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公开(公告)号:US20230140123A1
公开(公告)日:2023-05-04
申请号:US17899470
申请日:2022-08-30
发明人: Ethan SOKOL , Jay MOORE , Justin NEWBERG , Dexter JIN , Kuei-Ting CHEN , Russell MADISON
IPC分类号: G16B20/20 , C12Q1/6886 , G16B20/10 , G16B40/20
摘要: Described herein are methods, devices, and systems for identifying a subset of a plurality of features, using one or more feature importance metrics, for training and using a homologous repair deficiency (HRD) classification model. Further described are methods, devices, and systems for classifying a tumor of a cancer, such as pancreatic cancer, as likely HRD positive or likely HRD negative, and for calling the tumor as HRD positive or HRD negative. Also described herein are methods of treating a tumor of a cancer, such as pancreatic cancer, based on the classifications
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公开(公告)号:US20220399131A1
公开(公告)日:2022-12-15
申请号:US17885412
申请日:2022-08-10
发明人: Michael PELLINI , Gary PALMER , Mary Patricia LANCELOTTA , Matthew J. HAWRYLUK , Vincent A. MILLER
摘要: Provided are systems and methods for capturing outcome information associated with various cancer treatments. The system facilitates capture and analysis of cancer treatment information and associated outcome information. The treatment and outcome information can include genomic analysis and information on treatment of different cancers. The system can store and analyze any one or more of: tumor type, genomic alterations (e.g., genes and associated alterations, gene sequence mutations, alterations, amplifications, deletions, etc.), and treatment data (including, for example, treatments targeted to specific genes and/or genomic alterations). Users of the outcome system can supply and use the treatment and outcome information to facilitate diagnosis and therapy decisions. User interfaces within the system can be configured to allow users to easily locate outcome information associated with particular treatments of tumors having certain genomic alterations.
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公开(公告)号:US20220396839A1
公开(公告)日:2022-12-15
申请号:US17774452
申请日:2020-11-10
发明人: Dexter X. JIN , Ethan SOKOL , Sally TRABUCCO , Dean PAVLICK , Siraj ALI
IPC分类号: C12Q1/6886 , C12Q1/6806 , C12Q1/6881
摘要: Provided herein are methods for detecting a Ewing sarcoma breakpoint region 1 (EWSR1) fusion gene encoding a neoantigen (e.g., in a patient sample), as well as methods of prognosis and treatment related thereto, in some embodiments, the methods further comprise administering a cancer immunotherapy. In some embodiments, the EWSR1 fusion gene is a fusion gene between EWSR1 and WT1, Fill, ERG, FEV, NR4A3, ATF1, CREB1, CREM, CREB3L/CREB3L2, PA7Z1, NFATC2, KLFI5, C11orf93, ZNF444, PBX1, DDIT3, or TFCP2 that encodes a neoantigen.
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公开(公告)号:US11421265B2
公开(公告)日:2022-08-23
申请号:US16245301
申请日:2019-01-11
发明人: Doron Lipson , Geoffrey Alan Otto , Alexander Nevin Parker , Philip James Stephens , Sean R. Downing , Mima Jarosz , Mikhail G. Shapiro , Roman Yelensky
IPC分类号: C12Q1/6827 , C12Q1/6874 , C12Q1/6886 , G16B20/10 , G16B30/10 , G16B20/20 , G16B20/00 , G16B30/00
摘要: A method of analyzing a tumor sample comprising: (a) acquiring a library comprising a plurality of tumor members from a tumor sample; (b) contacting the library with a bait set to provide selected members; (c) acquiring a read for a subgenomic interval from a tumor member from said library; (d) aligning said read; and (e) assigning a nucleotide value (e.g., calling a mutation) from said read for the preselected nucleotide position, thereby analyzing said tumor sample.
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公开(公告)号:US20220145402A1
公开(公告)日:2022-05-12
申请号:US17535492
申请日:2021-11-24
IPC分类号: C12Q1/6886 , A61K45/06
摘要: Methods and compositions for treating a urothelial and/or a micropapillary carcinoma, such as a micropapillary urothelial carcinoma are disclosed.
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公开(公告)号:US11300570B2
公开(公告)日:2022-04-12
申请号:US16371589
申请日:2019-04-01
发明人: David Fabrizio , Garrett M. Frampton , Priti Hegde , Marcin Kowanetz , David Shames , Philip J. Stephens , James Xin Sun , Roman Yelensky , Wei Zou
IPC分类号: G01N33/574 , C07K16/28 , C12Q1/6886 , A61P35/04 , A61P35/00 , A61K38/17 , A61K39/395 , A61K45/06 , C07K14/705 , A61K39/00
摘要: The present invention provides therapeutic and diagnostic methods and compositions for cancer, for example, lung cancer (e.g., NSCLC), bladder cancer (e.g., UC), kidney cancer (e.g., RCC), breast cancer (e.g., TNBC), or melanoma. The invention provides methods of treating cancer (e.g., lung cancer (e.g., NSCLC), bladder cancer (e.g., UC), kidney cancer (e.g., RCC), breast cancer (e.g., TNBC), or melanoma), methods of determining whether a patient suffering from cancer (e.g., lung cancer (e.g., NSCLC), bladder cancer (e.g., UC), kidney cancer (e.g., RCC), breast cancer (e.g., TNBC), or melanoma) is likely to respond to treatment comprising a PD-L1 axis binding antagonist, methods of predicting responsiveness of a patient suffering from cancer (e.g., lung cancer (e.g., NSCLC), bladder cancer (e.g., UC), kidney cancer (e.g., RCC), breast cancer (e.g., TNBC), or melanoma) to treatment comprising a PD-L1 axis binding antagonist, and methods of selecting a therapy for a patient suffering from cancer (e.g., lung cancer (e.g., NSCLC), bladder cancer (e.g., UC), kidney cancer (e.g., RCC), breast cancer (e.g., TNBC), or melanoma), based on a tissue tumor mutational burden (tTMB) score, which reflects somatic mutation levels of genes in a tumor tissue sample obtained from the patient, alone or in combination with PD-L1 expression levels (e.g., PD-L1 expression levels in tumor or tumor-infiltrating immune cells in a tumor sample (tumor area) obtained from the patient).
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公开(公告)号:US11286532B2
公开(公告)日:2022-03-29
申请号:US15877035
申请日:2018-01-22
发明人: Maureen T. Cronin , Garrett Michael Frampton , Doron Lipson , Vincent A. Miller , Gary Palmer , Jeffrey S. Ross , Philip James Stephens , Roman Yelensky
IPC分类号: C12Q1/6886 , A61K31/565 , A61K31/4196 , A61K31/675 , A61K31/439 , A61K31/567 , A61K31/416 , A61K31/423 , A61K31/428 , A61K31/437 , A61K31/4439 , A61K31/472 , A61K31/536 , A61K31/5415 , A61K45/06 , C07K14/72 , C07K16/28 , A61K31/436
摘要: Novel mutant ESR1 molecules and uses are disclosed.
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公开(公告)号:US11158425B2
公开(公告)日:2021-10-26
申请号:US14463068
申请日:2014-08-19
发明人: Helena Futscher de Deus , Rachel Lauren Erbach , Ronald David Collette , Alexander N. Parker , Michael Pellini , Gary Palmer , Mary Pat Lancelotta , Matthew J. Hawryluk , Philip James Stephens , Eric Karl Neumann
摘要: Various embodiments provide interfaces to access genomic testing information and incorporate it into daily physician practice. According to one aspect, a graph-based data model is used that may be used to organizes and revise precision medicine knowledge. In one example structure, gene states are abstracted into alteration groups, where alteration groups are built using reverse engineering actionable information and storing that information within the graph-based data structure. Volumes of genomic alterations and associated information (e.g., journal articles, clinical trial information, therapies, etc.) are analyzed and synthesized into actionable information items viewable on an alteration system in a graph-based data format. According to one embodiment, the system can be configured to focus practitioners on discrete portions of the alteration information on which they can act. According to other aspects, curated information is provided on the system to enable practitioners to make informed decisions regarding the implications of the presence of specific genomic alterations.
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公开(公告)号:US20210283134A1
公开(公告)日:2021-09-16
申请号:US17204830
申请日:2021-03-17
发明人: Siraj Mahamed ALI , Matthew J. HAWRYLUK , Jie HE , Doron LIPSON , Vincent A. MILLER , Jeffrey S. ROSS , Philip James STEPHENS
IPC分类号: A61K31/5025 , C12N9/12 , A61K31/4412 , A61K45/06 , A61K31/47 , A61K31/435 , A61K31/506 , A61K31/519 , A61K31/4439 , A61K31/53 , A61K31/404 , A61K31/5383 , A61K31/498 , A61K31/496 , A61K31/517 , C12Q1/6886 , A61K31/553 , C07K14/705 , C07K14/71 , C07K16/40 , C12N15/113 , C12Q1/6883 , G01N33/573
摘要: Methods and compositions for treating cholangiocarcinoma.
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公开(公告)号:US11098368B2
公开(公告)日:2021-08-24
申请号:US15978701
申请日:2018-05-14
发明人: Maureen T. Cronin , Doron Lipson , Roman Yelensky
IPC分类号: C12Q1/6886 , C07K14/47 , C12N9/12 , A61K31/4545 , C07K16/40 , G01N33/50 , G01N33/574 , A61K38/00
摘要: Novel ALK and NTRK1 fusion molecules and uses are disclosed.
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