regulations of kashrut (dietary law) or food that may be consumed according to halakha (law). Kosher used in relation to meat relates particularly to a manner in which animals are prepared for consumption. According to Jewish tradition, meat may be considered kosher when the meat comes from animals that have been slaughtered according to Jewish law where the animal is killed by a single cut across the throat to a precise depth, severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and the oesophagus, no higher than the epiglottis and no lower than where cilia begin inside the trachea, causing the animal to bleed to death. Such slaughter is to be carried out using a large, razor-sharp knife, which is checked before each slaughter to ensure that it has no irregularities (such as nicks and dents). The slaughter is usually also carried out by a shochet or a rabbi. Kosher meat usually refers to most meats excluding pig. In particular, kosher meat may be selected from beef, chicken, lamb, mutton, goat meat and mixtures thereof. Kosher meat does not include shellfish, which under Jewish tradition is not permitted for consumption. Although Jewish traditions permit consumption of vertebrate fish, since there is no special method of slaughtering vertebrate fish, all vertebrate fish may be considered kosher. Any food or meat that does not fall within the definition of ‘kosher’ will then be considered as ‘non-kosher’.
The term ‘halal’ used in combination with food according to any aspect of the present invention refers to food that conforms to Islamic dietary laws and especially meat processed and prepared in accordance with those requirements. Similar to the way kosher meat is prepared, in Islamic tradition, animals are slaughtered according to Dhabīḥah where the animal is slaughtered using a cut across the neck with a non-serrated sharp blade in a single clean attempt to make an incision that cuts the front of the throat, oesophagus and jugular veins but not the spinal cord. In addition to the direction, permitted animals should be slaughtered upon utterance of the Islamic prayer Bismillah. The animal must also be drained of blood after the slaughter. The slaughter must be performed by an adult Muslim. Halal meat usually refers to most meats excluding pig. In particular, halal meat may be selected from beef, chicken, lamb, mutton, goat meat and mixtures thereof. Although Islamic traditions permit consumption of shellfish and vertebrate fish, since there is no special method of preparing shellfish, all shellfish and vertebrate fish may be considered halal. Any food or meat that does not fall within the definition of ‘halal’ will then be considered as ‘non-halal. The definition of halal is further provided in https://www.smiic.org/en/project/24 (Organisation of Islamic Cooperation (OIC)/Standards and Metrology Institute for the Islamic Countries (SMIIC), OIC/SMIIC 1:2019 General Requirements for Halal Food. accessed on 08 June 2022) The term “test” used in conjunction with the term subject and/ or animal in the present disclosure refers to an entity that is subjected to the method according to any aspect of the present invention and is the basis for an analysis application of the present invention. An “(individual) test subject”, an “(individual) group of test subjects” or a “test profile” or an ‘test animal derived product’ is therefore a (individual) subject or group of subjects being tested according to the invention or a profile being obtained or generated in this context. Conversely, the term “reference” shall denote, mostly predetermined, entities which are used for a comparison with the test entity. For example, the term ‘reference animal’ refers to an animal used for comparison or as a control in reference to the ‘test animal’. Similarly, the term ‘sample’ and/or ‘test animal-derived product sample’ used in accordance with any aspect of the present invention refers to an entity that may be subject to the method of the present invention. In particular, a sample may be any (test) animal-derived product that may be subject to the method of the present invention to determine the distinct certification by first determining the DNA methylation profile and then comparing this test methylation profile with a control. Blockchain may also be used to make the information easily available for the consumer. The method according to any aspect of the present invention may be used to identify an unknown sample (i.e. animal-derived product sample) based on DNA methylation patterns. These DNA methylation patterns may then be compared with reference DNA methylation patterns to trace the animal-derived product sample back to the slaughterhouse or farmhouse from which the sample originates and then determine whether the unknown sample corresponds to an animal which has been slaughtered according to Kosher, Halal, non-Kosher or non-Halal practices. In this way, a buyer or a consumer of meat can verify that meat being sold as or marketed as being Kosher or Halal is genuine.
As used herein, the term “comprising” is to be construed as encompassing both “including” and “consisting of”, both meanings being specifically intended, and hence individually disclosed aspects of the present invention. Where used herein, “and/or” is to be taken as specific disclosure of each of the two specified features or components with or without the other. For example, “A and/or B” is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each is set out individually herein. In the context of the present invention, the terms “about” and “approximately” denote an interval of accuracy that the person skilled in the art will understand to still ensure the technical effect of the feature in question. The term typically indicates deviation from the indicated numerical value by ±20%, ±15%, ±10%, and for example ±5%. As will be appreciated by the person of ordinary skill, the specific deviation for a numerical value for a given technical effect will depend on the nature of the technical effect. For example, a natural or biological technical effect may generally have a larger such deviation than one for a man-made or engineering technical effect. Where an indefinite or definite article is used when referring to a singular noun, e.g. "a", "an" or "the", this includes a plural of that noun unless something else is specifically stated. In context of the present invention, the terms “methylation profile”, “methylation pattern”, “methylation state” or “methylation status,” are used herein to describe the state, situation or condition of methylation of a genomic sequence, and such terms refer to the characteristics of a DNA segment at a particular genomic locus in relation to methylation. Such characteristics include, but are not limited to, whether any of the cytosine (C) residues within this DNA sequence are methylated, location of methylated C residue(s), percentage of methylated C at any particular stretch of residues, and allelic differences in methylation due to, e.g., difference in the origin of the alleles. The term "methylation status" refers to the status of a specific methylation site (i.e. methylated vs. non-methylated) which means a residue or methylation site is methylated or not methylated. Then, based on the methylation status of one or more methylation sites, a methylation profile may be determined. Accordingly, the term "methylation profile" or also “methylation pattern” refers to the relative or absolute concentration of methylated C residues or unmethylated C residues at any particular stretch of residues in the genomic material of a biological sample. For example, if cytosine (C) residue(s) not typically methylated within a DNA sequence are methylated, it may be referred to as "hypermethylated"; whereas if cytosine (C) residue(s) typically methylated within a DNA sequence are not methylated, it may be referred to as "hypomethylated". Likewise, if the cytosine (C) residue(s) within a DNA sequence (e.g., the DNA from a sample nucleic acid from a test subject) are methylated as compared to another sequence from a different region or from a different individual (e.g., relative to normal nucleic acid or to the standard nucleic acid of the reference sequence), that sequence is considered hypermethylated compared to the other sequence. Alternatively, if the cytosine (C) residue(s) within a DNA sequence are not methylated as compared to another sequence from a different region or from a different individual, that sequence is considered hypomethylated compared to the other sequence. These sequences are said to be "differentially methylated". Measurement of the levels of differential methylation may be
done by a variety of ways known to those skilled in the art. One method is to measure the methylation level of individual interrogated CpG sites determined by the bisulfite sequencing method, as a non-limiting example. The term “hypermethylation” refers to the average methylation state corresponding to an increased presence of 5-mCyt at one or a plurality of CpG dinucleotides within a DNA sequence of a test DNA sample, relative to the amount of 5-mCyt found at corresponding CpG dinucleotides within a normal control DNA sample. In particular, control refers to an animal derived product not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or not having been bled to death. The term “hypomethylation” refers to the average methylation state corresponding to a decreased presence of 5-mCyt at one or a plurality of CpG dinucleotides within a DNA sequence of a test DNA sample, relative to the amount of 5-mCyt found at corresponding CpG dinucleotides within a normal control DNA sample. In particular, control refers to an animal derived product not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or not having been bled to death. As used herein, a “methylated nucleotide” or a “methylated nucleotide base” refers to the presence of a methyl moiety on a nucleotide base, where the methyl moiety is usually not present in a recognized typical nucleotide base. For example, cytosine in its usual form does not contain a methyl moiety on its pyrimidine ring, but 5-methylcytosine contains a methyl moiety at position 5 of its pyrimidine ring. Therefore, cytosine in its usual form may not be considered a methylated nucleotide and 5-methylcytosine may be considered a methylated nucleotide. In another example, thymine may contain a methyl moiety at position 5 of its pyrimidine ring, however, for purposes herein, thymine may not be considered a methylated nucleotide when present in DNA. Typical nucleotide bases for DNA are thymine, adenine, cytosine and guanine. Typical bases for RNA are uracil, adenine, cytosine and guanine. Correspondingly a "methylation site" is the location in the target gene nucleic acid region where methylation has the possibility of occurring. For example, a location containing CpG is a methylation site wherein the cytosine may or may not be methylated. In particular, the term “methylated nucleotide” refers to nucleotides that carry a methyl group attached to a position of a nucleotide that is accessible for methylation. These methylated nucleotides are usually found in nature and to date, methylated cytosine that occurs mostly in the context of the dinucleotide CpG, but also in the context of CpNpG- and CpNpN-sequences may be considered the most common. In principle, other naturally occurring nucleotides may also be methylated but they will not be taken into consideration with regard to any aspect of the present invention. As used herein, a “CpG site” or “methylation site” is a nucleotide within a nucleic acid (DNA or RNA) that is susceptible to methylation either by natural occurring events in vivo or by an event instituted to chemically methylate the nucleotide in vitro.
As used herein, a “methylated nucleic acid molecule” refers to a nucleic acid molecule that contains one or more nucleotides that is/are methylated. The term ‘epigenetic change’ as used herein refers to a chemical (e.g., methylation) change or protein (e.g., histones) change that takes place to a gene body or a promoter thereof. Through epigenetic changes, environmental factors like. diet, stress and prenatal nutrition can make an imprint on genes passed from one generation to the next. The term “bisulfite” as used herein encompasses any suitable type of bisulfite, such as sodium bisulfite, or another chemical agent that is capable of chemically converting a cytosine (C) to a uracil (U) without chemically modifying a methylated cytosine and therefore can be used to differentially modify a DNA sequence based on the methylation status of the DNA, e.g., U.S. Pat. Pub. US 2010/0112595 (Menchen et al.). As used herein, a reagent that "differentially modifies" methylated or non-methylated DNA encompasses any reagent that modifies methylated and/or unmethylated DNA in a process through which distinguishable products result from methylated and non-methylated DNA, thereby allowing the identification of the DNA methylation status. Such processes may include, but are not limited to, chemical reactions (such as a C to U conversion by bisulfite) and enzymatic treatment (such as cleavage by a methylation-dependent endonuclease). Thus, an enzyme that preferentially cleaves or digests methylated DNA is one capable of cleaving or digesting a DNA molecule at a much higher efficiency when the DNA is methylated, whereas an enzyme that preferentially cleaves or digests unmethylated DNA exhibits a significantly higher efficiency when the DNA is not methylated. In context of the present invention also any “non-bisulfite-based method” and “non-bisulfite-based quantitative method” are comprised to test for a methylation status at any given methylation site to be tested. Such terms refer to any method for quantifying methylated or non-methylated nucleic acid that does not require the use of bisulfite. The terms also refer to methods for preparing a nucleic acid to be quantified that do not require bisulfite treatment. Examples of non-bisulfite-based methods include, but are not limited to, methods for digesting nucleic acid using one or more methylation sensitive enzymes and methods for separating nucleic acid using agents that bind nucleic acid based on methylation status. The terms "methyl-sensitive enzymes" and "methylation sensitive restriction enzymes" are DNA restriction endonucleases that are dependent on the methylation state of their DNA recognition site for activity. For example, there are methyl-sensitive enzymes that cleave or digest at their DNA recognition sequence only if it is not methylated. Thus, an unmethylated DNA sample will be cut into smaller fragments than a methylated DNA sample. Similarly, a hypermethylated DNA sample will not be cleaved. In contrast, there are methyl- sensitive enzymes that cleave at their DNA recognition sequence only if it is methylated. As used herein, the terms "cleave", "cut" and "digest" are used interchangeably.
A “biological sample” in context of the invention may comprise any biological material obtained from the subject or group of subjects that contains genomic material, and may be liquid, solid or both, may be tissue or bone, or a body fluid such as blood, lymph, etc. In particular, the biological sample useful for the present invention may comprise biological cells or fragments thereof. As used herein, the term “pre-selected methylation sites” refers to methylation sites that were selected from genes or regions that showed the highest degree of methylation variation during the training of the method and fulfils certain quality criteria such as a minimum sequencing coverage of ≥5x were considered and for ≥5 qualified CpG sites. Additionally, genes that have an average methylation level <0.1 or an average methylation level >0.9 can be excluded due to their limited dynamic range. “Reference methylation profiles” may be defined on the basis of multiple training samples using multivariate statistical methods, such as such as Principal Component analysis or Multi-Dimensional Scaling. In particular, the CpG site according to any aspect of the present invention, particularly in the pre-selected methylation sites is selected from the Table A below:
Table A Relevant CpG sites that are differentially methylated No chrom position No chrom position No chrom position No chrom position No chrom position 1 2 34511190 101 Z 16103001 201 28 2443299 301 2 85904873 401 3 7315133 2 2 57572893 102 5 27885744 202 Z 16048197 302 2 129933052 402 7 2239688 3 2 20693997 103 2 4575039 203 19 4088736 303 3 39148221 403 17 8377056 4 Z 17123376 104 33 431970 204 3 12789564 304 9 15812625 404 28 153360 5 Z 115673685 105 14 6596177 205 6 11221033 305 1 35484379 405 3 2421530 6 Z 24913614 106 7 301591 206 2 21010987 306 17 2360133 406 4 39771776 7 4 58554384 107 Z 72829308 207 9 10619341 307 8 1401347 407 6 9407093 8 18 8977183 108 5 43891403 208 9 7925956 308 2 66497871 408 17 5799733 9 4 45296016 109 10 18678519 209 6 1549721 309 15 5027241 409 4 45296889 10 7 18690074 110 3 38237516 210 5 23458500 310 12 7055474 410 28 3642946 11 2 123206194 111 19 5832481 211 28 1477408 311 2 3856589 411 2 13471116 12 1 49770596 112 1 50837347 212 19 50552 312 1 193821130 412 3 31394938 13 5 29057117 113 Z 33678917 213 26 3246923 313 13 18308448 413 6 22239587 14 21 2688710 114 4 89259160 214 8 6089739 314 1 68455273 414 8 25610078 15 1 47926496 115 19 5767147 215 1 3700593 315 2 114090502 415 1 153736291 16 13 11458665 116 4 40113483 216 13 16065472 316 4 60369319 416 8 6618970 17 5 19158349 117 5 14162871 217 4 53533077 317 27 4720035 417 10 2333800 18 11 18172296 118 10 10895845 218 5 52943689 318 10 967899 418 14 12811447 19 10 12400953 119 20 1000718 219 27 1541894 319 4 1985540 419 7 22755583 20 19 8867093 120 1 194401733 220 26 4856960 320 14 5059398 420 6 27262610 21 4 39537311 121 3 58874863 221 12 2372012 321 1 175460817 421 27 4719697 22 13 6729058 122 20 10511507 222 1 110237976 322 3 33946497 422 11 10256374 23 10 11406434 123 Z 81360739 223 1 84409963 323 12 2259754 423 11 11215844 24 4 21041627 124 15 8003087 224 1 39877658 324 3 12583058 424 3 12755221 25 26 5003532 125 6 17322989 225 5 11621859 325 24 804341 425 2 121422611 26 8 16729492 126 3 104905440 226 25 976468 326 Z 27444073 426 9 10594523 27 4 39536841 127 19 6022617 227 4 8695640 327 3 104543849 427 2 88162809 28 7 24170000 128 9 15414814 228 1 80519994 328 1 53092288 428 5 9737337 29 2 23153225 129 8 16295920 229 19 185280 329 1 14903055 429 17 1980788 30 1 130973501 130 3 32261769 230 3 48423158 330 1 122962624 430 1 24855132 31 19 8481362 131 2 62413006 231 1 39858634 331 3 76739886 431 1 71113923 32 1 14382900 132 2 118636996 232 8 16052167 332 8 11915537 432 11 10194539 33 10 6806714 133 21 927717 233 1 91422737 333 8 16296168 433 1 76766539 34 10 12500816 134 25 1946574 234 18 3777721 334 9 7724217 434 UN 64936 35 Z 7668187 135 3 22702842 235 12 7012484 335 9 4626749 435 3 38336190 36 1 48250341 136 5 12488676 236 1 77229485 336 4 60368609 436 17 8376829 37 26 1544666 137 1 169374378 237 3 49813062 337 Z 37529420 437 15 5989722 38 3 26860812 138 1 35104436 238 Z 27270228 338 13 3283054 438 7 15587386 39 3 40601306 139 28 153426 239 1 123415519 339 1 194236534 439 3 21854776 40 9 7624289 140 15 7003924 240 5 51772714 340 18 10185868 440 11 6629712 41 7 5077349 141 14 2268610 241 3 36638958 341 18 1708416 441 1 178990900 42 11 18808803 142 3 105678613 242 7 15096160 342 8 16374372 442 12 10134215 43 26 2590932 143 1 144628599 243 2 121482517 343 8 14713737 443 8 13384214 44 9 22225808 144 9 14072787 244 7 17289720 344 8 16589375 444 1 12877821 45 2 78548181 145 19 5363084 245 UN 5736 345 9 5089285 445 9 6855496 46 12 6363727 146 17 6765666 246 7 9938317 346 9 8479123 446 1 175461006 47 3 107890733 147 5 48084582 247 17 10895495 347 3 8952808 447 3 105678619 48 3 27258633 148 21 5073396 248 7 29790478 348 1 137293780 448 2 130013087 49 9 5216234 149 20 533436 249 2 125171980 349 13 13028604 449 14 8217810 50 20 5579795 150 11 10452379 250 9 9528198 350 5 53477916 450 14 10043625 51 27 3637822 151 4 49890681 251 7 16281087 351 8 28086175 451 17 9978114 52 19 2411046 152 5 52943641 252 2 1390782 352 2 26792587 452 2 42913387 53 17 6189674 153 2 46089114 253 26 1519097 353 12 1581381 453 19 5832942 54 3 105678589 154 23 1870014 254 Z 11047446 354 5 39173222 454 15 5823857 55 1 113283028 155 2 41841626 255 UN 28427 355 4 86456090 455 2 46089139 56 11 1459001 156 24 4885733 256 3 108708555 356 5 38166099 456 1 188916642 57 7 35189129 157 4 6740626 257 4 5202992 357 3 46066858 457 3 46372522 58 4 32571055 158 3 76507235 258 3 19170252 358 20 5519899 458 1 175460839 59 28 3800027 159 5 58997382 259 17 10895665 359 11 6629490 459 14 5261997 60 11 18808917 160 17 8203614 260 7 6603676 360 18 9435327 460 12 11951638 61 1 168855019 161 27 3464008 261 3 105215220 361 3 102971530 461 4 88992878 62 3 76755036 162 11 841570 262 26 1651982 362 19 4492763 462 3 51285929 63 1 34377737 163 4 43608241 263 10 10824700 363 23 4152128 463 1 65578611 64 3 76739615 164 7 22569247 264 4 39012274 364 Z 63907320 464 11 10578956 65 1 56825511 165 2 78548594 265 14 7327840 365 10 4390201 465 13 13224232 66 1 108957860 166 5 28115369 266 2 42356641 366 15 9763222 466 5 39113705 67 25 1876704 167 1 84532408 267 5 53918500 367 5 6746 467 21 1483434 68 1 130278359 168 6 12121146 268 4 57532309 368 19 199882 468 18 3699658 69 17 7904953 169 12 9675444 269 6 11915935 369 1 195334826 469 9 4676234 70 3 4193791 170 6 32236852 270 5 28318496 370 3 32362994 470 1 169234551 71 3 96461436 171 10 12734127 271 1 50488695 371 UN 7191 471 1 44860990 72 2 5096922 172 Z 11287708 272 7 11358921 372 23 2381593 472 10 2315851 73 12 15606143 173 8 16370376 273 1 15441151 373 19 7203329 473 13 17037566 74 2 20877142 174 19 1401235 274 6 10819414 374 Z 65981131 474 1 50703527 75 12 710959 175 1 144796538 275 1 39877753 375 5 13107975 475 9 4850885 76 Z 27177202 176 2 102562607 276 8 2118531 376 2 57948024 476 1 83226834 77 6 28147880 177 8 7548136 277 17 2935626 377 1 56521314 477 1 65578655 78 25 1107409 178 14 5000387 278 17 7463984 378 Z 34328034 478 4 73695235 79 2 115921454 179 1 56606169 279 20 5394896 379 4 34288785 479 14 6926191 80 15 7347328 180 9 9539267 280 17 4082722 380 3 30399012 480 2 111960400 81 2 4980847 181 18 3700175 281 15 7571659 381 18 3700112 481 1 153739829 82 10 15213509 182 1 61708721 282 1 144796614 382 13 12290255 482 1 53953094 83 2 127761601 183 8 29363057 283 1 165873085 383 7 35847537 483 7 22245891 84 2 15482005 184 6 11517878 284 4 66670233 384 20 8145679 484 1 88411659 85 24 3786074 185 4 88992493 285 16 168962 385 UN 3312 485 1 51088644 86 12 4380982 186 4 10802755 286 17 7673395 386 19 580436 486 1 92330716 87 21 2332328 187 3 12755149 287 17 5741333 387 5 9279301 487 1 65578725 88 Z 11287812 188 2 21041245 288 15 6891797 388 23 3739407 488 3 77142645 89 1 36508947 189 14 957744 289 18 2274676 389 24 375697 489 2 91651196 90 7 301604 190 Z 27177213 290 14 6696623 390 1 79199586 490 1 76766536 91 20 9983514 191 7 28179710 291 5 11091055 391 17 8205987 491 7 28205381 92 5 10355756 192 4 11719574 292 12 10148968 392 3 26344201 492 4 46058642 93 9 10672938 193 5 24369896 293 6 12121122 393 18 7373876 493 2 124732645 94 20 4533305 194 19 5384384 294 1 49441925 394 3 67720493 494 7 9697869 95 21 2332272 195 24 4459949 295 12 1581083 395 2 129925091 495 3 65294828 96 5 53496100 196 6 32533539 296 6 10819506 396 4 2123054 496 1 26767903 97 9 22079838 197 21 4836900 297 19 176255 397 20 10287258 497 2 93915362 98 2 49110506 198 1 16473870 298 11 10950629 398 6 24169226 498 1 88759238 99 10 3477178 199 1 110880942 299 7 11248389 399 5 48066943 499 1 92271976 100 1 165873023 200 8 28653132 300 2 121381306 400 26 3571402 500 5 480120
No chrom position No chrom position No chrom position No chrom position No chrom position 501 UN 11202 601 3 26264001 701 Z 72177473 801 1 155581060 901 5 14626826 502 10 10680859 602 3 26757632 702 13 14499771 802 5 38034094 902 5 14754310 503 1 175806942 603 3 26827383 703 13 15760688 803 5 44495103 903 5 15857395 504 1 7556524 604 3 31006184 704 13 17043224 804 5 45270723 904 5 16673990 505 1 54593907 605 3 31169966 705 13 17043375 805 5 51814426 905 5 18315526 506 1 44871524 606 3 31416605 706 14 2330596 806 5 52015072 906 5 19158441 507 1 56825448 607 2 50003872 707 14 2610614 807 5 53299189 907 5 19158446 508 1 79310370 608 2 60065457 708 14 6595973 808 5 53390948 908 5 19495119 509 10 2277642 609 2 60969061 709 14 7315747 809 5 53566111 909 5 22761531 510 10 16470610 610 2 62413026 710 14 7451783 810 5 54521468 910 5 25139165 511 13 13567090 611 2 66497875 711 14 12900892 811 5 54656647 911 5 26210040 512 14 8154906 612 2 75844300 712 14 13057958 812 5 56343550 912 5 26628736 513 17 10279957 613 2 79703088 713 15 4517586 813 5 58703602 913 5 27936505 514 19 934610 614 2 90554149 714 15 4987756 814 6 5064205 914 5 28451085 515 3 26827400 615 2 100917787 715 15 5106738 815 6 11151853 915 5 29056520 516 3 49135422 616 2 101292338 716 15 5986957 816 6 11188537 916 5 34703798 517 4 33043830 617 2 102813119 717 15 6018471 817 6 11582592 518 8 2489495 618 2 103329886 718 15 7042315 818 6 11761740 519 8 5304565 619 2 106422461 719 15 8003013 819 6 16194199 520 Z 10464173 620 2 108042776 720 15 11346421 820 6 21978838 521 3 33946905 621 2 108043217 721 15 12108868 821 6 22083181 522 3 33980543 622 2 108413855 722 16 105715 822 6 31431558 523 3 35737558 623 2 108413888 723 17 1439118 823 6 31473215 524 3 37962586 624 2 109563147 724 17 2457632 824 6 32181323 525 3 39178569 625 2 116530961 725 17 2588441 825 6 32533531 526 3 42000296 626 2 116531160 726 17 3817120 826 6 32568586 527 3 46066726 627 2 123333539 727 17 4082619 827 7 4813474 528 3 48325731 628 2 123333776 728 17 6717101 828 7 5038366 529 3 48792278 629 2 123623354 729 17 8592228 829 7 5060102 530 3 49036683 630 2 128974344 730 17 9171080 830 4 51454889 531 3 50934801 631 2 129932927 731 17 10088808 831 4 55109704 532 3 52022798 632 2 132629535 732 18 7515126 832 4 60528211 533 3 57998308 633 2 139673759 733 18 7875787 833 4 61707165 534 3 60009081 634 2 146178598 734 18 9697090 834 4 66670202 535 3 62286891 635 20 8162867 735 1 166728921 835 1 34681 536 3 72999617 636 20 10275863 736 1 183325914 836 1 524205 537 3 75813980 637 20 12592864 737 1 185282396 837 1 665546 538 3 77142698 638 21 1726961 738 1 188309833 838 1 959766 539 3 77740997 639 21 1824168 739 1 194782826 839 1 959793 540 3 77741067 640 21 2332382 740 1 195388710 840 1 1061369 541 3 77806851 641 18 10470282 741 1 196146823 841 1 20101427 542 3 79869584 642 19 1792458 742 10 968395 842 1 20529755 543 3 82094768 643 19 3779599 743 10 2096300 843 1 22090541 544 3 87049472 644 19 5325089 744 10 2277755 844 1 22105964 545 3 104543506 645 19 7633138 745 10 2505096 845 1 23223035 546 33 431964 646 19 7633191 746 10 6959419 846 1 24805622 547 3 37759 647 19 8867086 747 10 7035652 847 1 24806572 548 4 2503560 648 2 4915125 748 10 7767102 848 1 28910262 549 4 3023101 649 2 6233872 749 10 18093950 849 1 33609212 550 4 4377067 650 2 6287263 750 10 20006398 850 1 42851095 551 4 5154481 651 2 12592185 751 11 1329819 851 1 44172676 552 4 8581737 652 2 12854026 752 11 10194367 852 1 46517622 553 4 8734750 653 2 15015618 753 11 11467077 853 1 47827684 554 4 10712066 654 2 19106544 754 11 11492065 854 1 47828170 555 4 11020158 655 2 19555468 755 11 16009840 855 1 47996727 556 4 12409848 656 2 20654008 756 12 1444617 856 1 49461091 557 4 13440210 657 2 20877171 757 12 2401731 857 1 49770584 558 4 15354497 658 2 21020630 758 12 2575431 858 1 49923743 559 4 21510615 659 2 21776645 759 12 2911021 859 1 50116959 560 4 21597219 660 2 23152655 760 12 6759370 860 1 54593904 561 4 29981474 661 2 30653036 761 12 10178070 861 1 56606098 562 4 29981612 662 2 30964872 762 12 10809661 862 1 56825555 563 4 30237031 663 2 31517731 763 12 11952324 863 1 61015958 564 4 31634271 664 2 34511511 764 12 16343688 864 1 61016067 565 4 31775781 665 2 36807563 765 12 18132965 865 1 78401374 566 4 31797849 666 2 44148776 766 13 4123382 866 1 78401723 567 4 31798007 667 2 45606950 767 13 9484641 867 1 79293224 568 4 32235697 668 2 47274383 768 13 11458667 868 1 80519649 569 4 34147184 669 9 1125703 769 13 12045999 869 1 84657280 570 4 34634614 670 9 1432683 770 7 13949196 870 1 84657286 571 4 45304161 671 9 1621719 771 7 14319998 871 1 87297037 572 4 47198051 672 9 4819197 772 7 14832870 872 1 87498913 573 4 50421355 673 9 5216686 773 7 15906091 873 1 88405899 574 23 446710 674 9 5273930 774 7 25408321 874 1 89125947 575 23 1897115 675 9 7969508 775 7 26827807 875 1 102484686 576 23 4988905 676 9 8025607 776 8 2271335 876 1 105596806 577 24 2183046 677 9 8479246 777 8 5110731 877 1 105859382 578 24 2745230 678 9 9622397 778 8 7548409 878 1 110710757 579 25 976498 679 9 10672930 779 8 14361683 879 1 111034338 580 25 1102452 680 9 12209165 780 8 15791045 880 1 118204632 581 25 1922074 681 9 15449427 781 8 16370427 881 1 124980421 582 25 1946155 682 9 15664766 782 8 19012408 882 1 129210612 583 25 2053338 683 9 20353960 783 8 19105674 883 1 130493042 584 25 2379274 684 9 22079462 784 8 20844260 884 1 130543594 585 26 2591052 685 9 22364985 785 8 20862635 885 1 131937808 586 27 1273378 686 UN 10512 786 8 21330776 886 1 133908500 587 27 1528397 687 Z 2265489 787 8 27993362 887 4 77976506 588 27 1541617 688 Z 17067814 788 7 27306835 888 4 78949903 589 27 1609933 689 Z 24036072 789 7 27538837 889 4 83226239 590 27 3878658 690 Z 24036312 790 7 28565262 890 4 85487431 591 27 4209484 691 Z 24913899 791 7 29084206 891 4 88447258 592 28 700769 692 Z 27815215 792 7 29525425 892 4 88894627 593 28 785678 693 Z 31979924 793 7 30383908 893 4 88894964 594 28 799393 694 Z 35676605 794 7 30593598 894 4 89096143 595 28 2802446 695 Z 36792135 795 7 33455887 895 4 89309689 596 28 4072263 696 Z 40093320 796 7 33793138 896 5 10408062 597 3 12990210 697 Z 46063014 797 7 35330918 897 5 11924701 598 3 19773897 698 Z 50823119 798 7 35330947 898 5 12183678 599 3 24008503 699 Z 52080666 799 7 35848239 899 5 13200139 600 3 26263279 700 Z 52630840 800 1 155080938 900 5 14214536
The term “pre-determined reference profile” used in the context of the present invention refers to a typical or standard methylation profile of the genomic material of a type of reference animal-derived product that is confirmed to be correctly labelled or certified. In one example, the pre-determined reference profile may be used in the context of a control animal, where the control animal has been correctly certified (i.e. where the control animal has neither been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus nor of having been bled to death).The control animal may thus have been slaughtered using non-halal and non-kosher means of slaughtering that may be termed the normal means of slaughtering. A panel of pre-determined reference profiles for control animals may include profiles from different samples that have been obtained from different parts of control animals (not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus nor of having been bled to death). For example, the panel of pre-determined reference profiles may include at least one profile for egg, at least one profile for meat (muscle, tissue, organs etc.), at least one profile for milk and the like. Each of these samples may have its own unique pre-determined methylation reference profile that also forms a part of the panel of pre-determined reference profiles In another example, the pre-determined reference profile may be used in the context of reference animals that may have been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or having been bled to death. A panel of pre-determined reference profiles may be prepared for different samples that are from animals that have been confirmed to be slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or having been bled to death. Again here, there may be a panel of pre-determined reference profiles for each product that is derived from the animal that has been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or having been bled to death. For example, the panel of pre-determined reference profiles may include at least one profile for egg, at least one profile for meat (muscle, tissue, organs etc.), at least one profile for milk and the like from animals that have been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or having been bled to death. Each of these samples may have its own unique pre-determined methylation reference profile that also forms a part of the panel of pre-determined reference profiles For example, the control may a type of meat of the same species or the same animal taxon as the animal-derived product sample or unknown sample which has a known certification. Alternatively, the pre-determined reference profile may be obtained from different types of meat with a known certification. In one example, the control may be chicken meat that is certified ‘halal’. The halal chicken meat may be a mix of different parts of the chicken (i.e. breast, thigh, kidney, liver etc.). In another example, the halal chicken meat may be from one part of a chicken. From the halal chicken meat, a methylation profile may be obtained to be the pre-determined reference profile (the
control) that may be used to determine if the test sample (meat) is halal or non-halal by determining if the methylation profile of the test sample is significantly similar to the pre-determined reference profile. The methylation profile of different types of halal meat from one species of animal may be identical. The methylation profile of different types of halal meat from different species of animals may also be identical. In one example, the control may be chicken meat that is certified ‘kosher’. The kosher chicken meat may be a mix of different parts of the chicken (i.e. breast, thigh, kidney, liver etc.). In another example, the kosher chicken meat may be from one part of a chicken. From the kosher chicken meat, a methylation profile may be obtained to be the pre-determined reference profile (the control) that may be used to determine if the test sample (meat) is kosher or non- kosher by determining if the methylation profile of the test sample is significantly similar to the pre- determined reference profile. The methylation profile of different types of kosher meat from one species of animal may be identical. The methylation profile of different types of kosher meat from different species of animals may also be identical. There may be a compilation of several pre-determined reference profiles and comparing the methylation profile of the test sample with the pre-determined reference profiles in the compilation may enable identifying the specific pre-determined reference profile that is (significantly) similar to the methylation profile of the test sample and then the test sample may be confirmed to be slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or having been bled to death or not. In one example, the pre-determined reference profiles may include methylation profiles of different parts of meat (i.e. breast, thigh, kidney, liver, shoulder, ribs, intestines, etc.) from an animal (chicken, goat, cow, lamb, sheep etc.) that has been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or having been bled to death. In particular, the panel of predetermined reference methylation profiles according to any aspect of the present invention is distinct for different test animal-derived products. That is to say, each predetermined reference methylation profile is distinct for a single animal-derived product . The panel of predetermined reference methylation profiles may thus include many different predetermined reference methylation profiles from different parts of an animal or several animals of the same biological taxon as the test animal. There will also be different panels of predetermined reference methylation profiles for different animal taxon, and the relevant panel of predetermined reference methylation profiles unique for an animal taxon will depend on the animal taxon of the test animal. The term “significantly similar” in context of the present disclosure, and in particular in context with the comparison of methylation profiles (such as the comparison between test profiles (from test subject(s) (i.e. sample X) and reference profiles) shall mean a similarity observed by statistical means (i.e. by using bioinformatics) and/or also by observation using the eye. A significant similarity is observed for example if a test profile overlaps with a reference profile that is defined by
multiple training samples through multivariate statistical methods, such as Principal Component analysis or Multi-Dimensional Scaling. In particular, a test profile is significantly similar to the pre- determined reference profile if more than 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99% % of the methylation pattern/ profile overlaps with that of the reference profile. A similarity of a test profile to more than one, such as two, three or even all reference profile reduces the significance of the similarity. Of course, the similarity of the test methylation profile to the reference methylation profile takes into consideration the experimental error that occurs in all methods. The animal-derived product sample may be a single type of meat, different types of meat, a single part of a type of meat, different parts of a single type of meat or different parts of different types of meat. The sample may be from any biological entity having a DNA genome and DNA genome methylation. In particular, the methylation site is a CpG site. The biological entity may be any animal excluding a pig. In particular, the animal may be selected from the group consisting of chicken, lamb, camel, cow, goat, sheep, horse, donkey, turkey, duck, goose, quail, rabbit and mule. More in particular, the animal may be selected from the group consisting of cow, sheep, goat, camel, chicken, goose, duck and turkey. The term ‘meat’ herein may thus be understood to include chicken, lamb, beef, mutton, goat, camel, chicken, goose, duck, turkey and mixtures thereof. The one or more pre-selected methylation sites in (a) are methylation sites associated with tissue specific gene expression, preferably wherein the pre-selected methylation sites are associated with gene expression of one distinct tissue. The tissue may be selected from (i) metabolic tissue such as gut tissue, said gut tissue preferably being ileum or jejunum, (ii) muscular tissue, (iii) skin tissue, and (iv) organ tissue, said organ tissue preferably being hepatic and / or pancreatic tissue. According to yet another aspect of the present invention, there is provided a method of verifying certification of a test animal-derived product sample that has been certified to derive from a test animal that was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or that was bled to death, the method comprising the steps of: (a) determining a test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile obtained from (a) with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death
wherein a difference in the test methylation profile of (a) compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death and the test animal-derived product being correctly certified, and wherein a similarity in the test methylation profile of (a) compared to the reference methylation profile of the control animal, is indicative of the test animal not having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death and the test animal-derived product being wrongly certified, and wherein the pre-selected methylation sites are CpG sites selected from genes or regions of genomic DNA from the control and test animal that shows the highest degree of methylation variation during the training of the method. According to a further aspect of the present invention, there is provided a method for confirming or rejecting an assumed certification of an animal derived product sample, the method comprising - comparison of a test methylation profile obtained from genomic material of the animal derived product sample with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death, wherein a difference in the test methylation profile compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death wherein the assumed certification is that the test animal derived product sample is kosher or halal where the test animal is slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the test animal is bled to death. According to another aspect of the present invention, there is provided a method of determining if a test animal-derived product sample, is obtained from a test animal that has been bled to death or slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus the method comprising: - comparison of a test methylation profile obtained from genomic material of the test animal derived product sample with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death.
In particular, the certification is kosher or halal where the animal is slaughtered by a cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and/or the oesophagus. Additionally, or alternatively, the certification kosher or halal where the animal is drained of blood. According to yet a further aspect of the present invention, there is provided a certification of a test animal derived product sample certifying that the test animal was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and/or the oesophagus, wherein the method for determining that the test animal was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and/or the oesophagus comprises the steps of: (a) determining a test methylation profile of one or more pre-selected methylation sites within the genomic material contained in the test animal-derived product sample; and (b) comparing the test methylation profile determined in (a) with a panel of predetermined reference methylation profiles of the same biological taxon of the test animal from which the product sample derives, wherein each of the predetermined reference methylation profiles is from a different reference animal and/or different supplier, wherein if the test methylation profile of (a) is significantly similar to one of the predetermined reference methylation profiles, the test animal was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, the trachea and/or the oesophagus. Additionally, or alternatively, the test animal is drained of blood. According to yet another aspect of the present invention, there is provided a use of DNA methylation profiling for determining for certifying of an animal-derived product sample. In particular, the certification of the animal-derived product sample is kosher or halal where the test animal is slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the test animal is bled to death. BRIEF DESCRIPTIONS OF FIGURES Figure 1 is the results of Principle Component Analysis (PCA) of 6706643 CpG sites with min coverage 10 in all halal and non-halal samples. Figure 2 is the results of Principle Component Analysis (PCA) of 76339 Differentially methylated positions (DMPs) identified. EXAMPLES The foregoing describes preferred embodiments, which, as will be understood by those skilled in the art, may be subject to variations or modifications in design, construction or
operation without departing from the scope of the claims. These variations, for instance, are intended to be covered by the scope of the claims. Example 1 Wet-Lab methodology Halal and non halal chicken breast meat were purchased from five different vendors. The vendors for halal meat include Pasar, ZAC Butchery, Hego premium, RedMart and Keesong, whereas non halal meat was purchased from Pasar, Tegel, Farm fresh, Ryan and AW’s in Singapore. Genomic DNA was purified from the breast tissue samples using DNeasy Blood & Tissue Kit (Qiagen) and is quantified using PicroGreen or NanoDrop™ 2000. The genomic DNA (500ng) from breast tissue samples was used to prepare libraries for Whole Genome Bisulfite Sequencing (WGBS). The sequencing of the libraries was performed by a third party on a NovaSeq platform which generated 125GB data per sample with 20X coverage. Halal Non-Halal Brand Brand Pasar Pasar ZAC Butchery Tegel Hego premium Farm fresh RedMart Ryan Keesong AW's Computational methodology Processing: Sequenced reads were trimmed and mapped with BSMAP1 version 2.5 using the assembly version 5.0 of the chicken (Gallus gallus) genome as reference sequence. After deduplication using picard2 (http://broadinstitute.github.io/picard/), the methylation ratios were determined using a Python script (methratio.py) distributed with the BSMAP package. BSMAP is further explained in Xi, Y. et al., BMC Bioinform.10, 232 (2009). For all further analysis, only CpGs covered by at least ten reads were considered, which resulted in 6706643 CpG sites. Differential methylation analysis Differential methylation analysis was performed using MethylKit3 (version 1.12.0) between the halal and non-halal group. MethylKit uses logistic regression to calculate p-values and sliding linear model method4 to adjust the p-values to q-values. The use of the linear model method is further described here, Wang H-Q, et al., Bioinformatics.2011; 27:225–231. CpG sites with an FDR below 0.05 and a methylation change larger than 25% between the groups were considered as significantly differentially methylated Positions (DMPs), resulting in 76339 CpG sites.8000 of the exact positions of CpG sites are provided below in Table 1.
MethylKit generates a 'prcomp' object, which can be used to extract and plot the principal components. The use of MethylKit is disclosed in Akalin A, et al. Genome Biol.2012;13(10): R87. Principle Component Analysis (PCA) is a dimensionality-reduction method which can transform large data sets to a few principal components. The first few principal components generally retain most of the variation present in the dataset and are useful for emphasizing the grouping structure in the data Principle Component Analysis (PCA) of CpG sites with min coverage 10 in all samples: 6706643 as shown in Figure 1. Principle Component Analysis (PCA) of 76339 DMPs identified is shown in Figure 2. Plotting of the first two principal components of the CpGs before and after differential methylation analysis reveal meaningful clustering of the samples. Differentially methylated Positions (DMPs) were able to effectively cluster of the halal and non-halal groups in a meaningful way. Table 1.8000 CpG sites of the 76339 significantly differentially methylated Positions (DMPs) are provided.
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.18 Chrom.18 Chrom.19 Chrom.19 Chrom.19 Chrom.20 Chrom.20 Chrom.20 Chrom.21 Chrom.22 Chrom.23 Chrom.24 Chrom.2545 4749214 6735711 4724668 7583548 625393 6460722 13087908 433173 1663230 303275 126822 97800910 4808924 6760809 5451419 7604030 813936 6484087 13207717 912762 2100481 541486 149303 110245265 4841700 6818457 5465889 7633191 837059 7157261 13214456 1029141 2547055 573262 200583 110319252 4903508 6992754 5500154 7669414 911318 7305471 13215531 1390021 2552848 573539 284769 110969517 4913686 171630 5726543 7677916 927790 8111695 13216111 1554352 2729474 584175 1405250 115099934 5039644 271482 5747298 7757436 971372 8191456 13334571 1641909 2798914 609173 1421182 132000438 5517339 580436 5747488 8014377 974467 8408068 13344724 1653319 3700626 616284 1912123 132812036 5522749 747638 5830696 8071886 974560 8412195 13364176 1653357 3703666 648063 1986908 152888878 5602842 838192 5833728 8259175 978996 8443839 13483320 1831102 3704248 660965 1988653 166950336 5602848 876247 5833753 8300311 989001 8489417 1393885 2333072 3716675 663857 2059417 170421107 6141471 1003675 5841962 8416214 993560 8582641 2469788 664421 2059419 170424645 6189234 1408165 5891453 8434392 1000718 8789679 2559790 738474 2097033 177848532 6252403 1502032 5894315 9303967 1004332 8931031 2610337 772230 2123113 185681560 6633350 1505279 5965904 1073683 8938913 2618503 775923 2145047 205333890 6636041 1539817 5989183 1395259 8944640 2624195 792876 2330171 237927426 7358034 1547313 5989235 1404631 9254545 2688709 804158 2330498 249207260 7527461 1569669 6010174 1412280 9271756 2832321 808523 2652186 253436688 7540992 1580462 6020007 1419154 9286346 2974147 829432 2659757 42 7547309 1751180 6022617 1460398 9294047 2994600 853467 2688398 91 7574920 1796257 6025436 1530162 9325396 3001665 873415 2872478 28 8520358 1796923 6027194 1532476 9805264 3005099 874662 2873532 16 8892020 1809408 6047730 1538650 9849284 3024714 882886 2875411 80 9491434 1876738 6054505 1561203 10114240 3516402 1002478 2922961 64 9521363 1985088 6095664 1626986 10285739 3528476 1045090 2924593 43 9521864 2259820 6095884 1758206 10508386 3536570 1156676 2992122 13 9984590 2356804 6096481 1759384 10763997 3558629 1531846 3211402 88 9987506 2434748 6100849 1801935 10764208 3684754 1577757 3211739 18 10010477 2619904 6101015 2305416 10930631 3686478 1614192 3217940 70 10267891 2641336 6109977 2377369 10959899 3723987 1615332 3225884 62 2845568 6118616 2426602 10991662 4054918 1637697 3231008 31 3550591 6161955 2477792 11075418 4836900 1644570 3494353 38 3585622 6371540 2568813 11505812 4939003 1657014 3496578 04 3651040 6527535 2569043 11676390 4948026 1659546 3572763 74 3651331 6531519 2668097 11814885 4976109 1929541 3636773 39 3652052 6549159 2677844 11824650 4997453 1948145 3666284 06 3678657 6597719 2836739 11830800 5022715 2008332 3758125 56 3678661 6602651 2900096 12066976 5126628 2410540 3863025 39 3687105 6673957 2936787 12075797 5291715 2686617 4332717 17 3759136 6702522 2982291 12186799 5314232 2704778 4459949 07 3759162 7189659 2982302 12268210 5323538 2769886 4769482 43 3766184 7194757 2995437 12670983 5678012 2950084 5102087 63 3779485 7194939 3130379 12671317 5759162 3111000 5890836 04 3779599 7195075 3181759 12687999 5762368 3272938 6037678 37 3782009 7200145 3199954 12716334 5762381 3368358 51 3814901 7203329 3201300 12761427 5764164 3772854 20 3939895 7224289 3787277 12837139 6571837 4450830 66 3962214 7417096 4507226 12861404 6571938 4450876 86 4000300 7430290 4922176 12892794 6576343 4470184 00 4063257 7435989 5358625 12905265 6580599 4567627 51 4372316 7532028 6017404 12923319 4884561 12 4638239 7544763 6146979 12946708 4916097
.26 Chrom.27 Chrom.28 Chrom.33 Unlocalised Scaffolds 74 1432737 151802 414716 chr1_NT_456097v1_random: 4387418 1435380 151819 599116 chr1_NT_456113v1_random: 342957 1436167 1062404 1461466 chr1_NT_456143v1_random: 761483 1445658 1957082 1485829 chr1_NT_456856v1_random: 517061 1454549 2443298 chr1_NT_457819v1_random: 30884 1457215 2641875 chr13_NT_462202v1_random: 593331 1490347 2675966 chr14_NT_462351v1_random: 1924159 1490619 2791367 chr14_NT_462351v1_random: 1909557 1564845 2835337 chr3_NT_459020v1_random: 1205494 1565230 2912314 chr3_NT_459020v1_random: 11874497 1570143 2935182 chr3_NT_459020v1_random: 6401348 1571190 3218402 chr3_NT_459020v1_random: 10647159 1582033 3270473 chr3_NT_459020v1_random: 6428975 1591385 3491291 chr3_NT_459020v1_random: 1351429 1594214 3501746 chr4_NT_459801v1_random: 3163662 1596504 3548523 chr4_NT_459801v1_random: 16682836 1596914 3593309 chr5_NT_460430v1_random: 1834175 1601776 3623347 chr5_NT_460548v1_random: 726287 1603418 3635463 chr6_NT_460840v1_random: 2336624 1609162 3878808 chr22_NT_463002v1_random: 992961 1613400 3907769 chr33_NT_463452v1_random: 1502552 1619962 3985591 chr33_NT_463454v1_random: 5753136 1619971 3985871 chr33_NT_463456v1_random: 3615837 1619989 chrLGE64: 868044 75 1620516 chrUn_NT_464128v1: 67946 61 1625362 chrUn_NT_464135v1: 21542 57 1626371 chrUn_NT_464148v1: 5652 51 1639263 chrUn_NT_464215v1: 7282 50 1909749 chrUn_NT_464327v1: 17129 38 1949283 chrUn_NT_464492v1: 18892 90 2053097 chrUn_NT_465142v1: 16062 74 2053967 chrUn_NT_465200v1: 5520 75 2156431 chrUn_NT_466029v1: 6006 40 2752990 chrUn_NT_466029v1: 3712 60 2927799 chrUn_NT_466086v1: 822 25 2966444 chrUn_NT_466086v1: 8623 63 3052200 chrUn_NT_467376v1: 1658 15 3195680 chrUn_NT_467869v1: 10766 32 3458427 chrUn_NT_469469v1: 2442 55 3458886 chrUn_NT_469469v1: 2838 59 3475696 chrUn_NT_471611v1: 6225 68 3551689 chrUn_NT_473432v1: 5412 3632525 chrUn_NT_473478v1: 911 3637822 chrUn_NT_473624v1: 3973 3875240 chrUn_NT_473988v1: 822 3988099 chrUn_NT_479485v1: 871 4038299 chrUn_NT_479485v1: 432 4139773
Claims
CLAIMS 1. A method of certifying a test animal-derived product sample, the method comprising the steps of: (a) determining a test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile obtained from (a) with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death wherein a difference in the test methylation profile of (a) compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death and the test animal-derived product is certified so; and wherein the pre-selected methylation sites are CpG sites selected from genes or regions of genomic DNA from the control and test animal that shows the highest degree of methylation variation during the training of the method. 2. A method of certifying a test animal-derived product sample, the method comprising the steps of: (a) determining the test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile determined in (a) with a panel of predetermined reference methylation profiles of the same biological taxon of the test animal from which the product sample derives, wherein each of the predetermined reference methylation profiles is specific for a distinctly certified reference animal that - has been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus; and/or - bled to death; wherein if the test methylation profile is significantly similar to one of the predetermined reference methylation profiles, the test animal derived product sample has the same distinct certification as that of the predetermined reference methylation profile and is derived from a test animal that has been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or bled to death and the test animal-derived product is certified so; and
wherein the pre-selected methylation sites are CpG sites selected from genes or regions of genomic DNA from the control and test animal that shows the highest degree of methylation variation during the training of the method. 3. A method of certifying a test animal-derived product sample, the method comprising the steps of: (a) determining the methylation status of at least one CpG site within the genomic material obtained from the animal-derived product sample, (b) comparing the methylation status of the CpG site from (a) with that of a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death, wherein a difference in the test methylation status of (a) in the test animal compared to the CpG site in the control animal is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death and the test animal-derived product is certified so. 4. The method according to any one of the preceding claims, wherein test animal derived product sample is distinctly certified kosher or halal where the test animal is slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the test animal is bled to death. 5. A method of verifying certification of a test animal-derived product sample that has been certified to derive from a test animal that was slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or that was bled to death, the method comprising the steps of: (a) determining a test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and (b) comparing the test methylation profile obtained from (a) with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death wherein a difference in the test methylation profile of (a) compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular
veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death and the test animal-derived product being correctly certified, and wherein a similarity in the test methylation profile of (a) compared to the reference methylation profile of the control animal, is indicative of the test animal not having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death and the test animal-derived product being wrongly certified; and wherein the pre-selected methylation sites are CpG sites selected from genes or regions of genomic DNA from the control and test animal that shows the highest degree of methylation variation during the training of the method. 6. A method according to any one of the preceding claims, wherein the CpG site is selected from list provided in Table A. 7. A method for confirming or rejecting an assumed certification of an animal derived product sample, the method comprising - comparison of a test methylation profile obtained from genomic material of the animal derived product sample with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death, wherein a difference in the test methylation profile compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death wherein the assumed certification is that the test animal derived product sample is kosher or halal where the test animal is slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the test animal is bled to death. 8. A method of determining if a test animal-derived product sample, is obtained from a test animal that has been bled to death or slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus the method comprising: - comparison of a test methylation profile obtained from genomic material of the test animal derived product sample with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut
across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death. 9. The method according to claim 8, wherein the method comprises the steps of: a) determining the test methylation profile of one or more pre-selected methylation sites within the genomic material obtained from the test animal derived product sample; and b) comparing the test methylation profile determined in (a) with a panel of predetermined reference methylation profiles of the same biological taxon of the test animal from which the product sample derives, wherein with a reference methylation profile obtained from a control animal of the same biological taxon of the test animal from which the product sample is derived from, where the control animal is not slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the control animal is not bled to death, wherein a difference in the test methylation profile of (a) compared to the reference methylation profile from the control animal, is indicative of the test animal having been slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or of the test animal having been bled to death. 10. The method according to any one of the preceding claims, wherein the animal is selected from the group consisting of cow, sheep, goat, camel, chicken, goose, duck and turkey. 11. The method according to any one of the preceding claims, wherein the test animal-derived product sample is meat, eggs, milk and any other tissue or sample that provides genomic DNA. 12. The method according to any one of the preceding claims, wherein the test animal-derived product sample is meat. 13. The method according to any one of the preceding claims, wherein the difference is hypomethylation or hypermethylation. 14. Use of DNA methylation profiling for certifying of an animal-derived product sample, wherein the certification of the animal-derived product sample is kosher or halal where the test animal is slaughtered by a single cut across the throat severing both carotid arteries, both jugular veins, both vagus nerves, trachea and/or oesophagus and/or the test animal is bled to death.
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| EP22184431 | 2022-07-12 | ||
| PCT/EP2023/068584 WO2024012958A1 (en) | 2022-07-12 | 2023-07-05 | Certification of animal-derived product(s) based on dna-methylation |
Publications (1)
| Publication Number | Publication Date |
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| EP4555103A1 true EP4555103A1 (en) | 2025-05-21 |
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|---|---|---|---|
| EP23738732.9A Pending EP4555103A1 (en) | 2022-07-12 | 2023-07-05 | Certification of animal-derived product(s) based on dna-methylation |
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| EP (1) | EP4555103A1 (en) |
| KR (1) | KR20250036209A (en) |
| CN (1) | CN119907865A (en) |
| AR (1) | AR129848A1 (en) |
| AU (1) | AU2023308028A1 (en) |
| CA (1) | CA3261604A1 (en) |
| MX (1) | MX2025000359A (en) |
| WO (1) | WO2024012958A1 (en) |
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| AU2022338189B2 (en) * | 2021-09-06 | 2026-02-19 | Deutsches Krebsforschungszentrum Stiftung des öffentlichen Rechts | Dna-methylation-based certification of quality |
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| US7658288B2 (en) | 2004-11-08 | 2010-02-09 | Applied Biosystems, Llc | Bisulfite conversion reagent |
| CN109379186B (en) * | 2018-11-05 | 2021-06-25 | 上海信联信息发展股份有限公司 | Method and device for generating digital certificate for live poultry slaughter |
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2023
- 2023-07-05 WO PCT/EP2023/068584 patent/WO2024012958A1/en not_active Ceased
- 2023-07-05 CA CA3261604A patent/CA3261604A1/en active Pending
- 2023-07-05 EP EP23738732.9A patent/EP4555103A1/en active Pending
- 2023-07-05 KR KR1020257004369A patent/KR20250036209A/en active Pending
- 2023-07-05 CN CN202380065285.4A patent/CN119907865A/en active Pending
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| KR20250036209A (en) | 2025-03-13 |
| MX2025000359A (en) | 2025-04-02 |
| CA3261604A1 (en) | 2024-01-18 |
| AU2023308028A1 (en) | 2025-02-20 |
| CN119907865A (en) | 2025-04-29 |
| AR129848A1 (en) | 2024-10-02 |
| WO2024012958A1 (en) | 2024-01-18 |
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