Wellcome Trust Sanger Institute

Our Group

Experimental Cancer Genetics
Wellcome Trust Sanger Institute

 

Group Leader

Dr. David Adams
Senior Group Leader / CR UK Senior Fellow
Experimental Cancer Genetics
Wellcome Trust Sanger Institute
Hinxton, Cambs, CB10 1HH
Ph:  +44 (0) 1223 834 244
Fax: +44 (0) 1223 494 919

Victoria Russell-Hopkins (PA) vr4@sanger.ac.uk

 

Group Members

Louise van der Weyden          (Senior Staff Scientist)               – CR-UK Funded.
Annie Speak                              (Senior Staff Scientist)               – WT Funded.
Chi Wong                                   (Consultant in Haematology)   – WT Fellowship.
Vivek Iyer                                  (Principal Bioinformatician)     – WT Funded.
James Hewinson                     (Lab Manager)                              – WT Funded.
Marcela Sjoberg                      (Postdoc)                                        – EU Funded.
Nic Walker                               (Postdoc)                                        – EU Funded.
Emmanuelle Supper              (Postdoc)                                        – WT Fellowship.
Marco Ranzani                       (Postdoc)                                         – Marie Curie Funded.
Clara Alsinet-Armengol        (Postdoc)                                        – ERC Funded.
Kim Wong                               (Senior Computer Biologist)      – ERC Funded.
Sendu Bala                              (Senior Computer Biologist)      – EU Funded.
Mamun Rashid                      (Senior Computer Biologist)      – CR-UK funded.
Martin del Castillo                (PhD Student)                               – CR-UK studentship.
Gemma Turner                      (PhD Student)                               – MRC Funded.
Katharina Strege                    (PhD Student)                              – MRC Funded.
Richard Gunning                   (PhD Student)                              – BBSRC Funded.
Stefan Dentro                        (PhD Student)                               – WT Funded.
Nicky Thompson                  (Clinical PhD Student)                – WT Funded.
Sofia Chen                             (PhD Student)                               – EU Funded.
Aravind Sankar                    (PhD Student)                               – EU Funded.
Roy Rabbie                            (Clinical PhD Student)               – NHS/CR-UK Funded.
Daniela Robles                     (Visiting scientist)                       – Mexican Government.
Mairi Kusma                         (animal technician)                    – EU Funded.
Victoria                                  (animal technician)                    – EU Funded.

 

Research

Dr. David Adams and his group study the mechanisms of cancer development, particularly skin cancer (melanoma) and colorectal cancer. They sequence DNA from families with a high incidence of cancer, and also tumours from patients to understand why some people are at greater risk of tumour development and how cancers evolve. The group also performs functional studies in cultured cells and in mice to understand how factors such as DNA mutations and the immune system influence tumour growth.

 

Publications

Josep V. Forment, Mareike Herzog, Julia Coates, Tomasz Konopka, Bianca V. Gapp, Sebastian M. Nijman, Adams DJ, Keane TM,, Jackson SP. Genome-wide genetic screening with chemically-mutagenized haploid embryonic stem cells. Nature Structural and Molecular Biologyin press

Dickinson M., et al., Adams DJ, Lloyd K, McKerlie C, Beaudet AL, Bucan M, Murray SA. High-throughput discovery of novel developmental phenotypes. Nature – in press

McIntyre RE, Nicod J, Robles-Espinoza CD, Maciejowski J, Cai N, Hill J, Verstraten R, Iyer V, Rust AG, Balmus G, Mott R, Flint J, Adams DJ (2016) A Genome-Wide Association Study for Regulators of Micronucleus Formation in Mice. G3 in press

Nicod J, Davies RW, Cai N, Hassett C, Goodstadt L, Cosgrove C, Yee BK, Lionikaite V, McIntyre RE, Remme CA, Lodder EM, Gregory JS, Hough T, Joynson R, Phelps H, Nell B, Rowe C, Wood J, Walling A, Bopp N, Bhomra A, Hernandez-Pliego P, Callebert J, Aspden RM, Talbot NP, Robbins PA, Harrison M, Fray M, Launay JM, Pinto YM, Blizard DA, Bezzina CR, Adams DJ, Franken P, Weaver T, Wells S, Brown SD, Potter PK, Klenerman P, Lionikas A, Mott R, Flint J (2016) Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing. Nature genetics in press

van der Weyden L, Patton EE, Wood GA, Foote AK, Brenn T, Arends MJ, Adams DJ (2016) Cross-species models of human melanoma. The Journal of pathology 238: 152-165

Robles-Espinoza CD, Roberts ND, Chen S, Leacy FP, Alexandrov LB, Pornputtapong N, Halaban R, Krauthammer M, Cui R, Timothy Bishop D, Adams DJ (2016) Germline MC1R status influences somatic mutation burden in melanoma. Nature communications 7: 12064

Rabbie R, Adams DJ (2016) Desmoplastic melanoma: C>Ts and NF-kappaB. Pigment Cell Melanoma Res 29: 120-121

Kemper K, Krijgsman O, Kong X, Cornelissen-Steijger P, Shahrabi A, Weeber F, van der Velden DL, Bleijerveld OB, Kuilman T, Kluin RJ, Sun C, Voest EE, Ju YS, Schumacher TN, Altelaar AF, McDermott U, Adams DJ, Blank CU, Haanen JB, Peeper DS (2016) BRAF(V600E) Kinase Domain Duplication Identified in Therapy-Refractory Melanoma Patient-Derived Xenografts. Cell reports 16: 263-277

Harland M, Petljak M, Robles-Espinoza CD, Ding Z, Gruis NA, van Doorn R, Pooley KA, Dunning AM, Aoude LG, Wadt KA, Gerdes AM, Brown KM, Hayward NK, Newton-Bishop JA, Adams DJ, Bishop DT (2016) Germline TERT promoter mutations are rare in familial melanoma. Fam Cancer 15: 139-144

Robles-Espinoza CD, Velasco-Herrera Mdel C, Hayward NK, Adams DJ (2015) Telomere-regulating genes and the telomere interactome in familial cancers. Mol Cancer Res 13: 211-222

Ranzani M, Alifrangis C, Perna D, Dutton-Regester K, Pritchard A, Wong K, Rashid M, Robles-Espinoza CD, Hayward NK, McDermott U, Garnett M, Adams DJ (2015) BRAF/NRAS wild-type melanoma, NF1 status and sensitivity to trametinib. Pigment Cell Melanoma Res 28: 117-119

Perna D, Karreth FA, Rust AG, Perez-Mancera PA, Rashid M, Iorio F, Alifrangis C, Arends MJ, Bosenberg MW, Bollag G, Tuveson DA, Adams DJ (2015) BRAF inhibitor resistance mediated by the AKT pathway in an oncogenic BRAF mouse melanoma model. Proceedings of the National Academy of Sciences of the United States of America 112: E536-545

McCreery MQ, Halliwill KD, Chin D, Delrosario R, Hirst G, Vuong P, Jen KY, Hewinson J, Adams DJ, Balmain A (2015) Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers. Nat Med 21: 1514-1520

Kuilman T, Velds A, Kemper K, Ranzani M, Bombardelli L, Hoogstraat M, Nevedomskaya E, Xu G, de Ruiter J, Lolkema MP, Ylstra B, Jonkers J, Rottenberg S, Wessels LF, Adams DJ, Peeper DS, Krijgsman O (2015) CopywriteR: DNA copy number detection from off-target sequence data. Genome biology 16: 49

Kemper K, Krijgsman O, Cornelissen-Steijger P, Shahrabi A, Weeber F, Song JY, Kuilman T, Vis DJ, Wessels LF, Voest EE, Schumacher TN, Blank CU, Adams DJ, Haanen JB, Peeper DS (2015) Intra- and inter-tumor heterogeneity in a vemurafenib-resistant melanoma patient and derived xenografts. EMBO Mol Med 7: 1104-1118

Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Leopold V, Sjoberg M, Keane TM, Verma A, Ala U, Tay Y, Wu D, Seitzer N, Velasco-Herrera Mdel C, Bothmer A, Fung J, Langellotto F, Rodig SJ, Elemento O, Shipp MA, Adams DJ, Chiarle R, Pandolfi PP (2015) The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell 161: 319-332

Aoude LG, Pritchard AL, Robles-Espinoza CD, Wadt K, Harland M, Choi J, Gartside M, Quesada V, Johansson P, Palmer JM, Ramsay AJ, Zhang X, Jones K, Symmons J, Holland EA, Schmid H, Bonazzi V, Woods S, Dutton-Regester K, Stark MS, Snowden H, van Doorn R, Montgomery GW, Martin NG, Keane TM, Lopez-Otin C, Gerdes AM, Olsson H, Ingvar C, Borg A, Gruis NA, Trent JM, Jonsson G, Bishop DT, Mann GJ, Newton-Bishop JA, Brown KM, Adams DJ, Hayward NK (2015) Nonsense mutations in the shelterin complex genes ACD and TERF2IP in familial melanoma. J Natl Cancer Inst 107

Wong CC, Martincorena I, Rust AG, Rashid M, Alifrangis C, Alexandrov LB, Tiffen JC, Kober C, Green AR, Massie CE, Nangalia J, Lempidaki S, Dohner H, Dohner K, Bray SJ, McDermott U, Papaemmanuil E, Campbell PJ, Adams DJ(2014) Inactivating CUX1 mutations promote tumorigenesis. Nature genetics 46: 33-38

Robles-Espinoza CD, Harland M, Ramsay AJ, Aoude LG, Quesada V, Ding Z, Pooley KA, Pritchard AL, Tiffen JC, Petljak M, Palmer JM, Symmons J, Johansson P, Stark MS, Gartside MG, Snowden H, Montgomery GW, Martin NG, Liu JZ, Choi J, Makowski M, Brown KM, Dunning AM, Keane TM, Lopez-Otin C, Gruis NA, Hayward NK, Bishop DT, Newton-Bishop JA, Adams DJ (2014) POT1 loss-of-function variants predispose to familial melanoma. Nature genetics 46: 478-481

Yen J, White RM, Wedge DC, Van Loo P, de Ridder J, Capper A, Richardson J, Jones D, Raine K, Watson IR, Wu CJ, Cheng J, Martincorena I, Nik-Zainal S, Mudie L, Moreau Y, Marshall J, Ramakrishna M, Tarpey P, Shlien A, Whitmore I, Gamble S, Latimer C, Langdon E, Kaufman C, Dovey M, Taylor A, Menzies A, McLaren S, O’Meara S, Butler A, Teague J, Lister J, Chin L, Campbell P, Adams DJ, Zon LI, Patton EE, Stemple DL, Futreal PA (2013) The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models. Genome biology 14: R113

van der Weyden L, Arends MJ, Rust AG, Poulogiannis G, McIntyre RE, Adams DJ(2012) Increased tumorigenesis associated with loss of the tumor suppressor gene Cadm1. Molecular cancer 11: 29

Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, DeNicola G, Webster KA, Weiss D, Perez-Mancera PA, Krauthammer M, Halaban R, Provero P, Adams DJ, Tuveson DA, Pandolfi PP (2011) In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147: 382-395

Wood HM, Belvedere O, Conway C, Daly C, Chalkley R, Bickerdike M, McKinley C, Egan P, Ross L, Hayward B, Morgan J, Davidson L, MacLennan K, Ong TK, Papagiannopoulos K, Cook I, Adams DJ, Taylor GR, Rabbitts P (2010) Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic acids research 38: e151

Wong K, Keane TM, Stalker J, Adams DJ (2010) Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome biology 11: R128

University of Leeds

Prof Newton Bishop Group Shots 03

 

 

 

 

 

 

Our Group

Section of Epidemiology and Biostatistics
Leeds Institute of Cancer and Pathology
Cancer Genetics Building
St. James’s University Hospital
Leeds LS9 7TF

Group leader

Professor Julia A. Newton Bishop
Melanoma Group Leader
Section of Epidemiology and Biostatistics
Leeds Institute of Cancer and Pathology
Cancer Genetics Building
St. James’s University Hospital
Leeds LS9 7TF
E-mail: j.a.newton-bishop@leeds.ac.uk
Phone: 44 (0)113 2064668
Personal Assistant: Katie Cairns 44( 0) 1132064573
Fax: 44 (0)113 2340183
The Section of Epidemiology and Biostatistics in Leeds works to understand and identify genes predisposing to melanoma, bowel and testis cancers. It is also involved in developing statistical methods and applying these methods to the cancers being studied.
The group is also concerned with understanding how genes interact with lifestyle in determining risk of cancer and survival.

Melanoma research
In the melanoma group, lead by Professor Newton Bishop, we have studied high penetrance genes (familial melanoma genes) from families with multiple cases of melanoma. To investigate lower penetrance susceptibility genes and the interaction between genes and the environment (with respect to survival), we recruited a large cohort of melanoma patients (2184 patients participated in a study we call the Leeds Melanoma Cohort), their families and matched population controls.
We also study patients who have relapsed with melanoma and compared them to controls who have not relapsed in order to look at factors associated with prognosis. We have shown for example that patients with higher vitamin D levels when they are diagnosed are less likely to have further recurrence of their melanoma. Although we have stopped recruiting to the Leeds Melanoma Cohort we continue to use the data and samples we collected to try to understand recurrence and the effects that genes and lifestyles have on recurrence. We will continue to post summaries of the research as it is published on this web site within the information for patients.

Information for families with Melanoma taking part in research in Leeds
This Familial Melanoma Study has now ceased recruitment in the UK. We continue to work on the data and the samples collected however in order to identify genes which increase the risk of this form of skin cancer. We will continue to post summaries of the research as it is published on this web site within the information for patients.

Additional Links

Cancer Bacup
www.cancerbacup.org.uk/Home

This is the national cancer information service for people who have been diagnosed with cancer. There are comprehensive booklets for most of the cancers that can be ordered and information online about them. It also provides up-to-date information about trials and treatments.

Wessex Cancer Trust
www.wessexcancer.org

This is the UK’s only specialist skin cancer helpline and advice centre. The skin cancer section of the site provides information about the different skin cancers, skin disorders and sun protection.

Genetic Interest Group
www.gig.org.uk

This is a national alliance of patient organizations. Each of the organizations focuses on a different genetic disorder.

Human Genetics Commission
www.hgc.gov.uk

This is the UK government website on genetics.