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公开(公告)号：US20240287502A1
公开(公告)日：2024-08-29
申请号：US18397280
申请日：2023-12-27
发明人： Arvydas Lubys , Inga Cikotiene , Zana Kapustina , Arturas Berezniakovas , Justina Medziune , Simona Zeimyte , Mark Andersen , Michael Allen , Sihong Chen , Arseny Smirnov , Bryce Alves , Paul Rack
IPC分类号： C12N15/10 , C12N15/115 , C12Q1/6806
CPC分类号： C12N15/1065 , C12N15/115 , C12Q1/6806 , C12N2310/3517
摘要： The present disclosure describes oligonucleotide-tethered nucleotides, methods of making them, and methods of using them. The oligonucleotide-tethered nucleotides comprise, in some embodiments, a nucleotide linked to an oligonucleotide of from about 3 to about 100 nucleotides in length. These oligonucleotide-tethered nucleotides can be used to label a plurality of different types of nucleic acids in a plurality of different situations with a known oligonucleotide, which can serve as a barcode in some embodiments. The resulting oligonucleotide-labeled nucleic acids oligonucleotides can be used in a variety of nucleic acid sequencing methods.
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公开(公告)号：US11001836B2
公开(公告)日：2021-05-11
申请号：US16024175
申请日：2018-06-29
发明人： Mark Andersen , Daniel Mazur , Sihong Chen , Guobin Luo , Xinzhan Peng
IPC分类号： C12N15/10 , C12Q1/6806 , C12Q1/6853 , C12Q1/6855 , C12Q1/686 , C40B20/04 , C40B50/06 , C40B40/06
摘要： Provided are methods for preparing a library of target nucleic acid sequences, as well as compositions and uses therefor. Methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; repairing the digested target amplicons; and amplifying the repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the plurality of adaptor compositions comprise a handle and a targeted nucleic acid sequence and optionally one or more tag sequences. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences. Resulting library compositions are useful for a variety of applications, including sequencing applications.
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公开(公告)号：US20240102003A1
公开(公告)日：2024-03-28
申请号：US18345856
申请日：2023-06-30
发明人： Arvydas Lubys , Inga Cikotiene , Zana Kapustina , Arturas Berezniakovas , Justina Sulgaite , Simona Zeimyte , Mark Andersen , Michael Allen , Sihong Chen
IPC分类号： C12N15/10 , C12N15/115 , C12Q1/6806
CPC分类号： C12N15/1065 , C12N15/115 , C12Q1/6806 , C12N2310/3517
摘要： The present disclosure describes oligonucleotide-tethered nucleotides, methods of making them, and methods of using them. The oligonucleotide-tethered nucleotides comprise, in some embodiments, a nucleotide linked to an oligonucleotide of from about 3 to about 100 nucleotides in length. These oligonucleotide-tethered nucleotides can be used to label a plurality of different types of nucleic acids in a plurality of different situations with a known oligonucleotide, which can serve as a barcode in some embodiments. The resulting oligonucleotide-labeled nucleic acids oligo-nucleotides can be used in a variety of nucleic acid sequencing methods.
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4.发明公开公开(公告)号：US20230374574A1
公开(公告)日：2023-11-23
申请号：US18340581
申请日：2023-06-23
发明人： Michael Allen , Mark Andersen
IPC分类号： C12Q1/6858
CPC分类号： C12Q1/6858
摘要： Efficient methods for production of targeted libraries from complex samples is desirable for a variety of nucleic acid analyses. Provided are methods of selectively blocking abundant targets present in a sample for preparing libraries of target nucleic acid sequences, thereby allowing for rapid production of highly multiplexed targeted libraries and analysis of low frequency sequences, including sequencing applications. Methods optionally include use of unique tag sequences. Methods comprise contacting a nucleic acid sample with a plurality of target specific primers or adapters capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; ligating the digested target amplicons or repairing the digested target amplicons; and amplifying the ligated or repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the reactions further comprise target specific primers that are not capable of completely processing the workflow, resulting in non-useful amplicon production and thereby blocking selected target sequences, e.g., those present in high abundance in the sample. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences, which are optimized for detection of low frequency target sequences.
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公开(公告)号：US11739316B2
公开(公告)日：2023-08-29
申请号：US16908567
申请日：2020-06-22
发明人： Arvydas Lubys , Inga Cikotiene , Zana Kapustina , Arturas Berezniakovas , Justina Medziune , Simona Zeimyte , Mark Andersen , Michael Allen , Sihong Chen
IPC分类号： C12N15/10 , C12N15/115 , C12Q1/6806
CPC分类号： C12N15/1065 , C12N15/115 , C12Q1/6806 , C12N2310/3517
摘要： The present disclosure describes oligonucleotide-tethered nucleotides, methods of making them, and methods of using them. The oligonucleotide-tethered nucleotides comprise, in some embodiments, a nucleotide linked to an oligonucleotide of from about 3 to about 100 nucleotides in length. These oligonucleotide-tethered nucleotides can be used to label a plurality of different types of nucleic acids in a plurality of different situations with a known oligonucleotide, which can serve as a barcode in some embodiments. The resulting oligonucleotide-labeled nucleic acids oligonucleotides can be used in a variety of nucleic acid sequencing methods.
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公开(公告)号：US10829811B2
公开(公告)日：2020-11-10
申请号：US15965595
申请日：2018-04-27
发明人： John Leamon , Mark Andersen , Michael Thornton
IPC分类号： C12Q1/686 , C12Q1/6806 , C12Q1/6855 , C12N15/10 , C12Q1/6886 , C12Q1/6874
摘要： The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
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公开(公告)号：US11130984B2
公开(公告)日：2021-09-28
申请号：US16846932
申请日：2020-04-13
发明人： Mark Andersen , Steven Roman
IPC分类号： C12Q1/6806 , C12Q1/6853 , C07H21/00
摘要： The present invention provides methods, compositions, kits, systems and apparatus that are useful for isolating nucleic acid molecules from a sample. In particular, the methods generally relate to normalizing the concentration of target nucleic acid molecules from a sample. In one aspect, the invention relates to purifying a primer extension product from a primer extension reaction mixture. In some aspects, nucleic acid molecules obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing.
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公开(公告)号：US10266881B2
公开(公告)日：2019-04-23
申请号：US14796400
申请日：2015-07-10
发明人： John Leamon , Mark Andersen , Michael Thornton
IPC分类号： C12Q1/68 , C12Q1/6855 , C12Q1/6806 , C07H21/04
摘要： The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
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公开(公告)号：US09957552B2
公开(公告)日：2018-05-01
申请号：US14829297
申请日：2015-08-18
发明人： Mark Andersen , Steven Roman
CPC分类号： C12Q1/6806 , C07H21/00 , C12Q1/6853 , C12Q2525/301 , C12Q2527/107 , C12Q2563/131 , C12Q2563/149
摘要： The present invention provides methods, compositions, kits, systems and apparatus that are useful for isolating nucleic acid molecules from a sample. In particular, the methods generally relate to normalizing the concentration of target nucleic acid molecules from a sample. In one aspect, the invention relates to purifying a primer extension product from a primer extension reaction mixture. In some aspects, nucleic acid molecules obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing.
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公开(公告)号：US09885076B2
公开(公告)日：2018-02-06
申请号：US14796696
申请日：2015-07-10
发明人： John Leamon , Mark Andersen , Michael Thornton
CPC分类号： C12Q1/686 , C12N15/1065 , C12Q1/6806 , C12Q1/6855 , C12Q1/6874 , C12Q1/6886 , C12Q2600/16 , C12Q2521/307 , C12Q2525/101 , C12Q2525/191 , C12Q2537/143
摘要： The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
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