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@article{Farmery:2018:10.1038/s41598-017-14403-y,
author = {Farmery, JHR and Smith, ML and Lynch, AG and Huissoon, A and Furnell, A and Mead, A and Levine, AP and Manzur, A and Thrasher, A and Greenhalgh, A and Parker, A and Sanchis-Juan, A and Richter, A and Gardham, A and Lawrie, A and Sohal, A and Creaser-Myers, A and Frary, A and Greinacher, A and Themistocleous, A and Peacock, AJ and Marshall, A and Mumford, A and Rice, A and Webster, A and Brady, A and Koziell, A and Manson, A and Chandra, A and Hensiek, A and in't, Veld AH and Maw, A and Kelly, AM and Moore, A and Noordegraaf, AV and Attwood, A and Herwadkar, A and Ghofrani, A and Houweling, AC and Girerd, B and Furie, B and Treacy, CM and Millar, CM and Sewell, C and Roughley, C and Titterton, C and Williamson, C and Hadinnapola, C and Deshpande, C and Toh, C-H and Bacchelli, C and Patch, C and Van, Geet C and Babbs, C and Bryson, C and Penkett, CJ and Rhodes, CJ and Watt, C and Bethune, C and Booth, C and Lentaigne, C and McJannet, C and Church, C and French, C and Samarghitean, C and },
doi = {10.1038/s41598-017-14403-y},
journal = {Scientific Reports},
title = {Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data},
url = {http://dx.doi.org/10.1038/s41598-017-14403-y},
volume = {8},
year = {2018}
}

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TY  - JOUR
AB  - 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.
AU  - Farmery,JHR
AU  - Smith,ML
AU  - Lynch,AG
AU  - Huissoon,A
AU  - Furnell,A
AU  - Mead,A
AU  - Levine,AP
AU  - Manzur,A
AU  - Thrasher,A
AU  - Greenhalgh,A
AU  - Parker,A
AU  - Sanchis-Juan,A
AU  - Richter,A
AU  - Gardham,A
AU  - Lawrie,A
AU  - Sohal,A
AU  - Creaser-Myers,A
AU  - Frary,A
AU  - Greinacher,A
AU  - Themistocleous,A
AU  - Peacock,AJ
AU  - Marshall,A
AU  - Mumford,A
AU  - Rice,A
AU  - Webster,A
AU  - Brady,A
AU  - Koziell,A
AU  - Manson,A
AU  - Chandra,A
AU  - Hensiek,A
AU  - in't,Veld AH
AU  - Maw,A
AU  - Kelly,AM
AU  - Moore,A
AU  - Noordegraaf,AV
AU  - Attwood,A
AU  - Herwadkar,A
AU  - Ghofrani,A
AU  - Houweling,AC
AU  - Girerd,B
AU  - Furie,B
AU  - Treacy,CM
AU  - Millar,CM
AU  - Sewell,C
AU  - Roughley,C
AU  - Titterton,C
AU  - Williamson,C
AU  - Hadinnapola,C
AU  - Deshpande,C
AU  - Toh,C-H
AU  - Bacchelli,C
AU  - Patch,C
AU  - Van,Geet C
AU  - Babbs,C
AU  - Bryson,C
AU  - Penkett,CJ
AU  - Rhodes,CJ
AU  - Watt,C
AU  - Bethune,C
AU  - Booth,C
AU  - Lentaigne,C
AU  - McJannet,C
AU  - Church,C
AU  - French,C
AU  - Samarghitean,C
AU  - Halmagyi,C
AU  - Gale,D
AU  - Greene,D
AU  - Hart,D
AU  - Allsup,D
AU  - Bennett,D
AU  - Edgar,D
AU  - Kiely,DG
AU  - Gosal,D
AU  - Perry,DJ
AU  - Keeling,D
AU  - Montani,D
AU  - Shipley,D
AU  - Whitehorn,D
AU  - Fletcher,D
AU  - Krishnakumar,D
AU  - Grozeva,D
AU  - Kumararatne,D
AU  - Thompson,D
AU  - Josifova,D
AU  - Maher,E
AU  - Wong,EKS
AU  - Murphy,E
AU  - Dewhurst,E
AU  - Louka,E
AU  - Rosser,E
AU  - Chalmers,E
AU  - Colby,E
AU  - Drewe,E
AU  - McDermott,E
AU  - Thomas,E
AU  - Staples,E
AU  - Clement,E
AU  - Matthews,E
AU  - Wakeling,E
AU  - Oksenhendler,E
AU  - Turro,E
AU  - Reid,E
AU  - Wassmer,E
AU  - Raymond,FL
AU  - Hu,F
AU  - Kennedy,F
AU  - Soubrier,F
AU  - Flinter,F
AU  - Kovacs,G
AU  - Polwarth,G
AU  - Ambegaonkar,G
AU  - Arno,G
AU  - Hudson,G
AU  - Woods,G
AU  - Coghlan,G
AU  - Hayman,G
AU  - Arumugakani,G
AU  - Schotte,G
AU  - Cook,HT
AU  - Alachkar,H
AU  - Allen,HL
AU  - Lango-Allen,H
AU  - Stark,H
AU  - Stauss,H
AU  - Schulze,H
AU  - Boggard,HJ
AU  - Baxendale,H
AU  - Dolling,H
AU  - Firth,H
AU  - Gall,H
AU  - Watson,H
AU  - Longhurst,H
AU  - Markus,HS
AU  - Watkins,H
AU  - Simeoni,I
AU  - Emmerson,I
AU  - Roberts,I
AU  - Quinti,I
AU  - Wanjiku,I
AU  - Gibbs,JSR
AU  - Thaventhiran,J
AU  - Whitworth,J
AU  - Hurst,J
AU  - Collins,J
AU  - Suntharalingam,J
AU  - Payne,J
AU  - Thachil,J
AU  - Martin,JM
AU  - Martin,J
AU  - Carmichael,J
AU  - Maimaris,J
AU  - Paterson,J
AU  - Pepke-Zaba,J
AU  - Heemskerk,JWM
AU  - Gebhart,J
AU  - Davis,J
AU  - Pasi,J
AU  - Bradley,JR
AU  - Wharton,J
AU  - Stephens,J
AU  - Rankin,J
AU  - Anderson,J
AU  - Vogt,J
AU  - von,Ziegenweldt J
AU  - Rehnstrom,K
AU  - Megy,K
AU  - Talks,K
AU  - Peerlinck,K
AU  - Yates,K
AU  - Freson,K
AU  - Stirrups,K
AU  - Gomez,K
AU  - Smith,KGC
AU  - Carss,K
AU  - Rue-Albrecht,K
AU  - Gilmour,K
AU  - Masati,L
AU  - Scelsi
DO  - 10.1038/s41598-017-14403-y
PY  - 2018///
SN  - 2045-2322
TI  - Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data
T2  - Scientific Reports
UR  - http://dx.doi.org/10.1038/s41598-017-14403-y
UR  - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000443479700003&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
UR  - http://hdl.handle.net/10044/1/64876
VL  - 8
ER  -

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