公开(公告)号：US11901044B2

公开(公告)日：2024-02-13

申请号：US16739784

申请日：2020-01-10

申请人： KONINKLIJKE PHILIPS N.V.

发明人： Helen Cecile van Aggelen

IPC分类号： G16B40/10 ,  C12Q1/6869 ,  G06F12/0853 ,  G16B50/30 ,  G16B30/00

CPC分类号： G16B40/10 ,  C12Q1/6869 ,  G06F12/0853 ,  G16B30/00 ,  G16B50/30

摘要： A method for characterizing a sample comprising genetic information, comprising: (i) receiving a plurality of sequencing signals from a sequencing operation for a sample, each of the plurality of sequencing signals representing a genetic sequence; (ii) setting, based on a received sequencing signal, a bit within a bit array to a first value for the received sequencing signal, wherein a set of one or more bits is associated with a unique received sequencing signal; (iii) calculating a rate of change of bits within the bit array as new sequencing signals are received; (iv) comparing the rate of change to a predetermined threshold; and (v) identifying the sequencing operation as insufficient if the rate of change is at or above the predetermined threshold, or identifying the sequencing operation as sufficient if the rate of change is at or below the predetermined threshold.

公开(公告)号：US11901043B2

公开(公告)日：2024-02-13

申请号：US16185987

申请日：2018-11-09

申请人： National Cancer Center ,  MITSUI KNOWLEDGE INDUSTRY CO., LTD. ,  SYSMEX CORPORATION

发明人： Mamoru Kato ,  Hideya Kuwabara ,  Tomohiro Sakuma ,  Fumio Inoue ,  Kenichiro Suzuki

IPC分类号： G16B20/20 ,  C12Q1/6827 ,  C12Q1/6869 ,  G16B30/00 ,  G16B30/10 ,  G16B50/20 ,  G16B50/30 ,  G16B20/10 ,  G16B30/20 ,  G16B20/00

CPC分类号： G16B20/20 ,  C12Q1/6827 ,  C12Q1/6869 ,  G16B20/10 ,  G16B30/00 ,  G16B30/10 ,  G16B30/20 ,  G16B50/20 ,  G16B50/30 ,  G16B20/00 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2537/165 ,  C12Q1/6827 ,  C12Q2535/122 ,  C12Q2537/165

摘要： Disclosed is a sequence analysis method for analyzing nucleic acid sequence, the sequence analysis method including: obtaining a plurality of read sequences read from the nucleic acid sequence; and determining each nucleic acid sequence by aligning each read sequence with reference to a single reference sequence, wherein the reference sequence includes at least a first rearrangement sequence and a second rearrangement sequence that is different from the first rearrangement sequence.

公开(公告)号：US11901042B2

公开(公告)日：2024-02-13

申请号：US15976956

申请日：2018-05-11

申请人： Thuraiayah Vinayagamoorthy

发明人： Thuraiayah Vinayagamoorthy

IPC分类号： G16B20/20 ,  C12Q1/6886 ,  G16B5/00 ,  G16B10/00 ,  G16B15/00 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  G16B35/00 ,  G16B40/00 ,  G16B45/00 ,  G16B50/00

CPC分类号： G16B20/20 ,  C12Q1/6886 ,  G16B5/00 ,  G16B10/00 ,  G16B15/00 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  G16B35/00 ,  G16B40/00 ,  G16B45/00 ,  G16B50/00 ,  C12Q2600/154 ,  C12Q2600/156

摘要： Somatic mutations are associated with cancer progression and treatment using targeted therapies. Somatic mutations are not inherited and could be present at low concentrations in biopsy samples. Hence, there is a need for more sensitive assays to detect these changes in the presence of heterogeneous cell populations. The efficacy of such detection is determined by two factors; the ability to detect a minimum number of copies of the target mutation in the sample (Lower limit of detection), and the ratio of target mutation to that of wild-type in the sample (Tumor content). A new algorithm Detection Index (DI) is formulated to evaluate the efficacy of detection for a molecular testing method.

公开(公告)号：US20240047005A1

公开(公告)日：2024-02-08

申请号：US18221440

申请日：2023-07-13

申请人： KYUSHU UNIVERSITY, NATIONAL UNIVERSITY CORPORATION

发明人： Takahiro NAKAMURA ,  Yusuke Yagi ,  Keiko Kobayashi

IPC分类号： G16B15/00 ,  G16B30/00 ,  G16B35/00 ,  G16C20/60 ,  C07K14/415 ,  C12N15/82 ,  G16B20/50 ,  G16B20/30 ,  G16B30/10 ,  C12Q1/68 ,  G01N33/53

CPC分类号： G16B15/00 ,  G16B30/00 ,  G16B35/00 ,  G16C20/60 ,  C07K14/415 ,  C12N15/8216 ,  C12N15/8289 ,  G16B20/50 ,  G16B20/30 ,  G16B30/10 ,  C12Q1/68 ,  G01N33/5308 ,  C12N15/8287 ,  G16B20/00

摘要： A method for designing a protein capable of binding in an RNA base selective manner or RNA base sequence specific manner is provided. The protein of the present invention is a protein containing one or more of PPR motifs (preferably 2 to 14 PPR motifs) each consisting of a polypeptide of 30- to 38-amino acid length represented by the formula 1 (wherein Helix A is a moiety of 12-amino acid length capable of forming an α-helix structure, and is represented by the formula 2, wherein, in the formula 2, A1 to A12 independently represent an amino acid; X does not exist, or is a moiety of 1- to 9-amino acid length; Helix B is a moiety of 11- to 13-amino acid length capable of forming an α-helix structure; and L is a moiety of 2- to 7-amino acid length represented by the formula 3, wherein, in the formula 3, the amino acids are numbered “i” (−1), “ii” (−2), and so on from the C-terminus side, provided that Liii to Lvii may not exist), and combination of three amino acids A1, A4 and Lii, or combination of two amino acids A4, and Lii is a combination corresponding to a target RNA base or base sequence.

公开(公告)号：US20240043923A1

公开(公告)日：2024-02-08

申请号：US18313716

申请日：2023-05-08

申请人： Karius, Inc.

发明人： Fred C. Christians ,  Igor D. Vilfan ,  Michael Kertesz ,  Timothy A. Blauwkamp ,  Shivkumar Venkatasubrahmanyam ,  Michael Rosen ,  Rene Sit

IPC分类号： C12Q1/6874 ,  G16B30/00 ,  C12Q1/6869 ,  G16B30/10 ,  C12N15/10 ,  C12Q1/689

CPC分类号： C12Q1/6874 ,  G16B30/00 ,  C12Q1/6869 ,  G16B30/10 ,  C12N15/1065 ,  C12Q1/689 ,  C12Q2600/166

摘要： This disclosure provides methods for determining relative abundance of one or more non-host species in a sample from a host. Also provided are methods involving addition of known concentrations of synthetic nucleic acids to a sample and performing sequencing assays to identify non-host species such as pathogens. Also provided are methods of tracking samples, tracking reagents, and tracking diversity loss in sequencing assays.

公开(公告)号：US20240043907A1

公开(公告)日：2024-02-08

申请号：US18366149

申请日：2023-08-07

申请人： Waters Technologies Corporation

发明人： Martin Gilar ,  Catalin Doneanu ,  Matthew A. Lauber ,  Mame Maissa Gaye

IPC分类号： C12Q1/6806 ,  G16B30/00

CPC分类号： C12Q1/6806 ,  G16B30/00

摘要： The present disclosure describes methods, kits, and systems for digesting polyribonucleotides. The method involves selectively forming oligonucleotide (e.g., DNA:RNA or RNA:RNA) duplexes with single-stranded target RNA and then using sequence-specific nucleases that only act on RNA within duplexes to selectively cleave the target RNA into smaller fragments. Additional sequence-specific ribonucleases may be used to provide additional cuts of the target RNA at predetermined sites. By forming duplexes to increase the availability of nucleases that may be applied to cleave the single-stranded target RNA and selectively control where the target RNA is cleaved, the target RNA may be digested into fragments within controllable size ranges that are optimal for polynucletide analysis, such as by liquid chromatography and mass spectrometry.

公开(公告)号：US11887699B2

公开(公告)日：2024-01-30

申请号：US17932706

申请日：2022-09-16

申请人： LIFE TECHNOLOGIES CORPORATION

发明人： Cheng-Zong Bai

IPC分类号： G06F7/00 ,  G16B50/50 ,  H03M7/30 ,  G16B50/00 ,  G16B30/00 ,  G16B40/00 ,  G16B20/00 ,  G16B40/10 ,  G16B20/20 ,  G16B20/40 ,  C12Q1/6869 ,  G16B30/10

CPC分类号： G16B50/50 ,  G16B20/00 ,  G16B20/20 ,  G16B20/40 ,  G16B30/00 ,  G16B40/00 ,  G16B40/10 ,  G16B50/00 ,  H03M7/70 ,  C12Q1/6869 ,  G16B30/10 ,  C12Q1/6869 ,  C12Q2537/165

摘要： A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

公开(公告)号：US11881287B2

公开(公告)日：2024-01-23

申请号：US17161870

申请日：2021-01-29

申请人： PRECISIONLIFE LTD

发明人： Stephen Philip Gardner ,  Gert Lykke Sørensen Moller

IPC分类号： G16B40/20 ,  G16H10/40 ,  G16H20/00 ,  G06N5/00 ,  G06N5/02 ,  G16B30/00 ,  G16H50/30 ,  G06N5/022 ,  G06N5/01

CPC分类号： G16B40/20 ,  G06N5/01 ,  G06N5/022 ,  G16B30/00 ,  G16H10/40 ,  G16H20/00 ,  G16H50/30

摘要： There is provided a method for using a control apparatus to process one or more data inputs in a computing arrangement to provide one or more outputs comprising at least one of control outputs, analysis outputs, or recommendation outputs. The control apparatus is configured to execute real-time computing for a multi-dimensional system model spanned by state variables on one or more of finite domains or intervals. The one or more data inputs include one or more physical measurands of a system, and the one or more outputs provide a technical modification of the system. The method includes:



providing a system model in which all valid combinations and associated properties or object functions are stored as interconnected relations distributed on one or more computers; and
deducing one or more of:
(i) any sub-space, corresponding to an input statement of states or combinations spanned by one or more state variable or associated properties or object functions, by deriving consequences of the input statement by applying constraints defined by the input statement to the system model; or
(ii) any sub-space, corresponding to a query, of states or combinations spanned by one or more state variables or associated properties or object functions, by deriving consequences of the query by applying constraints defined by the query to the system model.

公开(公告)号：US11879158B2

公开(公告)日：2024-01-23

申请号：US17696524

申请日：2022-03-16

申请人： GUARDANT HEALTH, INC.

发明人： AmirAli Talasaz

IPC分类号： C12P19/34 ,  C12Q1/6886 ,  C12N15/10 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B30/00 ,  G16B30/10

CPC分类号： C12Q1/6886 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B30/00 ,  G16B30/10 ,  C12Q2600/118 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16 ,  C12Q1/6869 ,  C12Q2537/165 ,  C12Q2545/114

摘要： The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

公开(公告)号：US20240018581A1

公开(公告)日：2024-01-18

申请号：US18197641

申请日：2023-05-15

申请人： Massachusetts Institute of Technology

发明人： Philip Fremont-Smith ,  Chelsea Lynn Lennartz ,  Natalie Damaso

IPC分类号： C12Q1/6869 ,  G16B20/20 ,  G16B40/10 ,  G16B30/00

CPC分类号： C12Q1/6869 ,  G16B20/20 ,  G16B40/10 ,  G16B30/00

摘要： This patent application relates generally to mixture deconvolution systems and methods for identifying DNA profiles. Various embodiments of the present invention concern the deconvolution of unknown DNA profiles in a two-person DNA mixture into two DNA profiles. Deconvolution methods isolate distinct DNA profiles from a DNA mixture without the need to match against DNA reference profiles. Various embodiments include a mixture deconvolution pipeline that involves a series of mathematical steps and machine learning algorithms to achieve the desired performance and decision-support outputs. Various embodiments enable distant familial matching to existing investigative genetic genealogy (IGG; also known as forensic genetic genealogy (FGG)) databases. This capability enables the generation of investigative leads from unresolved casework samples (i.e., DNA mixtures) by identifying possible genealogical relationships to one or more person(s) of interest. Such aspects may be performed in association with one or more systems used for genetic identification.