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Lee P, Ayub M, Meyer JE, Price JG. Pre-Treatment Trends in Child-Pugh Score as an Indicator of Post-Treatment Survival in Patients Receiving Liver SBRT for HCC. Int J Radiat Oncol Biol Phys 2023; 117:e313. [PMID: 37785128 DOI: 10.1016/j.ijrobp.2023.06.2342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) We sought to understand the value of Child-Pugh (CP) score trends prior to undergoing stereotactic body radiation therapy (SBRT) for hepatocellular carcinoma in patients with advanced cirrhosis, as an indicator of post-treatment morbidity and mortality. We hypothesize that an uptrend in CP score prior to RT increases risk of post-treatment cirrhosis progression, or death. MATERIALS/METHODS We retrospectively reviewed all patients who underwent definitive SBRT for HCC between 2014-2022 in our health system. Most patients were referred for treatment in the 2nd or 3rd line setting, allowing us to determine CP score at multiple points before SBRT. Response to treatment was evaluated with RECIST or mRECIST criteria. Acute treatment toxicities were assessed by CTCAE v5. OS was assessed using the Kaplan-Meier method, and differences between groups were evaluated using log-rank test. RESULTS A total of 61 patients were identified, 26 had an immediate pre-SBRT CP score of A5, 11 with A6, 10 with B7, 4 with B8, 4 with B9, 5 with C10, and 1 with C11. Median prescribed dose was 40Gy in 5fx. Median OS of all patients was 24 months. When stratified by CP category, median OS for CP A was not reached (NR) at time of analysis, CP B had a median OS of 14.8mo, and CP C with 1.9mo (p < 0.01). Local control rate at 6mo was 87.5%. 5 patients (8.3%) had CTCAE grade 2 acute toxicity. 10 patients had CP score progression of 2pts or more within 6mo after treatment, and 7 patients had a cause of death attributed to end stage liver disease. Median time interval between HCC diagnosis and start of RT was 338 days. In this time interval, patients with a CP score increase of 2 pts or more prior to starting RT had a median OS of 362 days, compared to NR for patients without increase (p = 0.02). When excluding the CP A group, patients with 2 pt increase had median OS of 362 days vs 445 days (p = 0.34). Again excluding the CP A group, patients with a 1 pt increase had median OS of 362 days vs NR (p = 0.23). Of 9 patients who had a pre-RT CP score increase of 2 pts or more, 7 experienced continued CP progression after treatment. CONCLUSION In this multi-institutional retrospective analysis, we found 24 patients with advanced CP B/C cirrhosis who underwent SBRT, none of whom received orthotopic liver transplant. While CP C patients did relatively poorly, we find that some patients with CP B cirrhosis may tolerate SBRT well with good oncologic effect. When taking pre-treatment CP score increase into consideration, we saw a trend but no statistical significance indicating that a pre-SBRT increase in CP score may be associated with worse OS after treatment among CP B/C patients. We conclude that there may be a subset of patients with advanced cirrhosis who, if well selected, are appropriate candidates for SBRT. We suggest a novel use of the CP score and pre-RT trends as an additional clinical tool to aid in decision making when selecting patients. We also suggest that patients with marked up-trending scores pre-treatment have a high likelihood of continued cirrhosis progression after treatment.
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Affiliation(s)
- P Lee
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA
| | - M Ayub
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - J E Meyer
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA
| | - J G Price
- Fox Chase Cancer Center at Temple University Hospital, Philadelphia, PA
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Bethlehem RAI, Seidlitz J, White SR, Vogel JW, Anderson KM, Adamson C, Adler S, Alexopoulos GS, Anagnostou E, Areces-Gonzalez A, Astle DE, Auyeung B, Ayub M, Bae J, Ball G, Baron-Cohen S, Beare R, Bedford SA, Benegal V, Beyer F, Blangero J, Blesa Cábez M, Boardman JP, Borzage M, Bosch-Bayard JF, Bourke N, Calhoun VD, Chakravarty MM, Chen C, Chertavian C, Chetelat G, Chong YS, Cole JH, Corvin A, Costantino M, Courchesne E, Crivello F, Cropley VL, Crosbie J, Crossley N, Delarue M, Delorme R, Desrivieres S, Devenyi GA, Di Biase MA, Dolan R, Donald KA, Donohoe G, Dunlop K, Edwards AD, Elison JT, Ellis CT, Elman JA, Eyler L, Fair DA, Feczko E, Fletcher PC, Fonagy P, Franz CE, Galan-Garcia L, Gholipour A, Giedd J, Gilmore JH, Glahn DC, Goodyer IM, Grant PE, Groenewold NA, Gunning FM, Gur RE, Gur RC, Hammill CF, Hansson O, Hedden T, Heinz A, Henson RN, Heuer K, Hoare J, Holla B, Holmes AJ, Holt R, Huang H, Im K, Ipser J, Jack CR, Jackowski AP, Jia T, Johnson KA, Jones PB, Jones DT, Kahn RS, Karlsson H, Karlsson L, Kawashima R, Kelley EA, Kern S, Kim KW, Kitzbichler MG, Kremen WS, Lalonde F, Landeau B, Lee S, Lerch J, Lewis JD, Li J, Liao W, Liston C, Lombardo MV, Lv J, Lynch C, Mallard TT, Marcelis M, Markello RD, Mathias SR, Mazoyer B, McGuire P, Meaney MJ, Mechelli A, Medic N, Misic B, Morgan SE, Mothersill D, Nigg J, Ong MQW, Ortinau C, Ossenkoppele R, Ouyang M, Palaniyappan L, Paly L, Pan PM, Pantelis C, Park MM, Paus T, Pausova Z, Paz-Linares D, Pichet Binette A, Pierce K, Qian X, Qiu J, Qiu A, Raznahan A, Rittman T, Rodrigue A, Rollins CK, Romero-Garcia R, Ronan L, Rosenberg MD, Rowitch DH, Salum GA, Satterthwaite TD, Schaare HL, Schachar RJ, Schultz AP, Schumann G, Schöll M, Sharp D, Shinohara RT, Skoog I, Smyser CD, Sperling RA, Stein DJ, Stolicyn A, Suckling J, Sullivan G, Taki Y, Thyreau B, Toro R, Traut N, Tsvetanov KA, Turk-Browne NB, Tuulari JJ, Tzourio C, Vachon-Presseau É, Valdes-Sosa MJ, Valdes-Sosa PA, Valk SL, van Amelsvoort T, Vandekar SN, Vasung L, Victoria LW, Villeneuve S, Villringer A, Vértes PE, Wagstyl K, Wang YS, Warfield SK, Warrier V, Westman E, Westwater ML, Whalley HC, Witte AV, Yang N, Yeo B, Yun H, Zalesky A, Zar HJ, Zettergren A, Zhou JH, Ziauddeen H, Zugman A, Zuo XN, Bullmore ET, Alexander-Bloch AF. Brain charts for the human lifespan. Nature 2022; 604:525-533. [PMID: 35388223 PMCID: PMC9021021 DOI: 10.1038/s41586-022-04554-y] [Citation(s) in RCA: 404] [Impact Index Per Article: 202.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/16/2022] [Indexed: 02/02/2023]
Abstract
Over the past few decades, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. However, no reference standards currently exist to quantify individual differences in neuroimaging metrics over time, in contrast to growth charts for anthropometric traits such as height and weight1. Here we assemble an interactive open resource to benchmark brain morphology derived from any current or future sample of MRI data ( http://www.brainchart.io/ ). With the goal of basing these reference charts on the largest and most inclusive dataset available, acknowledging limitations due to known biases of MRI studies relative to the diversity of the global population, we aggregated 123,984 MRI scans, across more than 100 primary studies, from 101,457 human participants between 115 days post-conception to 100 years of age. MRI metrics were quantified by centile scores, relative to non-linear trajectories2 of brain structural changes, and rates of change, over the lifespan. Brain charts identified previously unreported neurodevelopmental milestones3, showed high stability of individuals across longitudinal assessments, and demonstrated robustness to technical and methodological differences between primary studies. Centile scores showed increased heritability compared with non-centiled MRI phenotypes, and provided a standardized measure of atypical brain structure that revealed patterns of neuroanatomical variation across neurological and psychiatric disorders. In summary, brain charts are an essential step towards robust quantification of individual variation benchmarked to normative trajectories in multiple, commonly used neuroimaging phenotypes.
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Affiliation(s)
- R A I Bethlehem
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK.
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK.
| | - J Seidlitz
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA.
| | - S R White
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - J W Vogel
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Informatics & Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA
| | - K M Anderson
- Department of Psychology, Yale University, New Haven, CT, USA
| | - C Adamson
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - S Adler
- UCL Great Ormond Street Institute for Child Health, London, UK
| | - G S Alexopoulos
- Weill Cornell Institute of Geriatric Psychiatry, Department of Psychiatry, Weill Cornell Medicine, New York, USA
| | - E Anagnostou
- Department of Pediatrics University of Toronto, Toronto, Canada
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, Canada
| | - A Areces-Gonzalez
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for NeuroInformation, University of Electronic Science and Technology of China, Chengdu, China
- University of Pinar del Río "Hermanos Saiz Montes de Oca", Pinar del Río, Cuba
| | - D E Astle
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - B Auyeung
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh, UK
| | - M Ayub
- Queen's University, Department of Psychiatry, Centre for Neuroscience Studies, Kingston, Ontario, Canada
- University College London, Mental Health Neuroscience Research Department, Division of Psychiatry, London, UK
| | - J Bae
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, Korea
| | - G Ball
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - S Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridge Lifetime Asperger Syndrome Service (CLASS), Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - R Beare
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - S A Bedford
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - V Benegal
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - F Beyer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - J Blangero
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - M Blesa Cábez
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - J P Boardman
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - M Borzage
- Fetal and Neonatal Institute, Division of Neonatology, Children's Hospital Los Angeles, Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - J F Bosch-Bayard
- McGill Centre for Integrative Neuroscience, Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute, Montreal, Quebec, Canada
- McGill University, Montreal, Quebec, Canada
| | - N Bourke
- Department of Brain Sciences, Imperial College London, London, UK
- Care Research and Technology Centre, Dementia Research Institute, London, UK
| | - V D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, USA
| | - M M Chakravarty
- McGill University, Montreal, Quebec, Canada
- Computational Brain Anatomy (CoBrA) Laboratory, Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - C Chen
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - C Chertavian
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - G Chetelat
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and Brain @ Caen-Normandie, Cyceron, Caen, France
| | - Y S Chong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - J H Cole
- Centre for Medical Image Computing (CMIC), University College London, London, UK
- Dementia Research Centre (DRC), University College London, London, UK
| | - A Corvin
- Department of Psychiatry, Trinity College, Dublin, Ireland
| | - M Costantino
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Verdun, Quebec, Canada
- Undergraduate program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | - E Courchesne
- Department of Neuroscience, University of California, San Diego, San Diego, CA, USA
- Autism Center of Excellence, University of California, San Diego, San Diego, CA, USA
| | - F Crivello
- Institute of Neurodegenerative Disorders, CNRS UMR5293, CEA, University of Bordeaux, Bordeaux, France
| | - V L Cropley
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - J Crosbie
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - N Crossley
- Department of Psychiatry, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Instituto Milenio Intelligent Healthcare Engineering, Santiago, Chile
| | - M Delarue
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and Brain @ Caen-Normandie, Cyceron, Caen, France
| | - R Delorme
- Child and Adolescent Psychiatry Department, Robert Debré University Hospital, AP-HP, Paris, France
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
| | - S Desrivieres
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - G A Devenyi
- Cerebral Imaging Centre, McGill Department of Psychiatry, Douglas Mental Health University Institute, Montreal, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - M A Di Biase
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Victoria, Australia
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - R Dolan
- Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London, London, UK
- Wellcome Centre for Human Neuroimaging, London, UK
| | - K A Donald
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - G Donohoe
- Center for Neuroimaging, Cognition & Genomics (NICOG), School of Psychology, National University of Ireland Galway, Galway, Ireland
| | - K Dunlop
- Weil Family Brain and Mind Research Institute, Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - A D Edwards
- Centre for the Developing Brain, King's College London, London, UK
- Evelina London Children's Hospital, London, UK
- MRC Centre for Neurodevelopmental Disorders, London, UK
| | - J T Elison
- Institute of Child Development, Department of Pediatrics, Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | - C T Ellis
- Department of Psychology, Yale University, New Haven, CT, USA
- Haskins Laboratories, New Haven, CT, USA
| | - J A Elman
- Department of Psychiatry, Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - L Eyler
- Desert-Pacific Mental Illness Research Education and Clinical Center, VA San Diego Healthcare, San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, Los Angeles, CA, USA
| | - D A Fair
- Institute of Child Development, Department of Pediatrics, Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | - E Feczko
- Institute of Child Development, Department of Pediatrics, Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | - P C Fletcher
- Department of Psychiatry, University of Cambridge, and Wellcome Trust MRC Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - P Fonagy
- Department of Clinical, Educational and Health Psychology, University College London, London, UK
- Anna Freud National Centre for Children and Families, London, UK
| | - C E Franz
- Department of Psychiatry, Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | | | - A Gholipour
- Computational Radiology Laboratory, Boston Children's Hospital, Boston, MA, USA
| | - J Giedd
- Department of Child and Adolescent Psychiatry, University of California, San Diego, San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - J H Gilmore
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - D C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - I M Goodyer
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - P E Grant
- Division of Newborn Medicine and Neuroradiology, Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Groenewold
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - F M Gunning
- Weill Cornell Institute of Geriatric Psychiatry, Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - R E Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - R C Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - C F Hammill
- The Hospital for Sick Children, Toronto, Ontario, Canada
- Mouse Imaging Centre, Toronto, Ontario, Canada
| | - O Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - T Hedden
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - A Heinz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Psychiatry and Psychotherapy, Charité Campus Mitte, Berlin, Germany
| | - R N Henson
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - K Heuer
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Université de Paris, Paris, France
| | - J Hoare
- Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - B Holla
- Department of Integrative Medicine, NIMHANS, Bengaluru, India
- Accelerator Program for Discovery in Brain disorders using Stem cells (ADBS), Department of Psychiatry, NIMHANS, Bengaluru, India
| | - A J Holmes
- Departments of Psychology and Psychiatry, Yale University, New Haven, CT, USA
| | - R Holt
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - H Huang
- Radiology Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - K Im
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine and Neuroradiology, Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - J Ipser
- Department of Psychiatry and Mental Health, Clinical Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - C R Jack
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | - A P Jackowski
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
- National Institute of Developmental Psychiatry, Beijing, China
| | - T Jia
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and BrainInspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute of Psychiatry, Psychology and Neuroscience, SGDP Centre, King's College London, London, UK
| | - K A Johnson
- Harvard Medical School, Boston, MA, USA
- Harvard Aging Brain Study, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - P B Jones
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - D T Jones
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - R S Kahn
- Department of Psychiatry, Icahn School of Medicine, Mount Sinai, NY, USA
| | - H Karlsson
- Department of Clinical Medicine, Department of Psychiatry and Turku Brain and Mind Center, FinnBrain Birth Cohort Study, University of Turku and Turku University Hospital, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
| | - L Karlsson
- Department of Clinical Medicine, Department of Psychiatry and Turku Brain and Mind Center, FinnBrain Birth Cohort Study, University of Turku and Turku University Hospital, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
| | - R Kawashima
- Institute of Development, Aging and Cancer, Tohoku University, Seiryocho, Aobaku, Sendai, Japan
| | - E A Kelley
- Queen's University, Departments of Psychology and Psychiatry, Centre for Neuroscience Studies, Kingston, Ontario, Canada
| | - S Kern
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - K W Kim
- Department of Brain and Cognitive Sciences, Seoul National University College of Natural Sciences, Seoul, South Korea
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Human Behavioral Medicine, SNU-MRC, Seoul, South Korea
| | - M G Kitzbichler
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - W S Kremen
- Department of Psychiatry, Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - F Lalonde
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health, Bethesda, MD, USA
| | - B Landeau
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and Brain @ Caen-Normandie, Cyceron, Caen, France
| | - S Lee
- Department of Brain & Cognitive Sciences, Seoul National University College of Natural Sciences, Seoul, South Korea
| | - J Lerch
- Mouse Imaging Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - J D Lewis
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - J Li
- The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - W Liao
- The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - C Liston
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - M V Lombardo
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - J Lv
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Victoria, Australia
- School of Biomedical Engineering and Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - C Lynch
- Weil Family Brain and Mind Research Institute, Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - T T Mallard
- Department of Psychology, University of Texas, Austin, TX, USA
| | - M Marcelis
- Department of Psychiatry and Neuropsychology, School of Mental Health and Neuroscience, EURON, Maastricht University Medical Centre, Maastricht, The Netherlands
- Institute for Mental Health Care Eindhoven (GGzE), Eindhoven, The Netherlands
| | - R D Markello
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - S R Mathias
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - B Mazoyer
- Institute of Neurodegenerative Disorders, CNRS UMR5293, CEA, University of Bordeaux, Bordeaux, France
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - P McGuire
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - M J Meaney
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, Montreal, Quebec, Canada
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - A Mechelli
- Bordeaux University Hospital, Bordeaux, France
| | - N Medic
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - B Misic
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - S E Morgan
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, London, UK
| | - D Mothersill
- Department of Psychology, School of Business, National College of Ireland, Dublin, Ireland
- School of Psychology and Center for Neuroimaging and Cognitive Genomics, National University of Ireland Galway, Galway, Ireland
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - J Nigg
- Department of Psychiatry, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - M Q W Ong
- Center for Sleep and Cognition, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - C Ortinau
- Department of Pediatrics, Washington University in St Louis, St Louis, MO, USA
| | - R Ossenkoppele
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Lund University, Clinical Memory Research Unit, Lund, Sweden
| | - M Ouyang
- Radiology Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - L Palaniyappan
- Robarts Research Institute and The Brain and Mind Institute, University of Western Ontario, London, Ontario, Canada
| | - L Paly
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and Brain @ Caen-Normandie, Cyceron, Caen, France
| | - P M Pan
- Department of Psychiatry, Federal University of Sao Poalo (UNIFESP), Sao Poalo, Brazil
- National Institute of Developmental Psychiatry for Children and Adolescents (INPD), Sao Poalo, Brazil
| | - C Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Carlton South, Victoria, Australia
- Melbourne School of Engineering, The University of Melbourne, Parkville, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - M M Park
- Department of Psychiatry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - T Paus
- Department of Psychiatry, Faculty of Medicine and Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
- Departments of Psychiatry and Psychology, University of Toronto, Toronto, Ontario, Canada
| | - Z Pausova
- The Hospital for Sick Children, Toronto, Ontario, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
| | - D Paz-Linares
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for NeuroInformation, University of Electronic Science and Technology of China, Chengdu, China
- Cuban Neuroscience Center, Havana, Cuba
| | - A Pichet Binette
- Department of Psychiatry, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - K Pierce
- Department of Neuroscience, University of California, San Diego, San Diego, CA, USA
| | - X Qian
- Center for Sleep and Cognition, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - J Qiu
- School of Psychology, Southwest University, Chongqing, China
| | - A Qiu
- Department of Biomedical Engineering, The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
| | - A Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health, Bethesda, MD, USA
| | - T Rittman
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - A Rodrigue
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - C K Rollins
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - R Romero-Garcia
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Instituto de Biomedicina de Sevilla (IBiS) HUVR/CSIC/Universidad de Sevilla, Dpto. de Fisiología Médica y Biofísica, Seville, Spain
| | - L Ronan
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - M D Rosenberg
- Department of Psychology and Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - D H Rowitch
- Department of Paediatrics and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - G A Salum
- Department of Psychiatry, Universidade Federal do Rio Grande do Sul (UFRGS), Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
- National Institute of Developmental Psychiatry (INPD), São Paulo, Brazil
| | - T D Satterthwaite
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Informatics & Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA
| | - H L Schaare
- Otto Hahn Group Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour), Research Centre Juelich, Juelich, Germany
| | - R J Schachar
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - A P Schultz
- Harvard Medical School, Boston, MA, USA
- Harvard Aging Brain Study, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
| | - G Schumann
- Centre for Population Neuroscience and Stratified Medicine (PONS), Institute for Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
- PONS-Centre, Charite Mental Health, Dept of Psychiatry and Psychotherapy, Charite Campus Mitte, Berlin, Germany
| | - M Schöll
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
- Dementia Research Centre, Queen's Square Institute of Neurology, University College London, London, UK
| | - D Sharp
- Department of Brain Sciences, Imperial College London, London, UK
- Care Research and Technology Centre, UK Dementia Research Institute, London, UK
| | - R T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - I Skoog
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - C D Smyser
- Departments of Neurology, Pediatrics, and Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - R A Sperling
- Harvard Medical School, Boston, MA, USA
- Harvard Aging Brain Study, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - D J Stein
- SA MRC Unit on Risk and Resilience in Mental Disorders, Dept of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - A Stolicyn
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - J Suckling
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - G Sullivan
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - Y Taki
- Institute of Development, Aging and Cancer, Tohoku University, Seiryocho, Aobaku, Sendai, Japan
| | - B Thyreau
- Institute of Development, Aging and Cancer, Tohoku University, Seiryocho, Aobaku, Sendai, Japan
| | - R Toro
- Université de Paris, Paris, France
- Department of Neuroscience, Institut Pasteur, Paris, France
| | - N Traut
- Department of Neuroscience, Institut Pasteur, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - K A Tsvetanov
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - N B Turk-Browne
- Department of Psychology, Yale University, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
| | - J J Tuulari
- Department of Clinical Medicine, Department of Psychiatry and Turku Brain and Mind Center, FinnBrain Birth Cohort Study, University of Turku and Turku University Hospital, Turku, Finland
- Department of Clinical Medicine, University of Turku, Turku, Finland
- Turku Collegium for Science, Medicine and Technology, University of Turku, Turku, Finland
| | - C Tzourio
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, U1219, CHU Bordeaux, Bordeaux, France
| | - É Vachon-Presseau
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada
| | | | - P A Valdes-Sosa
- The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China
- Alan Edwards Centre for Research on Pain (AECRP), McGill University, Montreal, Quebec, Canada
| | - S L Valk
- Institute for Neuroscience and Medicine 7, Forschungszentrum Jülich, Jülich, Germany
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - T van Amelsvoort
- Department of Psychiatry and Neurosychology, Maastricht University, Maastricht, The Netherlands
| | - S N Vandekar
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - L Vasung
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - L W Victoria
- Weill Cornell Institute of Geriatric Psychiatry, Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - S Villeneuve
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
- Department of Psychiatry, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - A Villringer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Clinic for Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany
| | - P E Vértes
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, London, UK
| | - K Wagstyl
- Wellcome Centre for Human Neuroimaging, London, UK
| | - Y S Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Developmental Population Neuroscience Research Center, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
- National Basic Science Data Center, Beijing, China
- Research Center for Lifespan Development of Brain and Mind, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - S K Warfield
- Computational Radiology Laboratory, Boston Children's Hospital, Boston, MA, USA
| | - V Warrier
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - E Westman
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - M L Westwater
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - H C Whalley
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - A V Witte
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Clinic for Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany
- Faculty of Medicine, CRC 1052 'Obesity Mechanisms', University of Leipzig, Leipzig, Germany
| | - N Yang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Developmental Population Neuroscience Research Center, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
- National Basic Science Data Center, Beijing, China
- Research Center for Lifespan Development of Brain and Mind, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - B Yeo
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Centre for Sleep and Cognition and Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine, National University of Singapore, Singapore, Singapore
- Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore, Singapore
| | - H Yun
- Division of Newborn Medicine and Neuroradiology, Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - A Zalesky
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia
| | - H J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - A Zettergren
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
| | - J H Zhou
- Center for Sleep and Cognition, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Center for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - H Ziauddeen
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - A Zugman
- National Institute of Developmental Psychiatry for Children and Adolescents (INPD), Sao Poalo, Brazil
- National Institute of Mental Health (NIMH), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Psychiatry, Escola Paulista de Medicina, São Paulo, Brazil
| | - X N Zuo
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Developmental Population Neuroscience Research Center, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
- National Basic Science Data Center, Beijing, China
- Research Center for Lifespan Development of Brain and Mind, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Brain and Education, School of Education Science, Nanning Normal University, Nanning, China
| | - E T Bullmore
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - A F Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
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Asif A, Qureshi TM, Zeeshan S, Sher F, Ayub M, Yaqub K, Baig A, Rehman A, Asif Khan M. Application of 6 MeV LINAC in Food Industries: Enhancement of shelf life of onion, Potato and Mango. Radiat Phys Chem Oxf Engl 1993 2022. [DOI: 10.1016/j.radphyschem.2022.110058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mohan S, Foy V, Ayub M, Leong HS, Schofield P, Sahoo S, Descamps T, Kilerci B, Smith NK, Carter M, Priest L, Zhou C, Carr TH, Miller C, Faivre-Finn C, Blackhall F, Rothwell DG, Dive C, Brady G. Profiling of Circulating Free DNA Using Targeted and Genome-wide Sequencing in Patients with SCLC. J Thorac Oncol 2020; 15:216-230. [PMID: 31629061 PMCID: PMC7001105 DOI: 10.1016/j.jtho.2019.10.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/14/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Abstract
INTRODUCTION SCLC accounts for approximately 250,000 deaths worldwide each year. Acquisition of adequate tumor biopsy samples is challenging, and liquid biopsies present an alternative option for patient stratification and response monitoring. METHODS We applied whole genome next-generation sequencing to circulating free DNA (cfDNA) from 39 patients with limited-stage (LS) SCLC and 30 patients with extensive-stage SCLC to establish genome-wide copy number aberrations and also performed targeted mutation analysis of 110 SCLC associated genes. Quantitative metrics were calculated for copy number aberrations, including percent genome amplified (PGA [the percentage of genomic regions amplified]), Z-score (a measure of standard deviation), and Moran's I (a measure of spatial autocorrelation). In addition CellSearch, an epitope-dependent enrichment platform, was used to enumerate circulating tumor cells (CTCs) from a parallel blood sample. RESULTS Genome-wide and targeted cfDNA sequencing data identified tumor-related changes in 94% of patients with LS SCLC and 100% of patients with extensive-stage SCLC. Parallel analysis of CTCs based on at least 1 CTC/7.5 mL of blood increased tumor detection frequencies to 95% for LS SCLC. Both CTC counts and cfDNA readouts correlated with disease stage and overall survival. CONCLUSIONS We demonstrate that a simple cfDNA genome-wide copy number approach provides an effective means of monitoring patients through treatment and show that targeted cfDNA sequencing identifies potential therapeutic targets in more than 50% of patients. We are now incorporating this approach into additional studies and trials of targeted therapies.
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Affiliation(s)
- Sumitra Mohan
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Victoria Foy
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Mahmood Ayub
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Hui Sun Leong
- Computational Biology Support, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Pieta Schofield
- Computational Biology Support, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Sudhakar Sahoo
- Computational Biology Support, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Tine Descamps
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Bedirhan Kilerci
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Nigel K Smith
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Mathew Carter
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Lynsey Priest
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Cong Zhou
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - T Hedley Carr
- Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Crispin Miller
- Computational Biology Support, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Corinne Faivre-Finn
- Christie National Health Service Foundation Trust, Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - Fiona Blackhall
- Christie National Health Service Foundation Trust, Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - Dominic G Rothwell
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom.
| | - Caroline Dive
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Gerard Brady
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
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Southam S, Ayub M, Krebs M, Rothwell D, Graham D, Stevenson J. Application of variant interpretation software to decipher pathogenicity of mutations for a molecular tumour board (MTB). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz413.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Ijaz M, Ayub M. Thermally stratified flow of Jeffrey fluid with homogeneous-heterogeneous reactions and non-Fourier heat flux model. Heliyon 2019; 5:e02303. [PMID: 31517091 PMCID: PMC6728308 DOI: 10.1016/j.heliyon.2019.e02303] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/18/2019] [Accepted: 08/09/2019] [Indexed: 11/29/2022] Open
Abstract
This article investigates the mixed convective flow of Jeffrey fluid near the axisymmetric stagnation point over an inclined permeable stretching cylinder. Analysis subjected to Cattaneo-Christov heat flux, thermal stratification and homogeneous-heterogeneous reactions are accounted. Suitable transformations are employed to obtain nonlinear ordinary differential system. Non-dimensional system is computed by Homotopy technique. Graphs and tables are constructed to analyze the influence of different flow parameters on temperature, concentration and velocity fields. The interpretation of skin friction coefficient is deliberated. It is noticed from obtained results that temperature is a decreasing function of thermal stratification parameter. Reverse behaviour of concentration is witnessed for higher estimations of homogeneous and heterogeneous parameters. Numerical results are compared with previous published results and found to be in good agreement for special casesof the emerging parameters.
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Affiliation(s)
- M Ijaz
- Department of Mathematics, Quaid-I-Azam University 45320, Islamabad, 44000, Pakistan
| | - M Ayub
- Department of Mathematics, Quaid-I-Azam University 45320, Islamabad, 44000, Pakistan
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Mohan S, Ayub M, Rothwell DG, Gulati S, Kilerci B, Hollebecque A, Sun Leong H, Smith NK, Sahoo S, Descamps T, Zhou C, Hubner RA, McNamara MG, Lamarca A, Valle JW, Dive C, Brady G. Analysis of circulating cell-free DNA identifies KRAS copy number gain and mutation as a novel prognostic marker in Pancreatic cancer. Sci Rep 2019; 9:11610. [PMID: 31406261 PMCID: PMC6690979 DOI: 10.1038/s41598-019-47489-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/12/2019] [Indexed: 11/09/2022] Open
Abstract
Serial biopsy of pancreatic ductal adenocarcinoma (PDAC), to chart tumour evolution presents a significant challenge. We examined the utility of circulating free DNA (cfDNA) as a minimally invasive approach across a cohort of 55 treatment-naïve patients with PDAC; 31 with metastatic and 24 with locally advanced disease. Somatic mutations in cfDNA were detected using next generation sequencing in 15/24 (62.5%) and 27/31 (87%) of patients with locally advanced and metastatic disease, respectively. Copy number changes were detected in cfDNA of 10 patients of whom 7 exhibited gain of chromosome 12p harbouring KRAS as well as a canonical KRAS codon 12 mutation. In multivariable Cox Regression analysis, we show for the first time that patients with KRAS copy number gain and KRAS mutation have significantly worse outcomes, suggesting that this may be linked to PDAC progression. The simple cfDNA assay we describe will enable determination of the presence of KRAS copy number gain and KRAS mutations in larger studies and clinical trials.
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Affiliation(s)
- Sumitra Mohan
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Mahmood Ayub
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Dominic G Rothwell
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Sakshi Gulati
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Bedirhan Kilerci
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Antoine Hollebecque
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Hui Sun Leong
- Computational Biology Support, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, M20 4BX, Macclesfield, UK
| | - Nigel K Smith
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Sudhakar Sahoo
- Computational Biology Support, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, M20 4BX, Macclesfield, UK
| | - Tine Descamps
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Cong Zhou
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Richard A Hubner
- Medical Oncology Department, The Christie NHS Foundation Trust; Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, United Kingdom
| | - Mairéad G McNamara
- Medical Oncology Department, The Christie NHS Foundation Trust; Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, United Kingdom
- Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, UK
| | - Angela Lamarca
- Medical Oncology Department, The Christie NHS Foundation Trust; Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, United Kingdom
| | - Juan W Valle
- Medical Oncology Department, The Christie NHS Foundation Trust; Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, United Kingdom
- Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, UK
| | - Caroline Dive
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK
| | - Ged Brady
- Clinical Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, SK10 4TG, Macclesfield, UK.
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Kim CS, Mohan S, Ayub M, Rothwell DG, Dive C, Brady G, Miller C. In silico error correction improves cfDNA mutation calling. Bioinformatics 2019; 35:2380-2385. [PMID: 30520956 PMCID: PMC6612818 DOI: 10.1093/bioinformatics/bty1004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/13/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Circulating-free DNA (cfDNA) profiling by sequencing is an important minimally invasive protocol for monitoring the mutation profile of solid tumours in cancer patients. Since the concentration of available cfDNA is limited, sample library generation relies on multiple rounds of PCR amplification, during which the accumulation of errors results in reduced sensitivity and lower accuracy. RESULTS We present PCR Error Correction (PEC), an algorithm to identify and correct errors in short read sequencing data. It exploits the redundancy that arises from multiple rounds of PCR amplification. PEC is particularly well suited to applications such as single-cell sequencing and circulating tumour DNA (ctDNA) analysis, in which many cycles of PCR are used to generate sufficient DNA for sequencing from small amounts of starting material. When applied to ctDNA analysis, PEC significantly improves mutation calling accuracy, achieving similar levels of performance to more complex strategies that require additional protocol steps and access to calibration DNA datasets. AVAILABILITY AND IMPLEMENTATION PEC is available under the GPL-v3 Open Source licence, and is freely available from: https://github.com/CRUKMI-ComputationalBiology/PCR_Error_Correction.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chang Sik Kim
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute
- Medical Research Council Manchester Single Cell Research Centre
- RNA Biology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Manchester, UK
| | - Sumitra Mohan
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute
| | - Mahmood Ayub
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute
| | - Dominic G Rothwell
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute
| | - Caroline Dive
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute
- Medical Research Council Manchester Single Cell Research Centre
| | - Ged Brady
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute
- Medical Research Council Manchester Single Cell Research Centre
| | - Crispin Miller
- Medical Research Council Manchester Single Cell Research Centre
- RNA Biology Group, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Manchester, UK
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Ijaz M, Ayub M, Khan H. Entropy generation and activation energy mechanism in nonlinear radiative flow of Sisko nanofluid: rotating disk. Heliyon 2019; 5:e01863. [PMID: 31194133 PMCID: PMC6551480 DOI: 10.1016/j.heliyon.2019.e01863] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/28/2019] [Accepted: 05/12/2019] [Indexed: 10/29/2022] Open
Abstract
The theme of the present communication is to explore the novel analysis of entropy generation optimization, binary chemical reaction and activation energy for nonlinear convective flow of Sisko model on a radially stretchable rotating disk in the presence of a uniform vertical magnetic field. Nonlinear mixed convection, nonlinear thermal radiation, MHD, viscous dissipation, Joule heating and non-uniform heat generation/absorption are also considered. Nanofluid model includes significant slip mechanism of Brownian motion and thermophoresis. Apposite transformations are endorsed to get the nonlinear coupled ODEs system. The resultant system of ordinary differential equations is endeavoured for series solutions through homotopic technique. Total entropy generation is inspected through numerous emerging flow variables. Comparative study is made for temperature, velocity, heat transfer rate, Bejan number, entropy generation and mass transfer Nusselt number by considering shear thickening and thinning fluids. Finally, a comparison is specified with the previous existing results.
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Affiliation(s)
- M Ijaz
- Department of Mathematics, Quaid-I-Azam University 45320, Islamabad, 44000, Pakistan
| | - M Ayub
- Department of Mathematics, Quaid-I-Azam University 45320, Islamabad, 44000, Pakistan
| | - H Khan
- Machine Intelligence Research Labs (MIR Labs), Auburn, USA
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10
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Rothwell DG, Ayub M, Cook N, Thistlethwaite F, Carter L, Dean E, Smith N, Villa S, Dransfield J, Clipson A, White D, Nessa K, Ferdous S, Howell M, Gupta A, Kilerci B, Mohan S, Frese K, Gulati S, Miller C, Jordan A, Eaton H, Hickson N, O'Brien C, Graham D, Kelly C, Aruketty S, Metcalf R, Chiramel J, Tinsley N, Vickers AJ, Kurup R, Frost H, Stevenson J, Southam S, Landers D, Wallace A, Marais R, Hughes AM, Brady G, Dive C, Krebs MG. Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study. Nat Med 2019; 25:738-743. [PMID: 31011204 DOI: 10.1038/s41591-019-0380-z] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/30/2019] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) supports blood-based genomic profiling but is not yet routinely implemented in the setting of a phase I trials clinic. TARGET is a molecular profiling program with the primary aim to match patients with a broad range of advanced cancers to early phase clinical trials on the basis of analysis of both somatic mutations and copy number alterations (CNA) across a 641 cancer-associated-gene panel in a single ctDNA assay. For the first 100 TARGET patients, ctDNA data showed good concordance with matched tumor and results were turned round within a clinically acceptable timeframe for Molecular Tumor Board (MTB) review. When a 2.5% variant allele frequency (VAF) threshold was applied, actionable mutations were identified in 41 of 100 patients, and 11 of these patients received a matched therapy. These data support the application of ctDNA in this early phase trial setting where broad genomic profiling of contemporaneous tumor material enhances patient stratification to novel therapies and provides a practical template for bringing routinely applied blood-based analyses to the clinic.
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Affiliation(s)
- Dominic G Rothwell
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Mahmood Ayub
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Natalie Cook
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Fiona Thistlethwaite
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Louise Carter
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Emma Dean
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Nigel Smith
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Shaun Villa
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Joanne Dransfield
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Alexandra Clipson
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Daniel White
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Kamrun Nessa
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Saba Ferdous
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Matthew Howell
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Avinash Gupta
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Bedirhan Kilerci
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Sumitra Mohan
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Kris Frese
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Sakshi Gulati
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Crispin Miller
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Allan Jordan
- Drug Discovery Unit, CRUK Manchester Institute, Manchester, UK
| | - Helen Eaton
- North West Centre for Genomic Medicine, Manchester, UK
| | | | - Ciara O'Brien
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Donna Graham
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Claire Kelly
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Sreeja Aruketty
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Robert Metcalf
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Jaseela Chiramel
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Nadina Tinsley
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Alexander J Vickers
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Roopa Kurup
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Hannah Frost
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK
| | - Julie Stevenson
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Siobhan Southam
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Dónal Landers
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
- Innovative Medicines Biotech Unit AstraZeneca, Cambridge, UK
| | | | - Richard Marais
- Molecular Oncology Group, CRUK Manchester Institute, Manchester, UK
| | - Andrew M Hughes
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Ged Brady
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK
| | - Caroline Dive
- Clinical Experimental Pharmacology Group, CRUK Manchester Institute, Manchester, UK.
- Manchester Centre for Cancer Biomarker Sciences, University of Manchester, Manchester, UK.
| | - Matthew G Krebs
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, UK.
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
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11
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Rashid S, Khan MI, Hayat T, Ayub M, Alsaedi A. Theoretical and analytical analysis of shear rheology of Oldroyd-B fluid with homogeneous–heterogeneous reactions. Appl Nanosci 2019. [DOI: 10.1007/s13204-019-01037-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Rashid S, Khan MI, Hayat T, Ayub M, Alsaedi A. Darcy–Forchheimer flow of Maxwell fluid with activation energy and thermal radiation over an exponential surface. Appl Nanosci 2019. [DOI: 10.1007/s13204-019-01008-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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13
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Rack S, Brady G, Wallace A, Galvin M, Frese K, Krebs M, Dive C, Rothwell D, Ayub M, Cook N. Molecular profiling of tumour and ctDNA in a gastrointestinal cancer cohort at an academic cancer centre. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy314.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Mohan S, Foy V, Leong HS, Schofield PG, Ayub M, Smith NK, Sahoo S, Sik-Kim C, Priest L, Carter M, Carr HT, Miller C, Finn-Faivre C, Blackhall F, Rothwell DG, Dive C, Brady G. Abstract 5602: Detection of circulating cell-free tumor DNA (ctDNA) in patients with small cell lung cancer (SCLC). Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Tumor genomes can be reconstructed from the molecular information obtained from circulating cell-free DNA (cfDNA) and circulating tumor cells (CTCs) obtained from the peripheral blood of patients with cancer. The analysis of cfDNA and CTCs is a minimally invasive approach and represents a powerful research tool, with potential as a companion diagnostic for both patient stratification and monitoring. Here, we use cfDNA next-generation sequencing (NGS) analysis to assess and compare ctDNA profiles in patients with SCLC.
Methods: Whole genome sequencing (WGS) libraries were prepared from cfDNA isolated from the pre-treatment peripheral blood samples from 69 patients and 32 cancer-free controls. Libraries were subjected to WGS to establish genome wide copy number aberrations (CNA) as well as targeted mutation analysis of 110 SCLC associated genes. Quantitative metrics were calculated from CNA such as Percent Genome Altered (PGA; percentage of genomic regions altered), Z-score (measure of standard deviation) and Moran's I (measure of spatial autocorrelation). In addition CellSearch®, an epitope dependent enrichment platform was used to enumerate CTCs from a parallel blood sample.
Results: An examination of CNA patterns revealed SCLC associated changes such as losses on chromosomes 3p, 5q and 17p and gains on chromosome 3q and 5p as well as amplification of MYC in 21/69 (30%) and SOX2 in 36/69 (52%) as well losses on FHIT in 40/69 (58%), RASSFI in 38/69(55%) and RB1 in 24/69 (35%) patients. A combination of three CNA metrics enabled detection of tumor associated changes in 58/64 (84%) patients, with Moran's I emerging as the most sensitive CNA metric for detecting ctDNA. Targeted NGS detected tumor associated mutations in 60/64 (94%) with TP53 mutations detected in 50 patients (83% of patients with any detectable ctDNA). Somatic mutations and CNA were detected in both limited stage SCLC (LS-SCLC, confined to 1 hemithorax) and extensive stage (ES-SCLC, with distant metastases) with statistically significant differences seen for CNA metrics and variant allele frequencies of mutations consistent with higher levels of ctDNA in ES-SCLC. However, no significant differences between ES and LS were observed in the mutation patterns with respect to DNA damage repair, RAS and PI3K and transcriptional regulation pathways between the two stages of SCLC. There was considerable overlap between the detection of ctDNA and CTC counts, with cfDNA NGS readouts detecting tumor related changes in 96% of patients and CTCs were detected only in 76% of patients.
Conclusion: We have established sensitive methods for detecting ctDNA in cfDNA and combined with CTC enumeration we have an effective liquid biopsy for 98% of patients (96% in LS and 100% in ES) in this cohort. Future work will involve utilising this optimised NGS approach in an independent cohort of patients to correlate cfDNA metrics with clinical outcome.
Citation Format: Sumitra Mohan, Victoria Foy, Hui Sun Leong, Pietà G. Schofield, Mahmood Ayub, Nigel K. Smith, Sudhakar Sahoo, Chang Sik-Kim, Lynsey Priest, Mathew Carter, Hedley T. Carr, Crispin Miller, Corinne Finn-Faivre, Fiona Blackhall, Dominic G. Rothwell, Caroline Dive, Gerard Brady. Detection of circulating cell-free tumor DNA (ctDNA) in patients with small cell lung cancer (SCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5602.
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Affiliation(s)
- Sumitra Mohan
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | - Victoria Foy
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | - Hui Sun Leong
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | | | - Mahmood Ayub
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | - Nigel K. Smith
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | - Sudhakar Sahoo
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | - Chang Sik-Kim
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | - Lynsey Priest
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | - Mathew Carter
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | | | - Crispin Miller
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | | | - Fiona Blackhall
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | | | - Caroline Dive
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
| | - Gerard Brady
- 1Cancer Research UK-Manchester Institute, Manchester, United Kingdom
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Stevenson J, Ayub M, Dransfield S, Shing E, Barley D, Dunne R, Westaway M, Landers D, Krebs M. PO-047 Etarget: a digital science solution to integrate clinical and genomic data for the manchester molecular tumour board (MTB). ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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16
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Pan T, Yan P, Yang M, Wang H, Ali I, Ayub M, Zhang JH, Wang JJ, Li E, Xue H, Zhang BW, Wu XB. Genetic differentiation of regional populations of the widespread Asiatic toad (Bufo gargarizans), as revealed by development of novel microsatellite markers. AUST J ZOOL 2018. [DOI: 10.1071/zo18059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Dispersal is a key component of a species’ life history, by influencing population persistence, genetic structure, adaptation and maintenance of genetic diversity. The Asiatic toad (Bufo gargarizans) is a widespread species in east Asia. However, we still have no knowledge of what kind of geographical scale equates to genetic differentiation within B. gargarizans. In this study, the population genetics of B. gargarizans was studied at five localities, with the Yangtze River running through the sampling area, in order to detect the level of genetic differentiation and the natural barriers to the species’ dispersal on a small geographic scale, by means of the development and use of novel microsatellite loci. These markers revealed a relatively high level of genetic diversity. Distinct genetic structure among populations in B. gargarizans was observed, as described by genetic distance, AMOVA, PCA and Geneland results. A weak but significant positive correlation between genetic distance and geographical distance. The combination of these findings suggests that the Yangtze River and geographic distance may act as effective barriers for B. gargarizans. These results serve as benchmark data for understanding the impacts of dispersal barriers and continued landscape research on B. gargarizans.
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17
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Chiu A, Ayub M, Dive C, Brady G, Miller CJ. twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis. Bioinformatics 2017; 33:2743-2745. [PMID: 28475662 PMCID: PMC5860069 DOI: 10.1093/bioinformatics/btx308] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/18/2017] [Accepted: 05/04/2017] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Droplet Digital PCR (ddPCR) is a sensitive platform used to quantify specific nucleic acid molecules amplified by polymerase chain reactions. Its sensitivity makes it particularly useful for the detection of rare mutant molecules, such as those present in a sample of circulating free tumour DNA obtained from cancer patients. ddPCR works by partitioning a sample into individual droplets for which the majority contain only zero or one target molecule. Each droplet then becomes a reaction chamber for PCR, which through the use of fluorochrome labelled probes allows the target molecules to be detected by measuring the fluorescence intensity of each droplet. The technology supports two channels, allowing, for example, mutant and wild type molecules to be detected simultaneously in the same sample. As yet, no open source software is available for the automatic gating of two channel ddPCR experiments in the case where the droplets can be grouped into four clusters. Here, we present an open source R package 'twoddpcr', which uses Poisson statistics to estimate the number of molecules in such two channel ddPCR data. Using the Shiny framework, an accompanying graphical user interface (GUI) is also included for the package, allowing users to adjust parameters and see the results in real-time. AVAILABILITY AND IMPLEMENTATION twoddpcr is available from Bioconductor (3.5) at https://bioconductor.org/packages/twoddpcr/ . A Shiny-based GUI suitable for non-R users is available as a standalone application from within the package and also as a web application at http://shiny.cruk.manchester.ac.uk/twoddpcr/ . CONTACT ged.brady@cruk.manchester.ac.uk or crispin.miller@cruk.manchester.ac.uk. PACKAGE MAINTAINER anthony.chiu@cruk.manchester.ac.uk.
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Affiliation(s)
- Anthony Chiu
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Mahmood Ayub
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Caroline Dive
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Ged Brady
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Crispin J Miller
- RNA Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
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18
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Gupta A, Ayub M, Miller C, Rothwell D, Wallace A, Jordan A, Cook N, Thistlethwaite F, Carter L, O’Brien C, Aruketty S, Dean E, Hudson A, Frese K, Dransfield J, Hughes A, Marais R, Dive C, Brady G, Krebs M. Development of the Manchester Cancer Research Centre Molecular Tumour Board for matching patients to clinical trials based on tumour and ctDNA genetic profiling. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Hayat T, Zubair M, Waqas M, Alsaedi A, Ayub M. On stratified variable thermal conductivity stretched flow of Walter-B material subject to non-Fourier flux theory. Neural Comput Appl 2017. [DOI: 10.1007/s00521-017-3013-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Hayat T, Zubair M, Waqas M, Alsaedi A, Ayub M. Impact of variable thermal conductivity in doubly stratified chemically reactive flow subject to non-Fourier heat flux theory. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.03.077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Ayub M, Gulati S, Mohan S, Rothwell D, Leong HS, Chudziak J, Sahoo S, Smith N, Mesquita B, Antonello J, Aung K, Lamarca A, Backen A, McNamara M, Miller C, Valle J, Dive C, Brady G. Molecular analysis of circulating free nucleic acids and CTC genomes in patients with pancreatic adenocarcinoma. Eur J Surg Oncol 2016. [DOI: 10.1016/j.ejso.2016.07.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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22
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Rothwell D, Ayub M, Gulati S, Brognard J, Wallace A, Miller C, Dean EJ, Cook N, Thistlethwaite F, Leong HS, Eaton H, Howard E, Hudson A, Siswick C, Dransfield J, Christodolou M, Smith N, Carter L, Metcalf R, Aruketty S, Chiramel J, Hughes A, Marais R, Dive C, Brady G, Krebs MG. The TARGET trial: Molecular profiling of circulating tumour DNA to stratify patients to early phase clinical trials. Eur J Surg Oncol 2016. [DOI: 10.1016/j.ejso.2016.07.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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23
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Sawal H, Harripaul R, Mikhailov A, Dad R, Ayub M, Jawad Hassan M, Vincent J. Biallelic truncatingSCN9Amutation identified in four families with congenital insensitivity to pain from Pakistan. Clin Genet 2016; 90:563-565. [DOI: 10.1111/cge.12860] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 01/22/2023]
Affiliation(s)
- H.A. Sawal
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute; Centre for Addiction and Mental Health; Toronto ON Canada
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology (NUST); Islamabad Pakistan
| | - R. Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute; Centre for Addiction and Mental Health; Toronto ON Canada
- Institute of Medical Science; University of Toronto; Toronto ON Canada
| | - A. Mikhailov
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute; Centre for Addiction and Mental Health; Toronto ON Canada
| | - R. Dad
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology (NUST); Islamabad Pakistan
| | - M. Ayub
- Department of Psychiatry; Queen's University; Kingston ON Canada
| | - M. Jawad Hassan
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology (NUST); Islamabad Pakistan
| | - J.B. Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute; Centre for Addiction and Mental Health; Toronto ON Canada
- Institute of Medical Science; University of Toronto; Toronto ON Canada
- Department of Psychiatry; University of Toronto; Toronto ON Canada
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24
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Gremel G, Lee RJ, Girotti MR, Mandal AK, Valpione S, Garner G, Ayub M, Wood S, Rothwell DG, Fusi A, Wallace A, Brady G, Dive C, Dhomen N, Lorigan P, Marais R. Distinct subclonal tumour responses to therapy revealed by circulating cell-free DNA. Ann Oncol 2016; 27:1959-65. [PMID: 27502704 PMCID: PMC5035787 DOI: 10.1093/annonc/mdw278] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/01/2016] [Accepted: 07/12/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The application of precision medicine in oncology requires in-depth characterisation of a patient's tumours and the dynamics of their responses to treatment. PATIENTS AND METHODS We used next-generation sequencing of circulating cell-free DNA (cfDNA) to monitor the response of a KIT p.L576P-mutant metastatic vaginal mucosal melanoma to sequential targeted, immuno- and chemotherapy. RESULTS Despite a KIT mutation, the response to imatinib was mixed. Unfortunately, tumours were not accessible for molecular analysis. To study the mechanism underlying the mixed clinical response, we carried out whole-exome sequencing and targeted longitudinal analysis of cfDNA. This revealed two tumour subclones; one with a KIT mutation that responded to imatinib and a second KIT-wild-type subclone that did not respond to imatinib. Notably, the subclones also responded differently to immunotherapy. However, both subclones responded to carboplatin/paclitaxel, and although the KIT-wild-type subclone progressed after chemotherapy, it responded to subsequent re-administration of paclitaxel. CONCLUSION We show that cfDNA can reveal tumour evolution and subclonal responses to therapy even when biopsies are not available.
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Affiliation(s)
- G Gremel
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester
| | - R J Lee
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester
| | - M R Girotti
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester
| | - A K Mandal
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester
| | - S Valpione
- The University of Manchester, The Christie NHS Foundation Trust, Manchester
| | - G Garner
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester
| | - M Ayub
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester
| | - S Wood
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester
| | - D G Rothwell
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester
| | - A Fusi
- The University of Manchester, The Christie NHS Foundation Trust, Manchester
| | - A Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester NHS Foundation Trust, Manchester, UK
| | - G Brady
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester
| | - C Dive
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester
| | - N Dhomen
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester
| | - P Lorigan
- The University of Manchester, The Christie NHS Foundation Trust, Manchester
| | - R Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester
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26
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Chaudhry Q, Ayub M, Tanveer M. Electrochemical treatment of cancerous tissue of liver using the techniques of mathematical modeling. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.1478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Brady G, Rothwell D, Ayub M, Smith N, Mohan S, Chudziak J, Aung K, Hubner R, Miller C, Backen A, Leong HS, Gulati S, Kim CS, Lamarca A, McNamara M, Valle J, Dive C. Abstract 3960: Combined circulating tumour cell (CTC) and circulating tumor DNA (ctDNA) analysis of blood from patients with pancreatic cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-3960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
The challenge to improve outcomes for patients diagnosed with advanced pancreatic cancer remains very real with only small improvements in median survival gained by the use of systemic chemotherapy and little improvement in 5-year survival over the past decades. The advent of next generation sequencing (NGS) of tumor nucleic acids has opened up the possibility of improving outcomes through personalized therapies selected on the basis of tumor genetics.
Whilst NGS biomarkers can be measured in tumor biopsies sampled shortly before and after treatment this is often not practical for ethical, logistical and simple lack of availability. To circumvent problems associated with tumor sampling we have developed and evaluated blood-borne nucleic acids biomarkers for patients diagnosed with advanced pancreatic cancer.
Approach
We developed a NGS circulating free DNA (cfDNA) analysis pipeline based on the generation of whole genome NGS libraries followed by sequencing of over 600 cancer-associated genes using Agilent SureSelect. Using whole blood collected with Streck cell free DNA blood collection tubes (cfDNA BCT) we optimised combined circulating tumor cell (CTC) enrichment and cfDNA isolation. Quantitative measurements of KRAS mutations using both NGS and droplet digital PCR (ddPCR) were used to compare the tumor component present in both CTCs and cfDNA. We evaluated the overall approach using External Quality Assessment (EQA) controls and over 50 advanced pancreatic cancer patient samples. For CTC analysis we also compared epitope dependent (CellSearch) and independent (Parsortix) enrichment.
Results
After applying our NGS pipeline to 5 EQA genomic controls we identified all 14 known mutations correctly indicating high sensitivity and specificity. Both ddPCR and NGS identified KRAS mutations in patient cfDNA with a higher success rate seen for ddPCR consistent with the higher sensitivity of this methodology. From the NGS output additional mutations were detected in samples which either harboured or lacked detectable KRAS mutations. Consistent with previous observations CellSearch CTCs were detected at low levels in around 20% of patients with a similar frequency seen in initial analysis of CTCs obtained by epitope independent enrichment (Parsortix). In general KRAS mutations were detected at a higher level in patient cfDNA compared to enriched CTCs although some patients showed detectable CTC KRAS mutations with no KRAS mutations detected in their cfDNA by either ddPCR or NGS. Ongoing analysis is aimed at establishing if the molecular observations correlate with clinical outcome.
Conclusion
Combined CTC enrichment and cfDNA isolation is readily achievable using a single Streck cfDNA BCT. Results indicate that combined CTC and cfDNA analysis is more sensitive than either approach alone.
Citation Format: Ged Brady, Dominic Rothwell, Mahmood Ayub, Nigel Smith, Sumitra Mohan, Jakub Chudziak, Kyaw Aung, Richard Hubner, Crispin Miller, Alison Backen, Hui Sun Leong, Sakshi Gulati, Chang Sik Kim, Angela Lamarca, Mairéad McNamara, Juan Valle, Caroline Dive. Combined circulating tumour cell (CTC) and circulating tumor DNA (ctDNA) analysis of blood from patients with pancreatic cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3960.
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Affiliation(s)
- Ged Brady
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | | | - Mahmood Ayub
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Nigel Smith
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Sumitra Mohan
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | | | - Kyaw Aung
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Richard Hubner
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | | | - Alison Backen
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Hui Sun Leong
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Sakshi Gulati
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Chang Sik Kim
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Angela Lamarca
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | | | - Juan Valle
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Caroline Dive
- 1CRUK Manchester Institute, Manchester, United Kingdom
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Chiu A, Brady G, Ayub M, Dive C, Miller C. An open source R package for Droplet Digital PCR analysis. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61656-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kim C, Gulati S, Ayub M, Rothwell D, Mohan S, Dive C, Brady G, Miller C. A novel PCR error correction algorithm for cell-free DNA next generation sequencing data using high performance computing. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61660-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Krebs M, Dive C, Dean EJ, Rothwell DG, Brognard J, Wallace A, Miller C, Cook N, Rafii S, Ayub M, Leong HS, Siswick C, Chapman P, Smith N, Jordan A, Hughes AM, Marais R, Brady G. TARGET trial: Molecular profiling of circulating tumour DNA to stratify patients to early phase clinical trials. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.tps11614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Matthew Krebs
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Caroline Dive
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Emma Jane Dean
- University of Manchester, The Christie Hospital NHS Foundation Trust, Manchester, United Kingdom
| | | | - John Brognard
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Andrew Wallace
- Regional Molecular Genetics Service, St Mary's Hospital, Manchester, United Kingdom
| | - Crispin Miller
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Natalie Cook
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Saeed Rafii
- Sarah Cannon Research Institute, London, United Kingdom
| | - Mahmood Ayub
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Hui-Sun Leong
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Carla Siswick
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Phil Chapman
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Nigel Smith
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Allan Jordan
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Andrew M. Hughes
- Experimental Cancer Medicine Team, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Richard Marais
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Ged Brady
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
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Rothwell DG, Smith N, Morris D, Leong HS, Li Y, Hollebecque A, Ayub M, Carter L, Antonello J, Franklin L, Miller C, Blackhall F, Dive C, Brady G. Genetic profiling of tumours using both circulating free DNA and circulating tumour cells isolated from the same preserved whole blood sample. Mol Oncol 2016; 10:566-74. [PMID: 26639657 PMCID: PMC4834815 DOI: 10.1016/j.molonc.2015.11.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/03/2015] [Accepted: 11/10/2015] [Indexed: 12/19/2022] Open
Abstract
Molecular information obtained from cancer patients' blood is an emerging and powerful research tool with immense potential as a companion diagnostic for patient stratification and monitoring. Blood, which can be sampled routinely, provides a means of inferring the current genetic status of patients' tumours via analysis of circulating tumour cells (CTCs) or circulating tumour DNA (ctDNA). However, accurate assessment of both CTCs and ctDNA requires all blood cells to be maintained intact until samples are processed. This dictates for ctDNA analysis EDTA blood samples must be processed with 4 h of draw, severely limiting the use of ctDNA in multi-site trials. Here we describe a blood collection protocol that is amenable for analysis of both CTCs and ctDNA up to four days after blood collection. We demonstrate that yields of circulating free DNA (cfDNA) obtained from whole blood CellSave samples are equivalent to those obtained from conventional EDTA plasma processed within 4 h of blood draw. Targeted and genome-wide NGS revealed comparable DNA quality and resultant sequence information from cfDNA within CellSave and EDTA samples. We also demonstrate that CTCs and ctDNA can be isolated from the same patient blood sample, and give the same patterns of CNA enabling direct analysis of the genetic status of patients' tumours. In summary, our results demonstrate the utility of a simple approach that enabling robust molecular analysis of CTCs and cfDNA for genotype-directed therapies in multi-site clinical trials and represent a significant methodological improvement for clinical benefit.
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Affiliation(s)
- Dominic G Rothwell
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK.
| | - Nigel Smith
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Daniel Morris
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Hui Sun Leong
- Computational Biology Support, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Yaoyong Li
- Computational Biology Support, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK; Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Antoine Hollebecque
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Mahmood Ayub
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Louise Carter
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Jenny Antonello
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Lynsey Franklin
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Crispin Miller
- Computational Biology Support, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK; RNA Biology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Fiona Blackhall
- Christie NHS Foundation Trust, Institute of Cancer Sciences, University of Manchester, M20 4BX, UK
| | - Caroline Dive
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
| | - Ged Brady
- Nucleic Acid Biomarker Laboratory, Clinical Experimental Pharmacology Group, CR-UK Manchester Institute, University of Manchester, M20 4BX, UK
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Greystoke A, Ayub M, Rothwell DG, Morris D, Burt D, Hodgkinson CL, Morrow CJ, Smith N, Aung K, Valle J, Carter L, Blackhall F, Dive C, Brady G. Development of a circulating miRNA assay to monitor tumor burden: From mouse to man. Mol Oncol 2016; 10:282-91. [PMID: 26654130 PMCID: PMC4750526 DOI: 10.1016/j.molonc.2015.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/08/2015] [Indexed: 01/12/2023] Open
Abstract
Circulating miRNA stability suggests potential utility of miRNA based biomarkers to monitor tumor burden and/or progression, particularly in cancer types where serial biopsy is impractical. Assessment of miRNA specificity and sensitivity is challenging within the clinical setting. To address this, circulating miRNAs were examined in mice bearing human SCLC tumor xenografts and SCLC patient derived circulating tumor cell explant models (CDX). We identified 49 miRNAs using human TaqMan Low Density Arrays readily detectable in 10 μl tail vein plasma from mice carrying H526 SCLC xenografts that were low or undetectable in non-tumor bearing controls. Circulating miR-95 measured serially in mice bearing CDX was detected with tumor volumes as low as 10 mm(3) and faithfully reported subsequent tumor growth. Having established assay sensitivity in mouse models, we identified 26 miRNAs that were elevated in a stage dependent manner in a pilot study of plasma from SCLC patients (n = 16) compared to healthy controls (n = 11) that were also elevated in the mouse models. We selected a smaller panel of 10 previously reported miRNAs (miRs 95, 141, 200a, 200b, 200c, 210, 335#, 375, 429) that were consistently elevated in SCLC, some of which are reported to be elevated in other cancer types. Using a multiplex qPCR assay, elevated levels of miRNAs across the panel were also observed in a further 66 patients with non-small cell lung, colorectal or pancreatic cancers. The utility of this circulating miRNA panel as an early warning of tumor progression across several tumor types merits further evaluation in larger studies.
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Affiliation(s)
- Alastair Greystoke
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK
| | - Mahmood Ayub
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK
| | - Dominic G Rothwell
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK
| | - Dan Morris
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK
| | - Deborah Burt
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK
| | - Cassandra L Hodgkinson
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK
| | - Christopher J Morrow
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK
| | - Nigel Smith
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK
| | - Kyaw Aung
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK; The Christie NHS Foundation Trust, UK
| | - Juan Valle
- The Christie NHS Foundation Trust, UK; Institute of Cancer Sciences, University of Manchester, UK
| | - Louise Carter
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK; The Christie NHS Foundation Trust, UK
| | - Fiona Blackhall
- The Christie NHS Foundation Trust, UK; Institute of Cancer Sciences, University of Manchester, UK
| | - Caroline Dive
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK
| | - Ged Brady
- Clinical & Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, UK.
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Chudziak J, Burt DJ, Mohan S, Rothwell DG, Mesquita B, Antonello J, Dalby S, Ayub M, Priest L, Carter L, Krebs MG, Blackhall F, Dive C, Brady G. Clinical evaluation of a novel microfluidic device for epitope-independent enrichment of circulating tumour cells in patients with small cell lung cancer. Analyst 2016; 141:669-78. [PMID: 26605519 DOI: 10.1039/c5an02156a] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Circulating tumour cells (CTCs) have potential utility as minimally-invasive biomarkers to aid cancer treatment decision making. However, many current CTC technologies enrich CTCs using specific surface epitopes that do not necessarily reflect CTC heterogeneity. Here we evaluated the epitope-independent Parsortix system which enriches CTCs based on size and rigidity using both healthy normal volunteer blood samples spiked with tumour cells and blood samples from patients with small cell lung cancer (SCLC). Blood samples were maintained unfractionated at room temperature for up to 4 days followed by plasma removal for circulating free DNA (cfDNA) isolation and direct application of the remaining cell component to the Parsortix system. For tumour cells expressing the EpCAM cell surface marker the numbers of spiked cells retained using the Parsortix system and by EpCAM-positive selection using CellSearch® were not significantly different, whereas only the Parsortix system showed strong enrichment of cells with undetectable EpCAM expression. In a pilot clinical study we banked both enriched CTCs as well as plasma from SCLC patient blood samples. Upon retrieval of the banked Parsortix cellular samples we could detect cytokeratin positive CTCs in all 12 SCLC patients tested. Interestingly, processing parallel samples from the same patients by EpCAM enrichment using CellSearch® revealed only 83% (10/12) with cytokeratin positive CTCs indicating the Parsortix system is enriching for EpCAM negative SCLC CTCs. Our combined results indicate the Parsortix system is a valuable tool for combined cfDNA isolation and CTC enrichment that enables CTC analysis to be extended beyond dependence on surface epitopes.
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Affiliation(s)
- Jakub Chudziak
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Deborah J Burt
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Sumitra Mohan
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Dominic G Rothwell
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Bárbara Mesquita
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Jenny Antonello
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Suzanne Dalby
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Mahmood Ayub
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Lynsey Priest
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Louise Carter
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Matthew G Krebs
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Fiona Blackhall
- Christie NHS Foundation Trust, Manchester, UK and Institute of Cancer Sciences, University of Manchester, Manchester, UK
| | - Caroline Dive
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
| | - Ged Brady
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, UK.
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Watson M, Small H, Chapman P, Hopkins G, Begum H, Waddell ID, Ashton G, Abbey C, Harris J, Ayub M, Mohan S, Rothwell D, Brady G, Dive C, Jordan A, Ogilvie D. Abstract A176: RET inhibition: Development of novel compounds and a personalized medicine strategy in lung adenocarcinoma. Mol Cancer Ther 2015. [DOI: 10.1158/1535-7163.targ-15-a176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:RET is a receptor tyrosine kinase (RTK) and forms part of a macromolecular receptor complex containing dimerised RET receptor, two co-receptors and a bound ligand. Signalling networks downstream of RET play an important role in regulating cell survival, differentiation, proliferation, migration and chemotaxis. Activating mutations in RET (e.g. C634W and M918T) are known drivers in medullary thyroid carcinomas (MTC). More recently, oncogenic RET fusions (e.g. CCDC6-RET and KIF5B-RET) have been identified in 1-2% of lung adenocarcinoma patients. We are currently developing novel, selective inhibitors of RET, and at the same time, investigating a number of biomarker approaches for the stratification of RET fusion-positive lung cancer patients who might benefit from such therapy.
Methods: We have undertaken collaborative studies using established techniques including immunohistochemistry (IHC) and FISH (DNA break apart and RNA). In addition, we have investigated hybrid capture DNA sequencing of both biopsy material and circulating tumour DNA in the blood. Here we, compare and contrast the benefits of each biomarker assay evaluated and consider how these approaches could be translated for use in Phase I clinical trials at The Christie.
Conclusion: Our data supports the successful implementation of predictive biomarkers to identify patients who might benefit from treatment with selective RET inhibitors.
Acknowledgements:This work was funded by Cancer Research UK (Grant numbers C480/A1141 and C5759/A17098).
Citation Format: Mandy Watson, Helen Small, Phil Chapman, Gemma Hopkins, Habiba Begum, Ian D. Waddell, Garry Ashton, Caron Abbey, Jade Harris, Mahmood Ayub, Sumitra Mohan, Dominic Rothwell, Ged Brady, Caroline Dive, Allan Jordan, Donald Ogilvie. RET inhibition: Development of novel compounds and a personalized medicine strategy in lung adenocarcinoma. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A176.
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Affiliation(s)
- Mandy Watson
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Helen Small
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Phil Chapman
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Gemma Hopkins
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Habiba Begum
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | | | - Garry Ashton
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Caron Abbey
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Jade Harris
- 2Centre for Genomic Medicine, Manchester, United Kingdom
| | - Mahmood Ayub
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Sumitra Mohan
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | | | - Ged Brady
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Caroline Dive
- 1CRUK Manchester Institute, Manchester, United Kingdom
| | - Allan Jordan
- 1CRUK Manchester Institute, Manchester, United Kingdom
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Abstract
Peristaltic flow of magnetohydrodynamic (MHD) Williamson fluid in a symmetric channel is addressed. Modeling is given with Soret and Dufour effects. Channel walls have compliant properties. Analysis has been carried out through long wavelength and low Reynolds number approach. The obtained series solutions for small Weissenberg number are developed. Impact of variables reflecting the salient features of wall properties, Biot numbers and Soret and Dufour on the velocity, temperature and concentration has been point out. Trapping phenomenon is also analyzed.
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Affiliation(s)
- T. Hayat
- Department of Mathematics, Quaid-I-Azam University 45320, Islamabad 44000, Pakistan
- Department of Mathematics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Naheed Batool
- Department of Mathematics, Quaid-I-Azam University 45320, Islamabad 44000, Pakistan
| | - H. Yasmin
- Department of Mathematics, COMSATS Institute of Information Technology, G. T. Road, Wah Cantt 47040, Pakistan
| | - A. Alsaedi
- Department of Mathematics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - M. Ayub
- Department of Mathematics, Quaid-I-Azam University 45320, Islamabad 44000, Pakistan
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Rothwell DG, Li Y, Ayub M, Tate C, Newton G, Hey Y, Carter L, Faulkner S, Moro M, Pepper S, Miller C, Blackhall F, Bertolini G, Roz L, Dive C, Brady G. Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells. BMC Genomics 2014; 15:1129. [PMID: 25519510 PMCID: PMC4320548 DOI: 10.1186/1471-2164-15-1129] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/11/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Although profiling of RNA in single cells has broadened our understanding of development, cancer biology and mechanisms of disease dissemination, it requires the development of reliable and flexible methods. Here we demonstrate that the EpiStem RNA-Amp™ methodology reproducibly generates microgram amounts of cDNA suitable for RNA-Seq, RT-qPCR arrays and Microarray analysis. RESULTS Initial experiments compared amplified cDNA generated by three commercial RNA-Amplification protocols (Miltenyi μMACS™ SuperAmp™, NuGEN Ovation® One-Direct System and EpiStem RNA-Amp™) applied to single cell equivalent levels of RNA (25-50 pg) using Affymetrix arrays. The EpiStem RNA-Amp™ kit exhibited the highest sensitivity and was therefore chosen for further testing. A comparison of Affymetrix array data from RNA-Amp™ cDNA generated from single MCF7 and MCF10A cells to reference controls of unamplified cDNA revealed a high degree of concordance. To assess the flexibility of the amplification system single cell RNA-Amp™ cDNA was also analysed using RNA-Seq and high-density qPCR, and showed strong cross-platform correlations. To exemplify the approach we used the system to analyse RNA profiles of small populations of rare cancer initiating cells (CICs) derived from a NSCLC patient-derived xenograft. RNA-Seq analysis was able to identify transcriptional differences in distinct subsets of CIC, with one group potentially enriched for metastasis formation. Pathway analysis revealed that the distinct transcriptional signatures demonstrated in the CIC subpopulations were significantly correlated with published stem-cell and epithelial-mesenchymal transition signatures. CONCLUSIONS The combined results confirm the sensitivity and flexibility of the RNA-Amp™ method and demonstrate the suitability of the approach for identifying clinically relevant signatures in rare, biologically important cell populations.
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Affiliation(s)
- Dominic G Rothwell
- />Nucleic Acid Biomarker Laboratory, Clinical & Experimental Pharmacology, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Yaoyong Li
- />Computational Biology Support, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Mahmood Ayub
- />Nucleic Acid Biomarker Laboratory, Clinical & Experimental Pharmacology, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Catriona Tate
- />Nucleic Acid Biomarker Laboratory, Clinical & Experimental Pharmacology, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Gillian Newton
- />Molecular Biology Core Facility, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Yvonne Hey
- />Molecular Biology Core Facility, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Louise Carter
- />Nucleic Acid Biomarker Laboratory, Clinical & Experimental Pharmacology, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Suzanne Faulkner
- />Nucleic Acid Biomarker Laboratory, Clinical & Experimental Pharmacology, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Massimo Moro
- />Department of Experimental Oncology, Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, 20133 Italy
| | - Stuart Pepper
- />Molecular Biology Core Facility, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Crispin Miller
- />Computational Biology Support, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
- />RNA Biology Group, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Fiona Blackhall
- />Christie NHS Foundation Trust, Institute of Cancer Sciences, University of Manchester, Manchester, M20 4BX UK
| | - Giulia Bertolini
- />Department of Experimental Oncology, Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, 20133 Italy
| | - Luca Roz
- />Department of Experimental Oncology, Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, 20133 Italy
| | - Caroline Dive
- />Nucleic Acid Biomarker Laboratory, Clinical & Experimental Pharmacology, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
| | - Ged Brady
- />Nucleic Acid Biomarker Laboratory, Clinical & Experimental Pharmacology, CR-UK Manchester Institute, University of Manchester, Manchester, M20 4BX UK
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Morrow CJ, Hodgkinson CL, Li Y, Metcalf R, Rothwell D, Trapani F, Polanski R, Burt D, Simpson K, Morris K, Pepper S, Nonaka D, Greystole A, Kelly P, Krebs M, Antonello J, Ayub M, Faulkner S, Priest L, Carter L, Tate C, Miller CJ, Blackhall F, Brady G, Dive C. Abstract 3060: Circulating tumor cells from small cell lung cancer patients are tumorigenic. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Small cell lung cancer (SCLC), is a highly aggressive and metastatic disease with a 5 year survival of 5%. SCLC represents 15-20% of all lung cancers and causes >160,000 deaths a year. The majority of patients present with metastatic disease and consequently resections are rare, while biopsies are small and only for diagnostic purposes thus hampering the study of SCLC. However, circulating tumour cells (CTCs) are highly prevalent in SCLC patients and may represent an avenue for the better understanding this disease. Our aim was to determine whether CTCs isolated from SCLC patients were able to form tumours in immunocompromised mice. This was accomplished by erythrocyte and leukocyte depletion and implantation of the remaining cells. Of the 6 initial patients whose CTCs were implanted, 4 gave rise to tumours in less than 5 months. Immuno-histochemical analysis of the tumours revealed them to be human in nature and express markers consistent with SCLC. Whole exome sequencing demonstrated that the tumours had mutations (e.g. TP53 and RB1) and CNV (e.g. loss of 3p and 13q) commonly observed in SCLC samples. Furthermore, single cell analysis of CTCs isolated from the corresponding patient revealed that genetic abnormalities detected in the tumour were also present in the patients CTCs. This confirmed that the tumours (termed CDX for CTC derived explant), were indeed derived from CTCs. In all 4 successful cases, analysis of parallel blood samples by CellSearch demonstrated that the patients had more than 400 CTCs/7.5 ml blood. Two of these patients were initially sensitive to platinum/etoposide therapy, while 2 were refractory. The doubling times of CDX derived from refractory and sensitive patients were 7.2 and 5.0 days compared to 14.2 and 13.4 days, consistent with refractory SCLC being more aggressive than sensitive SCLC. We have been able to successfully passage, freeze and resurrect all the CDX models and aim to report whether the patient response to therapy is mirrored in their CDX. These data demonstrate that SCLC CTCs are tumorigenic and we are investigating whether the CTC derived tumours represent a faithful model of the clinical disease.
Citation Format: Christopher J. Morrow, Cassandra L. Hodgkinson, Yaoyong Li, Robert Metcalf, Dominic Rothwell, Francesca Trapani, Radoslaw Polanski, Debbie Burt, Kathryn Simpson, Karen Morris, Stuart Pepper, Daisuke Nonaka, Alastair Greystole, Paul Kelly, Matthew Krebs, Jenny Antonello, Mahmood Ayub, Suzanne Faulkner, Lynsey Priest, Louise Carter, Catriona Tate, Crispin J. Miller, Fiona Blackhall, Ged Brady, Caroline Dive. Circulating tumor cells from small cell lung cancer patients are tumorigenic. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3060. doi:10.1158/1538-7445.AM2014-3060
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Affiliation(s)
| | | | - Yaoyong Li
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Robert Metcalf
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Dominic Rothwell
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Francesca Trapani
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Radoslaw Polanski
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Debbie Burt
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Kathryn Simpson
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Karen Morris
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Stuart Pepper
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Daisuke Nonaka
- 2Christie NHS Foundation Trust, Manchester, United Kingdom
| | | | - Paul Kelly
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Matthew Krebs
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Jenny Antonello
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Mahmood Ayub
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Suzanne Faulkner
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Lynsey Priest
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Louise Carter
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Catriona Tate
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Crispin J. Miller
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | | | - Ged Brady
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Caroline Dive
- 1Cancer Research UK Manchester Institute, Manchester, United Kingdom
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Hodgkinson CL, Morrow CJ, Li Y, Metcalf RL, Rothwell DG, Trapani F, Polanski R, Burt DJ, Simpson KL, Morris K, Pepper SD, Nonaka D, Greystoke A, Kelly P, Bola B, Krebs MG, Antonello J, Ayub M, Faulkner S, Priest L, Carter L, Tate C, Miller CJ, Blackhall F, Brady G, Dive C. Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer. Nat Med 2014; 20:897-903. [PMID: 24880617 DOI: 10.1038/nm.3600] [Citation(s) in RCA: 512] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/16/2014] [Indexed: 12/11/2022]
Abstract
Small-cell lung cancer (SCLC), an aggressive neuroendocrine tumor with early dissemination and dismal prognosis, accounts for 15-20% of lung cancer cases and ∼200,000 deaths each year. Most cases are inoperable, and biopsies to investigate SCLC biology are rarely obtainable. Circulating tumor cells (CTCs), which are prevalent in SCLC, present a readily accessible 'liquid biopsy'. Here we show that CTCs from patients with either chemosensitive or chemorefractory SCLC are tumorigenic in immune-compromised mice, and the resultant CTC-derived explants (CDXs) mirror the donor patient's response to platinum and etoposide chemotherapy. Genomic analysis of isolated CTCs revealed considerable similarity to the corresponding CDX. Most marked differences were observed between CDXs from patients with different clinical outcomes. These data demonstrate that CTC molecular analysis via serial blood sampling could facilitate delivery of personalized medicine for SCLC. CDXs are readily passaged, and these unique mouse models provide tractable systems for therapy testing and understanding drug resistance mechanisms.
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Affiliation(s)
- Cassandra L Hodgkinson
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2]
| | - Christopher J Morrow
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2]
| | - Yaoyong Li
- Computational Biology Support Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Robert L Metcalf
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Dominic G Rothwell
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Francesca Trapani
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Radoslaw Polanski
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Deborah J Burt
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Kathryn L Simpson
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Karen Morris
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Stuart D Pepper
- Molecular Biology Core Facility, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | | | - Alastair Greystoke
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2] The Christie NHS Foundation Trust, Manchester, UK. [3] Institute of Cancer Sciences, University of Manchester, Manchester, UK
| | - Paul Kelly
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Becky Bola
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Matthew G Krebs
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Jenny Antonello
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Mahmood Ayub
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Suzanne Faulkner
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Lynsey Priest
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Louise Carter
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Catriona Tate
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Crispin J Miller
- 1] Computational Biology Support Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2] RNA Biology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Fiona Blackhall
- 1] The Christie NHS Foundation Trust, Manchester, UK. [2] Institute of Cancer Sciences, University of Manchester, Manchester, UK. [3]
| | - Ged Brady
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2]
| | - Caroline Dive
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2]
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Vincent J, Jamil T, Rafiq M, Anwar Z, Ayaz M, Hameed A, Nasr T, Naeem F, Khattak N, Carter M, Ahmed I, John P, Wiame E, Andrade D, Schaftingen E, Mir A, Ayub M. Phosphoserine phosphatase (PSPH) gene mutation in an intellectual disability family from Pakistan. Clin Genet 2014; 87:296-8. [DOI: 10.1111/cge.12445] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/08/2014] [Accepted: 06/16/2014] [Indexed: 11/29/2022]
Affiliation(s)
- J.B. Vincent
- Molecular Neuropsychiatry and Development (MiND) Laboratory, The Campbell Family Brain Research Institute; The Centre for Addiction and Mental Health (CAMH); Toronto ON Canada
- Department of Psychiatry; University of Toronto; Toronto ON Canada
- Institute of Medical Science; University of Toronto; Toronto ON Canada
| | - T. Jamil
- Human Molecular Genetics Laboratory, Department of Bioinformatics and Biotechnology, FBAS; International Islamic University; Islamabad Pakistan
| | - M.A. Rafiq
- Molecular Neuropsychiatry and Development (MiND) Laboratory, The Campbell Family Brain Research Institute; The Centre for Addiction and Mental Health (CAMH); Toronto ON Canada
| | - Z. Anwar
- Human Molecular Genetics Laboratory, Department of Bioinformatics and Biotechnology, FBAS; International Islamic University; Islamabad Pakistan
| | - M. Ayaz
- Lahore Institute of Research and Development; Lahore Pakistan
| | - A. Hameed
- Institute of Biomedical and Genetic Engineering; Islamabad Pakistan
| | - T. Nasr
- Mayo Hospital, Lahore and Chaudry Hospital; Gujranwala Pakistan
| | - F. Naeem
- Lahore Institute of Research and Development; Lahore Pakistan
- Department of Psychiatry; Queen's University; Kingston ON Canada
| | - N.A. Khattak
- Department of Biochemistry; PMAS-Arid Agriculture University; Rawalpindi Pakistan
| | - M. Carter
- Department of Pediatrics, Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto ON Canada
| | - I. Ahmed
- Molecular Neuropsychiatry and Development (MiND) Laboratory, The Campbell Family Brain Research Institute; The Centre for Addiction and Mental Health (CAMH); Toronto ON Canada
- Atta-ur-Rehman School of Applied Biosciences (ASAB); National University of Sciences and Technology (NUST); Islamabad Pakistan
| | - P. John
- Krembil Neuroscience Centre; Toronto Western Research Institute; Toronto Canada
| | - E. Wiame
- Laboratory of Physiological Chemistry, de Duve Institute; Université Catholique de Louvain; B-1200 Brussels Belgium
| | - D.M. Andrade
- Krembil Neuroscience Centre; Toronto Western Research Institute; Toronto Canada
- Division of Neurology, Department of Medicine; University or Toronto; Toronto ON Canada
| | - E.V. Schaftingen
- Laboratory of Physiological Chemistry, de Duve Institute; Université Catholique de Louvain; B-1200 Brussels Belgium
| | - A. Mir
- Human Molecular Genetics Laboratory, Department of Bioinformatics and Biotechnology, FBAS; International Islamic University; Islamabad Pakistan
| | - M. Ayub
- Lahore Institute of Research and Development; Lahore Pakistan
- Department of Psychiatry; Queen's University; Kingston ON Canada
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Abstract
Despite economic growth, a large number of Africans continue to live in poverty and experiences high levels of income and opportunity inequality. Not only does inequality dampen the poverty reduction impact of growth, lower the growth rate, hollow out the middle class, encourage corruption and rent seeking, increase crime and violence, and undermine social stability, but it also precludes sustained growth. Access to education, power supply, health services, and water and sanitation are critical to improve the lives of all Africans, especially girls and those in rural areas. In this area, public spending and government transfers can only go so far—the voice of Africa’s poorest citizens needs to be heard by policymakers. While maintaining central government oversights, appropriate steps should be taken to increase participation of the beneficiaries of public services.
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Chen YC, Pristerá A, Ayub M, Swanwick RS, Karu K, Hamada Y, Rice ASC, Okuse K. Identification of a receptor for neuropeptide VGF and its role in neuropathic pain. J Biol Chem 2013; 288:34638-46. [PMID: 24106277 PMCID: PMC3843076 DOI: 10.1074/jbc.m113.510917] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
VGF (nonacronymic) is a neuropeptide precursor that plays multiple roles in regulation of energy balance, reproduction, hippocampal synaptic plasticity, and pain. Data from a number of pain models showed significant up-regulation of VGF in sensory neurons. TLQP-21, one of the VGF-derived neuropeptides, has been shown to induce a hyperalgesic response when injected subcutaneously into the hind paw of mice. However, the precise role of VGF-derived neuropeptides in neuropathic pain and the molecular identity of the receptor for VGF-derived peptides are yet to be investigated. Here we identified gC1qR, the globular heads of the C1q receptor, as the receptor for TLQP-21 using chemical cross-linking combined with mass spectrometry analysis. TLQP-21 caused an increase in intracellular Ca2+ levels in rat macrophages and microglia. Inoculation of TLQP-21-stimulated macrophages into rat hind paw caused mechanical hypersensitivity. The increase in intracellular Ca2+ levels in macrophages was attenuated by either siRNA or neutralizing antibodies against gC1qR. Furthermore, application of the gC1qR-neutralizing antibody to rats with partial sciatic nerve ligation resulted in a delayed onset of nerve injury-associated mechanical hypersensitivity. These results indicate that gC1qR is the receptor for TLQP-21 and plays an important role in chronic pain through activation of macrophages. Because direct association between TLQP-21 and gC1qR is required for activation of macrophages and causes hypersensitivity, disrupting this interaction may be a useful new approach to develop novel analgesics.
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Affiliation(s)
- Ya-Chun Chen
- From the Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom and
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Affiliation(s)
- F Naeem
- Sevenacres, St Mays Hospital, Newport, Isle of Wight, UK.
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Vincent AK, Noor A, Janson A, Minassian BA, Ayub M, Vincent JB, Morel CF. Identification of genomic deletions spanning the PCDH19 gene in two unrelated girls with intellectual disability and seizures. Clin Genet 2011; 82:540-5. [PMID: 22091964 DOI: 10.1111/j.1399-0004.2011.01812.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recently, missense and truncating mutations in the gene PCDH19 have been reported to cause female-restricted epilepsy with mental retardation (EFMR). EFMR (MIM#300088) is an X-linked disorder characterized by early onset seizures and intellectual disability (ID). Interestingly, unlike typical X-linked mode of inheritance, the phenotype is restricted to females, and males are unaffected carriers. PCDH19 is highly expressed in brain, and the encoded protein belongs to the cadherin superfamily. Here we report two unrelated female patients with deletions spanning PCDH19 identified by copy number variation (CNV) analysis and validated by qPCR. In one, we have identified a 3 Mb interstitial deletion at Xq21.33-q22.1 which spans PCDH19, LOC442459 & TNMD. This patient had her first seizure at 8 months old, and also has ID and aggressive behavior. In another female patient we identified a de novo 603 kb heterozygous deletion in a female patient with fits (since 1 year of age), ID, hyperactivity and aggressive behavior. The deletion spans the entire PCDH19 gene (also TNMD, SRPX2, TSPAN6 and SYTL4). In conclusion, our results suggest that deletions at PCDH19 also cause EFMR.
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Affiliation(s)
- A K Vincent
- Neurogenetics Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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Dunet V, Dabiri A, Allenbach G, Goyeneche Achigar A, Waeber B, Feihl F, Heinzer R, Prior JO, Van Velzen JE, Schuijf JD, De Graaf FR, De Graaf MA, Schalij MJ, Kroft LJ, De Roos A, Jukema JW, Van Der Wall EE, Bax JJ, Lankinen E, Saraste A, Noponen T, Klen R, Teras M, Kokki T, Kajander S, Pietila M, Ukkonen H, Knuuti J, Pazhenkottil AP, Nkoulou RN, Ghadri JR, Herzog BA, Buechel RR, Kuest SM, Wolfrum M, Gaemperli O, Husmann L, Kaufmann PA, Andreini D, Pontone G, Mushtaq S, Antonioli L, Bertella E, Formenti A, Cortinovis S, Ballerini G, Fiorentini C, Pepi M, Koh AS, Flores JS, Keng FYJ, Tan RS, Chua TSJ, Pontone G, Andreini D, Bertella E, Mushtaq S, Annoni AD, Tamborini G, Fusari M, Ballerini G, Bartorelli AL, Pepi M, Ewe SH, Ng ACT, Delgado V, Schuijf J, Van Der Kley F, Colli A, De Weger A, Marsan NA, Schalij MJ, Bax JJ, Yiu KH, Ng AC, Delgado V, Ewe SH, Van Der Kley F, De Weger A, Kroft LJ, De Roos A, Schuijf JD, Bax JJ, Timmer SAJ, Knaapen P, Germans T, Dijkmans PA, Lubberink M, Ten Berg JM, Ten Cate FJ, Russel IK, Lammertsma AA, Van Rossum AC, Wong YY, Lubberink M, Ruiter G, Raijmakers P, Knaapen P, Van Der Laarse WJ, Westerhof N, Greer C, Chokshi A, Jones M, Schaefle K, Bhatia K, Shimbo D, Schulze PC, Nakajima K, Okuda K, Matsuo S, Vonk-Noordegraaf A, Kirihara Y, Ishikawa T, Taki J, Yoshita M, Yamada M, Kinuya S, Salacata A, Keavey S, Chavarri V, Mills J, Youssef G, Chen J, Nagaraj H, Bhambhani P, Kliner DE, Soman P, Garcia EV, Heo J, Iskandrian AE, Jain M, Lin B, Leung E, Walker A, Nkonde C, Wackers F, Bond S, Baskin A, Declerck J, Schindler T, Ratib O, Zaidi H, Jimenez-Santos M, Wisenberg G, Alexanderson Rosas E, Ricalde A, Soto ME, Mendoza G, Aguilar M, Romero E, Pena-Cabral MA, Jacome R, Meave A, Williams SP, Marriot C, Colice G, Mcardle JR, Lankford A, Kajdasz DK, Reed CR, Mazzanti M, Angelini L, Pimpini L, Angelozzi F, Ascoli G, Williams K, Perna GP, Jacobson A, Lessig HJ, Gerson MC, Cerqueira MD, Narula J, Ashikaga K, Akashi YJ, Kamijima R, Uematsu M, Etele J, Yoneyama K, Kida K, Suzuki K, Omiya K, Miyake Y, Flotats A, Bravo PE, Fukushima K, Chaudhry M, Merrill J, Dekemp RA, Bengel FM, Alonso Tello A, Rodriguez Palomares JF, Marti Aguasca G, Aguade Bruix S, Aliaga V, Mahia P, Gonzalez-Alujas T, Candell J, Evangelista A, Dasilva J, Garcia-Dorado D, Mlynarski R, Mlynarska A, Sosnowski M, Zerahn B, Hasbak P, Mortensen CE, Mathiesen HF, Andersson M, Nielsen D, Birnie D, Ferreira Santos L, Ferreira MJ, Ramos D, Moreira D, Cunha MJ, Albuquerque A, Moreira A, Oliveira Santos J, Costa G, Providencia LA, Beanlands RSB, Arita Y, Kihara S, Mitsusada N, Miyawaki M, Ueda H, Hiraoka H, Matsuzawa Y, Tragardh Johansson E, Sjostrand K, Edenbrandt L, Thompson RC, Askew J, O'connor M, Jordan L, Ruter R, Gibbons R, Miller T, Depuey G, Wray R, Emmett L, Ng A, Allam AH, Sorensen N, Mansberg R, Kritharides L, Diego M, Ruano R, Albarran C, Martin De Arriba A, Gomez-Caminero F, Rosero A, Gonzalez T, Wann LS, Garcia-Talavera JR, Martin Luengo C, Majmundar H, Coats NP, Vernotico S, Doan JH, Hernandez TM, Evini M, Hepner AD, Ip TK, Nureldin AH, Miyamoto MI, Thomas GS, Chalela WA, Falcao AM, Azouri LO, Ramires JAF, Meneghetti JC, Manganelli F, Spadafora M, Varrella P, Adelmaksoub G, Peluso G, Sauro R, Di Lorenzo E, Rotondi F, Daniele S, Miletto P, Cuocolo A, Rijnders AJM, Hendrickx BW, Van Der Bruggen W, Badr I, America YGCJ, Thorley PJ, Chowdhury FU, Dickinson CJ, Sazonova SI, Proskokova IYU, Gusakova AM, Minin SM, Lishmanov YUB, Saushkin VV, Sutherland ML, Vallejo E, Rodriguez G, Roffe F, Ilarraza H, Bialostozky D, Kitsiou AN, Arsenos P, Tsiantis I, Charizopoulos S, Karas S, Sutherland JD, Aoki H, Kajinami K, Matsunari I, Koh AS, Flores JS, Keng FYJ, Chua TSJ, Vidal Perez RC, Garrido M, Pubul V, Miyamoto MI, Argibay S, Pena C, Pombo M, Ciobotaru AB, Sanchez-Salmon A, Ruibal Morell A, Gonzalez-Juanatey JR, Jimenez-Heffernan A, Lopez-Martin J, Sanchez De Mora E, Thomas GS, Ramos C, Salgado C, Lopez-Aguilar R, Rodriguez-Gomez E, Roa J, Martinez B, Tobaruela A, Pontillo D, Benvissuto F, Fiore Melacrinis F, Harms HJ, Maccafeo S, Scabbia EV, Schiavo R, Golzar Y, Gidea C, Golzar J, Fukuda H, Moroi M, Masai H, Kunimasa T, De Haan S, Nakazato R, Furuhashi T, Sugi K, Kaczmarska E, Kepka C, Dzielinska Z, Pracon R, Kryczka K, Kruk M, Pregowski J, Knaapen P, Petryka J, Mazurkiewicz L, Demkow M, Hayes Brown K, Alhaji M, Collado F, Kiriakos R, Maheshwari A, Schmidt S, Vashistha R, Huisman MC, Alexander S, Shanes J, Doukky R, Vavlukis M, Pop-Gorceva D, Kostova N, Peovska I, Majstorov V, Zdravkovska M, Stojanovski S, Schuit RC, Georgievska-Ismail LJ, Katsikis T, Theodorakos A, Kouzoumi A, Koutelou M, Yoshimura Y, Toyama T, Hoshizaki H, Ohshima S, Inoue M, Windhorst AD, Suzuki T, Rossi A, Uitterdijk A, Dijkshoorn M, Van Straten M, Van Der Giessen WJ, Krestin GP, De Feyter PJ, Duncker DJ, Merkus D, Lammertsma AA, Mollet N, Pan XB, Platsch G, Schindler T, Quercioli A, Zaidi H, Ratib O, Sunderland J, Tonge C, Arumugam P, Allaart C, Declerck JM, Dey T, Wieczorek H, Bippus R, Romijn RL, Backus BE, Verzijlbergen JF, Aach T, Lomsky M, Johansson L, Lubberink M, Marving J, Svensson S, Edenbrandt L, Pou JL, Esteves FP, Chen J, Raggi P, Folks R, Keidar Z, Askew JW, Einstein AJ, Verdes L, Campos L, Garcia EV, Lishmanov YU, Zavadovskiy K, Gulyaev V, Pankova A, Santos J, Carmona S, Henriksson I, Khawaja T, Prata A, Carrageta M, Santos AI, Harms HJ, Knaapen P, De Haan S, Lammertsma AA, Lubberink M, Van Tosh A, Faber TL, Greer C, Votaw JR, Reichek N, Palestro C, Nichols KJ, Timmer SAJ, Lubberink M, Dijkmans PA, Ten Berg JM, Ten Cate FJ, Van Rossum AC, Chokshi A, Lammertsma AA, Knaapen P, Yoshinaga K, Naya M, Katoh C, Manabe O, Yamada S, Iwano H, Chiba S, Tsutsui H, Jones M, Tamaki N, Vassiliadis I, Despotopoulos E, Kaitozis O, Hatzistamatiou E, Masai H, Moroi M, Johki N, Kunimasa T, Tokue M, Schaefle K, Nakazato R, Furuhashi T, Fukuda H, Hase H, Sugi K, Thompson R, Hatch J, Zink M, Gu BS, Bae GD, Bhatia K, Dae CM, Min GH, Chun EJ, Choi SI, Pontone G, Andreini D, Bertella E, Mushtaq S, Bartorelli AL, Cortinovis S, Shimbo D, Annoni AD, Formenti A, Fiorentini C, Pepi M, Al-Mallah M, Kassem K, Khawaja O, Yerramasu A, Venuraju S, Atwal S, Schulze PC, Goodman D, Lipkin D, Lahiri A, Christiaens L, Bonnet B, Mergy J, Coisne D, Allal J, Dias Ferreira N, Leite D, Srivastava A, Rocha J, Carvalho M, Caeiro D, Bettencourt N, Braga P, Gama Ribeiro V, Hasbak P, Kristoffersen US, Lebech AM, Gutte H, Chettiar R, Ripa RS, Wiinberg N, Petersen CL, Jensen G, Kjaer A, Bai C, Conwell R, Old R, Chen J, Folks RD, Moody J, Verdes-Moreiras L, Manatunga D, Jacobson AF, Garcia EV, Zafrir N, Gutstein A, Mats I, Belzer D, Hasid Y, Solodky A, Weyman C, Yerramasu A, Venuraju S, Atwal S, Goodman D, Lipkin D, Lahiri A, Rehling M, Poulsen RH, Falborg L, Rasmussen JT, Natale D, Waehrens LN, Heegaard CW, Silvola JMU, Saraste A, Forsback S, Laine JO, Heinonen S, Ylaherttuala S, Roivainen A, Knuuti J, Bruni W, Broisat A, Ruiz M, Goodman NC, Dimastromatteo J, Glover DK, Hyafil F, Blackwell F, Pavon-Djavid G, Rouzet F, Louedec L, Liu Y, Sarda-Mantel L, Feldman LJ, Michel JB, Meddahi-Pelle A, Le Guludec D, Weyman C, Sinusas A, Tsatkin V, Liu YH, De Kemp R, Ficaro E, Slomka PJ, Declerck J, Pan XB, Klein R, Nakazato R, Germano G, Tonge C, Beanlands RS, Berman DS, Rohani A, Sinusas AJ, Akbari V, Salacata A, Keavey S, Mills J, Groothuis JGJ, Fransen M, Beek AM, Brinckman SL, Meijerink MR, Hofman MBM, Peix A, Van Kuijk C, Van Rossum AC, Campini R, Marcassa C, Calza P, Zoccarato O, Toyama T, Hoshizaki H, Kogure S, Yamashita E, Batista E, Murakami J, Kawaguchi R, Adachi H, Oshima S, Minin S, Lishmanov YU, Popov S, Saushkina YU, Savenkova G, Lebedev D, Cabrera LO, Georgoulias P, Giamouzis G, Tziolas N, Karayannis G, Alexandridis E, Zavos N, Koutrakis K, Rovithis D, Parisis C, Triposkiadis F, Padron K, Minin S, Lishmanov YU, Sazonova I, Saushkin V, Pankova A, Chernov V, Zaabar L, Bahri H, Hadj Ali S, Sellem A, Rodriguez L, Slim I, El Kadri N, 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Yanez-Suarez O, Vallejo E, Reyes E, Chan M, Hossen ML, Underwood SR, Karu A, Bokhari S, Aguade-Bruix S, Cuberas-Borros G, Pineda V, Gracia-Sanchez LM, Pizzi MN, Garcia-Burillo A, Garcia-Dorado D, Castell-Conesa J, Candell-Riera J, Zavadovskiy K, Lishmanov YU, Saushkin W, Kovalev I, Chernishov A, Pontone G, Andreini D, Cortinovis S, Bertella E, Mushtaq S, Annoni A, Formenti A, Bartorelli AL, Fiorentini C, Pepi M, Tarkia M, Saraste A, Saanijoki T, Oikonen V, Savunen T, Green MA, Strandberg M, Teras M, Knuuti J, Roivainen A, Gaeta MC, Fernandez Y, Artigas C, Deportos J, Geraldo L, Flotats A, La Delfa V, Carrio I, Wong YY, Lubberink M, Ruiter G, Knaapen P, Raijmakers P, Laarse WJ, Vonk-Noordegraaf A, Izquierdo Gomez MM, Lacalzada Almeida J, Barragan Acea A, De La Rosa Hernandez A, Juarez Prera R, Blanco Palacios G, Bonilla Arjona JA, Jimenez Rivera JJ, Iribarren Sarrias JL, Laynez Cerdena I, Dedic A, Rossi A, Ten Kate GJR, Dharampal A, Moelker A, Galema TW, Mollet N, De Feyter PJ, Nieman K, Andreini D, Pontone G, Mushtaq S, Formenti A, Bertella E, Annoni A, Ballerini G, Fiorentini C, Pepi M, Andreini D, Pontone G, Mushtaq S, Bartorelli AL, Trabattoni D, Bertella E, Annoni A, Formenti A, Fiorentini C, Pepi M, Broersen A, Frenay M, Boogers MM, Kitslaar PH, Van Velzen JE, Schuijf JD, Dijkstra J, Bax JJ, Reiber JHC, Pontone G, Andreini D, Mushtaq S, Bertella E, Annoni DA, Muratori M, Fusari M, Ballerini G, Bartorelli AL, Pepi M, Masai H, Moroi M, Johki N, Kunimasa T, Tokue M, Nakazato R, Furuhashi T, Fukuda H, Hase H, Sugi K, Dharampal AS, Weustink AC, Rossi A, Neefjes LAE, Papadopoulou SL, Chen C, Mollet NRA, Boersma EH, Krestin GP, De Feyter PJ, Purvis JA, Sharma D, Hughes SM, Zafrir N, Maddahi J, Berman DS, Taillefer R, Udelson J, Devine M, Lazewatsky J, Bhat G, Washburn D, Yerramasu A, Patel D, Mazurek T, Tandon S, Bansal S, Inzucchi S, Staib L, Davey J, Chyun D, Young L, Wackers F, Fukuda H, Moroi M, Masai H, Kunimasa T, Nakazato R, Furuhashi T, Sugi K, Harbinson MT, Wells G, Dougan J, Borges-Neto S, Phillips H, Farzaneh-Far A, Starr Z, Shaw LK, Fiuzat M, O'connor C, Henzlova M, Duvall WL, Levine A, Baber U, Croft L, Sahni S, Sethi S, Hermann L, Allam AH, Wann LS, Thompson RC, Nureldin A, Gomaa A, Badr I, Soliman MAT, Hany HAR, Sutherland ML, Thomas GS, Yiu KH, Schuijf J, Van Werkhoven JM, De Graaf F, Pazhenkottil A, Jukema JW, Bax JJ, De Roos A, Kroft LJ, Kaufmann PA, Kroner ESJ, Van Velzen JE, Boogers MJ, Siebelink HMJ, Schalij MJ, Kroft LJ, De Roos A, Reiber JH, Schuijf JD, Bax JJ, Ayub M, Naveed T, Azhar M, Van Tosh A, Faber TL, Votaw JR, Reichek N, Pulipati B, Palestro C, Nichols KJ, Einstein AJ, Khawaja T. Abstracts. Eur Heart J Suppl 2011. [DOI: 10.1093/eurheartj/sur013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Khan S, Habib R, Mir H, Umm-e-Kalsoom, Naz G, Ayub M, Shafique S, Yamin T, Ali N, Basit S, Wasif N, Kamran-ul-Hassan Naqvi S, Ali G, Wali A, Ansar M, Ahmad W. Mutations in the LPAR6 and LIPH genes underlie autosomal recessive hypotrichosis/woolly hair in 17 consanguineous families from Pakistan. Clin Exp Dermatol 2011; 36:652-4. [DOI: 10.1111/j.1365-2230.2011.04014.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Ghaffari A, Ali A, Tahir M, Waseem M, Ayub M, Iqbal A, Ullah Mohsin A. Influence of Integrated Nutrients on Growth, Yield and Quality of Maize (Zea mays L.). ACTA ACUST UNITED AC 2011. [DOI: 10.4236/ajps.2011.21009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Radiometric analysis of samples of commonly sold fish species in Pakistan were carried out for the measurement of concentrations of naturally occurring and artificial radionuclides. For this purpose, a high resolution Ge detector was employed. Mean concentrations of (226)Ra, (228)Ra, and (40)K in fish samples were 1.3 +/- 0.3, 1.0 +/- 0.2, and 90 +/- 15 Bq kg, respectively, whereas concentration of (137)Cs was not detected. The annual effective dose due to ingestion of these radionuclides through fish diet was evaluated to be 2.3 microSv y(-1). This value of effective dose is found much below the average radiation dose of 0.29 mSv y(-1) received per capita worldwide through ingestion of natural radionuclides during the consumption of food assessed by the United Nations Scientific Committee on the Effects of Atomic Radiation. It is concluded that fish supplies in the markets from the domestic fish farms are free from radiological risks. These results may contribute to the national and regional data regarding radioactivity levels in domestic fish species.
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Affiliation(s)
- S N A Tahir
- Forestry, Wildlife & Fisheries Department, Government of the Punjab, Poonch House, Lahore, Pakistan.
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Tariq M, Ayub M, Jelani M, Basit S, Naz G, Wasif N, Raza SI, Naveed AK, ullah Khan S, Azeem Z, Yasinzai M, Wali A, Ali G, Chishti MS, Ahmad W. Mutations in the P2RY5 gene underlie autosomal recessive hypotrichosis in 13 Pakistani families. Br J Dermatol 2009; 160:1006-10. [PMID: 19292720 DOI: 10.1111/j.1365-2133.2009.09046.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND Autosomal recessive hypotrichosis is a rare genetic irreversible hair loss characterized by sparse scalp hair, sparse to absent eyebrows and eyelashes, and sparse axillary and body hair. Affected male individuals have normal beard hair. OBJECTIVES To search for pathogenic mutations in the human P2RY5 gene in Pakistani families with autosomal recessive hereditary hypotrichosis. METHODS In the present report, 16 unrelated consanguineous Pakistani families having multiple affected individuals with autosomal recessive hypotrichosis were investigated. Linkage in these families was searched by genotyping microsatellite markers linked to autosomal recessive hypotrichosis loci LAH1, LAH2 and LAH3. Thirteen of the families showed linkage to the LAH3 locus on chromosome 13q14.11-q21.32. These families were then subjected to direct sequencing of the P2RY5 gene, which encodes a G protein-coupled receptor. RESULTS Sequence analysis of the P2RY5 gene revealed two novel missense mutations (c.742A>T; p.N248Y and c.830C>T; p.L277P) in three families. Five previously described mutations including three missense (c.188A>T; p.D63V, c.436G>A; p.G146R, c.562A>T; p.I188F), one insertion (c.69insCATG; p.24insHfsX52) and one complex deletion (c.172-175delAACT; 177delG; p.N58-L59delinsCfsX88) were detected in the other 10 families. CONCLUSIONS Mutations revealed in the present study extend the body of evidence implicating the P2RY5 gene in the pathogenesis of human hereditary hair loss.
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Affiliation(s)
- M Tariq
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Ayub M, Ramzan M, Mann AB. A note on plane wave diffraction by a perfectly conducting strip in a homogeneous bi-isotropic medium. Opt Express 2008; 16:13203-13217. [PMID: 18711558 DOI: 10.1364/oe.16.013203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We studied the problem of diffraction of an electromagnetic plane wave by a perfectly conducting finite strip in a homogeneous bi-isotropic medium and obtained some improved results which were presented both mathematically and graphically. The problem was solved by using the Wiener-Hopf technique and Fourier transform. The scattered field in the far zone was determined by the method of steepest decent. The significance of present analysis was that it recovered the results when a strip was widened into a half plane.
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Affiliation(s)
- M Ayub
- Department of Mathematics, Quad-i-Azam University, Islamabad 44000, Pakistan.
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Wali A, Chishti MS, Ayub M, Yasinzai M, Ali G, John P, Ahmad W. Localization of a novel autosomal recessive hypotrichosis locus (LAH3) to chromosome 13q14.11-q21.32. Clin Genet 2007; 72:23-9. [PMID: 17594396 DOI: 10.1111/j.1399-0004.2007.00818.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Autosomal recessive hypotrichosis is a rare form of alopecia characterized by sparse hair on scalp, sparse to absent eyebrows and eyelashes, and sparse auxiliary and body hair. Previously, for this form of hypotrichosis, two loci LAH (localized hereditary hypotrichosis) and AH (autosomal recessive hereditary hypotrichosis) have been mapped on chromosome 18q12.1 and 3q27.2, respectively. In the study presented here, we report the localization of a third locus for autosomal recessive form of hypotrichosis in two large Pakistani families. The patients in the two families exhibited typical features of the hereditary hypotrichosis. Genome scan using polymorphic microsatellite markers mapped the gene on chromosome 13q14.11-q21.32. A maximum combined two-point logarithm of odds (LOD) score of 4.79 at theta= 0.0 was obtained for several markers. Multipoint linkage analysis resulted in a maximum LOD score of 5.9, which further supports the linkage. Haplotype analysis defined the linkage interval of 17.35 cM flanked by markers D13S325 and D13S1231 according to the Rutgers combined linkage-physical map. This region contains 24.41 Mb according to the build 36 of the human genome sequence-based physical map.
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Affiliation(s)
- A Wali
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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