101
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Bibby B, Thiruthaneeswaran N, Yang L, McArt D, O'Reilly P, Roberts D, Choudhury A, West C. OC-0382: Repurposing of FDA-approved drugs as novel radiosensitisers in hypoxic prostate cancer. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)30692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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102
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Irlam J, Bibby B, Thiruthaneeswaran N, Williamson A, Betts G, Yang L, Valentine H, Roberts D, Choudhury A, West C. EP-2284: Prospective validation of a hypoxia gene signature biomarker in the NIMRAD trial. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)32593-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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103
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Webb J, Chuter R, McWilliam A, Choudhury A, Van Herk M. EP-2073: The impact of the electron return effect on radiotherapy plan quality for peripheral sarcomas. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)32382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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104
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Thiruthaneeswaran N, Bibby B, Yang L, McArt D, Choudhury A, West C. Repurposing of FDA-approved Therapeutics to Identify Novel Radiosensitisers in Hypoxic Prostate Cancer. Clin Oncol (R Coll Radiol) 2018. [DOI: 10.1016/j.clon.2017.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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105
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Tharmalingam H, Tsang Y, Kennedy J, Choudhury A, Hoskin P. Whole Pelvis Irradiation Improves Biochemical Progression-free Survival in High-risk Prostate Cancer Patients Treated with External Beam Radiotherapy and High Dose Rate (HDR) Brachytherapy. Clin Oncol (R Coll Radiol) 2018. [DOI: 10.1016/j.clon.2017.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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106
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Stover DG, Parsons HA, Ha G, Freeman S, Barry B, Guo H, Choudhury A, Gydush G, Reed S, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TA, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Abstract GS3-07: Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-gs3-07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction:
Triple-negative breast cancer (TNBC) is a poor prognosis breast cancer subset characterized by relatively few mutations but extensive copy number alterations (CNAs). Cell-free DNA (cfDNA) offers the potential to overcome infrequent tumor biopsies in metastatic TNBC (mTNBC) and interrogate the genomics of chemotherapy resistance.
Methods:
506 archival or fresh plasma samples were identified from 164 patients with mTNBC who had previously received chemotherapy. We performed low coverage whole genome sequencing to determine genome-wide copy number and estimate 'tumor fraction' of cfDNA (TFx) using our recently-developed approach, ichorCNA. In patient samples with TFx >10%, we identified regions that were significantly gained or lost using GISTIC2.0. We compared CNAs of 20 paired primary-metastatic samples and also mTNBCs from cfDNA versus primary TNBCs from TCGA and METABRIC.
Results:
We successfully obtained high quality, low coverage whole genome sequencing data for 478 (94.5%) plasma samples from 158 patients, with 1 to 14 samples per patient. TFx and copy number profiles were highly concordant with paired metastatic biopsy (n=10, range 0-7 days from biopsy to blood draw) with sensitivity of 0.86 and specificity of 0.90 and reproducible in independently-processed blood draws (TFx intraclass correlation coefficient 0.984). Median overall survival from time of first blood draw was 8 months, and TFx was highly correlated independent of primary stage, primary receptor status, age at primary diagnosis, BRCA status, and metastatic line of therapy: adjusted hazard ratio between 4th and 1st quartiles = 2.14 (95% CI 1.40-3.28; p=0.00049). 101/158 patients (63.9%) had at least one sample with TFx >10%, our threshold for high confidence CNA calls. Copy number profiles and percent genome altered were remarkably similar between mTNBCs and primary TNBCs in TCGA and METABRIC (n=433), suggesting that large-scale chromosomal events are infrequent in TNBC metastatic progression. We identified chromosomal gains that demonstrated significant enrichment in mTNBCs relative to paired primary TNBCs (n=20) and also TCGA/METABRIC, including driver genes (NOTCH2, AKT2, AKT3) and putative antibody-drug conjugate targets. Finally, we identify a novel association of gains of 18q11 and/or 19p13 with poor metastatic prognosis, independent of clinicopathologic factors and TFx.
Conclusions:
Here, we present the first large-scale genomic characterization of metastatic TNBC to our knowledge, derived exclusively from cfDNA. 'Tumor fraction' of cfDNA is an independent prognostic marker in mTNBC. Primary and metastatic TNBC have remarkably similar copy number profiles yet we identify alterations enriched and prognostic in mTNBC. Collectively, these data have potential implications in the understanding of metastasis, therapeutic resistance, and novel therapeutic targets.
Citation Format: Stover DG, Parsons HA, Ha G, Freeman S, Barry B, Guo H, Choudhury A, Gydush G, Reed S, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TA, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS3-07.
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Mahil J, Van Herk M, Faivre-Finn C, Choudhury A, McWilliam A. Dose to the coronary arteries is significantly associated with overall survival in non-small-cell-lung-cancer (NSCLC) patients treated with curative-intent radiotherapy. Lung Cancer 2018. [DOI: 10.1016/s0169-5002(18)30184-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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108
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Choudhury A, Singh O. Histoenzymic distribution pattern in gall bladder of sheep. APPLIED BIOLOGICAL RESEARCH 2018. [DOI: 10.5958/0974-4517.2018.00010.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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109
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Joseph N, McWilliam A, Kennedy J, Haslett K, Faivre-Finn C, Choudhury A. Posttreatment Lymphocytopenia, Integral Heart Dose, and Overall Survival in Lung Cancer Patients Treated With Radical Radiation Therapy. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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110
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Choudhury A, Budgell G, MacKay R, Falk S, Faivre-Finn C, Dubec M, van Herk M, McWilliam A. The Future of Image-guided Radiotherapy. Clin Oncol (R Coll Radiol) 2017; 29:662-666. [DOI: 10.1016/j.clon.2017.04.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/11/2017] [Accepted: 04/28/2017] [Indexed: 11/16/2022]
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111
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Cicchetti A, Rancati T, Joseph N, Chang-Claude J, Giandini T, Fiorino C, Cozzarini C, Palorini F, Morlino S, Davidson S, Johnson K, Talbot C, Webb A, McWilliam A, West C, Valdagni R, Choudhury A. Weekly Integral Dose and Use of Lipid Lowering Drugs Are Associated With Worsening of Functional Outcomes in Prostate Cancer Patients Treated With IMRT. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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112
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Yang L, Williamson A, Irlam J, Helen D, Hoskin P, West C, Choudhury A. Molecular Subtyping of Muscle-Invasive Bladder Cancer Predicts Benefit of Hypoxia-Targeting Therapy. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.1134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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113
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Yang L, Roberts D, Takhar M, Bibby B, Cheng W, Haider S, Buffa F, Erho N, Hoskin P, West C, Choudhury A. Hypoxia Gene Expression Signature Independently Predicts Prognosis for Prostate Cancer Patients. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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114
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Mitin T, Choudhury A. The Folie à Trois. Int J Radiat Oncol Biol Phys 2017; 99:6. [PMID: 28816161 DOI: 10.1016/j.ijrobp.2017.05.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/13/2016] [Accepted: 05/30/2017] [Indexed: 11/26/2022]
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115
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Choudhury A, Jindal A, Maiwall R, Sharma MK, Sharma BC, Pamecha V, Mahtab M, Rahman S, Chawla YK, Taneja S, Tan SS, Devarbhavi H, Duan Z, Yu C, Ning Q, Jia JD, Amarapurkar D, Eapen CE, Goel A, Hamid SS, Butt AS, Jafri W, Kim DJ, Ghazinian H, Lee GH, Sood A, Lesmana LA, Abbas Z, Shiha G, Payawal DA, Dokmeci AK, Sollano JD, Carpio G, Lau GK, Karim F, Rao PN, Moreau R, Jain P, Bhatia P, Kumar G, Sarin SK. Liver failure determines the outcome in patients of acute-on-chronic liver failure (ACLF): comparison of APASL ACLF research consortium (AARC) and CLIF-SOFA models. Hepatol Int 2017; 11:461-471. [PMID: 28856540 DOI: 10.1007/s12072-017-9816-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/30/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND AIMS Acute-on-chronic liver failure (ACLF) is a progressive disease associated with rapid clinical worsening and high mortality. Early prediction of mortality and intervention can improve patient outcomes. We aimed to develop a dynamic prognostic model and compare it with the existing models. METHODS A total of 1402 ACLF patients, enrolled in the APASL-ACLF Research Consortium (AARC) with 90-day follow-up, were analyzed. An ACLF score was developed in a derivation cohort (n = 480) and was validated (n = 922). RESULTS The overall survival of ACLF patients at 28 days was 51.7%, with a median of 26.3 days. Five baseline variables, total bilirubin, creatinine, serum lactate, INR and hepatic encephalopathy, were found to be independent predictors of mortality, with AUROC in derivation and validation cohorts being 0.80 and 0.78, respectively. AARC-ACLF score (range 5-15) was found to be superior to MELD and CLIF SOFA scores in predicting mortality with an AUROC of 0.80. The point scores were categorized into grades of liver failure (Gr I: 5-7; II: 8-10; and III: 11-15 points) with 28-day cumulative mortalities of 12.7, 44.5 and 85.9%, respectively. The mortality risk could be dynamically calculated as, with each unit increase in AARC-ACLF score above 10, the risk increased by 20%. A score of ≥11 at baseline or persisting in the first week was often seen among nonsurvivors (p = 0.001). CONCLUSIONS The AARC-ACLF score is easy to use, dynamic and reliable, and superior to the existing prediction models. It can reliably predict the need for interventions, such as liver transplant, within the first week.
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Webster J, Larsen E, Marsh N, Choudhury A, Harris P, Rickard C. Chlorhexidine gluconate or polyhexamethylene biguanide disc dressing to reduce the incidence of central-line-associated bloodstream infection: a feasibility randomized controlled trial (the CLABSI trial). J Hosp Infect 2017; 96:223-228. [DOI: 10.1016/j.jhin.2017.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/09/2017] [Indexed: 01/02/2023]
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117
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Trainor S, Choudhury A, Huddart R, Kiltie AE, Kockelbergh R, Turner W, Birtle A, Crabb SJ. The National Institute for Health and Care Excellence (NICE) Guidance on Bladder Cancer; a Step in the Right Direction? Clin Oncol (R Coll Radiol) 2017; 29:344-347. [PMID: 28190637 DOI: 10.1016/j.clon.2017.01.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 01/19/2017] [Indexed: 01/08/2023]
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118
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West C, Yang L, Roberts D, Bibby B, Forker L, Haider S, Buffa F, Choudhury A. OC-0573: Development of hypoxia gene signatures as biomarkers for treatment stratification. Radiother Oncol 2017. [DOI: 10.1016/s0167-8140(17)31013-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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119
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Mee T, Kirkby N, Kirkby K, Jena R, Choudhury A. PV-0091: Quantifying the Gap Between Radiotherapy in the Elderly and the Demand for Age-Agnostic Treatment. Radiother Oncol 2017. [DOI: 10.1016/s0167-8140(17)30535-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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120
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Nightingale H, Conroy R, Elliott T, Coyle C, Wylie J, Choudhury A. A national survey of current practices of preparation and management of radical prostate radiotherapy patients during treatment. Radiography (Lond) 2017; 23:87-93. [DOI: 10.1016/j.radi.2017.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/18/2016] [Accepted: 01/03/2017] [Indexed: 11/26/2022]
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121
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Joseph N, McWilliam A, Haslett K, Kennedy J, Faivre-Finn C, Choudhury A. PO-0952: Integral heart dose and lymphocytopaenia in lung cancer patients treated with radical radiotherapy. Radiother Oncol 2017. [DOI: 10.1016/s0167-8140(17)31389-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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122
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Haque M, Choudhury A, Haque A, Blackwood R. The Prevalence of Depression and its Correlation with Healthcare Barriers
in Urban Islamabad. Ann Glob Health 2017. [DOI: 10.1016/j.aogh.2017.03.181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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123
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John M, Khan M, Quadir A, Choudhury A, Baba M, Dar F, Rafiq A. Sternal morphometry of common myna ( Acridotheres tristis), himalayan bulbul ( Pyconotus leucogenys) and house sparrow ( Passer domesticus). APPLIED BIOLOGICAL RESEARCH 2017. [DOI: 10.5958/0974-4517.2017.00034.9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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124
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Joseph N, Rancati T, Cicchetti A, Valdagni R, Chang-Claude J, Davidson S, Johnson K, Talbot C, Webb A, McWilliam A, West C, Choudhury A. A Higher Whole-Pelvic Integral Dose Is Associated With Worsening Fatigue and Functional Outcome in Prostate Cancer Patients Treated With Intensity Modulated Radiation Therapy. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2016.06.1300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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125
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Joseph N, McWilliam A, Kennedy J, Faivre-Finn C, Choudhury A. A Higher Integral Heart Dose Is Associated With Lymphocytopenia in Non-Small Cell Lung Cancer Patients Treated With Intensity Modulated Radiation Therapy and Concurrent Chemotherapy. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2016.06.1837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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