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

James H. R. Farmery, Mike L. Smith, Aarnoud Huissoon, Abigail Furnell, Adam Mead, Adam P. Levine, Adnan Manzur, Adrian Thrasher, Alan Greenhalgh, Alasdair Parker, Alba Sanchis-Juan, Alex Richter, Alice Gardham, Allan Lawrie, Aman Sohal, Amanda Creaser-Myers, Amy Frary, Andreas Greinacher, Andreas Themistocleous, Andrew J. PeacockAndrew Marshall, Andrew Mumford, Andrew Rice, Andrew Webster, Angie Brady, Ania Koziell, Ania Manson, Anita Chandra, Anke Hensiek, Anna Huis In'T. Veld, Anna Maw, Anne M. Kelly, Anthony Moore, Anton Vonk Noordegraaf, Antony Attwood, Archana Herwadkar, Ardi Ghofrani, Arjan C. Houweling, Barbara Girerd, Bruce Furie, Carmen M. Treacy, Carolyn M. Millar, Carrock Sewell, Catherine Roughley, Catherine Titterton, Catherine Williamson, Charaka Hadinnapola, Charu Deshpande, Cheng-Hock Toh, Chiara Bacchelli, Chris Patch, Chris Van Geet, Christian Babbs, Christine Bryson, Christopher J. Penkett, Christopher J. Rhodes, Christopher Watt, Claire Bethune, Claire Booth, Claire Lentaigne, Coleen McJannet, Colin Church, Courtney French, Crina Samarghitean, Csaba Halmagyi, Daniel Gale, Daniel Greene, Daniel Hart, David Allsup, David Bennett, David Edgar, David G. Kiely, David Gosal, David J. Perry, David Keeling, David Montani, Debbie Shipley, Deborah Whitehorn, Debra Fletcher, Deepa Krishnakumar, Detelina Grozeva, Dinakantha Kumararatne, Dorothy Thompson, Dragana Josifova, Eamonn Maher, Edwin K. S. Wong, Elaine Murphy, Eleanor Dewhurst, Eleni Louka, Elisabeth Rosser, Elizabeth Chalmers, Elizabeth Colby, Elizabeth Drewe, Elizabeth McDermott, Ellen Thomas, Emily Staples, Emma Clement, Emma Matthews, Emma Wakeling, Eric Oksenhendler, Ernest Turro, Evan Reid, Evangeline Wassmer, F. Lucy Raymond, Fengyuan Hu, Fiona Kennedy, Florent Soubrier, Frances Flinter, Gabor Kovacs, Gary Polwarth, Gautum Ambegaonkar, Gavin Arno, Gavin Hudson, Geoff Woods, Gerry Coghlan, Grant Hayman, Gururaj Arumugakani, Gwen Schotte, H. Terry Cook, Hana Alachkar, Hana Lango Allen, Hana Lango-Allen, Hannah Stark, Hans Stauss, Harald Schulze, Harm J. Boggard, Helen Baxendale, Helen Dolling, Helen Firth, Henning Gall, Henry Watson, Hilary Longhurst, Hugh S. Markus, Hugh Watkins, Ilenia Simeoni, Ingrid Emmerson, Irene Roberts, Isabella Quinti, Ivy Wanjiku, J. Simon R. Gibbs, James Thaventhiran, James Whitworth, Jane Hurst, Janine Collins, Jay Suntharalingam, Jeanette Payne, Jecko Thachil, Jennifer M. Martin, Jenny Carmichael, Jesmeen Maimaris, Joan Paterson, Joanna Pepke-Zaba, Johan W. M. Heemskerk, Johanna Gebhart, John Davis, John Pasi, John R. Bradley, John Wharton, Jonathan Stephens, Julia Rankin, Julie Anderson, Julie Vogt, Julie von Ziegenweldt, Karola Rehnstrom, Karyn Megy, Kate Talks, Kathelijne Peerlinck, Katherine Yates, Kathleen Freson, Kathleen Stirrups, Keith Gomez, Kenneth G. C. Smith, Kevin Rue-Albrecht, Kimberley Gilmour, Larahmie Masati, Laura Scelsi, Laura Southgate, Lavanya Ranganathan, Lionel Ginsberg, Lisa Devlin, Lisa Willcocks, Liz Ormondroyd, Lorena Lorenzo, Lorraine Harper, Louise Allen, Louise Daugherty, Manali Chitre, Manju Kurian, Marc Humbert, Marc Tischkowitz, Maria Bitner-Glindzicz, Marie Erwood, Marie Scully, Marijke Veltman, Mark Caulfield, Mark Layton, Mark McCarthy, Mark Ponsford, Mark Toshner, Marta Bleda, Martin Wilkins, Mary Mathias, Mary Reilly, Maryam Afzal, Matthew Brown, Matthew Rondina, Matthew Stubbs, Matthias Haimel, Melissa Lees, Michael A. Laffan, Michael Browning, Michael Gattens, Michael Richards, Michel Michaelides, Michele P. Lambert, Mike Makris, Minka de Vries, Mohamed Mahdi-Rogers, Moin Saleem, Moira Thomas, Muriel Holder, M. lanie Eyries, Naomi Clements-Brod, Natalie Canham, Natalie Dormand, Natalie Van Zuydam, Nathalie Kingston, Neeti Ghali, Nichola Cooper, Nicholas W. Morrell, Nigel Yeatman, Noémi Roy, Olga Shamardina, Omid S. Alavijeh, Paolo Gresele, Paquita Nurden, Patrick Chinnery, Patrick Deegan, Patrick Yong, Patrick Yu Wai Man, Paul A. Corris, Paul Calleja, Paul Gissen, Paula Bolton-Maggs, Paula Rayner-Matthews, Pavandeep K. Ghataorhe, Pavel Gordins, Penelope Stein, Peter Collins, Peter Dixon, Peter Kelleher, Phil Ancliff, Ping Yu, R. Campbell Tait, Rachel Linger, Rainer Doffinger, Rajiv Machado, Rashid Kazmi, Ravishankar Sargur, Remi Favier, Rhea Tan, Ri Liesner, Richard Antrobus, Richard Sandford, Richard Scott, Richard Trembath, Rita Horvath, Rob Hadden, Rob V. Mackenzieross, Robert Henderson, Robert MacLaren, Roger James, Rohit Ghurye, Rosa Dacosta, Rosie Hague, Rutendo Mapeta, Ruth Armstrong, Sadia Noorani, Sai Murng, Saikat Santra, Salih Tuna, Sally Johnson, Sam Chong, Sara Lear, Sara Walker, Sarah Goddard, Sarah Mangles, Sarah Westbury, Sarju Mehta, Scott Hackett, Sergey Nejentsev, Shahin Moledina, Shahnaz Bibi, Sharon Meehan, Shokri Othman, Shoshana Revel-Vilk, Simon Holden, Simon McGowan, Simon Staines, Sinisa Savic, Siobhan Burns, Sofia Grigoriadou, Sofia Papadia, Sofie Ashford, Sol Schulman, Sonia Ali, Soo-Mi Park, Sophie Davies, Sophie Stock, Souad Ali, Sri V. V. Deevi, Stefan Gräf, Stefano Ghio, Stephen J. Wort, Stephen Jolles, Steve Austin, Steve Welch, Stuart Meacham, Stuart Rankin, Suellen Walker, Suranjith Seneviratne, Susan Holder, Suthesh Sivapalaratnam, Sylvia Richardson, Taco Kuijpers, Taco W. Kuijpers, Tadbir K. Bariana, Tamam Bakchoul, Tamara Everington, Tara Renton, Tim Young, Timothy Aitman, Timothy Q. Warner, Tom Vale, Tracey Hammerton, Val Pollock, Vera Matser, Victoria Cookson, Virginia Clowes, Waseem Qasim, Wei Wei, Wendy N. Erber, Willem H. Ouwehand, William Astle, William Egner, Wojciech Turek, Yvonne Henskens, Yvonne Tan, Andy G. Lynch

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype.
Original languageEnglish
Article number1300
JournalScientific Reports
Volume8
Issue number1
DOIs
Publication statusPublished - 2018

Cite this

Farmery, J. H. R., Smith, M. L., Huissoon, A., Furnell, A., Mead, A., Levine, A. P., ... Lynch, A. G. (2018). Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data. Scientific Reports, 8(1), [1300]. https://doi.org/10.1038/s41598-017-14403-y