Leeds Institute of Cancer and Pathology

Pre-Cancer Genomics

Publications

Polycomb Repressor Complex 1 Member, BMI1 Contributes to Urothelial Tumorigenesis through p16-Independent Mechanisms. De Faveri LE, Hurst CD, Roulson JA, Wood H, Sanchez-Carbayo M, Knowles MA, Chapman EJ. Translational Oncology 2015 Oct;8(5):387-99.
Pubmed link

Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq. Conway C, Graham JL, Chengot P, Daly C, Chalkley R, Ross L, Droop A, Rabbitts P, Stead LF. Oncotarget. 2015. Epub ahead of print.
Pubmed link

The clonal relationships between pre-cancer and cancer revealed by ultra-deep sequencing. Henry M Wood, Caroline Conway, Catherine Daly, Rebecca Chalkley, Stefano Berri, Burcu Senguven, Lucy Stead, Lisa Ross, Philip Egan, Preetha Chengot, Jennifer Graham, Neeraj Sethi, Thian K Ong, Alec High, Kenneth MacLennan, Pamela Rabbitts. Journal of Pathology. 2015, Nov;237(3):296-306.
Pubmed link

Clinical and genomic analysis of a randomised phase II study evaluating anastrozole and fulvestrant in postmenopausal patients treated for large operable or locally-advanced hormone-receptor-positive breast cancer. Nathalie Quenel-Tueux, Marc Debled, Justine Rudewicz, Gaëtan MacGrogan, Marina Pulido, Louis Mauriac, Florence Dalenc, Thomas Bachelot, Barbara Lortal, Christelle Breton-Callu, Nicolas Madranges, Christine Tunon de Lara, Marion Fournier, Hervé Bonnefoi, Hayssam Soueidan, Macha Nikolski, Audrey Gros, Catherine Daly, Henry Wood, Pamela H Rabbitts, and Richard Iggo. British Journal of Cancer. 2015, Aug 11;113(4):585-94.
Pubmed link

A novel genomic signature reclassifies an oral cancer subtype. Manar Samman, Henry M Wood, Caroline Conway, Lucy Stead, Catherine Daly, Rebecca Chalkley, Stefano Berri, Burcu Senguven, Lisa Ross, Philip Egan, Preetha Chengot, Thian K Ong, Monica Pentenero, Sergio Gandolfo, Adele Cassenti, Paola Cassoni, Abdulaziz Al Ajlan, Alaa Samkari, William Barrett, Kenneth MacLennan, Alec High, Pamela Rabbitts. International Journal of Cancer. 2015. Nov 15;137(10):2364-73.
Pubmed link

Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data. Arief Gusnanto, Peter Tcherveniakov, Farag Shuweihdi, Manar Samman, Pamela Rabbitts, Henry M. Wood. Bioinformatics. 2015. Aug 15;31(16):2713-20.
Pubmed link

Diagnosis of fetal submicroscopic chromosomal abnormality in failed array CGH samples – copy number by sequencing as an alternative to microarrays for fetal invasive testing. Cohen K, Tzika A, Wood H, Berri S, Roberts P, Mason G, Sheridan. Ultrasound in Obstetrics & Gynecology. 2015 Apr;45(4):394-401.
Pubmed link

MicroRNAs and head and neck cancer: Reviewing the first decade of research. Sethi N, Wright A, Wood H, Rabbitts P. European Journal of Cancer. 2014 Oct;50(15):2619-35.
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Using common variants to indicate cancer genes. Stead, L.F., Thygesen, H.,Westhead, D.R. and Rabbitts, P. (2014)
International Journal of Cancer. 2014. Epub ahead of print.
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Next-Generation Sequencing Analysis for Detecting Human Papillomavirus in Oral Verrucous Carcinoma. Manar Samman; Henry M Wood; Caroline A Conway; Stefano Berri; Monica Pentenero; Sergio Gandolfo; Adele Cassenti; Paola Cassoni; Abdulaziz Al Ajlan; William A Barrett; Preetha Chengot; Pamela Rabbitts; Alec S High, FRCPath; Kenneth MacLennan, MD FRCPath. Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology. 2014 Jul;118(1):117-125
Pubmed link

Estimating optimal window size for analysis of low-coverage next-generation sequence data. Nafisah, I., Taylor, C., Wood, H., Rabbitts, P., Berri, S., Gusnanto, A. Bioinformatics. 2014, July; 30(13): 1823-9.
Pubmed link

No evidence for integrated viral DNA in the genome sequence of cutaneous squamous cell carcinoma. Michelle T Dimon, Henry M Wood, Pamela H Rabbitts, Wilson Liao, Raymond J Cho, Sarah T Arron. The Journal of Investigative Dermatology. 2014, July; 134(7): 2055-7.
Pubmed link

An Integrated Inspection of the Somatic Mutations in a Lung Squamous Cell Carcinoma using Next-Generation Sequencing. Stead L.F., Devery A., Conway C., Egan P., Daly C., Berri S., Wood H.M., Belvedere O., Papagiannopoulos K., Ryan A., Rabbitts P. PLOS One. 2013;8(11):e78823
PLOS One link

Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing; applications in tumour subclone resolution. Stead LF, Sutton KM, Taylor GR, Quirke P and Rabbitts, P. Human Mutation. 2013;34(10):1432-8
Pubmed link

IMSA: Integrated Metagenomic Sequence Analysis for Identification of Exogenous Reads in a Host Genomic Background. Dimon MT, Wood HM, Rabbitts PH, Arron ST. PLOS One. 2013;8(5):e64546.
Pubmed link

Diagnosis of Copy Number Variation by Illumina Next Generation Sequencing is comparable in performance to Oligonucleotide Array Comparative Genomic Hybridisation. Hayes JL and Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, Pendlebury M, Coates A, Willoughby L, Watson CM, Rabbitts P, Roberts P, Taylor GR. Genomics. 2013; 102(3): 174-181.
Pubmed link

Nonreciprocal Chromosomal Translocations in Renal Cancer Involve Multiple DSBs and NHEJ Associated with Breakpoint Inversion But Not Necessarily with Transcription. Hanif Ali, Angelika Daser, Paul Dear, Henry Wood, Pamela Rabbitts and Terence Rabbitts. Genes, Chromosomes and Cancer. 2013; 52: 402-409.
Pubmed link

Mutation detection by clonal sequencing of PCR amplicons and grouped read typing is applicable to clinical diagnostics. Chambers PA*, Stead LF*, Morgan JE, Carr IM, Sutton KM, Watson CM, Crowe V, Dickinson H, Roberts P, Mulatero C, Seymour M, Markham AF, Waring PM, Quirke P, Taylor GR. Human Mutation. 2013. 34(1):248-54.
Pubmed link
*These authors contributed equally to the work

The transcriptional consequences of somatic amplifications, deletions and rearrangements in a human lung squamous cell carcinomaLucy F. Stead, Stefano Berri, Henry M. Wood, Philip Egan, Caroline Conway, Catherine Daly, Kostas Papagiannopoulos and Pamela Rabbitts. Neoplasia. 2012; 14(11):1075-1086.
Pubmed link

Is next-generation sequencing an important tool in HPV subtype diagnosis?  Henry M Wood, Robert Bolt, Keith D Hunter. Expert Review of Molecular Diagnostics. 2012. 12(7):663-5.
Pubmed link

Next generation sequencing for simultaneous determination of HPV load, subtype and associated genomic copy number changes in tumors. Caroline Conway, Rebecca Chalkley, Alec High, Kenneth Maclennan, Stefano Berri, Preetha Chengot, Melissa Alsop, Philip Egan, Joanne Morgan, Graham R Taylor, John Chester, Mehmet Sen, Pamela Rabbitts, Henry M Wood. Journal of Molecular Diagnostics. 2012; 14(2):104-111
Pubmed link

A computational index derived from whole-genome copy number analysis is a novel tool for prognosis in early stage lung squamous cell carcinomaOrnella Belvedere, Stefano Berri, Rebecca Chalkley, Caroline Conway, Fabio Barbone, Federica Pisa, Kenneth MacLennan, Catherine Daly, Melissa Alsop, Joanne Morgan, Jessica Menis, Peter Tcherveniakov, Kostas Papagiannopoulos, Pamela Rabbitts, Henry M Wood. Genomics. 2012; 99(1):18-24
Pubmed link

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next generation sequence data. Arief Gusnanto, Henry M Wood, Yudi Pawitan, Pamela Rabbitts, Stefano Berri. Bioinformatics. 2012, 28(1):40-47
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Genomic evidence of preinvasive clonal expansion, dispersal and progression in bronchial dysplasia.
Frank McCaughan, Christodoulos P Pipinikas, Sam M Janes, P Jeremy George, Pamela H Rabbitts and Paul H Dear.
Journal of Pathology 2011; 224:153-9
Pubmed link

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens.
Henry M Wood, Ornella Belvedere, Caroline Conway, Catherine Daly, Rebecca Chalkley, Melissa Bickerdike, Claire McKinley, Phil Egan, Lisa Ross, Bruce Hayward, Joanne Morgan, Leslie Davidson, Ken MacLennan, Thian K Ong, Kostas Papagiannopoulos, Ian Cook, David J Adams, Graham R Taylor, Pamela Rabbitts.
Nucleic Acids Research. 2010; 38(14):e151
Pubmed link

Progressive 3q amplification consistently targets SOX2 in preinvasive squamous lung cancer.
Frank McCaughan, Jessica CM Pole , Alan T Bankier, Bernard A Konfortov, Bernadette Carroll, Mary Falzon, Terence H Rabbitts,  P Jeremy George, Paul H Dear, and Pamela H Rabbitts.
Am J Respir Crit Care Med. 2010; 182:83-91.
Pubmed link

µMCC – Unlocking Cancer Archives with Digital PCR.
McCaughan F, Darai-Ramqvist E, Bankier AT, Konfortov B, Foster N, George PJ, Rabbitts T, Kost-Alimova M, Rabbitts PH and Dear PH.
Journal of Pathology. 2008; 216:307-16
Pubmed link

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