公开(公告)号：US20240360516A1

公开(公告)日：2024-10-31

申请号：US18285435

申请日：2022-04-05

申请人： Peter MacCallum Cancer Institute

发明人： Sarah-Jane DAWSON ,  Mark Agnel Frederick DAWSON ,  Sandunie Dineika CHANDRANANDA ,  Paul Sung-Hao YEH

IPC分类号： C12Q1/6886 ,  C12Q1/6869

CPC分类号： C12Q1/6886 ,  C12Q1/6869 ,  C12Q2600/112 ,  C12Q2600/158 ,  G01N2800/52

摘要： The present disclosure relates generally to methods for the analysis of gene expression. In particular, the methods of the present disclosure are based on the measurement of gene expression from fragments of cell-free DNA (cfDNA), which is useful in non-invasive methods for monitoring disease status in cancer patients and in methods for the treatment of cancer patients.

公开(公告)号：US12119087B2

公开(公告)日：2024-10-15

申请号：US17574260

申请日：2022-01-12

申请人： ULTIMA GENOMICS, INC.

发明人： Mark Pratt ,  Gilad Almogy ,  Avishai Bartov

IPC分类号： G16B40/10 ,  C12Q1/6806 ,  C12Q1/6869 ,  G16B30/10 ,  G16B45/00

CPC分类号： G16B40/10 ,  C12Q1/6806 ,  C12Q1/6869 ,  G16B30/10 ,  G16B45/00

摘要： The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.

公开(公告)号：US12116627B2

公开(公告)日：2024-10-15

申请号：US17034024

申请日：2020-09-28

申请人： Tsinghua University

发明人： Ting Zhu ,  Xianyu Liu ,  Wenjun Jiang ,  Min Wang

IPC分类号： C12Q1/6869 ,  C12N15/10 ,  C12Q1/6806

CPC分类号： C12Q1/6869 ,  C12N15/1096 ,  C12Q1/6806

摘要： Methods of sequencing and producing nucleic acid sequences are provided. Accordingly there are provided methods of sequencing a nucleic acid sequence comprising L-nucleotides comprising subjecting the nucleic acid sequence comprising the L-nucleotides to a chemical sequencing method. Also provided is a method of reverse transcribing a ribose nucleic acid sequence into a deoxyribose nucleic acid sequence comprising catalyzing reverse transcription of the ribose nucleic acid sequence with a Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4).

公开(公告)号：US20240336965A1

公开(公告)日：2024-10-10

申请号：US18601772

申请日：2024-03-11

申请人： THE J. DAVID GLADSTONE INSTITUTES, A TESTAMENTARY TRUST ESTABLISHED UNDER THE WI ,  The Regents of the University of California ,  The Board of Trustees of the Leland Stanford Junior University

发明人： Vijay Ramani ,  Ke Wu ,  Hani Goodarzi ,  Arjun Scott Nanda ,  Sivakanthan Kasinathan

IPC分类号： C12Q1/6869 ,  C12N15/10 ,  C12Q1/44 ,  C12Q1/48 ,  C12Q1/6806

CPC分类号： C12Q1/6869 ,  C12N15/1065 ,  C12Q1/44 ,  C12Q1/485 ,  C12Q1/6806 ,  C12Q2600/154 ,  G01N2333/91245 ,  G01N2333/922

摘要： Methods are provided that implement tagmentation for single-molecule sequencing use 90-99% less input than current protocols: SMRT-Tag, which allows detection of genetic variation and CpG methylation, and SAMOSA-Tag, which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SAMOSA-Tag of 30,000-50,000 nuclei resolved single-fiber chromatin structure, CTCF binding, and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization.

公开(公告)号：US12111261B2

公开(公告)日：2024-10-08

申请号：US18330295

申请日：2023-06-06

申请人： Quantum-Si Incorporated

发明人： Jonathan M. Rothberg ,  Keith G. Fife ,  David M. Boisvert

IPC分类号： G01N21/64 ,  C12Q1/6869 ,  G01S7/4865 ,  H01L27/146 ,  H01L27/148 ,  H04N25/77

CPC分类号： G01N21/6428 ,  C12Q1/6869 ,  G01N21/64 ,  G01N21/6408 ,  G01S7/4865 ,  H01L27/14603 ,  H01L27/14612 ,  H01L27/14643 ,  H01L27/14687 ,  H01L27/14689 ,  H01L27/14812 ,  H04N25/77 ,  G01N21/6458

摘要： An integrated circuit includes a photodetection region configured to receive incident photons. The photodetection region is configured to produce a plurality of charge carriers in response to the incident photons. The integrated circuit includes at least one charge carrier storage region. The integrated circuit also includes a charge carrier segregation structure configured to selectively direct charge carriers of the plurality of charge carriers directly into the at least one charge carrier storage region based upon times at which the charge carriers are produced.

公开(公告)号：US20240327901A1

公开(公告)日：2024-10-03

申请号：US18653222

申请日：2024-05-02

申请人： President and Fellows of Harvard College

发明人： George M. Church ,  Evan R. Daugharthy ,  Richard C. Terry ,  Benjamin W. Pruitt ,  Brian M. Turczyk

IPC分类号： C12Q1/6832 ,  C12N15/10 ,  C12Q1/6806 ,  C12Q1/6816 ,  C12Q1/6844 ,  C12Q1/6869 ,  C12Q1/6874

CPC分类号： C12Q1/6832 ,  C12N15/1065 ,  C12N15/1093 ,  C12Q1/6806 ,  C12Q1/6816 ,  C12Q1/6844 ,  C12Q1/6869 ,  C12Q1/6874

摘要： The present disclosure provides a number of targeted nucleic acid FISSEQ library construction methods. Targeted FISSEQ can exhibit several benefits, such as enhanced sensitivity and/or shorter assay time in the detection, identification, quantification, and/or determining the nucleotide sequence of the target species, relative to “random” or “whole-omic” detection via FISSEQ.

公开(公告)号：US12106829B2

公开(公告)日：2024-10-01

申请号：US18352029

申请日：2023-07-13

申请人： Illumina, Inc.

发明人： Anindita Dutta ,  Gery Vessere ,  Dorna KashefHaghighi ,  Kishore Jaganathan ,  Amirali Kia

IPC分类号： G06N3/08 ,  G16B30/20 ,  G16B40/10 ,  C12Q1/6869

CPC分类号： G16B40/10 ,  G06N3/08 ,  G16B30/20 ,  C12Q1/6869

摘要： The technology disclosed relates to artificial intelligence-based base calling. The technology disclosed relates to accessing a progression of per-cycle analyte channel sets generated for sequencing cycles of a sequencing run, processing, through a neural network-based base caller (NNBC), windows of per-cycle analyte channel sets in the progression for the windows of sequencing cycles of the sequencing run such that the NNBC processes a subject window of per-cycle analyte channel sets in the progression for the subject window of sequencing cycles of the sequencing run and generates provisional base call predictions for three or more sequencing cycles in the subject window of sequencing cycles, from multiple windows in which a particular sequencing cycle appeared at different positions, using the NNBC to generate provisional base call predictions for the particular sequencing cycle, and determining a base call for the particular sequencing cycle based on the plurality of base call predictions.

公开(公告)号：US20240321395A1

公开(公告)日：2024-09-26

申请号：US18124670

申请日：2023-03-22

申请人： Helix, Inc.

发明人： Dana Wyman ,  Tracy Basler ,  Andrew Dei Rossi ,  Shishi Luo ,  William Lee ,  Efren Sandoval

IPC分类号： G16B30/00 ,  C12Q1/6869 ,  G16B20/00

CPC分类号： G16B30/00 ,  C12Q1/6869 ,  G16B20/00

摘要： Various embodiments disclosed relate to a method of quality control for a biological sample. The method can include receiving genetic data sequenced from the biological sample, determining whether an endogenous control is apparent in the genetic data, and in the event that the endogenous control is apparent in the genetic data, determining whether the biological sample is contaminated. The genetic data can be analyzed for sequences from both pathogen genetic material and mitochondrial genetic material. The endogenous control can be determined based on whether at least a threshold amount of the genetic data includes sequences for the mitochondrial genetic material.

公开(公告)号：US20240318246A1

公开(公告)日：2024-09-26

申请号：US18616750

申请日：2024-03-26

申请人： AXBIO INC.

发明人： Hui TIAN ,  Igor Constantin IVANOV ,  Vladimir Ivanovich BASHKIROV

IPC分类号： C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6855

CPC分类号： C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6855

摘要： The present disclosure provides methods for processing a nucleic acid sample. For example, a method of the present disclosure may simultaneously process two populations of nucleic acid (NA) templates for two different sequencing modalities: (i) a first population comprising circularized NA templates having a size smaller than a size threshold (e.g., smaller than 2 kilobase (kb)), and (ii) a second population comprising uncircularized NA templates having a size greater than or equal to the size threshold.

公开(公告)号：US20240316120A1

公开(公告)日：2024-09-26

申请号：US18628884

申请日：2024-04-08

申请人： The State of Israel, Ministry of Agriculture & Rural Development, Agricultural Research Organization

发明人： Itzhak MIZRAHI ,  Elie JAMI

IPC分类号： A61K35/74 ,  A23K10/18 ,  A23K20/195 ,  A23K50/10 ,  A23K50/60 ,  A61K35/66 ,  C12N1/20 ,  C12Q1/6869 ,  C12Q1/689

CPC分类号： A61K35/74 ,  A23K10/18 ,  A23K20/195 ,  A23K50/10 ,  A23K50/60 ,  A61K35/66 ,  C12N1/20 ,  C12Q1/6869 ,  C12Q1/689 ,  C12Q2600/124

摘要： A method of mimicking a phenotype of a first ruminating animal in a second ruminating animal is disclosed. The method comprises administering to the second ruminating animal a microbial composition comprising a plurality of microbes having a signature which is statistically significantly similar to the microbial signature of a rumen microbiome of the first ruminating animal, wherein the first and the second ruminating animal are of identical species, thereby mimicking the phenotype of the first ruminating animal in the second ruminating animal.