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：US20230360726A1

公开(公告)日：2023-11-09

申请号：US18130134

申请日：2023-04-03

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Earl HUBBELL ,  Sowmi UTIRAMERUR

IPC: C12Q1/6874 ,  C12Q1/6869 ,  G16B20/20 ,  G16B30/00 ,  G16B40/00

CPC classification number: G16B20/20 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B30/00 ,  G16B40/00

Abstract: A method comprises receiving an ensemble of sequencing reads based on measurements from a plurality of microwells of a sensor array; assigning measured values to the ensemble of sequencing reads; calculating model-predicted values utilizing a predictive model of nucleotide incorporations resulting from flows of nucleotide species according to a predetermined order; modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands, the modifying based on variations between model-predicted values for different hypothesized sequences obtained using the predictive model of nucleotide incorporations resulting from the flows of nucleotide species according to the predetermined order; calculating a measurement confidence value for each read in the ensemble of sequencing reads, the confidence value representing variations between the measured values and the modified model-predicted values; and identifying a plurality of reads in the ensemble as corresponding to a variant sequence.

公开(公告)号：US20230340585A1

公开(公告)日：2023-10-26

申请号：US18152813

申请日：2023-01-11

Applicant: Life Technologies Corporation

Inventor： Sameh El-Difrawy

IPC: C12Q1/6869 ,  C12Q1/6809 ,  C12Q1/6886 ,  G16B50/00 ,  G16B40/20 ,  G16B20/00

CPC classification number: C12Q1/6869 ,  C12Q1/6809 ,  C12Q1/6886 ,  G16B50/00 ,  G16B40/20 ,  G16B20/00 ,  C12Q2600/156

Abstract: Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

公开(公告)号：US20230314369A1

公开(公告)日：2023-10-05

申请号：US18108471

申请日：2023-02-10

Applicant: LIFE TECHNOLOGIES CORPORATION ,  INTEGENX INC.

Inventor： Jen-Kuei LIU ,  Bharti SOLANKI ,  Hans Michael WENZ ,  Frank MERCER ,  Cevat AKIN ,  Achim KARGER ,  Annelise BARRON ,  Scott MACK

IPC: G01N27/447 ,  C08L33/26

CPC classification number: G01N27/44747 ,  C08L33/26 ,  C08L2203/02 ,  C08L2205/025

Abstract: Provided herein is an electrophoresis separation medium comprising: (a) a non-crosslinked or sparsely cross-linked polymer or copolymer; (b) one or more denaturant compounds, in an amount sufficient to inhibit re-naturation of single stranded polynucleotides; (c) an aqueous solvent; (d) optionally, a wall-coating material suited to inhibition of electroosmotic flow; and (e) optionally, an organic water miscible solvent such as DMSO or acetonitrile, wherein the electrophoresis separation medium exhibits functional stability for at least seven days at 23° C.
Also provided herein are sieving compositions, including polymer-based sieving compositions, for molecular sieving as well as related kits, devices and methods of use. Such compositions can be useful for separation of biomolecules such as nucleic acids, proteins, glycoproteins and glycans.

公开(公告)号：US20230307095A1

公开(公告)日：2023-09-28

申请号：US18191477

申请日：2023-03-28

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Christian KOLLER ,  Marcin SIKORA ,  Peter VANDER HORN

IPC: G16B40/10 ,  G16B5/00 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00

CPC classification number: G16B40/10 ,  G16B5/00 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  C12Q1/6869

Abstract: A method for nucleic acid sequencing includes receiving nucleic acid sequencing data from a sequencing instrument that receives and processes a sample nucleic acid in a sequencing-by-synthesis process. The method also includes generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for candidate sequences using a simulation framework. The simulation framework incorporates an estimated carry forward rate (CFR), an estimated incomplete extension rate (IER), an estimated droop rate (DR), an estimated reactivated molecules rate (RMR), and an estimated termination failure rate (TFR), the RMR being greater than or equal to zero and the TFR being lesser than one. The method also includes identifying, from the set of candidate sequences of bases, a candidate sequence as corresponding to the sequence for the sample nucleic acid.

公开(公告)号：US11768156B2

公开(公告)日：2023-09-26

申请号：US17936947

申请日：2022-09-30

Applicant: Life Technologies Corporation

Inventor： Kyle Gee ,  Kathleen Kihn ,  Yi-Zhen Hu ,  Yexin Wu ,  Kathleen Free

IPC: G01N21/64 ,  C07D311/82 ,  C07D209/10 ,  C07F15/00 ,  C07F9/24

CPC classification number: G01N21/6486 ,  C07D209/10 ,  C07D311/82 ,  C07F9/2466 ,  C07F15/0093 ,  G01N21/6428

Abstract: Provided herein are compounds, compositions, kits, uses, and methods for assessing the viability of cells and/or quantifying the amount of live and dead cells in a mixture using differential stains. In some embodiments, the compounds are used in culture media or can function independently of fixation and/or permeabilization. In some embodiments, the compounds comprise a platinum atom. In some embodiments, the compounds comprise a nitrogen mustard moiety.

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：US20230221280A1

公开(公告)日：2023-07-13

申请号：US18084587

申请日：2022-12-20

Applicant: Life Technologies Holdings PTE Limited ,  Life Technologies Corporation

Inventor： Beng Heng LIM ,  Wuh Ken LOH ,  Hwee Siong KUAH ,  Jing Han WONG ,  Jefferson Cruz GANGCUANGCO ,  Jin Xin ONG ,  Soo Yong LAU ,  Yanping XU ,  Victor SHAPIRO ,  Zhi Da TEH ,  Chee Woei CHONG ,  Kuan Moon BOO

IPC: G01N27/447

CPC classification number: G01N27/44721

Abstract: A gel electrophoresis system includes a base module and a camera module. The base module includes a cassette slot for receiving a gel electrophoresis cassette, and a light element that functions to illuminate the gel electrophoresis cassette. The camera module is selectively attachable to and detachable from the base module. When attached to the base module, the camera module facilitates imaging of the gel electrophoresis cassette and provides additional imaging capabilities.

公开(公告)号：US20230204537A1

公开(公告)日：2023-06-29

申请号：US18056194

申请日：2022-11-16

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Keith G. Fife ,  Jungwook Yang

IPC: G01N27/414 ,  G06F30/392 ,  G06F30/394

CPC classification number: G01N27/4145 ,  G06F30/392 ,  G06F30/394 ,  G01N27/4148

Abstract: A high data rate integrated circuit, such as an integrated circuit including a large sensor array, may be implemented using clock multipliers in individual power domains, coupled to sets of transmitters, including a transmitter pair configuration. Reference clock distribution circuitry on the integrated circuit distributes a relatively low speed reference clock. In a transmitter pair configuration, each pair comprises a first transmitter and a second transmitter in a transmitter power domain. Also, each pair of transmitters includes a clock multiplier connected to the reference clock distribution circuitry, and disposed between the first and second transmitters, which produces a local transmit clock.

公开(公告)号：US20230193379A1

公开(公告)日：2023-06-22

申请号：US17811192

申请日：2022-07-07

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Vadim Mozhayskiy ,  Yutao FU ,  Earl HUBBELL

IPC: C12Q1/6874 ,  C12Q1/6825 ,  C12N15/10

CPC classification number: C12Q1/6874 ,  C12Q1/6825 ,  C12N15/1058

Abstract: A method for preparing a homopolymer recalibration panel includes: extracting, from a set of amplicons used in sequencing-by-synthesis, a set of candidate amplicons satisfying a first set of criteria, wherein the first set of criteria includes amplicons known to belong to high-confidence regions of a reference genome with no variants; and selecting, from the set of candidate amplicons, a reduced set of amplicons satisfying a second set of criteria, wherein the second set of criteria includes amplicons that together comprise at least a minimal threshold number of homopolymers of each homopolymer length between a predetermined minimal homopolymer length and a predetermined maximal homopolymer length for one or more of homopolymer types A, T, C, and G.