Methods for identifying biological samples
First Claim
1. A method of marking a plurality of biological samples with a detectable marker, said method comprising:
- obtaining a plurality of different nucleic acid marker molecules, where each marker molecule comprises a different nucleic acid tag sequence;
obtaining a plurality of biological samples;
adding an aliquot of each of at least 2 of the marker molecules to each of the biological samples to generate a plurality of barcoded biological samples, wherein each of the barcoded biological samples in the plurality comprises a different combination of marker molecules.
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Abstract
The present invention provides methods for marking nucleic acid samples with detectable markers by adding different combinations of marker molecules to each sample. Each sample may be marked with a different combination of two or more marker molecules each carrying a different tag nucleic acid sequences. The tag nucleic acid sequences may be random sequences that are not naturally occurring in the nucleic acid sample and do not cross hybridize to sequences naturally occurring in the nucleic acid sample. Methods of detecting the combination of tag sequences present in a sample, in parallel with methods of genetic analysis of the sample are disclosed. Kits containing marker molecules suitable for generating barcoded samples by mixing different combinations of marker molecules into each sample are also disclosed.
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Citations
42 Claims
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1. A method of marking a plurality of biological samples with a detectable marker, said method comprising:
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obtaining a plurality of different nucleic acid marker molecules, where each marker molecule comprises a different nucleic acid tag sequence;
obtaining a plurality of biological samples;
adding an aliquot of each of at least 2 of the marker molecules to each of the biological samples to generate a plurality of barcoded biological samples, wherein each of the barcoded biological samples in the plurality comprises a different combination of marker molecules. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14)
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15. A method of marking each sample in a plurality of biological samples so that each sample is marked with a detectable barcode marker that is different from the barcode marker of each of the other samples in the plurality, said method comprising:
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putting an aliquot of each sample in a different well of a multi-well plate comprising 12 columns and 8 rows;
obtaining 12 different first marker molecules and 8 different second marker molecules;
putting an aliquot of one of the first marker molecules into each well of each column so that each column has a different first marker molecules and all wells in a column have the same first marker molecule; and
,putting an aliquot of one of the second marker molecules into each well of each row so that each row has a different second marker molecules and all wells in a row have the same second marker molecule. - View Dependent Claims (16, 17)
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18. A method for marking a plurality of X genomic samples using Y different independent marker molecules, where Y is less than X, comprising:
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obtaining a plurality of X genomic DNA samples;
adding an aliquot of each of two of said Y different independent marker molecules to each of the X genomic DNA samples so that no two of the X genomic DNA samples has the same combination of independent marker molecules added. - View Dependent Claims (19, 20, 21, 22)
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23. A method of detecting contamination of a first sample with a second sample, wherein the first sample is marked with a first barcode and the second sample is marked with a second barcode, wherein a barcode comprises a known combination of 2 to 5 tag sequences and said first barcode and said second barcode are different:
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fragmenting the first sample with a restriction enzyme to generate restriction fragments;
ligating an adaptor to the restriction fragments to generate adaptor-ligated fragments;
amplifying the adaptor-ligated fragments by polymerase chain reaction using a primer complementary to the adaptor to generate amplified fragments;
labeling the amplified fragments;
generating a hybridization pattern for said first sample by hybridizing the labeled fragments to an array of probes comprising probes complementary to said tag sequences;
analyzing the hybridization pattern to determine which tag sequences are present in said first sample; and
,determining that said first sample is contaminated with said second sample if the barcode of the second sample is detected in the first sample. - View Dependent Claims (24, 25, 26)
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27. A method of determining the genotype of a sample at a plurality of single nucleotide polymorphisms and the identity of the sample, comprising:
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marking the sample to be analyzed with a barcode to generate a marked sample, wherein the barcode comprises a known combination of marker molecules each carrying a detectable tag sequence;
fragmenting an aliquot of the marked sample with a restriction enzyme to generate restriction fragments;
ligating adaptors to the restriction fragments to generate adaptor-ligated fragments;
amplifying the adaptor-ligated fragments;
labeling the amplified fragments and hybridizing the labeled fragments to an array, wherein the array comprises genotyping probes and probes complementary to tag sequences to generate a hybridization pattern; and
,analyzing the hybridization pattern to determine the genotype of the sample at said plurality of single nucleotide polymorphisms and to determine the barcode. - View Dependent Claims (28, 29, 30)
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- 31. A kit comprising a plurality of at least 10 different nucleic acid marker molecules wherein each marker molecule is physically separated from every other marker molecule and each comprises a different tag sequence.
- 36. A kit comprising a plurality of at least 20 different nucleic acid marker molecules wherein the marker molecules are provided in a multiwell container, so that different combinations of at least two marker molecules are present in each of a plurality of wells.
- 39. A kit comprising a plurality of barcode plasmids wherein each barcode plasmid comprises a different tag sequence, wherein cleavage of each barcode plasmid in the plurality with a selected restriction fragment releases the tag sequence on a restriction fragment that is between 200 and 2000 base pairs in length.
Specification