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CV (January 2014)

Carlos Caldas MD FACP FRCP FRCPath FMedSci

PERSONAL INFORMATION

Date of Birth: 27/06/60; Place of Birth: Oliveira de Frades, Portugal

Professional address: Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge

Research Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre,

Cambridge CB2 0RE, UK (E-mail: cc234@cam.ac.uk)

PRESENT ACADEMIC RANK AND POSITION

Professor of Cancer Medicine, Department of Oncology, University of Cambridge (since 11/02)

Senior Group Leader, Cancer Research UK Cambridge Research Institute (since 09/06)

NIHR Senior Investigator (since 04/12)

Director, Breast Cancer Research Unit, Cambridge University Hospitals NHS Foundation Trust and

NIHR Cambridge Biomedical Research Centre (since 07/08)

Lead, Cambridge Experimental Cancer Medicine Centre (since 04/07)

Co-Lead, Cancer Theme, NIHR Cambridge Biomedical Research Centre (since 10/11)

Honorary Consultant in Medical Oncology, Oncology Centre and Cambridge Breast Unit,

Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge (since

09/96)

EDUCATION

Medical School: MD, University of Lisbon, Portugal (1978-1984)

Residency: University of Texas Southwestern Medical School Affiliated Hospitals, Dallas, Texas, USA

(6-1988 to 6-1991)

Fellowship: The Johns Hopkins University Medical School and Hospital, Baltimore, Maryland, USA (7-

1991 to 7-1994)

QUALIFICATIONS

Board Certified in Internal Medicine (1991) and Medical Oncology (1993), American Board of Internal

Medicine, USA

European Certification in Medical Oncology (1994)

Specialist Register, General Medicine and Medical Oncology, General Medical Council (No: 4274278)

(1996)

HONORS AND AWARDS

MD with honours (“felicissime et honorifice”), University of Lisbon, 1984

ASCO (American Society for Clinical Oncology) Merit Award Recipient, 1994

European Union Human Capital and Mobility Fellowship, 1994-1996

Addenbrooke’s Hospital, Cambridge University Teaching Hospitals Trust, Outstanding Achievement

Award, 2003/2004

NHS Bronze Clinical Excellence Award, 2007

Order of St. James of the Sword (Ordem de Sant'Iago da Espada), Grade: Officer - decoration given by

the Portuguese Republic ["for outstanding services to science"], June 10th 2009

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Elected Fellow of the European Academy of Cancer Sciences (October 2010)

PREVIOUS PROFESSIONAL POSITIONS AND APPOINTMENTS

General Internship and Internal Medicine Resident, Santa Maria University Hospital, Lisbon, Portugal

(1985-1988)

Residency in Internal Medicine, Department of Internal Medicine, University of Texas Southwestern

Medical School Affiliated Hospitals, Dallas, Texas, USA (1988-91)

Senior Clinical Fellow, Medical Oncology, The Johns Hopkins Oncology Center, Baltimore, USA (1991-

4)

Research Fellow, The Institute of Cancer Research, Chester Beatty Laboratories, London, UK (1994-6)

Clinical Senior Research Associate, Department of Oncology, University of Cambridge (9/1996-10/2002)

Principal Investigator, Cambridge Institute for Medical Research, University of Cambridge (9/1998-

9/2001)

Senior Investigator, Cancer Genomics Program, Hutchison/MRC Research Centre, School of Clinical

Medicine, University of Cambridge (9/2001-1/2007)

Lead, Cambridge National Translational Cancer Research Centre (06/04-03/07)

PROFESSIONAL AND SOCIETY MEMBERSHIPS

Fellow, Society of Biology (FSB)- elected June 2011

Fellow, European Academy of Cancer Sciences- elected October 2010

Fellow, Royal College of Pathologists (FRCPath)- elected June 2008

Fellow, The Academy of Medical Sciences (FMedSci)- elected April 2004

Fellow, Royal College of Physicians (FRCP)- elected May 2002

Fellow, American College of Physicians (FACP)- elected July 1999

Member, American Association for Cancer Research

Member, European Association for Cancer Research

Member, The Johns Hopkins Medical and Surgical Association, Baltimore, USA

Full Register, General Medical Council, United Kingdom (Specialist Register of General Medicine and

Medical Oncology)

Member, Ordem dos Medicos, Portugal

Member, Colleges of Internal Medicine and Medical Oncology, Ordem dos Medicos, Portugal

Member, European Society for Medical Oncology (inactive)

Member, Association of Cancer Physicians (UK)

ADMINISTRATIVE RESPONSIBILITIES AND COMMITTEE MEMBERSHIPS

Current

Selection Committee, Serra Hunter Programme, Catalonia, Spain (2013-)

Chair, Advisory Council, IMM University of Lisbon Faculty of Medicine (2013-)

Scientific Council, Portuguese Association for Cancer Research (ASPIC) (2013-)

Board, Organisation of European Cancer Institutes [OECI] (elected 2013-2016)

NIHR Cambridge Biomedical Research Centre Executive Committee (2011-)

Cambridge Cancer Centre Clinical Strategy Committee (2011-)

Cambridge Cancer Centre Executive Committee (2011-)

Cancer Board, Cambridge University Hospitals NHS Foundation Trust (2010-)

Cambridge Cancer Centre Steering Committee (2006-)

College of Reviewers, Canada Research Chairs Program (2011-)

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Cancer Stem Cell Consortium Advisory Committee- Canada (2011-)

INSERM Expert (2006-)

External Advisory Committee, Research Centre of the Portuguese Cancer Institute Porto Centre (2004-)

Management Committee, Cambridge Computational Biology Institute (2003-)

Chairman, Steering Group, International Gastric Cancer Linkage Consortium (1999-)

Past

College of Reviewers and Full Application Review Committee, Genome Canada, 2012 Large-Scale

Applied Research Project Competition in Genomics and Personalized Health

Breast Cancer Campaign's Executive Advisory Board for Breast Cancer Research Gap Analysis 2012

German Consortium for Translational Cancer Research (DKTK) International Review Board (2010-2012)

Special Program Committee, (AICR) Italian Association for Cancer Research (2009)

Scientific Advisory Board, Cancer Research UK Stratified Medicine Programme (2010)

Cancer Research UK Cambridge Research Institute Senior Management Committee (2006-2009)

Scientific Advisory Board, Cancerôpole Ile-de-France (2008)

Scientific Advisory Board, GenoMed, Lisbon, Portugal (2006-2008)

NCRI Informatics Implementation Task Force (2004-2007)

International Scientific Advisory Board, IPATIMUP (Institute of Molecular Pathology and

Immunology), University of Porto, Portugal (1997-2007)

Cancer Services IT Steering Committee, Addenbrooke’s Hospital (2000-2007) (Chair, 2002-2007)

Medical and Scientific Advisory Panel, Leukaemia Research Fund (2003-6)

Clinical and Translational Research Committee, Cancer Research UK (2004-6)

Steering Group, Cambridge University DNA Microarrays Consortium (2000-2006)

International Panel of Referees, Translational Research in Clinical Trials, Cancer Research UK (2004-

2005)

Translational Research Committee, Cancer Research UK (2002-2004)

Management Committee, Hutchison/MRC Research Centre, University of Cambridge (2000-6)

Research Governance Committee, Addenbrooke’s Hospital (2001-2006)

Tissue Bank Management Committee (Faculty Board of Clinical Medicine Representative 01/2001-),

Addenbrooke’s Hospital, Cambridge (10/1999-10/2004)

Wellcome/MRC Building Management Committee, University of Cambridge (1996-2000)

Cambridge Institute for Medical Research Management Committee (1998-2000)

Information Strategy Committee, University of Cambridge School of Clinical Medicine (1996-2000)

Co-organizer, Cancer Biology/ Molecular Haemopoiesis Seminar Series, University of Cambridge (1997-

1999)

Organizer, Cancer Biology Seminar Series, University of Cambridge (2000)

Radiation Safety Committee, Cambridge Institute for Medical Research (1998-2001)

PEER-REVIEW ACTIVITIES

Section Editor (Systems Biology, Post-genomic Analyses and Emerging Technologies): BMC Cancer

Associate Editor (Cancer Genomics): Cancer Biology and Therapy

Editorial Board: Molecular Cancer Therapeutics, Molecular Oncology, Molecular Cancer Research,

BMC Medicine, Cellular Oncology, Expert Reviews in Molecular Medicine, Critical Reviews in

Oncogenesis, Hereditary Cancer in Clinical Practice

Scientific Reviewer: Nature, Nature Genetics, Nature Medicine, New England Journal of Medicine,

Science, Science Translational Medicine, The Lancet, The Lancet Oncology, PNAS, EMBO Molecular

Medicine, Gastroenterology, Cancer Research, Clinical Cancer Research, British Journal of Cancer,

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Genes Chromossomes & Cancer, Human Molecular Genetics, Oncogene, Journal of Medical Genetics,

European Journal of Cancer, International Journal of Cancer, Journal of Pathology.

Assessor of Grant Applications: Cancer Research UK; Medical Research Council [MRC]; Association

for International Cancer Research [AICR]; Leukaemia Research Fund [LRF]; Dutch Cancer Society; The

Wellcome Trust; Biotechnology and Biological Sciences Research Council [BBSRC]; Kay Kendal

Leukaemia Research Fund

Review Panel Membership: NIH-NCI; Canadian Cancer Society Research Institute (NCIC); EU

Innovative Medicines Initiative (IMI); EU FP-VII; Italian Association for Cancer Research; FCT Portugal;

German Consortium for Translational Cancer Research, German Federal Ministry of Education and

Research; College of Reviewers and Full Application Review Committee, Genome Canada .

MEETINGS

Presentations at Plennary Sessions

-PACABRUM 95, ‘Pancreatic Cancer: Molecular and Clinical Science’, March 1995, Birmingham, UK.

“Molecular Genetics in Pancreatic Cancer”

-VI National Cancer Conference of the Portuguese Society of Oncology, Plenary Session ‘Cellular and

Molecular Biology of Cancer’, October 1995, Lisbon, Portugal. “Molecular Biology of Leukaemias”

-XXI Annual Meeting of the Portuguese Society of Electron Microscopy and Cell Biology, Workshop

Oncogenes and Cell Proliferation, October 1996, Lisbon, Portugal. “MLL: a new oncogene”.

-1st Forum of the Society of Medical Sciences/Portuguese Academy of Medicine, Biology of Cancer, May

1997, Lisbon, Portugal. “Developmental control genes: a novel class of oncogenes”

-European School of Oncology, Advanced Course Molecular Biology for Clinicians, April 1998,

Cambridge, UK. “Developmental control genes and cancer”

-Second International From Gene to Cure Congress (Biliopancreatic malignancy: from gene to cure),

European Cancer Centre, February 1999, Amsterdam, the Netherlands. “Screening the at risk patient with

molecular markers”.

-19th International Symposium on Cancer, Sponsored by the Sapporo Cancer Seminar Foundation,

‘Cancer Genomics and Molecular Diagnosis’, Hokkaido University, July 1999, Sapporo, Japan. “Genetic

predisposition to gastric cancer: possibilities for molecular screening and diagnosis”

-The 1st Meeting of the International Collaborative Group on Hereditary Gastric Cancer, Cancer

Research Institute, Seoul National University, August 1999, Seoul, Korea. “Current status of hereditary

gastric cancer research in Europe and North America”

-Esophageal Cancer Symposium, RCP Edinburgh and RCS Edinburgh, March 2000, Edinburgh,

Scotland. “The genetics of oeasophageal carcinogenesis”

-Conference on Manipulating Human Life, Luso-American Development Foundation, April 2000,

Lisbon, Portugal. “Genetic testing for cancer predisposition”

-CRC (now CR UK) National Cancer Symposium, February 2001, Manchester, UK. “Amplicon profiling of

breast cancer”

-AACR International Conference: Molecular Mechanisms of Gastrointestinal Cancer Development and

its Clinical Application, 9-12 September 2001, Seoul, South Korea. “Hereditary Gastric Cancer: More than

E-cadherin?”

-8th European Workshop on Cytogenetics and Molecular Genetics of Human Solid Tumours, 12-15

September 2002, Barcelona, Spain. “Breast cancer genomics; towards clinical applications”

-IX National Cancer Conference of the Portuguese Society of Oncology, 15 October 2002, Lisbon,

Portugal. “Molecular genetics and the management of human cancer”

-27th ESMO Congress, Special Symposium- The role of genetics, infection and diet in gastrointestinal

tumours, 22 October 2002, Nice, France. “Genetic predisposition to gastric and oesophageal cancer”

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-Dutch Society of Pathology 2004 Annual Meeting, Ede, Netherlands, April 2004, State of the Art

Lecture “Cancer genomics and molecular pathology in the clinic”

-9th European Workshop on Cytogenetics and Molecular Genetics of Human Solid Tumours, 16-19

September 2004, Brno, Czech Republic. “EMSY- a new breast cancer oncogene”

-2005 ASCO Annual Meeting, Panel Discussant, Breast Cancer I Oral Presentation Session, , 13-17 May

2005, Orlando, USA

-9th Nottingham International Breast Cancer Conference, 13-16 September 2005, Nottingham “Molecular

classification and molecular prognostication of breast cancer: ready for practical clinical application?”

-2006 Pathological Society Winter Scientific Meeting, 4-6 January 2006, Cambridge “Breast cancer

pharmacogenomics and its clinical application”

-9th Scientific Symposium Lilly Foundation/CNIO- Cancer Epigenetics: from molecular knowledge to

therapy, 16-18 March 2006, El Escorial, Madrid, Spain “Differential expression of histone modifier genes in

human solid tumors: targets for diagnosis and therapy”

-2006 Annual Meeting of the British Society of Gastroenterology, 20-23 March 2006, Birmingham

“Hereditary diffuse gastric cancer”

-2nd IFOM-IEO (FIRC Molecular Oncology Institute/European Oncology Institute) Meeting, 5-8 May

2006, Milan, Italy “Breast cancer genomics”

-BRIC Symposium on Cancer Biology, 2 June 2006, Copenhagen, Denmark "New insights from breast

cancer genomics"

-Amsterdam Cancer Centre (at VUMC) Symposium, ‘Oncogenomics and proteomics’, 6 November 2006,

Amsterdam, Netherlands “Functional breast cancer genomics- biological and clinical implications”

-VI National Congress of the Portuguese Society of Breast Diseases, Inaugural Lecture, 8 November

2006, Lisbon, Portugal “Predictive and prognostic factors in breast cancer”

-97th Scientific Meeting of the British Division of the International Academy of Pathology, ‘A symposium

on breast pathology’, 24 November 2006, London “The molecular pathology of breast cancer”

-ASCO 2007 Gastrointestinal Cancers Symposium, 19-21 January 2007, Orlando, USA “Genetic

predisposition to gastric cancer”

-British Breast Group Meeting, 26 January 2007, Leicester “Prognostic and predictive markers, past, present

and future”

-2007 ASCO Annual Meeting, Speaker at Educational Session, June 1-5 2007, Chicago, USA “Familial

gastric cancer”

-10th Nottingham International Breast Cancer Conference, 18-20 September 2007, Nottingham “Molecular

taxonomy of breast cancer: the challenges of clinical application”

-Royal College of Pathologists Annual Conference, 3 October 2007, London “Prognostic and predictive

molecular diagnostics in oncology”

-1st Galway International Breast Cancer Conference, 19-21 June 2008, Galway, Ireland “The role of breast

cancer molecular classification in determining response” and “Molecular classification for breast cancer

prognosis”

-33rd European Symposium on Hormones and Cell regulation- Understanding the molecular and

cellular biology of endocrine-related cancers, 11-14 September 2008, Monte Ste Odile, Strasbourg, France

“Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis”

Chairmanships

▪Course Coordinator and Co-organizer: ‘Molecular Oncology: from the bench to the bedside’, Advanced

Courses in Molecular Medicine, Faculty of Medicine, University of Lisbon, April 5-9, 1999, Lisbon,

Portugal.

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▪Chairman, First Workshop of the International Gastric Cancer Linkage Consortium, June 4-5, 1999,

Churchill College, Cambridge, UK.

▪Session Co-chairperson, 19th International Symposium on Cancer, Sponsored by the Sapporo Cancer

Seminar Foundation, ‘Cancer Genomics and Molecular Diagnosis’, Hokkaido University, July 1999,

Sapporo, Japan.

▪Session Chairman, 2001 LRF Forum for Translational Research, February 2001, London, UK.

▪Workshop Panel Host, 2005 NCRI Cancer Conference, 5 October 2005, Birmingham, UK.

▪Co-Chairman (with Peter A. Jones and Manel Esteller), 9th Scientific Symposium Lilly

Foundation/CNIO- Cancer Epigenetics: from molecular knowledge to therapy, March 16-18 2006, El

Escorial, Madrid, Spain

▪Chairman, 2007 LRF Forum for Translational Research, Cancer Bioinformatics, 7 March 2007, London,

UK

▪Scientific and Organising Committee, 10th Nottingham International Breast Cancer Conference 2007

▪Co-organizer (with Jim Watson), Banbury Center Meeting, Champalimaud Foundation: Cancer

Research, 15-16 September 2007, Banbury Center, Cold Spring Harbor Laboratory, USA

▪ESMO Congress 2010 Scientific Committee

▪ESMO Congress 2012 Scientific Committee

▪EACR Summer Conference: Cancer Genomics 2013 Scientific Organising Committee (Chair)

▪European Multidisciplinary Cancer Congress (ECCO17/ESMO38/ESTRO32) 2013 Scientific Committee

▪European Breast Cancer Conference 2014 Executive Scientific Committee

▪ESMO Congress 2014 Scientific Committee

▪EACR-23 2014 Biennial Congress Scientific Review Committee

INVITED and VISITING LECTURES

*Closing Lecture, ‘Europe Against Cancer Programme’, National Programme Week, Portuguese Cancer

Institute (IPO), December 1995, Lisbon, Portugal. “Clinical applications of cancer genetics”

*Inaugural Lecture, GABBA Graduate Programme, University of Porto, Portugal, January 1998

“Trithorax-group genes: roles in development and cancer”

*Inaugural Lecture, Postgraduate Programme in Oncology, Portuguese Cancer Institute, Lisbon,

Portugal, October 1998 “Molecular Medicine: the new frontier in Oncology”

*Distinguished Visiting Lecturer, Department of Pathology and Laboratory Medicine, University of

British Columbia, Vancouver, Canada, October 2000 “From Cancer Genomics to Clinical Application. Breast

Cancer as a Model.”

*Special Lecture, Society of Medical Sciences/Portuguese Academy of Medicine, Lisbon, Portugal,

November 2000 “The impact of the Human Genome Project in Medicine. Molecular Oncology as a paradigm”

*Seminar, Singapore Genomics Program, National University of Singapore, Singapore, May 2001 “The

Cancer Genomics Program in Cambridge”

*Seminar, Department of Oncology, Queen’s University, Belfast, 12 June 2003 “Breast cancer-omics

towards clinical applications”

*Invited Speaker, IFOM/EIO, Milan, Italy, 14 July 2003 “The clinical cancer genomics program in Cambridge”

*Seminar, University of Leeds Cancer Research Centre, 25 February 2004, St James University Hospital,

Leeds “Breast cancer genomics- insights into biology and treatment”

*Keynote Speaker, Canadian Institutes of Health Research IRSC Partners Forum, 25 April 2004,

Vancouver, Canada “Knowledge translation: a UK perspective- the cancer research example”

*Distinguished Lecturer, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain, May 2004

“Clinical breast cancer genomics”

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*Guest Speaker, Cancer Interdisciplinary Research Group Awayday 2004, 1 October 2004, Cardiff

“Clinical cancer genomics”

*Invited Speaker, Symposium to mark the launch of the Queens University Centre for Cancer Research

and Cell Biology, 14-15 October 2004, Belfast “Translational cancer genomics”

*Invited Speaker, The Academy of Medical Sciences FORUM, Cancer Biomarkers and Imaging, 25

October 2004, London “Gene expression arrays”

*Invited Speaker, RCR Breast Group 2004 Annual Scientific Meeting, 1 November 2004, London

“Translational research implications for breast cancer”

*Invited Speaker, 1st Educational Meeting of the Anglo Celtic Cooperative Oncology Group, 19

November 2004, Edinburgh “Critical review of gene expression profiling in breast cancer”

*Seminar, Department of Oncology, IMM, University of Oxford, Oxford, 6 February 2005 “Breast cancer

genomics: insights into biology and potential clinical applications”

*Invited Speaker, Cancer Conference 2005, St James Hospital, 1 April 2005, Dublin, Ireland “Breast

cancer- translating cancer genomics into patient care”

*Invited Speaker, NCRI Cancer Informatics Workshop (2005 NCRI National Cancer Conference), 2

October 2005, Birmingham “CancerGRID- Developing open standards for clinical cancer informatics”

*Invited Speaker, West Midlands Cancer Intelligence Unit Quality Assurance Conference, 18 October

2005, Birmingham “Microarrays for breast cancer classification and prognostication”

*Invited Speaker, UK-Texas Bioscience Collaboration Meeting (DTI/NTRAC), 12-14 January 2006,

Oxford “Tailoring breast cancer treatment based on tumour biology”

*Invited Speaker, Institute of Molecular Medicine Symposium- Novel contributions of molecular

genetics to medicine, University of Lisbon, 24 February 2006, Lisbon, Portugal “Breast cancer genomics”

*Invited Speaker, Genentech, 27 February 2006, San Francisco, USA “Breast cancer genomics”

*Seminar, Christie Hospital Oncology Seminar Series, 3 March 2006, Manchester “Breast cancer genomics”

*Invited Speaker, IARC Meeting- Expression array analyses in breast cancer taxonomy, 10-11 May 2006,

Lyon, France “Array profiling of breast cancer- is it ready for clinical application now?”

*Invited Speaker, 2006 BGCS Spring Meeting “Translational research in gynaecological oncology”, 12

May 2006, Cambridge “What lessons can we learn from breast cancer”

*Invited Speaker, 2006 Cancer Genetics Group Spring Meeting, 22 May 2006, Birmingham “Familial

gastric cancer”

*Invited Speaker, 2006 “Weekend to End Breast Cancer” International Symposium, BC Cancer Research

Centre, 6 June 2006, Vancouver, Canada “New insights from breast cancer genomics”

*Speaker, Cambridge Cancer Centre Launch Symposium, 22 June 2007, Cambridge “Cambridge

Experimental Cancer Medicine Centre- molecular diagnostics/imaging/therapeutics”

*Invited Speaker, NCRI Late Phase Trials Forum, 5 July 2007, London “Genomics profiling in the context of

phase III clinical trials”

*Invited Speaker, 2007 “Weekend to End Breast Cancer” International Symposium, The Campbell

Family Institute for Breast Cancer Research, 30-31 July 2007, Toronto, Canada “Molecular heterogeneity of

breast carcinomas and the cancer stem cell hypothesis”

*Seminar, Cancer Research Nottingham University, 9 October 2007 “Unravelling the molecular

heterogeneity of human breast cancer”

*Invited Speaker, Gulbenkian Foundation Health Forum, 7 November 2007 Conference, Lisbon “The

genetic landscape of cancer…after the $1000USD genome”

*Seminar, Friedrich Miescher Institute (FMI) for Biomedical Research, Basel, 11 March 2008 “Micro-

RNAs in mammary devlopment and breast cancer”

*IFOM-IEO Campus Seminar, Milan, 22 May 2008 “Functional and translational breast cancer genomics”

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CLINICAL PRACTICE

Honorary Consultant in Medical Oncology, Oncology Center and Cambridge Breast Unit,

Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust

Main clinical interests: Treatment of metastatic and locally advanced breast cancer; Systemic adjuvant

therapy.

CURRENT RESEARCH GROUP

1- Associate Scientists

Suet-Feung Chin, PhD

Funding- Cancer Research UK Cambridge Institute (CI). Project- Breast cancer

genomics

Alejandra Bruna, PhD

Funding- Cancer Research UK Cambridge Institute (CI). Project- Breast cancer stem

cells

2- Clinical Lecturerers

Raza Ali, MD PhD

Funding- NIHR. Project- Molecular pathology of breast cancer

Emma Beddowes, MD PhD

Funding- NIHR. Project- ctDNA in metastatic breast cancer

3- PostDoctoral Fellows

Ana Gitt, PhD

Funding- EU FP-VII. Project- miRNAs in breast cancer

Oscar M Rueda, PhD

Funding- Cancer Research UK (CI). Project- Next-generation sequencing and

methylation-sequencing analysis; microarray analysis; prognostic and predictive

signatures

Roslin Russell, PhD

Funding- Cancer Research UK (CI). Project- Microarray analysis; RNA-sequencing

analysis

4- Graduate (PhD) Students

Ann Tufgedzic, BSc

Funding- Cancer Research UK (CI). Project- Breast cancer stem cells.

Bernard Pereira, MSc

Funding- Cancer Research UK (CI). Project- Sequencing bioinformatics.

Mae Goldgraben, MSc

Funding- MRC. Project- miRNAs in breast cancer

5- Research Assistants

Wendy Greenwood, BSc

Funding- Cancer Research UK (CI). Project- Breast cancer stem cells

6- Clinical Research Training Fellows (PhD Students)

Jose Sandoval, MD

Funding- FCT Portugal. Project- Breast cancer stem cells.

7- Computer Officers

Bin Liu, BSc

Funding- ECMC. Project- Development of genomics databases

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8- Research Nurses

Sue Richardson, RN

Funding- ECMC. Project- Familial Gastric Cancer Registry

Linda Jones, RN

Funding- ECMC. Project- Sample collections and translational trials in breast cancer

GRANTS

Current:

Cancer Research UK, Cambridge Research Institute, Program Grant, ~£3.5M, 5 years (2013-2018)

[“Breast Cancer Genomics Programme”]

Cancer Research UK/BBSRC (Co-applicant; Lead Applicant- Prof Kevin Brindle), ~£7,000,000, 5 years

(2013-2018) [“The Cambridge-Manchester Cancer Imaging Centre”]

Wellcome Trust Strategic Translation Award (Co-applicant; Lead Applicant- Prof Kevin Brindle),

£4,200,000, 4 years (2013-2017) [“Real time clinical imaging of tumour metabolism using hyperpolarized

13C magnetic resonance spectroscopy.”]

NIHR Senior Investigator Award, £60,000, 4 years (2012-2016)

Cancer Research UK/UK Departments of Health/NIHR (Lead Applicant), ~£2.5M, 5 years (2012-2017)

[“Cambridge Experimental Cancer Medicine Centre”]

Cancer Research UK TRICC Grant, ~£336,000, 5 years (2008-2014) [“Trans-PERSEPHONE and Trans-

PERSEPHONE-SNPs: the pharmacogenomics and pharmacogenetics of adjuvant Trastuzumab”]

EU FP-VII Project (Co-applicant), €645,900 (2010-14) ["RATHER- Rational Therapy for Breast Cancer:

Individualized Treatment for Difficult-to-Treat Breast Cancer Subtypes"]

EU FP-VII Network of Excellence (Co-applicant), €616,700 (2010-15) ["EurocanPlatform- A European

Platform for Translational Cancer Research"]

Past Grants:

EU FP-VII Project (Co-applicant), €138,000 (2010-13) ["BASIS- Breast Cancer Somatic Genetics Study"]

Cancer Research UK, Cambridge Research Institute, Program Grant, ~£3.5M, 5 years (2008-2013)

[“Breast Cancer Genomics Programme”]

Cancer Research UK BIDD Grant (Joint Lead Applicant), £60,000, 1 year (2012) [“Pharmacogenetics of

Breast Cancer Chemotherapy Toxicities - Part I”]

Cancer Research UK’s Science Committee, £200,000, 6 months (2012) ["Sequencing 150 breast cancer

genes in 2500 samples from the METABRIC cohort"]

Cancer Research UK Clinician Scientist Molecular Pathology Fellowship (Fellow- Dr. John Le Quesne

PhD), ~£600,000, 5 years (2007-2012)

Cancer Research UK/UK Departments of Health/NIHR (Lead Applicant), ~£2.5M, 5 years (2007-2012)

[“Cambridge Experimental Cancer Medicine Centre”]

EU FP7, Marie Curie Fellowship (Fellow- Dr. Alejandra Bruna), €180,783, 2 years (2010-2011) ["TGF-beta

and breast cancer stem cells"]

Cancer Research UK SEB Grant (Lead Applicant), £925,000, 3.5 years (2007-2010) [“METABRIC-

Generation of a robust molecular taxonomy of clinically annotated breast cancers”]

Cancer Research UK TRICC Grant, £180,000, 3.5 years (2006-2010) [“TANGO-Science: molecular

determinants of outcome in breast cancer patients treated with a taxane/anthracycline +/- gemcitabine-

containing adjuvant chemotherapy regime”]

Pfizer Limited, Investigator-Initiated Research Grant (Co-applicant; Lead Applicant- Dr Helena Earl),

£568,388, 3 years (2008-2011) [“Aromasin® Randomised TrIal +/-Sutent® as neoadjuvant Therapy for

post-menopausal women with breast cancer”]

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Cancer Research UK Clinical Research Training Fellowship (Fellow- Dr. Jean Abraham), ~£200,000, 3

years (2006-2009)

NIHR Capital Equipment Grant 2008 (Lead applicant), £420,000 (plus £154,000 capital charges)

STFC Grant (Co-applicant; Lead applicant: Dr Nick Walton), £87,000, 1 year (2008-2009) [“Automating

Tissue Microarray analysis: extending PathGrid”]

Cancer Research UK TRICC Grant (Co-PIs: Dr. Helena Earl, Dr. Jean Abrahm), £476,000, 4 years (2005-

2009) [“PG-SNPs: pharmacogenetics of early breast cancer chemotherapy”]

MRC Strategic Grant (Lead Applicant), ~£2.3M, 3.5 years (2005-2009) [“CancerGRID”]

Cancer Research UK CTRC Grant, ~£196,000, 2.5 years (2007-2009) [“Familial Gastric Cancer

Study/SOCS”]

Cancer Research UK Programme Grant, ~£1.2M, 5 years (2003-2008) [“Clinical breast cancer genomics”]

Cancer Research UK Programme Grant (co-PI with Bruce Ponder, Tony Kouzarides, Ashok

Venkitaraman, Sam Aparicio), ~£1.5M, 5 years (2003-2008) (~350K to Caldas lab) [“Cambridge BRCA2

collaborative]

Cambridge NTRAC Centre (Deputy Lead Applicant; Lead applicant: Prof. Bruce Ponder): ~£1.1M, 5

years (2002-2007)

BBSRC Exploiting Genomics Initiative (co-applicant; PI- Prof. Andrew Wylie): £1,700,000 [“Shared

genetic pathways in cell number control”- Core cDNA microarray facility]

Cancer Research UK/CRT: £100,000, 2 years (2003-2005) [“Using somatic knockouts for novel compound

screening and target validation”]

Cancer Research UK and Isaac Newton Trust (Co-PI): £58,500 (2001) [“Linux cluster for Bioinformatics”]

SUR IBM grant: ~£250,000 (2002) [“Linux cluster for Bioinformatics”]

JIF, MRC, HEFCE (Co-ordinating applicant and one of six coapplicants; PI- Prof. Bruce Ponder):

£3,364,876 (2000) [“Equiping a new centre for translational research in the University of Cambridge

School of Clinical Medicine”]

BBSRC (coapplicant; PI- Dr. Paul AW Edwards): £215,000, 3 years (2002-2005) [“Genomic microarrays to

examine chromosome rearrangement and evolution”]

EU: 150,000 Euros, 2 years (2003-2005) [“Genotyping of E-cadherin SNPs and tissue microarrays in

gastric cancers from the EPIC study”, EU-GAS consortium]

WellBeing Trust (with Bruce Ponder): £139,000, 3 years (2001-2004) [“Genetic profiles of ovarian

cancer”]

Cancer Research UK PhD Studentship, ~£80,000, 3 years (2000-2003) [“Molecular genetic and

cytogenetic analysis of normal and malignant breast tissue from patients in high risk families”]

Cancer Research UK (with Paul Edwards): £250,000, 3 years (2001-2004) [“Molecular cytogenetics of

carcinomas”]

Cancer Research UK (with James Brenton): £225,000, 3 years (2001-2004) [“Molecular profiling of

epithelial ovarian and breast cancer with simultaneous cDNA and CGH microarrays”]

BBSRC/LINK: £320,000, 2 years (2002-2004) [“Prototype protein biochip development for protein

expression profiling and novel antibody selection in breast cancer”]

Cancer Research UK: £220,000, 3 years (2000-2003) [“Molecular genetics of familial gastric cancer”]

MRC Clinical Training Fellowship (to Grace Callagy): £125,000, 3 years (2000-2003) [“Molecular

pathology of early progression in sporadic breast cancer”]

EU (Co-PI): £166,000, 3 years (2000-2003) [“Acetylases and deacetylases in human cancers”, Acetylon

consortium]

CRC/CRC-T: £195,000, 4.5 years (1997-2001) [“Molecular characterization of 13q12.3 deletions in

common human neoplasms”/“Cloning a new tumour suppressor gene at 13q12.3”]

JREI/MRC, Isaac Newton Trust (Co-PI): £100,000 (1998) [“Cytogenetics Facility”]

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LRF: £120,000, 3 years (1995-1998) [“Characterization of the locus for the MLL (Mixed Lineage

Leukaemia) gene by comparison with a model vertebrate genome (Fugu rubripes)”]

Addenbrooke’s Endowment Fund: £32,000, 1 year (1997) [“Identification of a novel tumour suppressor

gene at chromosome 13q12”]

Cambridge Cancer Research Fund: £17,200, 18 months (1997-1998) [“Search for a gene responsible for

familial gastric cancer”]

Addenbrooke’s Endowment Fund: £10,000, 1 year (1998) [“Molecular markers in metastatic breast

cancer”]

Addenbrooke’s Cancer Research Charity Fund: £23,500, 1 year (1998) [“Genetic predisposition to gastric

cancer”]

PUBLICATIONS

ORIGINAL ARTICLES

1. Caldas C, Sitzmann J, Trimble CL, and McGuire WP. Synchronous mature teratomas of the ovary and

liver: a case presenting 11 years following chemotherapy for immature teratoma. Gynecologic

Oncology, 47: 385-390, 1992

2. Caldas C, Bernicker E, Dal Nogare A, and Luby JP. Transverse myelitis associated with Epstein-Barr

virus infection. American Journal of Medical Sciences, 307: 45-48, 1994

3. Seymour AB, Hruban RH, Redston MS, Caldas C, Powell SM, Kinzler KW, Yeo CJ, and Kern SE.

Allelotype of pancreatic adenocarcinoma. Cancer Research, 54: 2761-2764, 1994

4. Redston MS, Caldas C, Seymour AB, Hruban RH, da Costa L, Yeo CJ, and Kern SE. P53 mutations in

pancreatic adenocarcinoma and evidence of common involvement of homocopolymer tracts in DNA

microdeletions. Cancer Research, 54: 3025-3033, 1994

5. Kern SE, Redston MS, Seymour AB, Caldas C, Powell SM, Kornackie S, and Kinzler KW. Molecular

genetic profiles of colitis-associated neoplasms. Gastroenterology, 107: 420-428, 1994

6. Caldas C, Hahn S , Hruban RH, Redston MS, Yeo CJ, and Kern SE. Detection of K-ras mutations in the

stool of patients with pancreatic carcinoma and pancreatic ductal hyperplasia. Cancer Research, 54:

3568-3573, 1994

7. Caldas C, Hahn SA, da Costa L, Redston MS, Schutte M, Seymour AB, Weinstein CL, Hruban RH, Yeo

CJ, and Kern SE. Frequent somatic mutations and homozygous deletions of the MTS1 gene in pancreatic

adenocarcinoma. Nature Genetics, 8: 27-32, 1994

8. Redston MS, Papadopoulos N, Caldas C, Kinzler KW, and Kern SE. Common APC and K-ras

mutations in the spectrum of colitis-associated neoplasias. Gastroenterology, 108: 383-392, 1995

9. Hahn SA, Seymour AB, Hoque ATMS, Schutte M, da Costa LT, Redston MS, Caldas C, Weinstein C

L, Fisher A, Yeo CJ, Hruban RH, and Kern SE. Allelotype of pancreatic adenocarcinoma using xenograft

enrichment. Cancer Research, 55: 4670-4675, 1995

10. Garcia-Marco JA*, Caldas C*, Price CM, Wiedemann LM, Ashworth A, and Catovsky D. Frequent

somatic deletion of the 13q12.3 locus encompassing BRCA2 in chronic lymphocytic leukemia. Blood,

88:1568-1575, 1996 (*These authors contributed equally to this work)

11. So CW, Caldas C, Liu M-M, Chen SJ, Huang Q-H, Gu L-J, Sham MH, Wiedemann LM, and Chan LC.

EEN encodes for a member of a new family of SH3-containing proteins and is the third gene located on

chromosome 19p13 which fuses to MLL in human leukemia. Proceedings of the National Academy of

Sciences of the USA, 94: 2563-2568, 1997

12. Gayther SA, Barski P, Batley SJ, Li L, de Foy KAF, Cohen SN, Ponder BAJ, and Caldas C. Aberrant

splicing of the TSG101 and FHIT genes occurs frequently in multiple malignancies and in normal

tissues and mimics alterations previously described in tumours. Oncogene, 15: 2119-2126, 1997

12

13. Garcia-Marco JA, Navarro B, and Caldas C. Confirmation of frequent somatic deletion of the 13q12.3

locus encompassing BRCA2 in chronic lymphocytic leukaemia [Letter]. British Journal of Haematology,

99: 708-709, 1997

14. Caldas C, So CW, MacGregor A, Ford AM, McDonald B, Chan LC, and Wiedemann LM. Exon

scrambling of MLL transcripts occur commonly and mimic partial genomic duplication of the gene.

Gene, 308: 167-176, 1998

15. Caldas C, Kim M-H, MacGregor A, Cain D, Aparicio S, and Wiedemann LM. Isolation and

characterization of a pufferfish MLL (mixed lineage leukemia)-like gene (fMll) reveals evolutionary

conservation in vertebrate genes related to Drosophila trithorax. Oncogene, 16: 3233-3241, 1998

16. Gayther SA, Gorringe KL, Ramus S, Huntsman D, Roviello F, Grehan N, Machado JC, Pinto E,

Seruca R, Halling K, MacLeod P, Powell SM, Jackson CE, Ponder BAJ, and Caldas C. Identification of

germline E-cadherin mutations in gastric cancer families of European origin. Cancer Research, 58: 4086-

4089, 1998

17. Huntsman D and Caldas C. Assignment of the E-cadherin gene (CDH1) to chromosome 16q22.1 by

radiation hybrid mapping. Cytogenetics and Cell Genetics, 83: 82-83,1998

18. Wiedemann LM, MacGregor A, and Caldas C. Analysis of the region of the 5' end of the MLL gene

involved in genomic duplication events. British Journal of Haematology, 105: 256-264, 1999

19. Pharoah PDP, Day NE, and Caldas C. Somatic mutations in the P53 gene and prognosis in breast

cancer: a meta-analysis. British Journal of Cancer, 80: 1968-1973, 1999

20. Berger W, Setinek U, Mohr T, Kindas-Mugge I, Vetterlein M, Dekan G, Eckersberger F, Caldas C,

and Micksche M. Evidence for an intracrine proliferative loop involving FGF-2 and FGF receptors in

non-small cell lung cancer cells. International Journal of Cancer, 83: 415-423, 1999

21. Caldas C, Carneiro F, Lynch HT, Yokota J, Wiesner G, Powell S, Lewis FR, Huntsman DG, Pharoah

PD, Jankowski JA, MacLeod P, Vogelsang H, Keller G, Park KGM, Richards FM, Maher ER, Gayther SA,

Oliveira C, Grehan N, Wight D, Seruca R, Roviello F, Ponder BAJ, and Jackson CE. Familial gastric

cancer: overview and guidelines for management. Journal of Medical Genetics, 36: 873-880, 1999

22. Huntsman DG, Chin S-F, Muleris M, Batley SJ, Collins VP, Wiedemann LM, Aparicio S, and Caldas

C. MLL2, the second human homolog of the Drosophila trithorax gene, maps to 19q13.1 and is amplified

in solid tumor cell lines. Oncogene, 18: 7975-7984, 1999

23. Gayther SA, Batley SJ, Linger L, Bannister L, Thorpe K, Chin S-F, Daygo Y, Russell P, Wilson A,

Sowter HM, Delhanty JDA, Ponder BAJ, Kouzarides T, and Caldas C. Mutations truncating the EP300

acetylase in human cancers. Nature Genetics, 24: 300-303, 2000

24. So CW, Sham MH, Chew SL, Cheung N, So CK, Chung SK, Caldas C, Wiedemann LM,

and Chan LC. Expression and protein-binding studies of the EEN gene family, new interacting

partners for dynamin, synaptojanin and huntingtin proteins. Biochemical Journal, 348: 447-58, 2000

25. Park J-G, Yang H-K, Kin WH, Caldas C, Yokota J, and Guilford P. Report on the first meeting of the

International Collaborative Group on Hereditary Gastric Cancer. Journal of the National Cancer

Institute, 92: 1781-2, 2000

26. Davidson JM, Gorringe KL, Chin S-F, Orsetti B, Besret C, Courtay-Cahen C, Roberts I , Theillet C,

Caldas C, and Edwards PAW. Molecular cytogenetic analysis of breast cancer cell lines. British Journal

of Cancer, 83: 1309-1317, 2000

27. Chin S-F, Wang Q, Puisieux A, and Caldas C. Absence of rearrangements in the BRCA2 gene in

human cancers. British Journal of Cancer, 84: 193-195, 2001

28. Huntsman DG, Carneiro F, Lewis F, MacLeod PM, Hayashi A, Monaghan K, Maung R, Seruca R,

Jackson CE, and Caldas C. Early gastric cancer in young asymptomatic germline E-cadherin mutation

carriers. New England Journal of Medicine, 344: 2904-2909, 2001

13

29. Daigo Y, Chin S-F, Gorringe K, Bobrow LG, Ponder BAJ, Pharoah PDP, and Caldas C. DOP-PCR

based array-CGH for extensive amplicon profiling of breast cancers: A new approach for the molecular

analysis of paraffin-embedded cancer tissue. American Journal of Pathology, 158: 1623-1631, 2001

30. Machado JC, Oliveira C, Carvalho R, Soares P, Berx G, Caldas C, Seruca R, Carneiro F, Sobrinho-

Simões M. E-cadherin gene (CDH1) promoter methylation as the second genetic hit in sporadic diffuse

gastric carcinoma. Oncogene, 20: 1525-1528, 2001

31. Lewis FR, Mellinger JD, Hayashi A, Lorelli D, Monaghan KG, Carneiro F, Huntsman DG, Jackson

CE, and Caldas C. Prophylactic total gastrectomy for familial gastric cancer. Surgery, 130: 612-619, 2001.

32. Machado JC, Pharoah PDP, Sousa S, Carvalho R, Oliveira C, Figueiredo C, Amorim A, Seruca R,

Caldas C, Carneiro F, Sobrinho-Simões M. Interleukin-1β and interleukin-1 receptor antagonist gene

polymorphisms are associated with increased risk of gastric carcinoma. Gastroenterology, 121: 823-829,

2001

33. Pharoah PDP, Guilford P, Caldas C and the International Gastric Cancer Linkage Consortium.

Incidence of stomach cancer and breast cancer in germline E-cadherin mutation carriers from hereditary

diffuse gastric cancer families. Gastroenterology, 121: 1348-1353, 2001

34. Oliveira C, Bordin MC, Grehan N, Huntsman DG, Suriano G, Machado JC, Kiviluoto T, Aaltonen L,

Jackson CE, Seruca R, and Caldas C. Screening E-cadherin in gastric cancer families reveals germ-line

mutations only in hereditary diffuse gastric cancer kindred. Human Mutation, 19: 510-517, 2002

35. Pharoah PDP, Oliveira C, Machado JC, Keller G, Vogelsang H, Laux H, Becker K-F, Hahn H,

Paprosli SM, Brown LA, Caldas C, and Huntsman DG. CDH1 C-160A promoter polymorphism is not

associated with risk of stomach cancer. International Journal of Cancer, 101: 196-197, 2002

36. Figueiredo C, Machado JC, Pharoah PDP, Seruca R, Sousa S, Carvalho R, Capelinha AF, Quint W,

Caldas C, van Doorn L-J, Carneiro F, and Sobrinho-Simões M. Helicobacter pylori and interleukin-1

genotyping: An opportunity to identify high-risk individuals for gastric carcinoma? Journal of the

National Cancer Institute, 94: 1680-1687, 2002

37. Ozdag H, Batley SJ, Forsti A, Yier NG, Daigo Y, Boutell J, Arends MJ, Ponder BAJ, Kouzarides T, and

Caldas C. Mutation analysis of CBP and PCAF reveals rare inactivating mutations in cancer cell lines but

not in primary tumours. British Journal of Cancer , 87: 1162-1165, 2002

38. Callagy G, Cattaneo E, Daigo Y, Bobrow LG, Pharoah PDP, and Caldas C. Molecular classification of

breast carcinomas using tissue microarrays. Diagnostic Molecular Pathology, 12: 27-34, 2003

39. Suriano G, Oliveira C, Ferreira P, Machado JC, Bordin MC, de Wever O, Bruyneel EA, Moguilevsky

N, Grehan N, Porter TR, Richards F, Hruban RH, Roviello F, Huntsman D, Mareel M, Carneiro F, Caldas

C* and Seruca R. Identification of CDH1 germline missense mutations associated with functional

inactivation of the E-cadherin protein in young gastric cancer probands. Human Molecular Genetics, 12:

575-582, 2003 [*co-corresponding author]

40. Machado JC, Figueiredo C, Canedo P, Pharoah P, Carvalho R, Nabais S, Alves CC, Campos ML, van

Doorn LJ, Caldas C, Seruca R, Carneiro F, and Sobrinho-Simões M. A pro-inflammatory genetic profile

increases the risk of chronic atrophic gastritis and gastric carcinoma. Gastroenterology, 125: 364-371,

2003

41. Daigo Y, Takayama I, Ponder BAJ, Caldas C, Ward SM, Sanders KM, and Fujino MA. Differential

gene expression in the murine gastric fundus lacking intersticial cells of Cajal. BMC Gastroenterology,

3: 14, 2003

42. Chin S-F, Daigo Y, Huang H-E, Iyer NG, Kranjac T, Callagy G, Gonzalez M, Sangan T, Earl H, and

Caldas C. A simple and reliable pre-treatment protocol facilitates fluorescent in situ hybridisation

(FISH) on tissue microarrays (TMAs) of paraffin-embedded tumour samples. Molecular Pathology, 56:

275-279, 2003

14

43. Daigo Y, Takayama I, Ponder BAJ, Caldas C, Ward SM, Sanders KM, and Fujino MA. Differential

gene expression profile in the small intestines of mice lacking pacemaker interstitial cells of Cajal. BMC

Gastroenterology, 3: 17, 2003

44. Hughes-Davies L, Huntsman D, Ruas M, Fuks F, Bye J, Chin S-F, Milner J, Brown LA, Hsu F, Gilks F,

Nielsen T, Schulzer M, Chia S, Ragaz J, Cahn A, Linger L, Ozdag H, Cattaneo E, Jordanova ES,

Schuuring E, Yu DS, Venkitaraman A, Ponder B, Doherty A, Aparicio S, Bentley D, Theillet C, Ponting

CP, Caldas C*, and Kouzarides T. EMSY links the BRCA2 pathway to sporadic breast and ovarian

cancer. Cell, 115: 523-535, 2003 [*co-corresponding author]

45. Daigo Y, Takayama I, Ponder BA, Caldas C, Ward SM, Sanders KM, Fujino MA. Novel human,

mouse and xenopus genes encoding a member of the RAS superfamily of low-molecular-weight GTP-

binding proteins and its downregulation in W/WV mouse jejunum. Journal of Gastroenterology and

Hepatology, 19: 211-217, 2004

46. Ahmed AA, Vias M, Iyer NG, Caldas C, and Brenton JD. Microarray segmentation methods

significantly influence data precision. Nucleic Acid Research, 32(5): E50, 2004

47. Naderi A, Ahmed AA, Barbosa-Morais NL, Aparicio S, Brenton JD, and Caldas C. Expression

microarray reproducibility is improved by optimising purification steps in RNA amplification and

labelling. BMC Genomics, 5: 9, 2004

48. Carneiro F, Huntsman DG, Smyrk T, Owen D, Seruca R, Pharoah P, Caldas C, and Sobrinho-Simoes

M. Model of early development of diffuse gastric cancer in E-cadherin mutation carriers and its

implications for patient screening. The Journal of Pathology, 203: 681-687, 2004

49. Grigorova M, Staines JM, Ozdag H, Caldas C, and Edwards PAW. Possible causes of chromosome

instability: comparison of chromosomal abnormalities in cancer cell lines with mutations in BRCA1,

BRCA2, CHK2 and BUB1. Cytogenetics and Genome Research, 104: 333-340, 2004

50. Brooks-Wilson AR, Kaurah P, Suriano G, Leach S, Senz J, Grehan N, Butterfield YSN, Jeyes J,

Schinas J, Bacani J, Kelsey M, Ferreira P, MacGillivray B, MacLeod P, Micek M, Ford J, Foulkes W,

Australie K, Greenberg C, LaPointe M, Gilpin C, Nikkel S, Gilchrist D, Hughes R , Jackson CE,

Monaghan KG, Oliveira MJ, Seruca R, Gallinger S, Caldas C*, and Huntsman D. Germline E-Cadherin

mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic

screening criteria. Journal of Medical Genetics, 41: 508-517, 2004 [*co-corresponding author]

51. Iyer NG, Chin S-F, Ozdag H, Daigo Y, Hu D-E, Cariati M, Brindle K, Aparicio S and Caldas C. p300

regulates p53-dependent apoptosis after DNA damage in colorectal cancer cells by modulation of

PUMA/p21 levels. Proceedings of the National Academy of Sciences of the USA, 101: 7386-7391, 2004

52. Huang H-E, Chin S-F, Ginestier C, Bardou V-J, Adelaide J, Iyer NG, Garcia MJ, Pole JC, Callagy GM,

Hewitt SM, Gullick WJ, Jacquemier J, Caldas C, Chaffanet M, Birnbaum D, and Edwards PAW. A

recurrent chromosome breakpoint in breast cancer targets the NRG1/neuregulin1/heregulin gene. Cancer

Research, 64: 6840-6844, 2004

53. Callagy G, Pharoah P, Chin S-F, Sangon T, Daigo Y, Jackson L, and Caldas C. Identification and

validation of prognostic markers in breast cancer with the complimentary use of array-CGH and tissue

microarrays. The Journal of Pathology, 205: 388-396, 2005

54. Gorringe KL, Chin S-F, Pharoah P, Staines JM, Oliveira C, Edwards PAW, and Caldas C. Evidence

that both genetic instability and selection contribute to the accumulation of chromosome alterations in

cancer. Carcinogenesis, 26: 923-930, 2005

55. Grigorova M, Lyman RC, Caldas C, and Edwards PAW. Chromosome abnormalities in ten lung

cancer cell lines of the NCI-H series analysed by Spectral Karyotyping. Cancer Genetics and

Cytogenetics, 162: 1-9, 2005

15

56. Garcia MJ, Pole JCM, Chin S-F, Teschendorff A, Naderi A, Ozdag H, Vias M, Kranjac T,

Subkhankulova T, Paish C, Ellis I, Brenton JD, Edwards PAW, and Caldas C. A 1Mb minimal amplicon

at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene, 24: 5235-5245, 2005

57. Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, Bonaldi T, Haydon C,

Ropero S, Petrie K, Iyer NG, Pérez-Rosado A, Calvo E, Lopez JA, Cano A, Calasanz MJ, Colomer D, Piris

MA, Ahn N, Imhof A, Caldas C, Jenuwein T and Esteller M. Loss of acetylated lysine 16 and

trimethylated lysine 20 of histone H4 is a common hallmark of human cancer. Nature Genetics, 37:391-

400, 2005

58. Teschendorff AE, Wang Y, Barbosa-Morais NL, Brenton JD and Caldas C. A variational Bayesian

mixture modeling framework for cluster analysis of gene expression data. Bioinformatics, 21: 3025-3033,

2005

59. Naderi A, Ahmed AA, Wang Y, Brenton JD and Caldas C. Optimal amounts of fluorescent dye

improve expression microarray results in tumor specimens. Molecular Biotechnology, 30:151-154, 2005

60. Onwuegbusi BA, Aitchison A, Chin S-F, Kranjac T, Mills I, Huang Y, Caldas C, and Fitzgerald RC.

Impaired TGFB signalling in Barrett’s carcinogenesis due to frequent SMAD4 inactivation. Gut, 55: 764-

774, 2006

61. van den Ijsell P, Tijssen M, Chin S-F, Eijk P, Carvalho B, Hopmans E, Holstege H, Bangarusamy DK,

Jonkers J, Meijer G, Caldas C, and Ylstra B. Human and mouse oligonucleotide-based array CGH.

Nucleic Acid Research, 33, e192, 2006

62. Su M, Chin SF, Li XY, Edwards P, Caldas C, and Fitzgerald RC. Comparative genomic hybridization

of esophageal adenocarcinoma and squamous cell carcinoma cell lines. Diseases of the Esophagus, 19:

10-14, 2006

63. Griffin JL, Blenkiron C, Valonen PK, Caldas C, and Kauppinen RA. High-Resolution Magic Angle

Spinning (1)H NMR Spectroscopy and Reverse Transcription-PCR Analysis of Apoptosis in a Rat

Glioma. Analytical Chemistry, 78:1546-1552, 2006

64. Boyer J, Allen WL, McLean EG, Wilson PM, McCulla A, Moore S, Longley DB, Caldas C, and

Johnston PG. Pharmacogenomic identification of novel determinants of response to chemotherapy in

colon cancer. Cancer Research, 66:2765-2777, 2006

65. Pole JCM, Courtay-Cahen C, Blood KA, Cooke SL, Alsop AE, Tse DML, Garcia MJ, Caldas C,

Edwards PAW. High-resolution analysis of chromosome rearrangements on 8p in breast, colon and

pancreatic cancer reveals a complex pattern of loss, gain and rearrangement. Oncogene, 25:5693-5706,

2006

66. Camps J, Salaverria I, Garcia MJ, Prat E, Bea S, Pole JC, Hernandez L, Rey JD, Cigudosa JC, Bernues

M, Caldas C, Colomer D, Miro R, and Campo E. Genomic imbalances and patterns of karyotypic

variability in mantle-cell lymphoma cell lines. Leukemia Research, 30: 923-934, 2006

67. Brachner A, Sasgary S, Priker C, Rodgarkia C, Mikula M, Mikulitis W, Bergmeister H, Setinek U,

Wieser M, Chin S-F, Caldas C, Micksche M, Cerni C, and Berger W. Telomerase- and ALT-independent

stabilization in a metastasis-derived human NSCLC cell line; impact of ectopic hTERT. Cancer Research,

66: 3584-3592, 2006

68. Callagy GM, Pharoah PD, Pinder SE, Hsu FD, Nielsen TO, Ragaz J, Ellis IO, Huntsman D, and

Caldas C. Bcl-2 is a prognostic marker in breast cancer independently of the Nottingham Prognostic

Index (NPI). Clinical Cancer Research, 12: 2468-2475, 2006

69. Bundy JG, Iyer NG, Gentile MS, Hu D-E, Maia A-T, Thorne NP, Brenton JD, Caldas C, and Brindle

KM. Metabolic consequences of p300 gene deletion in human colon cancer cells. Cancer Research, 66:

7606-7614, 2006

16

70. Krubasik D, Iyer NG, English WR, Ahmed AA, Vias M, Wu C, Roskelley C, Brenton JD, Caldas C,

and Murphy G. Absence of p300 induces cellular phenotypic changes characteristic of epithelial to

mesenchyme transition. British Journal of Cancer, 94: 1326-1332, 2006

71. Özdağ H, Teschendorff AE, Ahmed AA, Hyland SJ, Blenkiron C, Bobrow L, Veerakumarasivam A,

Burtt G, Subkhankulova T, Arends MJ, Collins VP, Bowtel D, Kouzarides T, Brenton JD, and Caldas C.

Differential expression of selected histone modifier genes in human solid cancers. BMC Genomics, 7:90,

2006

72. Teschendorff AE, Naderi A, Barbosa-Morais NL, and Caldas C. PACK: Profile Analysis using

Clustering and Kurtosis to find molecular classifiers of cancer. Bioinformatics, 22: 2269-2275, 2006

73. Rodriguez-Sanjuan JC, Fontalba A, Mayorga M, Bordin MC, Hyland SJ, Trugeda S, Garcia RA,

Gomez-Fleitas M, Fernandez F, Caldas C, Fernandez-Luna JL. A novel mutation in the E-cadherin gene

in the first family with hereditary diffuse gastric cancer reported in Spain. European Journal of Surgical

Oncology, 32: 1110-1113, 2006

74. Kunapuli P, Kasyapa CS, Chin S-F, Caldas C, and Cowell JK. ZNF198, a zinc finger protein

rearranged in myeloproliferative disease, localizes to the PML nuclear bodies and interacts with SUMO-

1 and PML. Experimental Cell Research, 312: 3739-3751, 2006

75. Teschendorff AE, Naderi A, Barbosa-Morais NL, Pinder SE, Ellis IO, Aparicio S, Brenton JD, and

Caldas C A consensus prognostic gene expression classifier for ER positive breast cancer. Genome

Biology, 7: R101, 2006

76. Iyer NG, Xian J, Chin S-F, Bannister AJ, Daigo Y, Aparicio S, Kouzarides T and Caldas C. P300 is

required for orderly G1/S transition in human cancer cells. Oncogene, 26: 21-29, 2007

77. Naderi A, Teschendorff AE, Barbosa-Morais NL, Pinder SE, Green AR, Powe DG, Robertson JFR,

Aparicio S, Ellis IO, Brenton JD, and Caldas C. A gene-expression signature to predict survival in breast

cancer across independent data sets. Oncogene, 26: 1499-1506, 2007

78. Jong K, Marchiori E, van der Vaart A, Carvalho B, Chin S-F, Oudejans JJ, Grabsch H, Quirke P, van

den Ijsell P, Meijer GA, Caldas C, and Ylstra B. Cross-platform array comparative genomic

hybridization (array CGH) meta-analysis separates hematopoietic and mesenchymal from epithelial

tumors. Oncogene, 26: 1499-1506, 2007

79. Chin S-F, Wang Y, Thorne NP, Teschendorff AE, Pinder SE, Vias M, Naderi A, Roberts I, Barbosa-

Morais NL, Garcia MJ, Iyer NG, Kranjac T, Robertson JFR, Aparicio S, Tavaré S, Ellis IO, Brenton JD, and

Caldas C. Using array-comparative genomic hybridization to define molecular portraits of primary

breast cancers. Oncogene, 26: 1959-1970, 2007

80. Melchor L, Garcia M, Honrado E, Pole J, Alvarez S, Edwards P, Caldas C, Brenton J, and Benitez J.

Genomic analysis of the 8p11-12 amplicon in familial breast cancer. International Journal of Cancer,

120: 714-717, 2007

81. Paterson A, Pole J, Blood K, Garcia M, Cooke S, Teschendorff A, Wang Y, Chin S-F, Ylstra B, Caldas

C, and Edwards P. Co-amplification of 8p12 and 11q13 in breast cancers is not the result of a single

genomic event. Genes Chromosomes & Cancer, 46: 427-439, 2007

82. Lujambio A, Ropero S, Ballestar E, Fraga MF, Cerrato C, Setien F, Casado S, Gitt A, Spiteri I, Caldas

C, Miska E, and Esteller M. Genetic unmasking of an epigenetically silenced microRNA in human

cancer cells. Cancer Research, 67: 1424-1429, 2007

83. Carneiro F, Moutinho C, Pera G, Caldas C, Fenger C, Offerhaus J, Save V, Stenling R, Nesi G, Mahlke

U, Blaker H, Torrado J, Roukos DH, Sabourin JC, Boeing H, Palli D, Bueno-de-Mesquita HB, Overvad K,

Bingham S, Clavel-Chapelon F, Lund E, Trichopoulou A, Manjer J, Riboli E, and Gonzalez CA.

Pathology findings and validation of gastric and esophageal cancer cases in a European cohort

(EPIC/EUR-GAST). Scandinavian Journal of Gastroenterology, 42: 618-627, 2007

17

84. Flinterman MB, Mymryk JS, Klanrit P, Yousef AF, Lowe SW, Caldas C, Gaken J, Frazaneh F, and

Tavassoli M. p400 function is required for the adenovirus E1A mediated suppression of EGFR and

tumour cell killing. Oncogene, 26: 6863-6874, 2007

85. Udler M, Maia A-T, Cebrian A, Brown C, Rashbass J, Shah M, Caldas C, Dunning A, Easton D,

Ponder B, and Pharoah P. Common variation in anti-oxidant defense genes and survival after diagnosis

of breast cancer. Journal of Clinical Oncology, 25: 3015-3023, 2007

86. Naderi A, Teschendorff AE, Beigel J, Cariati M, Ellis IO, Brenton JD, and Caldas C. Bex2 is

overexpressed in a subset of primary breast cancers and mediates NGF/NF-kB inhibition of apoptosis in

breast cancer cell lines. Cancer Research, 67: 6725-6736, 2007

87. Teschendorff AE, Journée M, Absil P-A, Sepulchre R, and Caldas C. Elucidating the altered

transcriptional programs in breast cancer using Independent Component Analysis. PLoS

Computational Biology, 3: e161, 2007

88. Teschendorff AE, Miremadi A, Pinder S, Ellis IO, and Caldas C. An immune response gene

expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer.

Genome Biology, 8: R157, 2007

89. Blenkiron C, Goldstein LD, Thorne NP, Spiteri I, Chin S-F, Dunning M, Barbosa-Morais NL,

Teschendorff AE, Green AR, Ellis IO, Tavare S, Caldas C*, and Miska EA. MicroRNA expression

profiling of human breast cancer identifies new markers of tumour subtype. Genome Biology, 8: R214,

2007 [*co-corresponding author]

90. Chin S-F, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa J, Pinder SE,

van de Wiel MA, Green AR, Ellis IO, Porter PL, Tavare S, Brenton JD, Ylstra B, and Caldas C. High-

resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast

cancer. Genome Biology 8:R215, 2007

91. Ahmed AA, Mills AD, Ibrahim AEK, Temple J, Blenkiron C, Vias M, Massie CE, Iyer NG, McGeoch

A, Crawford R, Nicke B, Downward J, Swanton C, Bell S, Earl HM, Laskey RA, Caldas C, and Brenton

JD. The extracellular matrix protein TGFBI induces microtubule stabilization and sensitizes ovarian

cancers to paclitaxel. Cancer Cell, 12: 514-527, 2007

92. Foo RS-Y, Nam Y-J, Ostreicher MJ, Metzl MD, Whelan RS, Peng C-F, Ashton AW, Fu W, Mani K,

Chin S-F, Provenzano E, Ellis I, Figg N, Pinder S, Bennett MR, Caldas C, and Kitsis RN. Regulation of

p53 tetramerization and nuclear export by ARC. Proceedings of the National Academy of Sciences of the

USA, 104: 20826-20831, 2007

93. Cariati M, Naderi A, Brown JP, Smalley MJ, Pinder SE, Caldas C, and Purushotham AD. Alpha-6

integrin is necessary for the tumourgenicity of a stem cell-like subpopulation within the MCF7 breast

cancer cell line. International Journal of Cancer, 122: 298-304, 2008

94. Veerakumarasivam A, Scott H, Chin S-F, Warren A, Wallard M, Grimmer D, Ichimura K, Caldas C,

Collins VP, Neal D, and Kelly J. High-resolution array-based comparative genomic hybridization of

bladder cancers identifies MDM4 as an amplification target exclusive of MDM2 and p53. Clinical

Cancer Research, 14: 2527-2534, 2008

95. Stuart-Harris R, Caldas C, Pinder SE, and Pharoah P. Proliferation markers and survival in early

breast cancer: a systematic review and meta-analysis of 85 studies in 32,825 patients. The Breast, 17: 323-

334, 2008

96. Meyer KB, Maia A-T, O’Reilly M, Teschendorff AE, Chin S-F, Caldas C, and Ponder BAJ. Allele-

specific up-regulation of FGFR2 increases susceptibility to breast cancer. PLoS Biology, 6: e108, 2008

97. Azzato EM, Driver K, Leseuer F, Shah M, Greenberg D, Easton DF, Teschendorff A, Caldas C,

Caporaso NE, Pharoah PDP. Effects of common germline genetic variation in cell cycle control genes on

breast cancer survival: results from a population-based cohort. Breast Cancer Research, 10: R47, 2008

18

98. Callagy GM, Webber MJ, Pharoah PDP, and Caldas C. Meta-analysis confirms BCL2 is an

independent prognostic marker in breast cancer. BMC Cancer, 8: 153, 2008

99. Git A, Spiteri I, Blenkiron C, Dunning M, Pole JCM, Chin S-F, Wang Y, Smith J, Livesey FJ, and

Caldas C. PMC42, a breast progenitor cancer cell line, has normal-like mRNA and miRNA

transcriptomes. Breast Cancer Research, 10: R54, 2008

100. Brown LA, Hoog J, Chin S-F, Tao Y, Zayed AA, Chin K, Teschendorff AE, Quackenbush JF, Marioni

JC, Leung S, Perou CM, Nielsen TO, Ellis M, Gary JW, Bernard PS, Hunstman DG, and Caldas C. ESR1

gene amplification in breast cancer: a common phenomenon? Nature Genetics, 40: 806-807, 2008

101. Capellá G, Pera G, Sala N, Agudo A, Rico F, Del Giudicce G, Plebani M, Palli D, Boeing H, Bueno-

de-Mesquita HB, Carneiro F, Berrino F, Vineis P, Tumino R, Panico S, Berglund G, Simán H, Nyrén O,

Hallmans G, Martinez C, Dorronsoro M, Barricarte A, Navarro C, Quirós JR, Allen N, Key T, Bingham

S, Caldas C, Linseisen J, Nagel G, Overvad K, Tjonneland A, Boshuizen HC, Peeters PH, Numans ME,

Clavel-Chapelon F, Trichopoulou A, Lund E, Jenab M, Kaaks R, Riboli E, and González CA. DNA repair

polymorphisms and the risk of stomach adenocarcinoma and severe chronic gastritis in the EPIC-

EURGAST study. International Journal of Epidemiology, 37: 1316-1325, 2008

102. Crusius JB, Canzian F, Capellá G, Peña AS, Pera G, Sala N, Agudo A, Rico F, Del Giudice G, Palli D,

Plebani M, Boeing H, Bueno-de-Mesquita HB, Carneiro F, Pala V, Save VE, Vineis P, Tumino R, Panico

S, Berglund G, Manjer J, Stenling R, Hallmans G, Martínez C, Dorronsoro M, Barricarte A, Navarro C,

Quirós JR, Allen N, Key TJ, Binghan S, Caldas C, Linseisen J, Kaaks R, Overvad K, Tjønneland A,

Büchner FC, Peeters PH, Numans ME, Clavel-Chapelon F, Trichopoulou A, Lund E, Jenab M, Rinaldi S,

Ferrari P, Riboli E, and González CA. Cytokine gene polymorphisms and the risk of adenocarcinoma of

the stomach in the European prospective investigation into cancer and nutrition (EPIC-EURGAST).

Annals of Oncology, 19: 1894-1902, 2008

103. Barber M, Murrell A, Ito Y, Maia AT, Hyland S, Oliveira C, Carneiro F, Paterson AL, Grehan N,

Dwerryhouse S, Caldas C, and Fitzgerald RC. Mechanisms and sequelae of E-cadherin silencing in

hereditary diffuse gastric cancer. The Journal of Pathology, 216: 295-306, 2008

104. Barber M, Save V, Carneiro F, Dwerryhouse S, Lao-Sirieix P, Hardwick R, Caldas C*, and Fitzgerald

RC. Histopathological and molecular analysis of gastrectomy specimens from hereditary diffuse gastric

cancer patients has implications for endoscopic surveillance of individuals at risk. The Journal of

Pathology, 216: 286-294, 2008 [*corresponding author]

105. Teschendorff AE, and Caldas C. A robust classifier of high predictive value to identify good

prognosis patients in ER negative breast cancer. Breast Cancer Research, 10: R73, 2008

106. Cooke SL, Pole JCM, Chin S-F, Ellis IO, Caldas C, and Edwards PAW. High-resolution array CGH

clarifies events on 8p in carcinogenesis. BMC Cancer, 8: 288, 2008

107. Reyal F, Van Vliet MH, Armstrong NJ, Horlings HM, de Visser KE, Kok M, Teschendorff AE, Mook

S, Van't Veer L, Caldas C, Salmon RJ, Van de Vijver MJ, Wessels LFA. A comprehensive analysis of

prognostic signatures reveals the high predictive capacity of proliferation, immune response and RNA

splicing modules in breast cancer. Breast Cancer Research, 10: R93, 2008

108. Oliveira C, Senz J, Kaurah P, Pinheiro H, Sanges R, Haegert A, Corso G, Schouten J, Fitzgerald R,

Vogelsang H, Keller G, Dwerryhouse S, Grimmer D, Chin S-F, Yang H-K, Jackson CE, Seruca R, Roviello

F, Stupka E, Caldas C, and Huntsman D. Germline CDH1 deletions in hereditary diffuse gastric cancer

families. Human Molecular Genetics, 18: 1545-1555, 2009

109. Morales C, García MJ, Ribas M, Miró R, Muñoz M, Caldas C, and Peinado MA. Dihydrofolate

reductase amplification and sensitization to methotrexate of methotrexate-resistant colon cancer cells.

Molecular Cancer Therapeutics, 8: 424-432, 2009

110. Udler MS, Azzato EM, Healey CS, Ahmed S, Pooley KA, Greenberg D, Shah M, Teschendorff AE,

Caldas C, Dunning AM, Ostrander EA, Caporaso NE, Easton D, and Paul D. Pharoah PD. Common

19

germline polymorphisms in COMT, CYP19A1, ESR1, PGR, SULT1E1 and STS and survival after a

diagnosis of breast cancer. International Journal of Cancer, 125: 2687-2696, 2009

111. Britton P, Duffy SW, Sinnatamby R, Wallis MG, Barter S, Gaskarth M, O'Neill A, Caldas C, Brenton

JD, Forouhi P, Wishart GC. One-stop diagnostic breast clinics: how often are breast cancers missed?

British Journal of Cancer, 100: 1873-1878, 2009

112. Pickard MR, Green AR, Ellis IO, Caldas C, VL, Mourtada-Maarabouni M, and Williams GT.

Deregulated expression of Fau and MELK is associated with poor prognosis in breast cancer. Breast

Cancer Research, 11: R60, 2009

113. Maia AT, Spiteri I, Lee AJX, O'Reilly M, Jones L, Caldas C, and Ponder BAJ. Extent of differential

allelic expression of candidate breast cancer genes is similar in blood and breast. Breast Cancer

Research, 11: R88, 2009

114. Chua YL, Y Ito Y, Pole JCM, Chin S-F, Ellis IO, Caldas C, O'Hare MJ, Murrell AM, Edwards PAW.

The NRG1 gene is frequently silenced by methylation in breast cancers and is a strong candidate for the

8p tumour suppressor gene. Oncogene, 28: 4041-4052, 2009

115. Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin S-F, Brenton JD, Tavare S,

and Caldas C. The pitfalls of platform comparison: DNA copy number array technologies assessed.

BMC Genomics, 10: 588, 2009

116. Dawson SJ, Duffy SW, Blows FM, Driver KE, Provenzano E, Le Quesne J, Greenberg DC, Pharoah

P, Caldas C, and Wishart GC. Molecular characteristics of screen-detected vs symptomatic breast

cancers and their impact on survival. British Journal of Cancer, 101: 1338-1344, 2009

117. Papatheodorou I, Crichton C, Morris L, Maccallum P, METABRIC group, Davies J, Brenton JD and

Caldas C. A Metadata approach for clinical data management in translational genomics studies in

breast cancer. BMC Medical Genomics, 2: 66, 2009

118. Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R,

Send J, Steidl C, Holt RA, Jones S, Sun M, Leung G, Moore R, Severson T, Taylor GA, Teschendorff AE,

Tse K, Turashvili G, Varhol R, Warren RL, Watson P, Zhao Y, Caldas C, Huntsman D, Hirst M, Marra

MA, and Aparicio S. Mutational evolution in a lobular breast tumour profiled at single nucleotide

resolution. Nature, 461: 809-813, 2009

119. Sassen S, Goldstein LD, Stingl J, Blenkiron C, Le Quesne J, Spiteri I, Karagavriilidou K, Watson CJ,

Tavare S, Miska EA, and Caldas C. Characterisation of microRNA expression in post-natal mouse

mammary gland development. BMC Genomics, 10: 548, 2009

120. Wishart GC, Azzato E, Greenberg D, Rashbass J, Kearins O, Lawrence G, Caldas C, and Pharoah P.

PREDICT: A new UK prognostic model that predicts survival following surgery for invasive breast

cancer. Breast Cancer Research, 12: R1, 2010

121. Bartlett JMS, Munro AF, Dunn JA, McConkey Jordan CS, Twelves CJ, Cameron DA, Thomas

Campbell JF, Rea DW, Provenzano E, Caldas C, Pharoah P, Hiller L, Earl H, and Poole CJ. Predictive

markers of anthracycline benefit: a prospectively planned analysis of the UK National Epirubicin

Adjuvant Trial (NEAT/BR9601). The Lancet Oncology, 11: 266-274, 2010

122. Frye M, Dragoni I, Chin S-F, Spiteri I, Kurowski A, Provenzano E, Green A, Ellis IO, Grimmer D,

Teschendorff A, Zouboulis CC, Caldas C, and Watt FM. Genomic gain of 5p15 leads to over-expression

of Misu (NSUN2) in breast cancer. Cancer Letters, 289: 71-80, 2010

123. Zhang H, Rakha EA, Ball GR, Spiteri I, Aleskandarany M, Paish EC, Powe DG, Macmillam RD,

Caldas C, Ellis IO, and Green AR. The proteins FABP7 and OATP2 are associated with the basal

phenotype and patient outcome in human breast cancer. Breast Cancer Research and Treatment, 121:

41-51, 2010

20

124. Git A, Dvinge H, Salmon-Divon M, Osborne M, Cutter C, Bertone P, Hadfield J, and Caldas C.

Systematic comparison of microarray profiling, real-time PCR and next-generation sequencing for

measuring differential microRNA expression. RNA, 16: 991-1006, 2010

125. Fitzgerald RC, Hardwick R, Huntsman D, Carneiro F, Guilford P, Blair V, Chung DC, Norton J,

Ragunath K, Van Krieken JH, Dwerryhouse S, and Caldas C, on behalf of the International Gastric

Cancer Linkage Consortium. Hereditary diffuse gastric cancer: updated consensus guidelines for

clinical management and directions for future research. Journal of Medical Genetics, 47: 436-444, 2010

126. Obrador-Hevia A, Chin S-F, González S, Rees J, Vilardell F, Greenson JK, Cordero D, Moreno V,

Caldas C, and Capellá G. Oncogenic KRAS is not necessary for Wnt signalling activation in APC-

associated FAP adenomas. The Journal of Pathology, 221: 57-67, 2010

127. Ahmed AA, Etemadmoghadam D, Temple J, Lynch AG, Riad M, Sharma R, Stewart C, Fereday S,

Caldas C, deFazio A, Bowtell D, and Brenton JD. Driver mutations in TP53 are ubiquitous in high-grade

serous carcinoma of the ovary. The Journal of Pathology, 221: 49-56, 2010

128. Blows FM, Driver KE, Schmidt MK, Broeks A, van Leeuwen FE, Wesseling J, Cheang MC, Gelmon

K, Nielson TO, Blomqvist C, Heikkila P, Heikkinen T, Nevanlinna H, Akslen LA, Begin LR, Foulkes

WD, Couch FJ, Wang X, Cafourek V, Olsen JE, Baglietto L, Giles GG, Severi G, McLean CA, Southey

MC, Rakha E, Green AR, Ellis IO, Sherman ME, Lissowska J, Anderson WF, Cox A, Cross SS, Reed

MWR, Provenzano E, Dawson S-J, Dunning AM, Humphreys M, Easton DF, Garcia-Closas M, Caldas C,

Pharoah PD, and Huntsman D. Subtyping of breast cancer by immunohistochemistry to investigate a

relationship between subtype and short and long term survival: a collaborative analysis of data for

10,159 cases from 12 studies. PLoS Medicine, 7: e10000279, 2010

129. Udler MS, Ahmed S, Healey CS, Meyer K, Struewing J, Maranian M, Kwon EM, Zhang J, Tyrer J,

Karlins E, Platte R, Kalmyrzaev B, Dicks E, Field H, Maia A-T, Prathalingam R, Teschendorff A,

McArthur S, Doody DR, Luben R, Caldas C, Bernstein L, Kolonel LK, Henderson BE, Wu AH, Le

Marchand L, Ursin G, Press MF, Lindblom A, Margolin S, Shen C-Y, Yang S-L, Chia-Ni C-N, Kang D,

Yoo K-Y, Noh D-Y, Ahn S-H, Malone KE, Haiman CA, Pharoah PD, Ponder BAJ, Ostrander EA, Easton

DF, and Dunning AM. Fine scale mapping of the breast cancer 16q12 locus. Human Molecular Genetics,

19: 2507-2515, 2010

130. Azzato EM, Lee AJX, Teschendorff A, Ponder BAJ, Pharoah P, Caldas C, and Maia AT. Common

germ-line polymorphism of C1QA and breast cancer survival. British Journal of Cancer, 102: 1294-1299,

2010

131. The International Cancer Genome Consortium*. International network of cancer genome projects.

Nature, 464: 993-998, 2010 [*co-author]

132. Dawson S-J, Makretsov N, Blows FM, Driver K, Provenzano E, Le Quesne J, Baglietto L, Severi G,

Giles GG, McLean CA, Callagy G, Green AR, Ellis I, Gelmon K, Turashvili G, Leung S, Aparicio S,

Huntsman D, Caldas C*, and Pharoah P. BCL2 in breast cancer: a favourable prognostic marker across

molecular subtypes and independent of adjuvant therapy received. British Journal of Cancer, 103: 668-

675, 2010 [*corresponding author]

133. Peters CJ, Rees JRE, Hardwick RH, Hardwick JS, Vowler SL, Ong C-A J, Zhang C, Save V,

O'Donovan M, Rassl D, Alderson D, Caldas C, Fitzgerald RC, on behalf of the OCCAMS Study Group. A

four gene signature predicts survival in resected adenocarcinoma of the esophagus, junction and gastric

cardia. Gastroenterology, 139: 1995-2004, 2010

134. Russnes HG, Vollan HKM, Lingjærde OC, Krasnitz A, Lundin P, Naume B, Sørlie T, Borgen E, Rye

IH, Langerød A, Chin S-F, Teschendorff AE, Stevens P, Månér S, Schlichting E, Baumbusch LO, Nesland

JM, Kåresen R, Stratton MP, Wigler M, Caldas C, Zetterberg A, Hicks J, and Børresen-Dale A-L.

Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Science

Translational Medicine, 2: 38ra47, 2010

21

135. Abraham JE, Maranian MJ, Driver KE, Platte R, Kalmyrzaev B, Baynes C, Luccarini C, Shah M,

Ingle S, Greenberg D, Earl HM, Dunning AM, Pharoah PDP and Caldas C. CYP2D6 gene variants:

Association with breast cancer specific survival in a cohort of breast cancer patients from the United

Kingdom treated with adjuvant tamoxifen. Breast Cancer Research, 12: R64, 2010

136. Walton NA, Brenton JD, Caldas C, Irwin MJ, Akram A, Gonzalez-Solares E, Lewis JR, Maccallum

PH, Morris LJ, and Rixon GT. PathGrid: a service-orientated architecture for microscopy image analysis.

Philosophical Transactions of the Royal Society A, 368: 3937-3952, 2010

137. Dunning MJ, Curtis C, Barbosa-Morais NL, Caldas C, Tavaré S, and Lynch AG. The importance of

platform annotation in interpreting microarray data. The Lancet Oncology, 11: 717, 2010

138. Teschendorff AE, Gomez S, Arenas A, El-Ashry D, Schmidt M, Gehrmann M, and Caldas C.

Improved prognostic classification of breast cancer defined by antagonistic activation patterns of

immune response pathway modules. BMC Cancer, 10: 604, 2010

139. Habashy HO, Powe DG, Glaab E, Ball G, Spiteri I, Krasnogor N, Garibaldi JM, Rakha EA, Green

AR, Caldas C, and Ellis IO. RERG (Ras-like, oestrogen-regulated, growth-inhibitor) expression in breast

cancer: a marker of ER-positive luminal-like subtype. Breast Cancer Research and Treatment, 128: 315-

326, 2011

140. Ali AMG, Dawson S-J, Blows FM, Provenzano E, IO Ellis IO, Baglietto L, Huntsman D, Caldas C,

Pharoah PD. Comparison of methods for handling missing data on immunohistochemical markers in

survival analysis of breast cancer. British Journal of Cancer, 104: 693-699, 2011

141. Holland D, Burleigh A, Git A, Goldgraben MA, Perez-Mancera PA, Chin S-F, Hurtado A, Bruna A,

Ali R, Greenwood W, Dunning MJ, Samarajiwa S, Menon S, Rueda OM, Lynch AG, McKinney S, Ellis

IO, Eaves CJ, Carroll JS, Curtis C, Aparicio S, and Caldas C. ZNF703 is a common Luminal B breast

cancer oncogene that differentially regulates luminal and basal progenitors in human mammary

epithelium. EMBO Molecular Medicine, 3: 167-180, 2011

142. Wishart GC, Bajdik CD, Azzato EM, Dicks E, Greenberg DC, Rashbass J, Caldas C, and Pharoah

PDP. A population-based validation of the prognostic model PREDICT for early breast cancer. European

Journal of Surgical Oncology, 37: 411-417, 2011

143. Goh XY, Rees JRE, Paterson AL, Chin S-F, Marioni JC, Save V, O'Donovan M, Eijk PP, Alderson D,

YIstra B, Caldas C, and Fitzgerald RC. Integrative analysis of array comparative genomic hybridisation

and matched gene expression profiling data reveals novel genes with prognostic significance in

oesophageal adenocarcinoma. Gut, 60: 1317-1326, 2011

144. Storr SJ, Mohammed RA, Woolston CM, Green AR, Parr T, Spiteri I, Caldas C, Ball GR, Ellis IO, and

Martin SG. Calpastatin is associated with lymphovascular invasion in breast cancer. The Breast, 20: 413-

418, 2011

145. Abraham JE, Maranian M, Driver KE, Platte R, Kalmyrzaev B, Baynes C, Luccarini C, Earl HM,

Dunning AM, Pharoah PD, and Caldas C. CYP2D6 gene variants and their association with breast

cancer susceptibility. Cancer Epidemiology, Biomarkers and Prevention, 20: 1255-1258, 2011

146. Broeks A, Schmidt MK, Sherman ME, Couch FJ, Hopper JL, Dite GS, Apicella C, Smith LD,

Hammet F, Southey MC, Veer LJ, de Groot R, VTHBM, Fasching PA, Beckmann MW, Jud S, Ekici AB,

Hartmann A, Hein A, Schulz-Wendtland R , Burwinkel B, Marme F, Schneeweiss A, Sinn H-P, Sohn C,

Tchatchou S, Bojesen SE, Nordestgaard BG, Flyger H, Ørsted DD, Kaur-Knudsen D, Milne RL, Pérez

JIA, Zamora P, Rodríguez PM, Benítez J, Brauch H, Justenhoven C, Ko Y-D, Hamann U, Fischer H-P,

Brüning T, Pesch B, Chang-Claude J, Wang-Gohrke S, Bremer M, Karstens JH, Hillemanns P, Dörk T,

Nevanlinna HA, Heikkinen T, Heikkilä P, Blomqvist C, Aittomäki K, Aaltonen K, Lindblom A,

Margolin S, Mannerma A, Kosma V-M, Kauppinen JM, Kataja V, Auvinen P, Eskelinen M ,Soini Y,

Chenevix-Trench G, Spurdle AB, Beesley J, Chen X, Holland H, Lambrechts D, Claes B, Vandorpe T,

Neven P, Wildiers H, Flesch-Janys D, Hein R, Löning T, Kosel M, Fredericksen ZS, Wang X, Giles GG,

22

Baglietto L, Severi G, McLean C, Haiman CA, Henderson BE , Le Marchand L, Kolonel LN, Alnæs GG,

Kristensen V, Børresen-Dale A-L, Hunter DJ , Hankinson SE, Andrulis IL, Mulligan AM, O'Malley FP,

Devilee P, Huijts P, Tollenaar RAEM, van Asperen CJ, Seynaeve C, Chanock SJ, Lissowska J, Brinton L,

Peplonska B, Figueroa J, Yang XR, Hooning MJ, Hollestelle A, Oldenburg RA, Jager A, Kriege M,

Ozturk B, van Leenders GJLH (RBCS), Hall P, Czene K, Humphreys K, Liu J (SASBAC), Cox A, Connley

D, Cramp HE, Cross SS, Balasubramanian SP, Reed MWR (SBCS), Dunning AM, Easton DF, Humphreys

MK, Caldas C (SEARCH), Lubinski J, Jakubowska A, Huzarski T, Byrski T, Cybulski C, Gorski B,

Gronwald J, Brennan P, Sangrajrang S, Gaborieau V, Shen C-Y, Hsiung C-N, Yu J-C, Chen S-T, Hsu G-C,

Hou M-F, Huang C-S, Anton-Culver H, Ziogas A, Pharoah PDP, and Garcia-Closas M. Low penetrance

breast cancer susceptibility loci are associated with specific breast tumor subtypes: Findings from the

Breast Cancer Association Consortium. Human Molecular Genetics, 20: 3289-3303, 2011

147. Ali HR, Dawson S-J, Blows FM, Provenzano E, Pharoah PD, and Caldas C. Cancer stem cell

markers in breast cancer: pathological, clinical and prognostic significance. Breast Cancer Research, 13:

R118, 2011

148. Yuan Y, Curtis C, Caldas C, and Markowetz F. A sparse regulatory network of copy-number driven

gene expression reveals putative breast cancer oncogenes. IEEE/ACM Transactions on Computational

Biology and Bioinformatics, 9: 947-954, 2012

149. Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Brown GD, Gojis O, Ellis IO, Green

AR, Ali S, Chin S-F, Palmieri C, Caldas C*, and Carroll JS. Differential oestrogen receptor binding is

associated with clinical outcome in breast cancer. Nature, 481: 389-393, 2012 [*co-corresponding/co-

senior author]

150. Ali HR, Dawson S-J, Blows FM, Provenzano E, Leung S, Nielsen T, Pharoah PD, and Caldas C. A

Ki67/BCL2 index based on immunohistochemistry is highly prognostic in ER positive breast cancer. The

Journal of Pathology, 226: 97-107, 2012

151. Le Quesne J, Jones J, Warren J, Dawson S-J, Ali R, Bardwell H, Blows F, Pharoah P, Caldas C.

Biological and prognostic associations of miR‐205 and let‐7b in breast cancer revealed by In Situ

Hybridisation analysis of micro‐RNA expression in arrays of archival tumour tissue. The Journal of

Pathology, 227: 306-314, 2012

152. Curtis C, Shah SP, Chin S-F, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG,

Samarajiwa S, Yuan Y, Graf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S, METABRIC

Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L,

Ellis I, Purushotham A, Børresen-Dale A-L, Brenton JD, Tavare S, Caldas C*, and Aparicio S. The

genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature, 486:

346-352, 2012 [*co-corresponding/co-senior author]

153. Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G,

Bashashati A, Prentice L, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan

A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K,

Chan S, Griffith M, Moradian A, Cheng S-WG, Morin G, Watson P, Gelmon K, Chia S, Chin S-F, Curtis

CN, Rueda O, Pharoah P, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M,

Gascard P, Tlsty T, Costello J, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M,

Caldas C*, Marra MA, and Aparicio S. The clonal and mutational evolution spectrum of primary triple-

negative breast cancers. Nature, 486: 395-399, 2012 [*co-corresponding/co-senior author]

154. Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, Zainal SN, Martin S, Varela

I, Bignell GR, Yates LR, Papaemmanuil E, Beare D, Butler A, Cheverton A, Gamble J, Hinton J, Jia MM,

Jayakumar A, Jones D, Lattimer C, Lau KW, McLaren S, McBride D, Menzies A, Mudie L, Raine K, Rad

R, Teague J, Easton D, Langerod A, OSBREAC Consortium, Lee MTM, Shen C-Y, Tee BTK, Huimin BW,

Broeks A, Vargas AC, Turashvili G, Martens J, Fatima A, Miron P, Chin S-F, Thomas G, Boyault S,

23

Mariani O, Lakhani SR, van de Vijver M, van't Veer L, Foekens J, Desmedt C, Sotiriou C, Tutt A, Caldas

C, Reis-Filho JS, Aparicio SAJR, Salomon AV, Børresen-Dale A-L, Richardson A, Campbell PJ, Futreal

PA, and Stratton MR. The landscape of cancer genes and mutational processes in breast cancer. Nature,

486: 400-404, 2012

155. Liu R, Maia AT, Russell R, Caldas C, Ponder BA, and Ritchie ME. Allele-specific expression analysis

methods for high-density SNP microarray data. Bioinformatics, 28: 1102-1108, 2012

156. Maia A-T, Antoniou AC, OReilly M, Samarajiwa S, Dunning M, Kartsonaki C, Chin S-F, Curtis CN,

McGuffog L, Domchek SM, EMBRACE, Easton DF, Peock S, Frost D, Evans G, Eeles R, Izatt L, Adlard J,

Eccles D, GEMO, Sinilnikova OM, Mazoyer S, Stoppa-Lyonnet D, Gauthier-Villars M, Faivre L, Venat-

Bouvet L, Delnatte C, Nevanlinna H, Couch FJ, Godwin AK, Caligo M-A, SWE-BRCA, Barkardottir RB,

kConFab, Chen X, Beesley J, Healey S, Caldas C, Chenevix-Trench G, and Ponder BAJ. Effects of BRCA2

cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers. Breast Cancer

Research, 14: R63, 2012

157. Ali HR, Dawson S-J, Blows FM, Provenzano E, Pharoah PD, and Caldas C. Aurora kinase A

outperforms Ki67 as a prognostic marker in ER positive breast cancer. British Journal of Cancer, 106:

1798-1806, 2012

158. Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DWY, Kaper F, Dawson S-J, Piskorz A, Jimenez-

Linan M, Bentley D, Hadfield J, May AP, Caldas C, Brenton JD, and Rosenfeld N. Non-invasive

identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Science

Translational Medicine, 4: 136ra68, 2012

159. Abraham JE, Maranian MJ, Spiteri I, Russell R, Ingle S, Luccarini C, Earl HM, Pharoah PDP,

Dunning AM, and Caldas C. Saliva samples are a viable alternative to blood samples as a source of

DNA for high throughput genotyping. BMC Medical Genomics, 5: 19, 2012

160. Ha G, Roth A, Lai D, Bashashati A, Ding J, Goya R, Giuliany R, Rosner J, Oloumi A, Shumansky K,

Chin S-F, Turashvili G, Hirst M, Caldas C, Marra MA, Aparicio S, and Shah SP. Integrative analysis of

genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals

disrupted pathways in triple negative breast cancer. Genome Research, 22: 1995-2007, 2012

161. Wishart GC, Bajdik CD, Dicks E, Provenzano E, Schmidt MK, Sherman M, Greenberg DC, Green

AR, Gelmon KA, Kosma V-M, Olson JE, Beckmann MW, Winqvist R, Cross SS, Severi G, Huntsman D,

Pylkäs K, Ellis I, Nielsen TO, Giles G, Blomqvist C, Fasching PA, Couch FJ, Rakha E, Foulkes WD, Blows

FM, Bégin LR, van't Veer LJ, Southey M, Nevanlinna H, Mannermaa A, Cox A, Cheang M, Baglietto L,

Caldas C, Garcia-Closas M, and Pharoah PDP. PREDICT Plus: development and validation of a

prognostic model for early breast cancer that includes HER2. British Journal of Cancer, 107: 800-807,

2012

162. Earl HM, Hiller L, Dunn JA, Vallier A-L, Jordan S, Bardwell H, Grieve R, Spooner DA, Agrawal R,

Fernando I, Brunt AM, O’Reilly SM, Crawford SM, Rea DW, Simmonds P, Mansi JL, Stanley A, Harvey

P, McAdam K, Foster L, Leonard RCF, Twelves CJ, Bartlett JMS, Pharoah P, Caldas C, and Poole CJ for

the NEAT Investigators and the SCTBG. Adjuvant Epirubicin followed by Cyclophosphamide,

Methotrexate and Fluorouracil (CMF) versus CMF in early breast cancer: Results with over seven years

median follow-up from the randomised phase III NEAT/BR9601 trials. British Journal of Cancer, 107:

1257-1267, 2012

163. Lynch AG, Chin S-F, Dunning MJ, Caldas C, Tavare S, and Curtis C. Calling sample mixups in

cancer population studies. PLoS One, 7: e41815, 2012

164. Bruna A, Greenwood W, Le Quesne J, Teschendorff A, Miranda-Saavedra D, Rueda OM,

Sandoval JL, Tufegdzic-Vidakovic A, Saadi A, Pharoah P, Stingl J, and Caldas C. TGF β induces the

formation of tumour-initiating cells in claudin-low breast cancer cell lines. Nature Communications, 3:

1055, 2012

24

165. Yuan Y, Failmezger H, Rueda OM, Ali HR, Graf S, Chin S-F, Schwarz RF, Curtis C, Dunning MJ,

Bardwell H, Provenzano E, Johnson N, Doyle S, Turashvili G, Aparicio S, Caldas C, and Markowetz F.

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.

Science Translational Medicine, 4: 157ra143, 2012

166. Shehata M, Teschendorff A, Sharp G, Novcic N, Russell A, Avril S, Prater M, Eirew P, Caldas C,

Watson CJ, and Stingl J. Phenotypic and functional characterization of the luminal cell hierarchy of the

mammary gland. Breast Cancer Research, 14: R134, 2012

167. Pharoah PD, Abraham J, and Caldas C. Re: CYP2D6 genotype and tamoxifen response in

postmenopausal women with endocrine-responsive breast cancer: the Breast International Group 1-98

trial and Re: CYP2D6 and UGT2B7 genotype and risk of recurrence in tamoxifen-treated breast cancer

patients. Journal of the National Cancer Institute, 104: 1263-1264, 2012

168. Aleskandarany MA, Negm OH, Rakha EA, Ahmed MA, Nolan CC, Ball GR, Caldas C, Green AR,

Tighe PJ, and Ellis IO. TOMM34 expression in early invasive breast cancer: a biomarker associated with

poor outcome. Breast Cancer Research and Treatment, 136: 419-427, 2012

169. Nilsen G, Liestøl K, Van Loo P, Vollan HKM, Eide MB, Rueda OM, Chin S-F, Russell R, Baumbusch

LO, Caldas C, Børresen-Dale A-L, and Lingjaerde O-C. Copy number: Efficient algorithms for single-

and multi-track copy number segmentation. BMC Genomics, 13: 591, 2012

170. Schulte I, Batty EM, Pole JCM, Blood KA, Steven Mo, Cooke SL, Ng C, Howe KL, Chin S-F, Brenton

JD, Caldas C, Howarth KD, and Edwards PAW. Structural analysis of the genome of breast cancer cell

line ZR-75-30 identifies twelve expressed fusion genes. BMC Genomics, 13: 719, 2012

171. Bashashati A, Haffari G, Ding J, Ha G, Liu K, Rosner J, Huntsman D, Caldas C, Aparicio S, and

Shah S. DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in

cancer. Genome Biology, 13: R124, 2012

172. Ali HR, Irwin M, Morris L, Dawson S-J, Blows FM, Provenzano E, Mahler-Araujo B , Pharoah PD,

Walton NA, Brenton JD , and Caldas C. Astronomical algorithms for the automated analysis of

immunohistochemical stains in breast cancer. British Journal of Cancer, 108: 602-612, 2013

173. Provenzano E, Vallier A-L, Walland K, Champ R, Bowden S, Grier A, Fenwick N, Abraham J,

Iddawela M, Caldas C, Hiller L, Dunn J, and Earl HM. A central review of histopathology reports after

breast cancer neoadjuvant chemotherapy in the Neo-tAnGo trial. British Journal of Cancer, 108: 866-

872, 2013

174. Baker BG, Ball GR, Rakha EA, Nolan CC, Caldas C, Ellis IO, and Green AR. Lack of expression of

the proteins GMPR2 and PPARα are associated with the basal phenotype and patient outcome in breast

cancer. Breast Cancer Research and Treatment, 137: 127-137, 2013

175. Ali A, Provenzano E, Abraham J, Driver K, Bartlett JMS, Munro AF, Twelves C, Poole CJ, Hiller L,

Dunn J, Earl HM, Caldas C, and Pharoah PDP. Prognosis of early breast cancer by

immunohistochemistry defined intrinsic subtypes in patients treated with adjuvant chemotherapy in

the NEAT/BR9601 trial. International Journal of Cancer, 133: 1470-1479, 2013

176. Mohammed H, D’Santos C, Serandour AA, Ali HR, Brown GD, Atkins A, Rueda OM, Holmes KA,

Theodorou V, Robinson JLL, Zwart W, Saadi A, Ross-Innes CS, Chin S-F, Menon S, Stingl J, Palmieri C,

Caldas C, and Carroll JS. Endogenous purification reveals GREB1 as a key estrogen receptor regulatory

factor. Cell Reports, 3: 342-349, 2013

177. Dawson S-J, Tsui DWY, Murtaza M, Biggs H, Rueda OM, Chin S-F, Dunning MJ, Gale D, Forshew

T, Mahler-Araujo B, Rajan S, Humphray S, Becq J, Halsall D, Wallis M, Bentley D, Caldas C*, and

Rosenfeld N. Analysis of circulating tumor DNA to monitor metastatic breast cancer. The New England

Journal of Medicine, 368: 1199-1209, 2013 [*co-corresponding/co-senior author]

178. Murtaza M, Dawson S-J, Tsui DWY, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin S-F,

Kingsbury Z, Wong ASC, Marass F, Humphray S, Hadfield J, Bentley D, Chin TM, Brenton JD, Caldas

25

C*, and Rosenfeld N. Noninvasive analysis of acquired resistance to cancer therapy by exome

sequencing of plasma DNA. Nature, 497: 108-112, 2013 [*co-corresponding/co-senior author]

179. Morris LJ, Tsui A, Crichton C, Harris S, Maccallum P, Howat W, Davies J, Brenton JD, and Caldas

C. A metadata-aware application for remote scoring and exchange of tissue microarray images. BMC

Bioinformatics, 14: 147, 2013

180. Dvinge H, Git A, Graf S, Salmon-Divon M, Curtis C, Sottoriva A, Zhao Y, Hirst M, Armisen J, Miska

EA, Chin S-F, Provenzano E, Turashvili G, Green A, Ellis I, Aparicio S, and Caldas C. The shaping and

functional consequences of the miRNA landscape in breast cancer. Nature, 497: 378-382, 2013

181. Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine B, Shimoni Y, Vollan

HKM, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale

A-L, Caldas C, Califano A, Friend S, Ideker T, Schadt EE, Stolovitzky GA, and Margolin AA. Improving

breast cancer survival analysis through competition-based multidimensional modelling. PLoS

Computational Biology, 9: e1003047, 2013

181. Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR,

Mangravite LM, Furia MD, Vollan HKM, Rueda OM, Guinney J, Deflaux NA, Hoff B, Schildwachter X,

Russnes HG, Park D, Vang VO, Pirtle T, Youseff L, Citro C, Curtis C, The Sage DREAM Breast Cancer

Challenge Consortium, Kristensen VN, Hellerstein J, Friend SH, Stolovitzky G, Aparicio S, Caldas C*,

and Borresen-Dale A-L. Systematic analysis of challenge-driven improvements in molecular prognostic

models for breast cancer. Science Translational Medicine, 5: 181re1, 2013 [*co-senior author]

182. McLuckie KI, Di Antonio M, Zecchini H, Xian J, Caldas C, Krippendorff BF, Tannahill D, Lowe C,

and Balasubramanian S. G-Quadruplex DNA as a molecular target for induced synthetic lethality in

cancer cells. Journal of the American Chemical Society, 135: 9640-9643, 2013

183. Rajan S, Foreman J, Wallis MG, Caldas C, and Britton P. Multidisciplinary decisions in breast

cancer: does the patient receive what the team has recommended? British Journal of Cancer, 108: 2442-

2447, 2013

184. Fletcher MNC, Castro MAA, Wang X, de Santiago I, O’Reilly M, Chin S-F, Rueda OM, Caldas C,

Ponder BAJ, Markowetz F, and Meyer KB. Master regulators of FGFR2 signalling and breast cancer risk.

Nature Communications, 4: 2464, 2013

185. Alexandrov L, Nik-Zainal S, Wedge D, Aparicio S, Behjati S, Biankin A, Bignell G, Bolli N, Borg A,

Børresen-Dale A-L, Boyault S, Burkhardt B, Butler A, Caldas C, Davies H, Desmedt C, Eils R, Eyfjörð JE,

Foekens J, Greaves M, Hosoda F, Hutter B, Ilicic T, Imbeaud S, Imielinsk M, Jäger N, Jones D,

Knappskog S, Kool M, Lakhani S, Lopez-Otin C, Martin S, Munshi N, Nakamura H, Northcott P, Pajic

M, Papaemmanuil E, Paradiso A, Pearson J, Puente X, Raine K, Ramakrishna M, Richardson A, Richter

J, Rosenstiel P, Schlesner M, Schumacher T, Span P, Teague J, Totoki Y, Tutt A, Valdés-Mas R, Van 't

Veer L, van Buuren M, Vincent-Salomon A, Waddell N, Yates L, Australian Pancreatic Cancer Genome

Initiative, ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, ICGC PedBrain, Zucman-

Rossi J, Futreal A, McDermott U, Lichter P, Meyerson M, Grimmond S, Siebert R, Campo E, Shibata T,

Pfister S, Campbell P, and Stratton MR. Signatures of mutational processes in human cancer. Nature,

500: 415-421, 2013

186. Niemczyk M, Ito Y, Huddleston J, Git A, Abu-Amero S, Caldas C, Moore GE, Stojic L, and Murrell

A. Imprinted chromatin around DIRAS3 regulates alternative splicing of GNG12-AS1, a long noncoding

RNA. American Journal of Human Genetics, 93: 224-235, 2013

187. Levine DM, Ek WE, Zhang R, Liu X, Onstad L, Sather C, Lao-Sirieix P, Gammon MD, Corley DA,

Shaheen NJ, Bird NC, Hardie LJ, Murray LJ, Reid BJ, Chow W-H, Risch HA, Nyrén O, Ye A, Liu G,

Romero Y, Bernstein L, Wu AH, Casson AG, Chanock S, Harrington P, Caldas I, Debiram-Beecham I,

Caldas C, Hayward NK, Pharoah P, Fitzgerald R, MacGregor S, Whiteman DC, and Vaughan TL. A

26

genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and

Barrett’s esophagus. Nature Genetics, 45: 1487 – 1493, 2013

188. Jones JO, Chin SF, Wong-Taylor LA, Leaford D, Ponder BA, Caldas C, and Maia AT. TOX3

mutations in breast cancer. PLoS One, 8: e74102, 2013

189. Lee U, Frankenberger C, Yun J, Bevilacqua E, Caldas C, Chin SF, Rueda OM, Reinitz J, and Rosner

MR. A prognostic gene signature for metastasis-free survival of triple negative breast cancer patients.

PLoS One, 8: e82125, 2013

190. Horne HN, Sherman ME, Garcia-Closas M, Pharoah PD, Blows FM, Yang XR, Hewitt SM, Conway

C, Lissowska J, Brinton LA, Dawson S-J, Caldas C, Easton D, Chanock SJ, and Figueroa JD. Breast

cancer susceptibility risk associations and heterogeneity by E-cadherin tumor tissue expression. Breast

Cancer Research and Treatment, 143: 181-187, 2014

191. Earl HM, Vallier A-L, Hiller L, Fenwick N, Young J, Iddawela M, Abraham J, Hughes-Davies L,

Gounaris I, McAdam K, Houston S, Hickish T, Skene A, Chan S, Dean S, Ritchie D, Laing R, Harries M,

Gallagher C, Wishart G, Dunn J, Provenzano E, and Caldas C, for the NeotAnGo Investigators. Effects

of the addition of gemcitabine, and paclitaxel-first sequencing, in neoadjuvant sequential epirubicin,

cyclophosphamide, and paclitaxel for women with high-risk early breast cancer (Neo-tAnGo): an open-

label, 2 x 2 factorial randomised phase 3 trial. The Lancet Oncology, 15: 201-212, 2014

192. Abraham JE, Guo Q, Dorling L, Tyrer J, Ingle S, Hardy R, Vallier A-L, Hiller L, Burns R, Jones L,

Bowden SJ, Dunn JA, Poole CJ, Caldas C*, Pharoah PPD, and Earl HM. Replication of genetic

polymorphisms reported to be associated with taxane-related sensory neuropathy in breast cancer

patients treated with neo-adjuvant and adjuvant paclitaxel. Clinical Cancer Research, 2014 (in press)

[*co-corresponding/co-senior author]

193. Abdel-Fatah TMA, Russell R, Agarwal D, Moseley P , Ayotunde AM, Perry C, Ball G, Chan S,

Caldas C, Ellis IO, and Madhusudan S. DNA polymerase β deficiency is linked to aggressive breast

cancer: a comprehensive analysis of gene copy number, mRNA and protein expression in multiple

cohorts. Molecular Oncology, 2014 (in press)

194. Worster E, Liu X, Richardson S, Hardwick RH, Dwerryhouse S, Caldas C*, and Fitzgerald RC. The

impact of prophylactic total gastrectomy on health-related quality of life: a prospective cohort study.

Annals of Surgery, 2014 (in press) [*co-senior author]

195. Bidard F-C, Peeters D, Fehm T, Nole F, Gisbert-Criado R, Mavroudis D, Grisanti S, Generali D,

Garcia-Saenz JA, Stebbing J, Caldas C, Gazzaniga P, Manso L, Zamarchi R, de Lascoiti AF, de Mattos-

Arruda L, Ignatiadis M, Lebofsky R, van Laere SJ, Meier-Stiegen F, Sandri M-T, Vidal-Martinez J,

Politaki E, Consoli F, Bottini A, Diaz-Rubio E, Krell J, Dawson S-J, Raimondi C, Rutten A, Janni W,

Munzone E, Carañana V, Agelaki S, Almici C, Dirix L, Solomayer E, Zorzino L, Johannes H, Reis-Filho

JS, Pantel K, Pierga J-Y, and Michiels S. Clinical validity of circulating tumour cells in patients with

metastatic breast cancer: a pooled analysis of European studies. The Lancet Oncology, 2014 (in press)

196. Lim YC, di Pietro M, O'Donovan M, Richardson S, Debiram I, Dwerryhouse S, Hardwick RH,

Tischkowitz M, Caldas C*, Ragunath K, and Fitzgerald RC. Prospective cohort study assessing outcomes

of patients from families fulfilling criteria for hereditary diffuse gastric cancer undergoing endoscopic

surveillance. Gastrointestinal Endoscopy, 2014 (in press)

197. Viré E, Curtis C, Davalos V, Git A, Robson S, Villanueva A, Vidal A, Aparicio S, Esteller M, Caldas

C, and Kouzarides T. The breast cancer oncogene EMSY represses transcription of anti-metastatic

microRNA miR-31. Molecular Cell, 2014 (in press)

198. Ong C-AJ, Shannon NB, Ross-Innes CS, O'Donovan M, Rueda OM, Hu D, Kettunen MI, Walker CE,

Noorani A, Hardwick RH, Caldas C, Brindle K, and Fitzgerald RC. Discovery of TRIM44 amplification

couples a prognostic target with a potential therapeutic strategy. Journal of the National Cancer

Institute, 2014 (in press)

27

REVIEWS/EDITORIALS

1. Caldas C and McGuire WP. Taxol in epithelial ovarian cancer. Journal of the National Cancer

Institute Monographs, 15: 155-158, 1993

2. Caldas C and McGuire WP. Paclitaxel (Taxol) therapy in ovarian carcinoma. Seminars in Oncology, 20

(suppl 3): 50-55, 1993

3. Caldas C, Morris L, and McGuire WP. Salvage therapy in ovarian cancer. Obstetrics and Gynecology

Clinics of North America, 21: 179-194, 1994

4. Caldas C, and Ambinder R. Epstein-Barr virus infection and bone-marrow transplantation. Current

Opinions in Oncology, 7: 102-106, 1995

5. Caldas C, and Kern SE. K-ras mutation and pancreatic adenocarcinoma. International Journal of

Pancreatology, 18: 1-6, 1995

6. Caldas C and Ponder BAJ. Cancer genes and molecular oncology in the clinic. The Lancet, 349 (suppl

II): 16-18, 1997

7. Caldas C. Molecular staging of cancer: is it time? [Editorial] The Lancet, 350: 231, 1997

8. Caldas C. Science, Medicine and the future: Molecular assessment of cancer. British Medical Journal,

316: 1360-1363, 1998.

9. Pharoah PDP and Caldas C. Molecular genetics and the assessment of human cancers. Expert

Reviews in Molecular Medicine, (99) 00052-6h.htm, 1999

10. Caldas C. Biliopancreatic malignancy: Screening the at risk patient with molecular markers. Annals

of Oncology, 10 Suppl 4:153-156, 1999

11. Caldas C, and Aparicio S. Cell memory and cancer - the story of the trithorax and polycomb group

genes. Cancer and Metastasis Reviews, 18: 313-329, 1999

12. Emilien G, Ponchon M, Caldas C, Isacson O, and Maloteaux J-M. Impact of genomics on drug

discovery and clinical medicine. Quarterly Journal of Medicine, 93: 391-423, 2000

13. Aparicio SAJR, Caldas C, and Ponder BAJ. Does massively parallel analysis signify the end of

histopathology as we know it? Genome Biology, 1:, 2000

14. Brenton JD, Aparicio SAJR, and Caldas C. Molecular profiling of breast cancer: portraits but not

physiognomy. Breast Cancer Research, 3: 77-80, 2001

15. Caldas C, and Aparicio SAJ. Cancer: The molecular outlook. [News and Views] Nature, 415: 484-485,

2002

16. Fitzgerald RC, and Caldas C. E-cadherin mutations in hereditary gastric cancer: prevention by

resection? Digestive Diseases, 20: 23-31, 2002

17. Oliveira C, Seruca R, and Caldas C. Genetic screening for hereditary diffuse gastric cancer. Expert

Review of Molecular Diagnostics, 3: 201-215, 2003

18. Brenton JD, and Caldas C. Predictive cancer genomics- what do we need? [Editorial] The Lancet, 362:

340-341, 2003

19. Iyer NG, Ozdag H, and Caldas C. p300/CBP and cancer. Oncogene, 23: 4225-4231, 2004

20. Fitzgerald RC, and Caldas C. Clinical implications of E-cadherin associated hereditary diffuse gastric

cancer. Gut, 53: 775-778, 2004

21. Capella G, and Caldas C. MTAP homozygous deletion: an Achilles heel of human cancers ready for

clinical use? [Commentary] Cancer Biology and Therapy, 4: 347, 2005

22. Caldas C and Brenton JD. Sizing up miRNAs as cancer genes. [News and Views] Nature Medicine,

11: 712-714, 2005

23. Santos-Rosa H, and Caldas C. Chromatin modifier enzymes, the histone code and cancer. European

Journal of Cancer, 41: 2381-2402, 2005

28

24. Brenton JD, Carey LA, Ahmed AA, and Caldas C. Molecular classification and molecular forecasting

of breast cancer: ready for clinical application? Journal of Clinical Oncology, 23: 7350-7360, 2005

25. Fitzgerald RC and Caldas C. Familial gastric cancer- clinical management. Best Practice & Research

Clinical Gastroenterology, 20: 735-743, 2006

26. Barber M, Fitzgerald RC and Caldas C. Familial gastric cancer- aetiology and pathogenesis. Best

Practice & Research Clinical Gastroenterology, 20: 721-734, 2006

27. Abraham J, Earl H, Pharoah PD, and Caldas C. Pharmacogenetics of cancer chemotherapy.

Biochimica et Biophysica Acta- Reviews on Cancer, 1766: 168-183, 2006

28. Caldas C. Genomics and predicting drug sensitivity. Biochimica et Biophysica Acta- Reviews on

Cancer, 1766: 167, 2006

29. Caldas C and Edwards PAW. A quantum leap in our knowledge of breast cancer mutations. Breast

Cancer Research, 8: 304, 2006

30. Miremadi A, Oestergaard MZ, Pharoah PDP and Caldas C. Cancer genetics of epigenetic genes.

Human Molecular Genetics, 16: R28-R49, 2007

31. Stingl J and Caldas C. Molecular heterogeneity of breast carcinomas and the cancer stem cell

hypothesis. Nature Reviews Cancer, 7: 791-799, 2007

32. Costa JL, Meijer G, Ylstra B, and Caldas C. Array CGH copy number profiling: a new tool for

translational research in solid malignancies. Seminars in Radiation Oncology, 18: 98-104, 2008

33. Sassen S, Miska E, and Caldas C. MicroRNA- implications for cancer. Virchows Archive, 452: 1-10,

2008

34. Swanton C and Caldas C. Molecular classification of solid cancers: towards pathway-driven

therapeutics. British Journal of Cancer, 100: 1517-1522, 2009

35. Teschendorff AE and Caldas C. The breast cancer somatic ’muta-ome’: tackling the complexity.

Breast Cancer Research, 11: 301, 2009

36. Dawson SJ, Provenzano E, and Caldas C. Triple negative breast cancers: Clinical and prognostic

implications. European Journal of Cancer, 45: S27-S40, 2009

37. Hughes-Davies L, Caldas C, and Wishart GC. Tamoxifen: the drug that came in from the cold.

British Journal of Cancer, 101: 875-878, 2009

38. Lao-Sirieix P, Caldas C, and Fitzgerald RC. Genetic predisposition to gastro-oesophageal cancer.

Current Opinion in Genetics & Development, 20: 210-217, 2010

39. LeQuesne J and Caldas C. Micro-RNA and breast cancer. Molecular Oncology, 4: 230-241, 2010

40. Swanton C and Caldas C. From genomic landscapes to personalized cancer management- is there a

roadmap? Annals of the New York Academy of Sciences, 1210: 2931-2940, 2010

41. Pharoah PD and Caldas C. How to validate a breast cancer prognostic signature. [News and Views]

Nature Reviews Clinical Oncology, 7: 615-616, 2010

42. Teschendorff AE, Jiao Y, and Caldas C. Prognostic gene network modules in breast cancer hold

promise. Breast Cancer Research, 12: 317, 2010

43. Vollan HKM and Caldas C. The breast cancer genome- a key for better oncology. BMC Cancer, 11:

501, 2011

44. Caldas C. Cancer sequencing unravels clonal evolution. [News and Views]. Nature Biotechnology,

30: 408-410, 2012

45. Aparicio S and Caldas C. The implications of clonal genome evolution for cancer medicine. The New

England Journal of Medicine, 368: 842-851, 2013

46. Caldas C and Tannock IF. Tamoxifen: when more might be better. [News and Views] Nature

Reviews Clinical Oncology, 10: 125-126, 2013

47. Dawson S-J, Rueda OM, Aparicio S, and Caldas C. A new genome-driven integrated classification

of breast cancer and its implications. EMBO Journal, 32: 617-628, 2013

29

48. Baird RD and Caldas C. Genetic heterogeneity in breast cancer – the road to personalised medicine?

BMC Medicine, 11: 151, 2013

49. Caldas C. Video Q&A: molecular profiling of breast cancer. BMC Medicine, 11: 150, 2013

50. Yarden Y, and Caldas C, on behalf of the European Association for Cancer Research. Basic cancer

research is essential for the success of personalised medicine. European Journal of Cancer, 49: 2619-2620,

2013

51. Dawson SJ, Rosenfeld N, and Caldas C. Circulating tumor DNA to monitor metastatic breast cancer.

[correspondence]. The New England Journal of Medicine, 369: 93-94, 2013

52. Rajan A, Caldas C, van Luenen H, Saghatchian M, and van Harten WH. Assessing excellence in

translational cancer research: a consensus based framework. Journal of Translational Medicine, 11: 274,

2013

BOOK CHAPTERS

1. Carneiro F and Caldas C. Helicobacter Pilory. In, Encyclopedia of Genetics, Academic Press, Eds.

Brenner S and Miller JH, 2001

2. Caldas C and Venkitaraman A. Tumor suppressor genes. In, Encyclopedia of Genetics, Academic

Press, Eds. Brenner S and Miller JH, Pgs.: 2081-2088, 2001

3. Callagy G, Jackson LA and Caldas C. Laser capture microdissection and comparative genomic

hybridisation. In, Methods in Molecular Biology, vol 293, Laser Capture Microdissection Methods and

Protocols, Human Press, Eds. Murray GI and Curran S, Pgs: 39-55, 2005

4. Fitzgerald RC and Caldas C. The genetics of upper gastrointestinal malignancy. In, The effective

management of upper gastrointestinal malignancies, UK Key Advances in Clinical Practice Series,

Aesculapius Medical Press, Eds. Cunningham D, Jankowski J and Miles A, Pgs.: 23-37, 2005

5. Rueda OM, Diaz-Uriarte R, and Caldas C. Finding common regions of alteration in copy number data.

In, Methods in Molecular Biology, vol 973, Pgs: 339-353, 2013