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For: Peng H, Lu L, Zhou Z, Liu J, Zhang D, Nan K, Zhao X, Li F, Tian L, Dong H, Yao Y. CNV Detection from Circulating Tumor DNA in Late Stage Non-Small Cell Lung Cancer Patients. Genes (Basel) 2019;10:E926. [PMID: 31739500 DOI: 10.3390/genes10110926] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 01/10/2023] Open

For:	Peng H, Lu L, Zhou Z, Liu J, Zhang D, Nan K, Zhao X, Li F, Tian L, Dong H, Yao Y. CNV Detection from Circulating Tumor DNA in Late Stage Non-Small Cell Lung Cancer Patients. Genes (Basel) 2019;10:E926. [PMID: 31739500 DOI: 10.3390/genes10110926] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 01/10/2023] Open

Number

Cited by Other Article(s)

Grebnev PA, Meshkov IO, Ershov PV, Makhotenko AV, Azarian VB, Erokhina MV, Galeta AA, Zakubanskiy AV, Shingalieva OS, Tregubova AV, Asaturova AV, Yudin VS, Yudin SM, Makarov VV, Keskinov AA, Makarova AS, Snigir EA, Skvortsova VI. Benchmarking of Approaches for Gene Copy-Number Variation Analysis and Its Utility for Genetic Aberration Detection in High-Grade Serous Ovarian Carcinomas. Cancers (Basel) 2024;16:3252. [PMID: 39409874 PMCID: PMC11475927 DOI: 10.3390/cancers16193252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 09/20/2024] [Accepted: 09/21/2024] [Indexed: 10/20/2024] Open

Affiliation(s)

Pavel Alekseevich Grebnev Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Ivan Olegovich Meshkov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Pavel Viktorovich Ershov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Antonida Viktorovna Makhotenko Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Valentina Bogdanovna Azarian Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Marina Vyacheslavovna Erokhina Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anastasiya Aleksandrovna Galeta Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Aleksandr Vladimirovich Zakubanskiy Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Olga Sergeevna Shingalieva Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anna Vasilevna Tregubova Federal State Budgetary Institution “National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov”, Ministry of Healthcare of The Russian Federation, Oparina Street, Bld. 4, 117997 Moscow, Russia; (A.V.T.); (A.V.A.)
Aleksandra Vyacheslavovna Asaturova Federal State Budgetary Institution “National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov”, Ministry of Healthcare of The Russian Federation, Oparina Street, Bld. 4, 117997 Moscow, Russia; (A.V.T.); (A.V.A.)
Vladimir Sergeevich Yudin Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Sergey Mihaylovich Yudin Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Valentin Vladimirovich Makarov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anton Arturovich Keskinov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anna Sergeevna Makarova Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Ekaterina Andreevna Snigir Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Veronika Igorevna Skvortsova Federal Medical Biological Agency (FMBA of Russia), Volokolamskoye Shosse, 30, 123182 Moscow, Russia;

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Lam WKJ, Bai J, Ma MJL, Cheung YTT, Jiang P. Circulating tumour DNA analysis for early detection of lung cancer: a systematic review. ANNALS OF TRANSLATIONAL MEDICINE 2024;12:64. [PMID: 39118954 PMCID: PMC11304429 DOI: 10.21037/atm-23-1572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 01/11/2024] [Indexed: 08/10/2024]

Affiliation(s)

W. K. Jacky Lam Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong, China Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
Jinyue Bai Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong, China Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China
Mary-Jane L. Ma Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong, China Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China
Y. T. Tommy Cheung Department of Pathology, Princess Margaret Hospital, Kwai Chung, Hong Kong, China
Peiyong Jiang Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong, China Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China

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Jiang R, Cheng X, Li P, Meng E, Wu X, Wu H. Plasma circulating tumor DNA unveils the efficacy of PD-1 inhibitors and chemotherapy in advanced gastric cancer. Sci Rep 2024;14:14027. [PMID: 38890392 PMCID: PMC11189402 DOI: 10.1038/s41598-024-63486-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/29/2024] [Indexed: 06/20/2024] Open

Abstract

Programmed Death Receptor 1 (PD-1) inhibitors, when combined with chemotherapy, have exhibited notable effectiveness in enhancing the survival outcomes of patients afflicted with advanced gastric cancer. However, it is important to acknowledge that not all patients derive substantial benefits from this therapeutic approach, highlighting the crucial necessity of identifying efficacious biomarkers to inform immunotherapy interventions. In this study, we sought to investigate the predictive utility of circulating tumor DNA (ctDNA) as a biomarker in a cohort of 30 patients diagnosed with advanced gastric cancer, all of whom underwent first-line treatment involving PD-1 inhibitor administration alongside chemotherapy. We procured peripheral blood samples both at baseline and following the completion of two treatment cycles. Additionally, baseline tissue specimens were collected for the purpose of genomic alteration assessment, employing both 47-gene and 737-gene next-generation sequencing panels for plasma and tumor tissue, respectively. We delineated a ctDNA response as the eradication of maximum variant allele frequencies relative to baseline levels. Notably, the objective response rate among individuals exhibiting a ctDNA response proved significantly superior in comparison to non-responders (P = 0.0073). Furthermore, patients who manifested a ctDNA response experienced markedly prolonged progression-free survival (PFS) and overall survival (OS) when juxtaposed with those devoid of a ctDNA response (median PFS: 15.6 vs. 6.0 months, P = 0.003; median OS: not reached [NR] vs. 9.0 months, P = 0.011). In summation, patients with advanced gastric cancer receiving first-line treatment with PD-1 inhibitors and chemotherapy, dynamic changes in ctDNA can serve as a potential biomarker for predicting treatment efficacy and long-term outcomes.

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Kimura TDC, Scarini JF, Lavareze L, Kowalski LP, Coutinho-Camillo CM, Krepischi ACV, Egal ESA, Altemani A, Mariano FV. MicroRNA copy number alterations in the malignant transformation of pleomorphic adenoma to carcinoma ex pleomorphic adenoma. Head Neck 2024;46:985-1000. [PMID: 38482546 DOI: 10.1002/hed.27717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 04/10/2024] Open

Li W, Huang X, Patel R, Schleifman E, Fu S, Shames DS, Zhang J. Analytical evaluation of circulating tumor DNA sequencing assays. Sci Rep 2024;14:4973. [PMID: 38424110 PMCID: PMC10904763 DOI: 10.1038/s41598-024-54361-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open

Ye L, Chu X, Ni J, Chu L, Yang X, Zhu Z. NGS-based Tissue-Blood TMB Comparison and Blood-TMB Monitoring in Stage-III Non-Small Cell Lung Cancer Treated with Concurrent Chemoradiotherapy. Cancer Invest 2024;42:165-175. [PMID: 38390854 DOI: 10.1080/07357907.2024.2316297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/05/2024] [Indexed: 02/24/2024]

Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023;25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open

Risinskaya N, Gladysheva M, Abdulpatakhov A, Chabaeva Y, Surimova V, Aleshina O, Yushkova A, Dubova O, Kapranov N, Galtseva I, Kulikov S, Obukhova T, Sudarikov A, Parovichnikova E. DNA Copy Number Alterations and Copy Neutral Loss of Heterozygosity in Adult Ph-Negative Acute B-Lymphoblastic Leukemia: Focus on the Genes Involved. Int J Mol Sci 2023;24:17602. [PMID: 38139431 PMCID: PMC10744257 DOI: 10.3390/ijms242417602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open

Affiliation(s)

Natalya Risinskaya National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Maria Gladysheva National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Abdulpatakh Abdulpatakhov National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Yulia Chabaeva National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Valeriya Surimova National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Olga Aleshina National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Anna Yushkova National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Olga Dubova National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.) Institute of Biodesign and Modeling of Complex Systems, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
Nikolay Kapranov National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Irina Galtseva National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Sergey Kulikov National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Tatiana Obukhova National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Andrey Sudarikov National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
Elena Parovichnikova National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)

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Xu Z, Wang X, Song X, An Q, Wang D, Zhang Z, Ding X, Yao Z, Wang E, Liu X, Ru B, Xu Z, Huang Y. Association between the copy number variation of CCSER1 gene and growth traits in Chinese Capra hircus (goat) populations. Anim Biotechnol 2023;34:1377-1383. [PMID: 35108172 DOI: 10.1080/10495398.2022.2025818] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]

Kwon HJ, Park UH, Goh CJ, Park D, Lim YG, Lee IK, Do WJ, Lee KJ, Kim H, Yun SY, Joo J, Min NY, Lee S, Um SW, Lee MS. Enhancing Lung Cancer Classification through Integration of Liquid Biopsy Multi-Omics Data with Machine Learning Techniques. Cancers (Basel) 2023;15:4556. [PMID: 37760525 PMCID: PMC10526503 DOI: 10.3390/cancers15184556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open

Affiliation(s)

Hyuk-Jung Kwon Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.) Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea
Ui-Hyun Park Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Chul Jun Goh Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Dabin Park Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Yu Gyeong Lim Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Isaac Kise Lee Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.) Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea NGENI Foundation, San Diego, CA 92123, USA
Woo-Jung Do Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Kyoung Joo Lee Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Hyojung Kim Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Seon-Young Yun Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Joungsu Joo Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Na Young Min Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Sunghoon Lee Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
Sang-Won Um Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea;
Min-Seob Lee Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.) Diagnomics, Inc., 5795 Kearny Villa Rd., San Diego, CA 92123, USA

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Hsu R, Benjamin DJ, Nagasaka M. The Development and Role of Capmatinib in the Treatment of MET-Dysregulated Non-Small Cell Lung Cancer-A Narrative Review. Cancers (Basel) 2023;15:3561. [PMID: 37509224 PMCID: PMC10377299 DOI: 10.3390/cancers15143561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open

Gao Z, Huang D, Chen H, Yang Y, An K, Ding C, Yuan Z, Zhai Z, Niu P, Gao Q, Cai J, Zeng Q, Wang Y, Hong Y, Rong W, Huang W, Lei F, Wang X, Chen S, Zhao X, Bai Y, Gu J. Development and validation of postoperative circulating tumor DNA combined with clinicopathological risk factors for recurrence prediction in patients with stage I-III colorectal cancer. J Transl Med 2023;21:63. [PMID: 36717891 PMCID: PMC9887832 DOI: 10.1186/s12967-023-03884-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/10/2023] [Indexed: 01/31/2023] Open

Abstract

BACKGROUND

Circulating tumor DNA (ctDNA) detection following curative-intent surgery could directly reflect the presence of minimal residual disease, the ultimate cause of clinical recurrence. However, ctDNA is not postoperatively detected in ≥ 50% of patients with stage I-III colorectal cancer (CRC) who ultimately recur. Herein we sought to improve recurrence risk prediction by combining ctDNA with clinicopathological risk factors in stage I-III CRC.

METHODS

Two independent cohorts, both consisting of early-stage CRC patients who underwent curative surgery, were included: (i) the discovery cohort (N = 124) with tumor tissues and postoperative plasmas for ctDNA determination; and (ii) the external validation cohort (N = 125) with available ctDNA results. In the discovery cohort, somatic variations in tumor tissues and plasmas were determined via a 733-gene and 127-gene next-generation sequencing panel, respectively.

RESULTS

In the discovery cohort, 17 of 108 (15.7%) patients had detectable ctDNA. ctDNA-positive patients had a significantly high recurrence rate (76.5% vs. 16.5%, P < 0.001) and short recurrence-free survival (RFS; P < 0.001) versus ctDNA-negative patients. In addition to ctDNA status, the univariate Cox model identified pathologic stage, lymphovascular invasion, nerve invasion, and preoperative carcinoembryonic antigen level associated with RFS. We combined the ctDNA and clinicopathological risk factors (CTCP) to construct a model for recurrence prediction. A significantly higher recurrence rate (64.7% vs. 8.1%, P < 0.001) and worse RFS (P < 0.001) were seen in the high-risk patients classified by the CTCP model versus those in the low-risk patients. Receiver operating characteristic analysis demonstrated that the CTCP model outperformed ctDNA alone at recurrence prediction, which increased the sensitivity of 2 year RFS from 49.6% by ctDNA alone to 87.5%. Harrell's concordance index, calibration curve, and decision curve analysis also suggested that the CTCP model had good discrimination, consistency, and clinical utility. These results were reproduced in the validation cohort.

CONCLUSION

Combining postoperative ctDNA and clinical risk may better predict recurrence than ctDNA alone for developing a personalized postoperative management strategy for CRC.

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Affiliation(s)

Zhaoya Gao grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Dandan Huang grid.452694.80000 0004 0644 5625Department of Oncology, Peking University Shougang Hospital, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Hui Chen Medical Affairs, 3D Medicines, Inc., Shanghai, China
Yong Yang grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Ke An grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Changmin Ding grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Zheping Yuan Medical Affairs, 3D Medicines, Inc., Shanghai, China
Zhichao Zhai grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Pengfei Niu grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Qingkun Gao grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Jinping Cai Medical Affairs, 3D Medicines, Inc., Shanghai, China
Qingmin Zeng grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Yanzhao Wang grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Yuming Hong grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Wanshui Rong grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Wensheng Huang grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Fuming Lei grid.452694.80000 0004 0644 5625Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Xiaodong Wang grid.452694.80000 0004 0644 5625Department of Oncology, Peking University Shougang Hospital, Beijing, China ,3grid.11135.370000 0001 2256 9319Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China
Shiqing Chen Medical Affairs, 3D Medicines, Inc., Shanghai, China
Xiaochen Zhao Medical Affairs, 3D Medicines, Inc., Shanghai, China
Yuezong Bai Medical Affairs, 3D Medicines, Inc., Shanghai, China
Jin Gu Department of Gastrointestinal Surgery, Peking University Shougang Hospital, No.9 Jinyuanzhuang Road, Shijingshan District, Beijing, China. .,Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Disease, Peking University Health Science Center, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China. .,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, China. .,Peking University International Cancer Institute, Beijing, China.

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Tyler LC, Le AT, Chen N, Nijmeh H, Bao L, Wilson TR, Chen D, Simmons B, Turner KM, Perusse D, Kasibhatla S, Christiansen J, Dudek AZ, Doebele RC. MET gene amplification is a mechanism of resistance to entrectinib in ROS1+ NSCLC. Thorac Cancer 2022;13:3032-3041. [PMID: 36101520 PMCID: PMC9626307 DOI: 10.1111/1759-7714.14656] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/07/2023] Open

Abstract

BACKGROUND

ROS1 tyrosine kinase inhibitors (TKIs) have demonstrated significant clinical benefit for ROS1+ NSCLC patients. However, TKI resistance inevitably develops through ROS1 kinase domain (KD) modification or another kinase driving bypass signaling. While multiple TKIs have been designed to target ROS1 KD mutations, less is known about bypass signaling in TKI-resistant ROS1+ lung cancers.

METHODS

Utilizing a primary, patient-derived TPM3-ROS1 cell line (CUTO28), we derived an entrectinib-resistant line (CUTO28-ER). We evaluated proliferation and signaling responses to TKIs, and utilized RNA sequencing, whole exome sequencing, and fluorescence in situ hybridization to detect transcriptional, mutational, and copy number alterations, respectively. We substantiated in vitro findings using a CD74-ROS1 NSCLC patient's tumor samples. Last, we analyzed circulating tumor DNA (ctDNA) from ROS1+ NSCLC patients in the STARTRK-2 entrectinib trial to determine the prevalence of MET amplification.

RESULTS

CUTO28-ER cells did not exhibit ROS1 KD mutations. MET TKIs inhibited proliferation and downstream signaling and MET transcription was elevated in CUTO28-ER cells. CUTO28-ER cells displayed extrachromosomal (ecDNA) MET amplification without MET activating mutations, exon 14 skipping, or fusions. The CD74-ROS1 patient samples illustrated MET amplification while receiving ROS1 TKI. Finally, two of 105 (1.9%) entrectinib-resistant ROS1+ NSCLC STARTRK-2 patients with ctDNA analysis at enrollment and disease progression displayed MET amplification.

CONCLUSIONS

Treatment with ROS1-selective inhibitors may lead to MET-mediated resistance. The discovery of ecDNA MET amplification is noteworthy, as ecDNA is associated with more aggressive cancers. Following progression on ROS1-selective inhibitors, MET gene testing and treatments targeting MET should be explored to overcome MET-driven resistance.

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Hassan S, Shehzad A, Khan SA, Miran W, Khan S, Lee YS. Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management. Biomedicines 2022;10:2047. [PMID: 36009594 PMCID: PMC9405989 DOI: 10.3390/biomedicines10082047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 11/20/2022] Open

Ding J, Huang M, Huang B, Peng X, Wu G, Peng C, Zhang H, Mao C, Wu X. Identification of a dysregulated ceRNA network modulated by copy number variation-driven lncRNAs in lung squamous cell carcinoma. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022;63:351-361. [PMID: 36161731 DOI: 10.1002/em.22509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/02/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]

Wang Z, Wang X, Xu Y, Li J, Zhang X, Peng Z, Hu Y, Zhao X, Dong K, Zhang B, Gao C, Zhao X, Chen H, Cai J, Bai Y, Sun Y, Shen L. Mutations of PI3K-AKT-mTOR pathway as predictors for immune cell infiltration and immunotherapy efficacy in dMMR/MSI-H gastric adenocarcinoma. BMC Med 2022;20:133. [PMID: 35443723 PMCID: PMC9022268 DOI: 10.1186/s12916-022-02327-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/09/2022] [Indexed: 12/24/2022] Open

Abstract

BACKGROUND

A significant subset of mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) gastric adenocarcinomas (GAC) are resistant to immune checkpoint inhibitors (ICIs), yet the underlying mechanism remains largely unknown. We sought to investigate the genomic correlates of the density of tumor-infiltrating immune cells (DTICs) and primary resistance to ICI treatment.

METHODS

Four independent cohorts of MSI-H GAC were included: (i) the surgery cohort (n = 175) with genomic and DTIC data, (ii) the 3DMed cohort (n = 32) with genomic and PD-L1 data, (iii) the Cancer Genome Atlas (TCGA) cohort (n = 73) with genomic, transcriptomic, and survival data, and (iv) the ICI treatment cohort (n = 36) with pre-treatment genomic profile and ICI efficacy data.

RESULTS

In the dMMR/MSI-H GAC, the number of mutated genes in the PI3K-AKT-mTOR pathway (NMP) was positively correlated with tumor mutational burden (P < 0.001) and sensitivity to PI3K-AKT-mTOR inhibitors and negatively correlated with CD3⁺ (P < 0.001), CD4⁺ (P = 0.065), CD8⁺ (P = 0.004), and FOXP3⁺ cells (P = 0.033) in the central-tumor rather than invasive-margin area, and the transcription of immune-related genes. Compared to the NMP-low (NMP = 0/1) patients, the NMP-high (NMP ≥ 2) patients exhibited a poorer objective response rate (29.4% vs. 85.7%, P < 0.001), progression-free survival (HR = 3.40, P = 0.019), and overall survival (HR = 3.59, P = 0.048) upon ICI treatment.

CONCLUSIONS

Higher NMP was identified as a potential predictor of lower DTICs and primary resistance to ICIs in the dMMR/MSI-H GAC. Our results highlight the possibility of using mutational data to estimate DTICs and administering the PI3K-AKT-mTOR inhibitor as an immunotherapeutic adjuvant in NMP-high subpopulation to overcome the resistance to ICIs.

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Affiliation(s)

Zhenghang Wang Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
Xinyu Wang Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
Yu Xu Medical Affairs, 3D Medicines, Inc, Shanghai, China
Jian Li Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
Xiaotian Zhang Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
Zhi Peng Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
Yajie Hu Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
Xinya Zhao Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
Kun Dong Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
Bei Zhang Medical Affairs, 3D Medicines, Inc, Shanghai, China
Chan Gao Medical Affairs, 3D Medicines, Inc, Shanghai, China
Xiaochen Zhao Medical Affairs, 3D Medicines, Inc, Shanghai, China
Hui Chen Medical Affairs, 3D Medicines, Inc, Shanghai, China
Jinping Cai Medical Affairs, 3D Medicines, Inc, Shanghai, China
Yuezong Bai Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China
Yu Sun Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China.
Lin Shen Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China.

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Lee JW, Park YS, Choi JY, Chang WJ, Lee S, Sung JS, Kim B, Lee SB, Lee SY, Choi J, Kim YH. Genetic Characteristics Associated With Drug Resistance in Lung Cancer and Colorectal Cancer Using Whole Exome Sequencing of Cell-Free DNA. Front Oncol 2022;12:843561. [PMID: 35402275 PMCID: PMC8987589 DOI: 10.3389/fonc.2022.843561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022] Open

Affiliation(s)

Jong Won Lee Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, South Korea Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
Young Soo Park Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea
Jung Yoon Choi Division of Hematology–Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, South Korea
Won Jin Chang Division of Hematology–Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, South Korea
Soohyeon Lee Division of Hematology–Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, South Korea
Jae Sook Sung Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea
Boyeon Kim Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, South Korea
Saet Byeol Lee Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, South Korea
Sung Yong Lee Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Medical Center, Korea University College of Medicine, Seoul, South Korea
Jungmin Choi Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
Yeul Hong Kim Cancer Research Institute, Korea University College of Medicine, Seoul, South Korea Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, South Korea Division of Hematology–Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, South Korea *Correspondence: Yeul Hong Kim,

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Sturgill EG, Misch A, Lachs R, Jones CC, Schlauch D, Jones SF, Shastry M, Yardley DA, Burris HA, Spigel DR, Hamilton EP, McKenzie AJ. Next-Generation Sequencing of Patients With Breast Cancer in Community Oncology Clinics. JCO Precis Oncol 2022;5:1297-1311. [PMID: 34994634 DOI: 10.1200/po.20.00469] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open

Abstract

PURPOSE

Molecular biomarkers informing disease diagnosis, prognosis, and treatment decisions in patients with breast cancer are being uncovered by next-generation sequencing (NGS) technologies. In this study, we survey how NGS is used for patients with breast cancer in real-world settings with a focus on physician behaviors and sequencing results.

METHODS

We conducted a retrospective analysis of patients with breast cancer who received NGS testing from commercial vendors as part of standard of care from 2014 to 2019. A total of 2,635 NGS reports from 2,316 unique breast cancer patients were assessed. Hormone receptor and human epidermal growth factor receptor 2 statuses were abstracted from patient medical records. Comparative gene amplification and mutation frequencies were analyzed using Pearson's correlation and Lin's concordance statistics.

RESULTS

The number of physicians ordering NGS tests for patients with breast cancer increased more than six-fold from 2014 to 2019. Tissue- and plasma-based tests were ordered roughly equally by 2019, with plasma-based testing ordered most frequently in hormone receptor-positive subtypes. Patients with triple-negative breast cancer were most likely to receive NGS testing. Gene amplifications including ERBB2 were detected less frequently in our real-world data set as compared to previous genomic landscape studies, whereas the opposite was true for gene mutations including ESR1. Pathogenic mutations in the PI3K pathway (38.6%) and DNA damage repair pathway (11.0%) were frequently reported. Alterations were also reported across other cellular pathways.

CONCLUSION

Overall, we found that an increasing number of physicians in community settings are adopting NGS in the care of patients with breast cancer. Discrepancies between our real-world NGS data and previous genomic landscape studies are likely owed to the prevalence of plasma-based testing in community oncology clinics, as the reference data were from tissue-based NGS alone.

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Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer. J Clin Med 2021;10:jcm10194487. [PMID: 34640513 PMCID: PMC8509146 DOI: 10.3390/jcm10194487] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open

Liquid Biopsy Biomarkers for Immunotherapy in Non-Small Cell Lung Carcinoma: Lessons Learned and the Road Ahead. J Pers Med 2021;11:jpm11100971. [PMID: 34683113 PMCID: PMC8540302 DOI: 10.3390/jpm11100971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/26/2022] Open

Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z, Novoradovskaya N, Willey JC, Jones W, Kusko R, Chen G, Madala BS, Blackburn J, Stevanovski I, Bhandari A, Close D, Conroy J, Hubank M, Marella N, Mieczkowski PA, Qiu F, Sebra R, Stetson D, Sun L, Szankasi P, Tan H, Tang LY, Arib H, Best H, Burgher B, Bushel PR, Casey F, Cawley S, Chang CJ, Choi J, Dinis J, Duncan D, Eterovic AK, Feng L, Ghosal A, Giorda K, Glenn S, Happe S, Haseley N, Horvath K, Hung LY, Jarosz M, Kushwaha G, Li D, Li QZ, Li Z, Liu LC, Liu Z, Ma C, Mason CE, Megherbi DB, Morrison T, Pabón-Peña C, Pirooznia M, Proszek PZ, Raymond A, Rindler P, Ringler R, Scherer A, Shaknovich R, Shi T, Smith M, Song P, Strahl M, Thodima VJ, Tom N, Verma S, Wang J, Wu L, Xiao W, Xu C, Yang M, Zhang G, Zhang S, Zhang Y, Shi L, Tong W, Johann DJ, Mercer TR, Xu J. Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Nat Biotechnol 2021;39:1115-1128. [PMID: 33846644 PMCID: PMC8434938 DOI: 10.1038/s41587-021-00857-z] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/15/2021] [Indexed: 02/08/2023]

Affiliation(s)

Ira W Deveson Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
Binsheng Gong Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
Kevin Lai Bioinformatics, Integrated DNA Technologies, Inc., Coralville, IA, USA
Jennifer S LoCoco Illumina, Inc., San Diego, CA, USA
Todd A Richmond Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
Jeoffrey Schageman Clinical Sequencing Division, Thermo Fisher Scientific, Austin, TX, USA
Zhihong Zhang Research and Development, Burning Rock Biotech, Shanghai, China
Natalia Novoradovskaya Agilent Technologies, La Jolla, CA, USA
James C Willey Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, Toledo, OH, USA
Wendell Jones Q2 Solutions - EA Genomics, Morrisville, NC, USA
Rebecca Kusko Immuneering Corporation, Cambridge, MA, USA
Guangchun Chen Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
Bindu Swapna Madala Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
James Blackburn Cancer Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
Igor Stevanovski Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
Ambica Bhandari ResearchDx, Inc., Irvine, CA, USA
Devin Close R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
Jeffrey Conroy OmniSeq, Inc., Buffalo, NY, USA
Michael Hubank NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
Narasimha Marella Cancer Genetics, Inc., Rutherford, NJ, USA
Piotr A Mieczkowski Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
Fujun Qiu Research and Development, Burning Rock Biotech, Shanghai, China
Robert Sebra Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Daniel Stetson Astrazeneca Pharmaceuticals, Waltham, MA, USA
Lihyun Sun Elim Biopharmaceuticals, Inc., Hayward, CA, USA
Philippe Szankasi R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
Haowen Tan Primbio Genes Biotechnology, East Lake High-tech Development Zone, Wuhan, Hubei, China
Lin-Ya Tang Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
Hanane Arib Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Hunter Best R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA Departments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
Blake Burgher OmniSeq, Inc., Buffalo, NY, USA
Pierre R Bushel National Institute of Environmental Health Sciences, Research Triangle Park, Morrisville, NC, USA
Fergal Casey Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
Simon Cawley Clinical Sequencing Division, Thermo Fisher Scientific, South San Francisco, CA, USA
Chia-Jung Chang Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
Jonathan Choi Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
Jorge Dinis Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
Daniel Duncan Cancer Genetics, Inc., Rutherford, NJ, USA
Agda Karina Eterovic Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
Liang Feng Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
Abhisek Ghosal ResearchDx, Inc., Irvine, CA, USA
Kristina Giorda Marketing, Integrated DNA Technologies, Inc., Coralville, IA, USA
Sean Glenn OmniSeq, Inc., Buffalo, NY, USA
Scott Happe Agilent Technologies, Cedar Creek, TX, USA
Nathan Haseley Illumina, Inc., San Diego, CA, USA
Kyle Horvath ResearchDx, Inc., Irvine, CA, USA
Li-Yuan Hung Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
Mirna Jarosz NGS Products and Services, Integrated DNA Technologies, Inc., Coralville, IA, USA
Garima Kushwaha Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
Dan Li Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
Quan-Zhen Li Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
Zhiguang Li Intramural Research Program, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
Liang-Chun Liu Clinical Diagnostic Division, Thermo Fisher Scientific, Fremont, CA, USA
Zhichao Liu Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
Charles Ma Cancer Genetics, Inc., Rutherford, NJ, USA
Christopher E Mason Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, USA
Dalila B Megherbi CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, MA, USA
Tom Morrison Accugenomics, Inc., Wilmington, NC, USA
Carlos Pabón-Peña Agilent Technologies, Santa Clara, CA, USA
Mehdi Pirooznia Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
Paula Z Proszek NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
Amelia Raymond Astrazeneca Pharmaceuticals, Waltham, MA, USA
Paul Rindler R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
Rebecca Ringler ResearchDx, Inc., Irvine, CA, USA
Andreas Scherer Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine, HiLIFE Unit, Biomedicum Helsinki 2U (D302b), University of Helsinki, Helsinki, Finland EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
Rita Shaknovich Cancer Genetics, Inc., Rutherford, NJ, USA
Tieliu Shi Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
Melissa Smith Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Ping Song Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
Maya Strahl Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Venkat J Thodima Cancer Genetics, Inc., Rutherford, NJ, USA
Nikola Tom EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
Suman Verma ResearchDx, Inc., Irvine, CA, USA
Jiashi Wang Research and Development, Integrated DNA Technologies, Inc., Coralville, IA, USA
Leihong Wu Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
Wenzhong Xiao Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
Chang Xu Research and Development, QIAGEN Sciences, Inc., Frederick, MD, USA
Mary Yang Department of Information Science, University of Arkansas at Little Rock, Little Rock, AR, USA
Guangliang Zhang Clinical Laboratory, Burning Rock Biotech, Guangzhou, China
Sa Zhang Clinical Laboratory, Burning Rock Biotech, Guangzhou, China
Yilin Zhang Elim Biopharmaceuticals, Inc., Hayward, CA, USA
Leming Shi State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, China Human Phenome Institute, Fudan University, Shanghai, China Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, China
Weida Tong Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
Donald J Johann Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Timothy R Mercer St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia. Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia. Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Queensland, QLD, Australia.
Joshua Xu Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.

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Zhao J, Sun G, Zhu S, Dai J, Chen J, Zhang M, Ni Y, Zhang H, Shen P, Zhao X, Zhang B, Pan X, Nie L, Yin X, Liang J, Zhang X, Wang Z, Zhu X, Liao B, Liu Z, Armstrong CM, Gao AC, Huang H, Chen N, Zeng H. Circulating tumour DNA reveals genetic traits of patients with intraductal carcinoma of the prostate. BJU Int 2021;129:345-355. [PMID: 34185954 DOI: 10.1111/bju.15530] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/05/2021] [Accepted: 06/22/2021] [Indexed: 02/05/2023]

Abstract

OBJECTIVES

To investigate the genetic alterations of patients with prostate cancer (PCa) with and without intraductal carcinoma of the prostate (IDC-P).

PATIENTS AND METHODS

We performed targeted sequencing of plasma cell-free DNA on 161 patients with prostate adenocarcinoma (PAC) with IDC-P and 84 without IDC-P. Genomic alterations were compared between these two groups. The association between genetic alterations and patients' survival outcomes was also explored.

RESULTS

We identified that 29.8% (48/161) and 21.4% (18/84) of patients with and without IDC-P harboured genomic alterations in DNA repair pathways, respectively (P = 0.210). Pathogenic germline DNA repair alterations were frequently detected in IDC-P carriers compared to IDC-P non-carriers (11.8% [19/161] vs 2.4% [two of 84], P = 0.024). Germline BReast CAncer type 2 susceptibility protein (BRCA2) and somatic cyclin-dependent kinase 12 (CDK12) defects were specifically identified in IDC-P carriers relative to PAC (BRCA2: 8.7% [14/161] vs 0% and CDK12: 6.8% [11/161] vs 1.2% [one of 84]). Patients with IDC-P had a distinct androgen receptor (AR) pathway alteration, characterised by an enrichment of nuclear receptor corepressor 2 (NCOR2) mutations compared with patients with pure PAC (21.1% [34/161] vs 6.0% [five of 84], P = 0.004). Increased AR alterations were detected in patients harbouring tumours with an IDC-P proportion of ≥10% vs those with an IDC-P proportion of <10% (6.4% [five of 78] vs 18.1% [15/83], P = 0.045). For IDC-P carriers, tumour protein p53 (TP53) mutation was associated with shorter castration-resistant-free survival (median 10.9 vs 28.9 months, P = 0.026), and BRCA2 alteration was related to rapid prostate-specific antigen progression for those receiving abiraterone treatment (median 9.1 vs 11.9 months, P = 0.036).

CONCLUSION

Our findings provide genomic evidence explaining the aggressive phenotype of tumours with IDC-P, highlighting the potential therapeutic strategies for this patient population.

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Affiliation(s)

Jinge Zhao Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Guangxi Sun Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Sha Zhu Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Jindong Dai Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Junru Chen Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Mengni Zhang Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
Yuchao Ni Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Haoran Zhang Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Pengfei Shen Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Xiaochen Zhao Departments of Biochemistry and Molecular Biology and Urology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
Bei Zhang Departments of Biochemistry and Molecular Biology and Urology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
Xiuyi Pan Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
Ling Nie Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
Xiaoxue Yin Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
Jiayu Liang Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Xingming Zhang Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Zhipeng Wang Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Xudong Zhu Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Banghua Liao Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Zhenhua Liu Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
Cameron M Armstrong Department of Urology, University of California Davis, Davis, CA, USA
Allen C Gao Department of Urology, University of California Davis, Davis, CA, USA
Haojie Huang 3DMedicines Inc., Shanghai, China
Ni Chen Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
Hao Zeng Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China

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Circulating tumor DNA in lung cancer: real-time monitoring of disease evolution and treatment response. Chin Med J (Engl) 2021;133:2476-2485. [PMID: 32960843 PMCID: PMC7575184 DOI: 10.1097/cm9.0000000000001097] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open

Yang X, Li D, Tu C, He W, Meng L, Tan YQ, Lu G, Du J, Zhang Q. Novel variants of the PCCB gene in Chinese patients with propionic acidemia. Clin Chim Acta 2021;519:18-25. [PMID: 33798502 DOI: 10.1016/j.cca.2021.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/20/2021] [Indexed: 10/21/2022]

Affiliation(s)

Xiaoxuan Yang Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
Dongyan Li Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
Chaofeng Tu Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China; Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
Wenbing He Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China; Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
Lanlan Meng Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
Yue-Qiu Tan Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China; Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
Guangxiu Lu Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
Juan Du Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China; Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.
Qianjun Zhang Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China; Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.

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Zhao Y, Gao Y, Xu X, Zhou J, Wang H. Multi-omics analysis of genomics, epigenomics and transcriptomics for molecular subtypes and core genes for lung adenocarcinoma. BMC Cancer 2021;21:257. [PMID: 33750346 PMCID: PMC7942004 DOI: 10.1186/s12885-021-07888-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/08/2021] [Indexed: 02/07/2023] Open

Riedl JM, Hasenleithner SO, Pregartner G, Scheipner L, Posch F, Groller K, Kashofer K, Jahn SW, Bauernhofer T, Pichler M, Stöger H, Berghold A, Hoefler G, Speicher MR, Heitzer E, Gerger A. Profiling of circulating tumor DNA and tumor tissue for treatment selection in patients with advanced and refractory carcinoma: a prospective, two-stage phase II Individualized Cancer Treatment trial. Ther Adv Med Oncol 2021;13:1758835920987658. [PMID: 33717225 PMCID: PMC7923987 DOI: 10.1177/1758835920987658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/17/2020] [Indexed: 11/22/2022] Open

Abstract

BACKGROUND

Molecular profiling (MP) represents an opportunity to match patients to a targeted therapy and when tumor tissue is unavailable, circulating tumor deoxyribonucleic acid (ctDNA) can be harnessed as a non-invasive analyte for this purpose. We evaluated the success of a targeted therapy selected by profiling of ctDNA and tissue in patients with advanced and refractory carcinoma.

PATIENTS AND METHODS

A blood draw as well as an optional tissue biopsy were obtained for MP. Whole-genome sequencing and a cancer hotspot panel were performed, and publicly available databases were used to match the molecular profile to targeted treatments. The primary endpoint was the progression-free survival (PFS) ratio (PFS on MP-guided therapy/PFS on the last evidence-based therapy), whereas the success of the targeted therapy was defined as a PFS ratio ⩾1.2. To test the impact of molecular profile-treatment matching strategies, we retrospectively analyzed selected cases via the CureMatch PreciGENE™ decision support algorithm.

RESULTS

Interim analysis of 24 patients yielded informative results from 20 patients (83%). A potential tumor-specific drug could be matched in 11 patients (46%) and eight (33%) received a matched treatment. Median PFS in the matched treatment group was 61.5 days [interquartile range (IQR) 49.8-71.0] compared with 81.5 days (IQR 68.5-117.8) for the last evidence-based treatment, resulting in a median PFS ratio of 0.7 (IQR 0.6-0.9). Hence, as no patient experienced a PFS ratio ⩾1.2, the study was terminated. Except for one case, the CureMatch analysis identified either a two-drug or three-drug combination option.

CONCLUSIONS

Our study employed a histotype-agnostic approach to harness molecular profiling data from both ctDNA and metastatic tumor tissue. The outcome results indicate that more innovative approaches to study design and matching algorithms are necessary to achieve improved patient outcomes.EU Clinical Trials Registry (https://www.clinicaltrialsregister.eu): EudraCT: 2014-005341-44.

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Affiliation(s)

Jakob M. Riedl Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
Samantha O. Hasenleithner Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
Gudrun Pregartner Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
Lukas Scheipner Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
Florian Posch Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria Center for Biomarker Research in Medicine (CBmed Ges.m.b.H.), Graz, Austria
Karin Groller Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
Karl Kashofer Institute of Pathology, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
Stephan W. Jahn Institute of Pathology, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
Thomas Bauernhofer Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
Martin Pichler Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
Herbert Stöger Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
Andrea Berghold Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
Gerald Hoefler Institute of Pathology, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
Michael R. Speicher Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
Ellen Heitzer Diagnostic and Research Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Auenbruggerplatz 2, Graz 8036, Austria Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
Armin Gerger Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria Center for Biomarker Research in Medicine (CBmed Ges.m.b.H.), Graz, Austria

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Copy number variation: Characteristics, evolutionary and pathological aspects. Biomed J 2021;44:548-559. [PMID: 34649833 PMCID: PMC8640565 DOI: 10.1016/j.bj.2021.02.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open

Hu H, Xu H, Lu F, Zhang J, Xu L, Xu S, Jiang H, Zeng Q, Chen E, He Z. Exploring the Effect of Differentially Expressed Long Non-coding RNAs Driven by Copy Number Variation on Competing Endogenous RNA Network by Mining Lung Adenocarcinoma Data. Front Cell Dev Biol 2021;8:627436. [PMID: 33585468 PMCID: PMC7876300 DOI: 10.3389/fcell.2020.627436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022] Open

Abstract

Lung cancer is the first cause of cancer death, and gene copy number variation (CNV) is a vital cause of lung cancer progression. Prognosis prediction of patients followed by medication guidance by detecting CNV of lung cancer is emerging as a promising precise treatment in the future. In this paper, the differences in CNV and gene expression between cancer tissue and normal tissue of lung adenocarcinoma (LUAD) from The Cancer Genome Atlas Lung Adenocarcinoma data set were firstly analyzed, and greater differences were observed. Furthermore, CNV-driven differentially expressed long non-coding RNAs (lncRNAs) were screened out, and then, a competing endogenous RNA (ceRNA) regulatory network related to the gene CNV was established, which involved 9 lncRNAs, seven microRNAs, and 178 downstream messenger RNAs (mRNAs). Pathway enrichment analyses sequentially performed revealed that the downstream mRNAs were mainly enriched in biological pathways related to cell division, DNA repair, and so on, indicating that these mRNAs mainly affected the replication and growth of tumor cells. Besides, the relationship between lncRNAs and drug effects was explored based on previous studies, and it was found that LINC00511 and LINC00942 in the CNV-associated ceRNA network could be used to determine tumor response to drug treatment. As examined, the drugs affected by these two lncRNAs mainly targeted metabolism, target of rapamycin signaling pathway, phosphatidylinositol-3-kinase signaling pathway, epidermal growth factor receptor signaling pathway, and cell cycle. In summary, the present research was devoted to analyzing CNV, lncRNA, mRNA, and microRNA of lung cancer, and nine lncRNAs that could affect the CNV-associated ceRNA network we constructed were identified, two of which are promising in determining tumor response to drug treatment.

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Copy Number Variation: Methods and Clinical Applications. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11020819] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]

Hofman P. Detecting Resistance to Therapeutic ALK Inhibitors in Tumor Tissue and Liquid Biopsy Markers: An Update to a Clinical Routine Practice. Cells 2021;10:168. [PMID: 33467720 PMCID: PMC7830674 DOI: 10.3390/cells10010168] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/16/2022] Open

Bourrier C, Pierga JY, Xuereb L, Salaun H, Proudhon C, Speicher MR, Belic J, Heitzer E, Lockhart BP, Guigal-Stephan N. Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival. Cancers (Basel) 2020;12:cancers12061481. [PMID: 32517171 PMCID: PMC7353062 DOI: 10.3390/cancers12061481] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022] Open

Affiliation(s)

Chantal Bourrier Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France; (C.B.); (B.P.L.)
Jean-Yves Pierga Department of Medical Oncology, Institut Curie, 26 rue d’Ulm, 75005 Paris, France; (J.-Y.P.); (H.S.) Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, 26 rue d’Ulm, 75005 Paris, France; Université de Paris, 75005 Paris, France
Laura Xuereb Division of Methodology and Valorisation of Data, Servier Research and Development Institute, 50 rue carnot, 92150 Suresnes, France;
Hélène Salaun Department of Medical Oncology, Institut Curie, 26 rue d’Ulm, 75005 Paris, France; (J.-Y.P.); (H.S.) Université de Paris, 75005 Paris, France
Charlotte Proudhon Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, 26 rue d’Ulm, 75005 Paris, France;
Michael R. Speicher Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; (M.R.S.); (J.B.); (E.H.) BioTechMed-Graz, 8010 Graz, Austria
Jelena Belic Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; (M.R.S.); (J.B.); (E.H.)
Ellen Heitzer Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; (M.R.S.); (J.B.); (E.H.) BioTechMed-Graz, 8010 Graz, Austria Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, 8010 Graz, Austria
Brian Paul Lockhart Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France; (C.B.); (B.P.L.)
Nolwen Guigal-Stephan Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France; (C.B.); (B.P.L.) Correspondence: ; Tel.: +33-155-722-532

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Innovating Computational Biology and Intelligent Medicine: ICIBM 2019 Special Issue. Genes (Basel) 2020;11:genes11040437. [PMID: 32316483 PMCID: PMC7231250 DOI: 10.3390/genes11040437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/03/2022] Open