公开(公告)号：US20240287502A1

公开(公告)日：2024-08-29

申请号：US18397280

申请日：2023-12-27

Applicant: Thermo Fisher Scientific Baltics UAB ,  Life Technologies Corporation

Inventor： 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: C12N15/10 ,  C12N15/115 ,  C12Q1/6806

CPC classification number: C12N15/1065 ,  C12N15/115 ,  C12Q1/6806 ,  C12N2310/3517

Abstract: 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.

公开(公告)号：US11001836B2

公开(公告)日：2021-05-11

申请号：US16024175

申请日：2018-06-29

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Mark Andersen ,  Daniel Mazur ,  Sihong Chen ,  Guobin Luo ,  Xinzhan Peng

IPC: C12N15/10 ,  C12Q1/6806 ,  C12Q1/6853 ,  C12Q1/6855 ,  C12Q1/686 ,  C40B20/04 ,  C40B50/06 ,  C40B40/06

Abstract: 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.

公开(公告)号：US20240102003A1

公开(公告)日：2024-03-28

申请号：US18345856

申请日：2023-06-30

Applicant: Thermo Fisher Scientific Baltics UAB ,  Life Technologies Corporation

Inventor： Arvydas Lubys ,  Inga Cikotiene ,  Zana Kapustina ,  Arturas Berezniakovas ,  Justina Sulgaite ,  Simona Zeimyte ,  Mark Andersen ,  Michael Allen ,  Sihong Chen

IPC: C12N15/10 ,  C12N15/115 ,  C12Q1/6806

CPC classification number: C12N15/1065 ,  C12N15/115 ,  C12Q1/6806 ,  C12N2310/3517

Abstract: 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.

公开(公告)号：US20230374574A1

公开(公告)日：2023-11-23

申请号：US18340581

申请日：2023-06-23

Applicant: Life Technologies Corporation

Inventor： Michael Allen ,  Mark Andersen

IPC: C12Q1/6858

CPC classification number: C12Q1/6858

Abstract: 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.

公开(公告)号：US11739316B2

公开(公告)日：2023-08-29

申请号：US16908567

申请日：2020-06-22

Applicant: THERMO FISHER SCIENTIFIC BALTICS UAB ,  LIFE TECHNOLOGIES CORPORATION

Inventor： Arvydas Lubys ,  Inga Cikotiene ,  Zana Kapustina ,  Arturas Berezniakovas ,  Justina Medziune ,  Simona Zeimyte ,  Mark Andersen ,  Michael Allen ,  Sihong Chen

IPC: C12N15/10 ,  C12N15/115 ,  C12Q1/6806

CPC classification number: C12N15/1065 ,  C12N15/115 ,  C12Q1/6806 ,  C12N2310/3517

Abstract: 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.

公开(公告)号：US10829811B2

公开(公告)日：2020-11-10

申请号：US15965595

申请日：2018-04-27

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： John Leamon ,  Mark Andersen ,  Michael Thornton

IPC: C12Q1/686 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12N15/10 ,  C12Q1/6886 ,  C12Q1/6874

Abstract: 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.

公开(公告)号：US12065643B2

公开(公告)日：2024-08-20

申请号：US17302674

申请日：2021-05-10

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Mark Andersen ,  Daniel Mazur ,  Sihong Chen ,  Guobin Luo ,  Xinzhan Peng

IPC: C12N15/10 ,  C12Q1/6806 ,  C12Q1/6853 ,  C12Q1/6855 ,  C12Q1/686 ,  C40B40/06 ,  C40B20/04 ,  C40B50/06

CPC classification number: C12N15/1068 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q1/6853 ,  C12Q1/6855 ,  C12Q1/686 ,  C40B20/04 ,  C40B40/06 ,  C40B50/06 ,  C12Q1/6806 ,  C12Q2521/531 ,  C12Q2525/119 ,  C12Q2525/121 ,  C12Q2525/131 ,  C12Q2525/155 ,  C12Q2525/179 ,  C12Q2531/113 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2549/119 ,  C12Q2563/179 ,  C12Q1/6853 ,  C12Q2521/531 ,  C12Q2525/119 ,  C12Q2525/121 ,  C12Q2525/131 ,  C12Q2525/155 ,  C12Q2525/179 ,  C12Q2531/113 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2549/119 ,  C12Q2563/179

Abstract: 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.

公开(公告)号：US11965809B2

公开(公告)日：2024-04-23

申请号：US17525477

申请日：2021-11-12

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Mark Andersen ,  Michael Pallas ,  Haopeng Wang

IPC: C12Q1/6816 ,  C12Q1/686 ,  G01N15/04

CPC classification number: G01N15/04 ,  C12Q1/6816 ,  C12Q1/686 ,  C12Q1/6816 ,  C12Q2563/107 ,  C12Q2563/159 ,  C12Q2565/607 ,  C12Q2565/629

Abstract: A method of aligning a plurality of targets is provided. The method includes generating a plurality of targets. A third phase includes the plurality of targets. The method further includes combining a first phase, a second phase, and the third phase in a volume. The first phase, the second phase, and the third phase are substantially immiscible, and the third phase is in fluid communication with the first phase and the second phase, and the first phase, the second phase, and the third phase are operable to be in a configuration of the third phase between the first phase and the second phase in the volume.

公开(公告)号：US11851703B2

公开(公告)日：2023-12-26

申请号：US16949159

申请日：2020-10-15

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： John Leamon ,  Mark Andersen ,  Michael Thornton

IPC: C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/686 ,  C12N15/10 ,  C12Q1/6886 ,  C12Q1/6874

CPC classification number: C12Q1/686 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6874 ,  C12Q1/6886 ,  C12Q2600/16 ,  C12Q1/6855 ,  C12Q2521/307 ,  C12Q2525/101 ,  C12Q2525/191 ,  C12Q2537/143

Abstract: 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.

公开(公告)号：US11193872B2

公开(公告)日：2021-12-07

申请号：US16222664

申请日：2018-12-17

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Mark Andersen ,  Michael Pallas ,  Haopeng Wang

IPC: C12Q1/6816 ,  G01N15/04 ,  C12Q1/686

Abstract: A method of aligning a plurality of targets is provided. The method includes generating a plurality of targets. A third phase includes the plurality of targets. The method further includes combining a first phase, a second phase, and the third phase in a volume. The first phase, the second phase, and the third phase are substantially immiscible, and the third phase is in fluid communication with the first phase and the second phase, and the first phase, the second phase, and the third phase are operable to be in a configuration of the third phase between the first phase and the second phase in the volume.