Publications by authors named "Andy G Lynch"

48Publications

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Sci Rep 2018 Sep 3;8(1):13376. Epub 2018 Sep 3.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1038/s41598-018-31524-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120886PMC
September 2018

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Sci Rep 2018 01 22;8(1):1300. Epub 2018 Jan 22.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1038/s41598-017-14403-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778012PMC
January 2018

New Model for Estimating Glomerular Filtration Rate in Patients With Cancer.

J Clin Oncol 2017 Aug 7;35(24):2798-2805. Epub 2017 Jul 7.

Tobias Janowitz, Edward H. Williams, Stephen J. Sammut, Andy G. Lynch, Duncan I. Jodrell, Simon Tavaré, and Helena Earl, Cancer Research UK Cambridge Institute, Tobias Janowitz, Peter B. Thomas, and Duncan I. Jodrell, University of Cambridge, Addenbrooke's Hospital, Cambridge; Andrea Marshall, University of Warwick, Coventry; Nicola Ainsworth, Queen Elizabeth Hospital, King's Lynn; Scott Shepherd, Royal Marsden Hospital, London; Jeff White, NHS Greater Glasgow and Clyde; and Patrick B. Mark, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom.

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http://dx.doi.org/10.1200/JCO.2017.72.7578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5562175PMC
August 2017

Mining Human Prostate Cancer Datasets: The "camcAPP" Shiny App.

EBioMedicine 2017 Mar 2;17:5-6. Epub 2017 Mar 2.

Cancer Research UK Cambridge Institute, Cambridge Biomedical Campus, UK; Department of Genito-urinary Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Academic Urology Group, Department of Surgery, University of Cambridge, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2017.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5360593PMC
March 2017

Whole blood mRNA in prostate cancer reveals a four-gene androgen regulated panel.

Endocr Relat Cancer 2016 10 30;23(10):797-812. Epub 2016 Aug 30.

Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Molecular Diagnostics and Therapeutics GroupUniversity College London, London, UK

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http://dx.doi.org/10.1530/ERC-16-0287DOI Listing
October 2016

The importance of DNA methylation in prostate cancer development.

J Steroid Biochem Mol Biol 2017 02 24;166:1-15. Epub 2016 Apr 24.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09600760163010
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http://dx.doi.org/10.1016/j.jsbmb.2016.04.009DOI Listing
February 2017

Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target.

J Natl Cancer Inst 2016 May 11;108(5). Epub 2015 Dec 11.

Affiliations of authors:Cancer Research UK Cambridge Institute, University of Cambridge , Cambridge, UK (MA, CEM, NP, HIZ, AQ, AB, SM, BM, CE, SL, SW, VRZ, GS, RR, HM, AGL, CD, CT, AL, RS, JY, RS, JSC, JRG, ST, DEN); School of Medical Sciences, University of Aberdeen , Aberdeen, UK (FO, IJM); Department of Pathology, Addenbrooke's Hospital , Cambridge, UK (AYW, NS); Institute of Human Genetics, Jena University Hospital , Jena , Germany (ME, KL, WH, AB); Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, Faculty of Health Sciences, University of Adelaide , Australia (LAS, WDT); Freemasons Foundation Centre for Men's Health, School of Medicine, Faculty of Health Sciences, University of Adelaide , Australia (LAS, WDT); Diatherix , Huntsville, AL (EG); Masonic Cancer Center, University of Minnesota , Minneapolis, MN (SMD); The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia , Vancouver BC , Canada (PSR); Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital , Oslo , Norway (IGM); Department of Cancer Prevention, Institute of Cancer Research and Department of Urology, Oslo University Hospital , Oslo , Norway (IGM); Prostate Cancer UK/Movember Centre of Excellence, Queens University , Belfast , UK (IGM); Department of Oncology, Addenbrooke's Hospital , Cambridge, UK (MA, DEN).

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http://jnci.oxfordjournals.org/content/108/5/djv371.full.pdf
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http://jnci.oxfordjournals.org/lookup/doi/10.1093/jnci/djv37
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http://dx.doi.org/10.1093/jnci/djv371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849803PMC
May 2016

multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples.

Nucleic Acids Res 2015 May 26;43(9):e61. Epub 2015 Feb 26.

Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK

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http://dx.doi.org/10.1093/nar/gkv135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482059PMC
May 2015

HES5 silencing is an early and recurrent change in prostate tumourigenesis.

Endocr Relat Cancer 2015 Apr 5;22(2):131-44. Epub 2015 Jan 5.

Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK

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http://dx.doi.org/10.1530/ERC-14-0454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335379PMC
April 2015

Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data.

Front Genet 2014 14;5:399. Epub 2014 Nov 14.

Cancer Research UK Cambridge Institute, University of Cambridge Cambridge, UK.

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http://dx.doi.org/10.3389/fgene.2014.00399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231950PMC
December 2014

Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes.

Science 2014 Aug;345(6196):1251343

Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.

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http://dx.doi.org/10.1126/science.1251343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380235PMC
August 2014

BeadArray expression analysis using bioconductor.

PLoS Comput Biol 2011 Dec 1;7(12):e1002276. Epub 2011 Dec 1.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.

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http://dx.doi.org/10.1371/journal.pcbi.1002276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228778PMC
December 2011

BayesPeak--an R package for analysing ChIP-seq data.

Bioinformatics 2011 Mar 17;27(5):713-4. Epub 2011 Jan 17.

Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042177PMC
March 2011

BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies.

Cancer Inform 2010 Sep 29;9:217-27. Epub 2010 Sep 29.

Department of Oncology, University of Cambridge, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956622PMC
September 2010

The cost of reducing starting RNA quantity for Illumina BeadArrays: a bead-level dilution experiment.

BMC Genomics 2010 Oct 6;11:540. Epub 2010 Oct 6.

Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK.

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http://dx.doi.org/10.1186/1471-2164-11-540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091689PMC
October 2010

Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data.

BMC Bioinformatics 2010 Apr 27;11:208. Epub 2010 Apr 27.

Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1186/1471-2105-11-208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880029PMC
April 2010

Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary.

J Pathol 2010 May;221(1):49-56

Functional Genomics of Ovarian Cancer Laboratory, Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1002/path.2696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262968PMC
May 2010

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

BMC Genomics 2009 Dec 8;10:588. Epub 2009 Dec 8.

Department of Oncology, University of Cambridge, Addenbrooke's Hopsital, Hills Road, Cambridge CB20XZ, UK.

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http://dx.doi.org/10.1186/1471-2164-10-588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797821PMC
December 2009

BayesPeak: Bayesian analysis of ChIP-seq data.

BMC Bioinformatics 2009 Sep 21;10:299. Epub 2009 Sep 21.

Statistical Laboratory, Centre for Mathematical Sciences, Wilberforce Road, Cambridge, UK.

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http://dx.doi.org/10.1186/1471-2105-10-299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760534PMC
September 2009

Spike-in validation of an Illumina-specific variance-stabilizing transformation.

BMC Res Notes 2008 Jun 4;1:18. Epub 2008 Jun 4.

Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1186/1756-0500-1-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518281PMC
June 2008

Statistical issues in the analysis of Illumina data.

BMC Bioinformatics 2008 Feb 6;9:85. Epub 2008 Feb 6.

Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1186/1471-2105-9-85DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2291044PMC
February 2008

New androgen receptor genomic targets show an interaction with the ETS1 transcription factor.

EMBO Rep 2007 Sep 17;8(9):871-8. Epub 2007 Aug 17.

Uro-Oncology Research Group, Department of Oncology, University of Cambridge, Cancer Research UK Cambridge, Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1038/sj.embor.7401046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950328PMC
September 2007

Missing channels in two-colour microarray experiments: combining single-channel and two-channel data.

BMC Bioinformatics 2007 Jan 25;8:26. Epub 2007 Jan 25.

Department of Oncology, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1186/1471-2105-8-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797192PMC
January 2007