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Oligonucleotide sequences that identify species of animal

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20120270223 patent thumbnailZoom

Oligonucleotide sequences that identify species of animal


The present invention provides a method for identifying animal species, said method comprises a step of amplifying a DNA fragment by PCR using a DNA in a sample as a template and animal-specific DNA sequences as a primer pair, wherein the animal-specific DNA sequences are derived from a ATP synthase subunit 8 gene or a region proximal thereto of a mitochondrial genome; and a step of detecting the amplified DNA fragment.
Related Terms: Dna Sequences

Browse recent National Institute Of Agrobiological Sciences patents - Tsukuba-shi, JP
Inventors: Toyoko Kusama, Koichi Kadowaki, Tetsuya Nomura
USPTO Applicaton #: #20120270223 - Class: 435 612 (USPTO) - 10/25/12 - Class 435 


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The Patent Description & Claims data below is from USPTO Patent Application 20120270223, Oligonucleotide sequences that identify species of animal.

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CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Division of application Serial No. 12/707,828 filed Feb. 18, 2010, which is a Continuation of application Ser. No. 10/826,119 filed Apr. 16, 2004,the entire contents of both of which is hereby incorporated by reference. Applicants request use of the compliant computer readable “Sequence Listing” that is already on file for application Ser. No. 10/826,119 filed Apr. 16, 2004 and state that the paper or compact disc copy of the “Sequence Listing” in this application is identical to the computer readable copy filed for application Ser. No. 10/826,119 filed Apr. 16, 2004.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to methods for identifying animal species and animal-derived DNA-specific primer pairs used therein. More specifically, the present invention relates to methods for identifying animal species that include a step of amplifying an animal-specific DNA sequence derived from the ATP synthase subunit 8 gene of a mitochondrial genome, and primer pairs used in this amplification step.

2. Description of the Related Art

Currently, there is a problem that cattle is infected with bovine spongiform encephalopathy (BSE) by giving feed containing meat and bonemeal derived from cattle infected with BSE. It has been shown that BSE-like diseases may be present in various livestock as well. Accordingly, since the emergence of BSE, there has been a need to develop sensitive and effective method to identify feed contaminated bone and bonemeal, and this has become a particularly urgent matter for authorities.

Immunological methods and gene identification methods using nuclear gene conventionally have been used as methods for identifying animal species. Examples of immunological methods include ELISA and immunoblotting. PCR is an example of a gene identification method using nuclear gene. However, there are many problems with methods for identifying the animal species that are currently employed. For example, in meat and bonemeal that has been heat-treated, there is a high likelihood that nucleic acids have been fragmented. Furthermore, majority of feed in which meat and bonemeal has been mixed is composed of plant-derived material. Therefore, it is necessary to analyze trace amounts of animal-derived components. There is a dire need for the development of a detection method that is highly sensitive and effective and that can be executed with respect to such heat-treated samples.

Accordingly, a method other than immunological methods and gene identification methods employing nuclear gene that is for detecting and identifying the animal species of animal-derived components that are present in trace amounts is desirable. In particular, it is crucial to identify the type of animal meat, meat and bonemeal, or fishmeal used in feed given to livestock and pets. Furthermore, it is desirable that the detection method is highly sensitive and differentiate species of animal DNA present in trace amounts from among large quantities of plant DNA or DNA of other animal species.

SUMMARY

OF THE INVENTION

The inventors of the present application focused on the mitochondrial genome, which is inherited maternally and exists in a greater number of copies than nuclear genome, and investigated the use of mitochondrial gene as a target for identifying animal species. Their research indicated that the homologous sequence with ATP synthase subunit 8 gene (atp8 gene) from animal mitochondrial genome is not present in plant (Oryza sativa) mitochondrial genome. Thus, the inventors found that the DNA derived from the atp8 gene can serve as a material for specific detection of trace amounts of animal DNA among plant-based feed, in other word, plant atp8 gene is very diverged from animal atp8 gene, and also that specific DNA sequences of the animal mitochondrial atp8 gene can be used to identify the animal species, thereby arriving at the present invention.

The present invention provides a method for identifying animal species, said method comprises:

amplifying a DNA sequence by PCR using a DNA in a sample as a template and animal-specific DNA sequences as a primer pair, wherein the animal-specific DNA sequences are derived from a ATP synthase subunit 8 gene or a region proximal thereto of a mitochondrial genome, and

detecting the amplified DNA sequence.

In a preferred embodiment, the animal is a mammal, and further preferably, the primer pair is a combination of the DNA sequence of SEQ ID NO: 1 and the DNA sequence of SEQ ID NO: 2.

In a further preferred embodiment, the mammal is selected from the group consisting of cattle, sheep, goat, deer, pig, horse, rabbit, and whale.

In a preferred embodiment, the animal is a ruminant, and further preferably, the primer pair is a combination of the DNA sequence of SEQ ID NO: 3 and the DNA sequence of SEQ ID NO: 4, or a combination of the DNA sequence of SEQ ID NO: 5 and the DNA sequence of SEQ ID NO: 6.

In a further preferred embodiment, the ruminant is selected from the group consisting of cattle, sheep, goat, and deer.

In a preferred embodiment, the animal is a cattle, and further preferably, the primer pair is a combination of DNA sequences selected from the group consisting of the following DNA sequence combinations: SEQ ID NO: 9 and SEQ ID NO: 13; SEQ ID NO: 9 and SEQ ID NO: 12; SEQ ID NO: 11 and SEQ ID NO: 13; SEQ ID NO: 10 and SEQ ID NO: 12; SEQ ID NO: 11 and SEQ ID NO: 12; SEQ ID NO: 8 and SEQ ID NO: 12; and SEQ ID NO: 14 and SEQ ID NO: 15.

In a preferred embodiment, the animal is a pig, and further preferably, the primer pair is a combination of the DNA sequence of SEQ ID NO: 17 and the DNA sequence of SEQ ID NO: 19, or a combination of the DNA sequence of SEQ ID. NO: 18 and the DNA sequence of SEQ ID NO: 22.

In a preferred embodiment, the animal is a sheep, and further preferably, the primer pair is a combination of the DNA sequence of SEQ ID NO: 23 and the DNA sequence of SEQ ID NO: 24.

In a preferred embodiment, the animal is a goat, and further preferably, the primer pair is a combination of the DNA sequence of SEQ ID NO: 25 and the DNA sequence of SEQ ID NO: 26.

In a preferred embodiment, the animal is a chicken, and further preferably, the primer pair is a combination of the DNA sequence of SEQ ID NO: 28 and the DNA sequence of SEQ ID NO: 30.

In a preferred embodiment, the animal is a fish, and further preferably, the primer pair is a combination of the DNA sequence selected from the group consisting of SEQ ID NOS: 32, 34, 38 and 39 and the DNA sequence selected from the group consisting of SEQ ID NOS: 33, 35, 36, 37, 40, and 41.

In a further preferred embodiment, the fish is selected from the group consisting of sardine, flatfish, salmon, Alaska Pollack, tuna, and lady crab.

In a further preferred embodiment, the sample is selected from a group consisting of raw meat, raw fish, processed meat food products, processed fish food products, food products containing processed meat, food products containing processed fish, blood, hair, body fluids, milk, milk processing products, meat and bonemeal, bonemeal, fishmeal, fish soluble, and feed, fertilizer, and feed additive containing them.

The present invention also provides a primer pair for detection of a mammal-specific DNA, the primer pair being a combination of the DNA sequence of SEQ ID NO: 1 and the DNA sequence of SEQ ID NO: 2.

In a preferred embodiment, the mammal is selected from the group consisting of cattle, sheep, goat, deer, pig, horse, rabbit, and whale.

The present invention also provides a primer pair for detection of a ruminant-specific DNA, the primer pair being a combination of the DNA sequence of SEQ ID NO: 3 and the DNA sequence of SEQ ID NO: 4, or a combination of the DNA sequence of SEQ ID NO: 5 and the DNA sequence of SEQ ID NO: 6.

In a preferred embodiment, the ruminant is selected from the group consisting of cattle, sheep, goat, and deer.

The present invention also provides a primer pair for detection of a cattle-specific DNA, the primer pair being a combination of DNA sequences selected from the group consisting of the, following DNA sequence combinations: SEQ ID NO: 9 and SEQ ID NO: 13; SEQ ID NO: 9 and SEQ ID NO: 12; SEQ ID NO: 11 and SEQ ID NO: 13; SEQ ID NO: 10 and SEQ ID NO: 12; SEQ ID NO: 11 and SEQ ID NO: 12; SEQ ID NO: 8 and SEQ ID NO: 12; and SEQ ID NO: 14 and SEQ ID NO: 15.

The present invention also provides a primer pair for detection of a pig-specific DNA, the primer pair being a combination of the DNA sequence of SEQ ID NO: 17 and the DNA sequence of SEQ ID NO: 19, or a combination the DNA sequence of SEQ ID NO: 18 and the DNA sequence of SEQ ID NO: 22.

The present invention also provides a primer pair for detection of a sheep-specific DNA, the primer pair being a combination of the DNA sequence of SEQ ID NO: 23 and the DNA sequence of SEQ ID NO: 24.

The present invention also provides a primer pair for detection of a goat-specific DNA, the primer pair being a combination of the DNA sequence of SEQ ID NO: 25 and the DNA sequence of SEQ ID NO:'26.

The present invention also provides a primer pair for detection of a chicken-specific DNA, the primer pair being a combination of the DNA sequence of SEQ ID NO: 28 and the DNA sequence of SEQ ID NO: 30.

The present invention also provides a primer pair for detection of a fish-specific DNA, the primer pair being a combination of the DNA sequence selected from the group consisting of SEQ ID NOS: 32, 34, 38 and 39 and the DNA sequence selected from the group consisting of SEQ ID NOS: 33, 35, 36, 37, 40, and 41.

In a preferred embodiment, the fish is selected from the group consisting of sardine, flatfish, salmon, Alaska Pollack, tuna, and lady crab.

The present invention also provides a primer pair for detection of a plant-specific DNA, the primer pair being a combination of the DNA sequence of SEQ ID NO: 42 and the DNA sequence of SEQ ID NO: 43.

Further, the present invention provides a method for detecting animal-derived components present in mixed feed, said method comprises:

amplifying a DNA sequence by PCR using a DNA in a sample as a template and animal-specific DNA sequences as a primer pair, wherein the animal-specific DNA sequences are derived from a ATP synthase subunit 8 gene or a region proximal thereto of a mitochondrial genome, and

detecting the amplified DNA sequence.

The present invention also provides a kit for detecting an animal-derived component present in a sample, said kit comprises at least one of primer pair specific for any animal described above.

In a preferred embodiment, the kit further comprises a primer pair for detection of a plant-specific DNA, said primer pair is a combination of the DNA sequence of SEQ ID NO: 42 and the DNA sequence of SEQ ID NO: 43.

Further, the present invention provides a method for detecting plant-derived components present in sample, said method comprises:

amplifying a DNA sequence by PCR using a DNA in a sample as a template and plant-specific DNA sequences as a primer pair, wherein the plant-specific DNA sequences are derived from a ATP synthase subunit 8 gene or a region proximal thereto of a mitochondrial genome, and

detecting the amplified DNA sequence.

Using the method of the present invention, it is possible to detect, with high sensitivity, trace amounts of animal-derived DNA in a sample. It is thus applicable to identify the animal species of trace amounts of meat and bonemeal mixed into feed. More particularly, detection is possible even if trace amounts of cattle-derived meat and bonemeal are mixed into mixed feed for livestock. Further, the primers for the detection of fish-specific DNA according to the present invention are useful for detecting a wide range of fishmeal derived from various fish species that has been mixed into mixed feed or the like.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 shows a sequence alignment of mitochondrial atp8 genes derived from various types of animals.

FIG. 2 shows a sequence alignment of chicken, cattle, and pig mitochondrial atp8 genes.

FIG. 3 shows a sequence alignment of mitochondrial atp8 genes, and nearby regions, derived from various types of animals.

FIG. 4 shows the positional relationship on the mitochondrial atp8 gene of the primers used to specifically detect cattle-derived DNA sequences.

FIG. 5 is a photograph showing the results of electrophoresis after performing PCR using a primer pair (anicon5 and anicon3) for detecting mammal-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 6 is a photograph showing the results of electrophoresis after performing PCR using a primer pair (rumicon5 and rumicon3) for detecting ruminant-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 7 is a photograph showing the results of electrophoresis after performing PCR using a primer pair (Fpr-F and Fpr-R) for detecting ruminant-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 8 is a photograph showing the results of electrophoresis after performing PCR using a primer pair (cow3 and cow51) for detecting cattle-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 9 is a photograph showing the results of electrophoresis after performing PCR using various primer pairs for detecting cattle-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 10 is a photograph showing the results of electrophoresis after performing PCR using various primer pairs for detecting cattle-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 11 is a photograph showing the results of electrophoresis after performing PCR using a primer pair (Fpc-F and Fpc-R) for detecting cattle-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 12 is a photograph showing the results of electrophoresis after performing PCR using a primer pair (pig51 and pig3) for detecting pig-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 13 is a photograph showing the results of electrophoresis after performing PCR using a primer pair (pig5-3 and pig32-2) for detecting pig-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 14 is a photograph showing the results of electrophoresis after , performing PCR using a primer pair (sheep5 and sheep3) for detecting sheep-specific DNA sequences and a primer pair (goat5 and goat3) for detecting goat-specific DNA sequences, and with DNAs derived from various types of animals serving as templates.

FIG. 15 is a photograph showing the results of electrophoresis after performing PCR using a primer pair for detecting chicken-specific DNA sequences and with DNAs derived from various types of animals serving as templates.

FIG. 16 is an electrophoresis photograph showing the results of the detection of DNA, using mammal-specific primer pairs, using various primer pairs, in mixed feed for livestock that contains cattle meat and bonemeal.

FIG. 17 is an electrophoresis photograph showing the results of the detection of DNA, using ruminant-specific primer pairs, in mixed feed for livestock that includes cattle meat and bonemeal.

FIG. 18 is an electrophoresis photograph showing the results of the detection of DNA, using cattle-specific primer pairs, in mixed feed for livestock that contains cattle meat and bonemeal.

DESCRIPTION OF THE PREFERRED EMBODIMENT

The mitochondrial genome is essential for the biosynthesis of the enzymes required for oxidative phosphorylation (electron transport system), and mitochondrial DNA codes for ATP synthase and cytochrome c oxidase, and the like. ATP synthase is composed of several subunits, and as discussed above, the inventors found that the ATP synthase subunit 8 gene (atp8 gene) is present in the animal mitochondrial genome but homologous sequence with animal atp8 gene is not present in the plant (Oryza sativa) mitochondrial genome. It thus became possible to identify animal species even when plant-derived DNA is present in large quantities in the feed.

Several animal atp8 genes are known. For example, taking the cattle atp8 DNA sequence (cattle) as a reference, the atp8 DNA sequences of several animal species were aligned so that homology with the cow sequence is achieved, and this is shown in FIG. 1. FIG. 1 shows the DNA sequence of the atp8 gene of 1: cattle, 2: alpaca, 3: cat, 4: dog, 5: goat (1), 6: goat (2), 7: horse, 8: antelope, 9: mouse, 10: rabbit, 11: rat, 12: donkey, 13: sheep, 14: deer, 15: sperm whale, and 16: razorback whale. It should be noted that the arrow in the diagram indicates the start position of the cattle atp8 reading frame.

FIG. 2 shows the atp8 genes of cattle, chicken, and pig aligned with one another. Further, FIG. 3 shows the atp8 genes of fish, chicken, cattle, sheep, and pig aligned with one another, and the underlined portion indicates the position of the atp8 gene of a pilchard.

As shown in FIGS. 1 to 3, there is diversity of DNA sequences among the atp8 genes. This diversity can be used to detect specific sequences in various types of animals, thereby allowing various animal species to be identified.

To identify various types of animals, examples of methods for detecting a DNA sequence specific to an animal species include Southern Blotting and PCR (polymerase chain reaction). PCR is preferably used in the present invention because it permits detection even with very small DNA samples and it allows accuracy to be improved. In the present invention, PCR is carried out using a pair of primers including a DNA sequence specific to a target animal species, and a DNA fragment that is amplified is detected.

PCR is for example carried out as follows. First, two regions are selected as primers from any of regions of the atp8 gene and regions proximal thereto having a DNA sequence specific to a target animal species, and the selected primers are synthesized. Using this pair of primers, the DNA fragment of the region sandwiched between the two primers is amplified by PCR. A sample containing the amplified DNA fragments is then subjected to electrophoresis to determine whether that DNA fragment is present.

A primer is a DNA sequence of nucleotides in any length, and is suitably selected based on the sequence alignment of the atp8 genes of various types of animals in publicly available databases. For example, in order to detect DNA specific to mammals, a region having higher homology with mammals and low homology with non-mammals and having appropriate nucleotide at the 3′ end can be chosen. In order to detect DNA specific to a certain animal, a region having specificity to that animal and low specificity with other animals can be chosen. Since primers are used in pairs, two regions, that is, a region on the 5′ side and a region on the 3′ side, are selected. If more than two regions can be selected as primers, then it is possible to use various primer combinations.

For example, FIG. 4 shows a DNA sequence of cattle mitochondrial atp8 gene, and the markings in the diagram are the regions (sequences) that can be used as primers for detecting cattle-specific DNA. DNA sequences for specifically detecting mammals (anicon5 [SEQ ID NO: 1] and anicon3 [SEQ ID NO: 2]) and DNA sequences for specifically detecting ruminants (rumicon5 [SEQ ID NO: 3] and rumicon3 [SEQ ID NO: 4]) are also shown in FIG. 4. A more detailed explanation follows in the Examples. For example, mammal specific DNA can be detected when anicon5 is used as the 5′ primer and anicon3 is used as the 3′ primer. Likewise, ruminant specific DNA can be detected when rumicon5 and rumicon3 are used as primers. Alternatively, although not shown, it is also possible to combine Fpr-F [SEQ ID NO: 5] and Fpr-R [SEQ ID NO: 6] to detect ruminant specific DNA with greater accuracy. As the 5′ primer, any one of cow5 [SEQ ID NO: 7], cow51 [SEQ ID NO: 8], cow52 [SEQ ID NO: 9], cow53 [SEQ ID NO: 10], and cow54 [SEQ ID NO: 11] is used, and as the 3′ primer, either cow3 [SEQ ID NO: 12] or cow31 [SEQ ID NO: 13] is used. For example, the primer pairs of cow52 and cow31, cow52 and cow3, cow54 and cow31, cow53 and cow3, cow54 and cow3, and cow51 and cow3 are capable of detecting cattle-specific DNA. Alternatively, although not shown, it is also possible to combine Fpc-F [SEQ ID NO: 14] and Fpc-R [SEQ ID NO: 15] to detect cattle-specific DNA with greater accuracy.

The regions surrounded by squares in FIGS. 1 to 3 indicate examples of DNA sequences used in tests for specifically detecting DNAs derived from the respective animal species.

The DNA sequences of the regions selected as primers are synthesized by normally employed methods. Typically, nucleotides are extended on a support medium using an automated DNA synthesizer, then removed from protecting group and cleaved from the support medium. Then, they can be purified using a normally employed method (such as column chromatography) to obtain primers of interest.

Samples that can be measured include raw meat, raw fish, processed meat food products, processed fish food products, food products containing processed meat, food products containing processed fish, blood, hair, body fluids, milk, milk processing products, meat and bonemeal, bonemeal, fishmeal, fish soluble, and feed, fertilizer, and feed additive containing them. Extraction of mitochondrial DNA from these samples is, for example, perforated. as follows. Approximately 50 mg to 500 mg of a sample (for example, 50 mg in the case of raw meat, 100 mg to 500 mg in the case of a dried powder sample) is suspended in about 10 times that amount of buffered solution, ground using a bead grinding method, for example, and then extracted using a commercially available tissue cell mitochondrial DNA extraction kit (manufactured by Wako Pure Chemical Industries, Ltd., for example). Such kits allow purer mitochondrial DNA to be collected in that little genome DNA in the tissue cells is contaminated. For example, to the sample ground is added a reagent in the kit, and centrifuged, and the pellets are collected to concentrate. It is thus possible to more efficiently extract mitochondrial DNA with little contamination of genome DNA, which is present in large quantities in the sample. The method for extracting DNA is not limited to those described herein, and it is apparent to those skilled in the art to employ other methods for extracting DNA.

There are no particular limitations regarding the amount of primer used, but generally is it preferable that approximately 0.4 μM is used.

PCR is performed on the pretreated sample, that is, either the mitochondrial DNA or total DNA extracted from the sample, using the primer pair selected above, so as to amplify the DNA fragment of the region sandwiched between the primers. PCR is executed under conditions in which it is ordinarily performed, and conditions that are appropriate for each primer pair are set. For example, DNA fragment is, firstly, heat denatured at 95° C. for 9 minutes; then subjected to the cycle of reactions of denaturing at 92° C. for 30 seconds to one minute, annealing at 40 to 65° C. for 30 seconds to two minutes, and extending at 72° C. for 30 seconds to two minutes, which is repeated 30 to 50 times; and finally, allowed to react at 72° C. for five minutes to finish PCR. AmpliTaq GOLD polymerase or the like is used as the DNA polymerase. The size of the PCR product (DNA fragment) amplified by the primer pair can be approximately 100 by to approximately 300 bp, although this varies depending on the number of bases between the primer pair that has been selected. The PCR product is then subjected to agarose or polyacrylamide gel electrophoresis, for example, under conditions in which the above DNA fragments can be separated.

The DNA fragments on the gel subjected to electrophoresis can be detected by detection means normally employed by those skilled in the art, such as ethidium bromide staining, silver staining, fluorescence detection, and Southern hybridization, and can be confirmed by DNA sequencing.

Thus, if mitochondrial DNA derived from a species of interest is present in the sample, then, amplified DNA fragments can be detected on the gel. Limits to detection may vary depending on various factors, such as the type and combination of the primer pair used, the amount of sample, the PCR conditions, and the detection method. If appropriate conditions are selected, then the presence of DNA can be detected with high sensitivity even in trace samples. For example, if appropriate conditions are selected when the sample is a mixed feed that contains cattle-derived meat and bonemeal, then contamination of only 0.001 wt % cattle meat and bonemeal in the feed can be detected using a specific cattle-specific primer pair.

It should be noted that when a sample is a mixed feed, if a plant DNA-specific primer pair (for example, the combination of placon5 [SEQ ID NO: 42] and placon3 [SEQ ID NO: 43]) is used as a control experiment, then it is possible to confirm whether or not DNA has been appropriately extracted from the sample. Furthermore, by using a plant DNA-specific primer pair, a plant-derived component present in a sample can be detected.

The primer pairs of the present invention may be provided in the form of a kit for detecting an animal-derived component present in a sample. The kit comprises at least one of primer pair specific for any animal described above. Preferably, the kit further comprises the plant DNA-specific primer pair as a control.

It should be noted that the primer sequence has been specified in the Examples discussed below, but there is no intention to limit the present invention to the following Examples. It is intended that the present invention includes in its scope sequences that include those primer sequences, or those sequences with one or more base sequence substitutions, deletions, or insertions or addition of nucleotide sequences to the 5′ end, and sequences which by changing the hybridizing conditions can hybridize with a DNA of interest and allow a DNA derived from a specific animal species to be detected specifically.

EXAMPLES

Primer Synthesis

Primer regions to be used in the following Examples were selected based on the sequence alignment of the atp8 gene and regions proximal thereto of various animals shown in FIGS. 1 to 3. The DNA sequences of the selected regions were synthesized using an automated DNA synthesizer.

Example 1 Specific Detection of Mammal-Derived DNA Sequence


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stats Patent Info
Application #
US 20120270223 A1
Publish Date
10/25/2012
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File Date
12/18/2014
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