Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

Fiona Allum; Xiaojian Shao; Frédéric Guénard; Marie Michelle Simon; Stephan Busche; Maxime Caron; John Lambourne; Julie Lessard; Karolina Tandre; Åsa K. Hedman; Tony Kwan; Bing Ge; Lars Rönnblom; Mark I. McCarthy; Panos Deloukas; Todd Richmond; Daniel Burgess; Timothy D. Spector; André Tchernof; Simon Marceau; Mark Lathrop; Marie Claude Vohl; Tomi Pastinen; Elin Grundberg; Kourosh R. Ahmadi; Chrysanthi Ainali; Amy Barrett; Veronique Bataille; Jordana T. Bell; Alfonso Buil; Emmanouil T. Dermitzakis; Antigone S. Dimas; Richard Durbin; Daniel Glass; Neelam Hassanali; Catherine Ingle; David Knowles; Maria Krestyaninova; Cecilia M. Lindgren; Christopher E. Lowe; Eshwar Meduri; Paola Di Meglio; Josine L. Min; Stephen B. Montgomery; Frank O. Nestle; Alexandra C. Nica; James Nisbet; Stephen O'Rahilly; Leopold Parts; Simon Potter; Johanna Sandling; Magdalena Sekowska; So Youn Shin; Kerrin S. Small; Nicole Soranzo; Gabriela Surdulescu; Mary E. Travers; Loukia Tsaprouni; Sophia Tsoka; Alicja Wilk; Tsun Po Yang; Krina T. Zondervan

doi:10.1038/ncomms8211

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

Fiona Allum, Xiaojian Shao, Frédéric Guénard, Marie Michelle Simon, Stephan Busche, Maxime Caron, John Lambourne, Julie Lessard, Karolina Tandre, Åsa K. Hedman, Tony Kwan, Bing Ge, Lars Rönnblom, Mark I. McCarthy, Panos Deloukas, Todd Richmond, Daniel Burgess, Timothy D. Spector, André Tchernof, Simon MarceauMark Lathrop, Marie Claude Vohl, Tomi Pastinen, Elin Grundberg^*, Kourosh R. Ahmadi, Chrysanthi Ainali, Amy Barrett, Veronique Bataille, Jordana T. Bell, Alfonso Buil, Emmanouil T. Dermitzakis, Antigone S. Dimas, Richard Durbin, Daniel Glass, Neelam Hassanali, Catherine Ingle, David Knowles, Maria Krestyaninova, Cecilia M. Lindgren, Christopher E. Lowe, Eshwar Meduri, Paola Di Meglio, Josine L. Min, Stephen B. Montgomery, Frank O. Nestle, Alexandra C. Nica, James Nisbet, Stephen O'Rahilly, Leopold Parts, Simon Potter, Johanna Sandling, Magdalena Sekowska, So Youn Shin, Kerrin S. Small, Nicole Soranzo, Gabriela Surdulescu, Mary E. Travers, Loukia Tsaprouni, Sophia Tsoka, Alicja Wilk, Tsun Po Yang, Krina T. Zondervan

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

85 Citations (SciVal)

Original language	English
Article number	7211
Journal	Nature Communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms8211
Publication status	Published (VoR) - 29 May 2015

Funding

We thank J. Wendt (Roche NimbleGen) for useful input on the experiments. We also thank W. Cheung, M. Turgeon and C. Greenwood at McGill University for bioinformatics and statistical support. This work was supported by a Canadian Institute of Health Research (CIHR) team grant awarded to E.G., A.T., M.C.V. and M.L. (TEC-128093) and the CIHR funded Epigeneome Mapping Centre at McGill University (EP1-120608) awarded to T.P. and M.L., and the Swedish Research Council, Knut and Alice Wallenberg Foundation and the Torsten Söderberg Foundation awarded to L.R. F.A. holds studentship from The Research Institute of the McGill University Health Center (MUHC). F.G. is a recipient of a research fellowship award from the Heart and Stroke Foundation of Canada. A.T. is the director of a Research Chair in Bariatric and Metabolic Surgery. M.C.V. is the recipient of the Canada Research Chair in Genomics Applied to Nutrition and Health (Tier 1). E.G. and T.P. are recipients of a Canada Research Chair Tier 2 award. The MuTHER Study was funded by a programme grant from the Wellcome Trust (081917/Z/07/Z) and core funding for the Wellcome Trust Centre for Human Genetics (090532). TwinsUK was funded by the Wellcome Trust; European Community’s Seventh Framework Programme (FP7/2007-2013). The study also receives support from the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London. T.D.S. is a holder of an ERC Advanced Principal Investigator award. SNP genotyping was performed by The Wellcome Trust Sanger Institute and National Eye Institute via NIH/CIDR. Finally, we thank the NIH Roadmap Epigenomics Consortium and the Mapping Centers (http://nihroadmap.nih.gov/epigenomics/) for the production of publicly available reference epigenomes. Specifically, we thank the mapping centre at MGH/BROAD for generation of human adipose reference epigenomes used in this study.

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Allum, F., Shao, X., Guénard, F., Simon, M. M., Busche, S., Caron, M., Lambourne, J., Lessard, J., Tandre, K., Hedman, Å. K., Kwan, T., Ge, B., Rönnblom, L., McCarthy, M. I., Deloukas, P., Richmond, T., Burgess, D., Spector, T. D., Tchernof, A., ... Zondervan, K. T. (2015). Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nature Communications, 6, Article 7211. https://doi.org/10.1038/ncomms8211

@article{ebb7a5b1ca2f42cc9a055fa4f6ce94ad,

title = "Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants",

author = "Fiona Allum and Xiaojian Shao and Fr{\'e}d{\'e}ric Gu{\'e}nard and Simon, \{Marie Michelle\} and Stephan Busche and Maxime Caron and John Lambourne and Julie Lessard and Karolina Tandre and Hedman, \{{\AA}sa K.\} and Tony Kwan and Bing Ge and Lars R{\"o}nnblom and McCarthy, \{Mark I.\} and Panos Deloukas and Todd Richmond and Daniel Burgess and Spector, \{Timothy D.\} and Andr{\'e} Tchernof and Simon Marceau and Mark Lathrop and Vohl, \{Marie Claude\} and Tomi Pastinen and Elin Grundberg and Ahmadi, \{Kourosh R.\} and Chrysanthi Ainali and Amy Barrett and Veronique Bataille and Bell, \{Jordana T.\} and Alfonso Buil and Dermitzakis, \{Emmanouil T.\} and Dimas, \{Antigone S.\} and Richard Durbin and Daniel Glass and Neelam Hassanali and Catherine Ingle and David Knowles and Maria Krestyaninova and Lindgren, \{Cecilia M.\} and Lowe, \{Christopher E.\} and Eshwar Meduri and \{Di Meglio\}, Paola and Min, \{Josine L.\} and Montgomery, \{Stephen B.\} and Nestle, \{Frank O.\} and Nica, \{Alexandra C.\} and James Nisbet and Stephen O'Rahilly and Leopold Parts and Simon Potter and Johanna Sandling and Magdalena Sekowska and Shin, \{So Youn\} and Small, \{Kerrin S.\} and Nicole Soranzo and Gabriela Surdulescu and Travers, \{Mary E.\} and Loukia Tsaprouni and Sophia Tsoka and Alicja Wilk and Yang, \{Tsun Po\} and Zondervan, \{Krina T.\}",

note = "Funding Information: We thank J. Wendt (Roche NimbleGen) for useful input on the experiments. We also thank W. Cheung, M. Turgeon and C. Greenwood at McGill University for bioinformatics and statistical support. This work was supported by a Canadian Institute of Health Research (CIHR) team grant awarded to E.G., A.T., M.C.V. and M.L. (TEC-128093) and the CIHR funded Epigeneome Mapping Centre at McGill University (EP1-120608) awarded to T.P. and M.L., and the Swedish Research Council, Knut and Alice Wallenberg Foundation and the Torsten S{\"o}derberg Foundation awarded to L.R. F.A. holds studentship from The Research Institute of the McGill University Health Center (MUHC). F.G. is a recipient of a research fellowship award from the Heart and Stroke Foundation of Canada. A.T. is the director of a Research Chair in Bariatric and Metabolic Surgery. M.C.V. is the recipient of the Canada Research Chair in Genomics Applied to Nutrition and Health (Tier 1). E.G. and T.P. are recipients of a Canada Research Chair Tier 2 award. The MuTHER Study was funded by a programme grant from the Wellcome Trust (081917/Z/07/Z) and core funding for the Wellcome Trust Centre for Human Genetics (090532). TwinsUK was funded by the Wellcome Trust; European Community{\textquoteright}s Seventh Framework Programme (FP7/2007-2013). The study also receives support from the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy{\textquoteright}s and St Thomas{\textquoteright} NHS Foundation Trust in partnership with King{\textquoteright}s College London. T.D.S. is a holder of an ERC Advanced Principal Investigator award. SNP genotyping was performed by The Wellcome Trust Sanger Institute and National Eye Institute via NIH/CIDR. Finally, we thank the NIH Roadmap Epigenomics Consortium and the Mapping Centers (http://nihroadmap.nih.gov/epigenomics/) for the production of publicly available reference epigenomes. Specifically, we thank the mapping centre at MGH/BROAD for generation of human adipose reference epigenomes used in this study. Publisher Copyright: {\textcopyright} 2015 Macmillan Publishers Limited. All rights reserved.",

year = "2015",

month = may,

day = "29",

doi = "10.1038/ncomms8211",

language = "English",

volume = "6",

journal = "Nature Communications",

publisher = "Nature Research",

}

Allum, F, Shao, X, Guénard, F, Simon, MM, Busche, S, Caron, M, Lambourne, J, Lessard, J, Tandre, K, Hedman, ÅK, Kwan, T, Ge, B, Rönnblom, L, McCarthy, MI, Deloukas, P, Richmond, T, Burgess, D, Spector, TD, Tchernof, A, Marceau, S, Lathrop, M, Vohl, MC, Pastinen, T, Grundberg, E, Ahmadi, KR, Ainali, C, Barrett, A, Bataille, V, Bell, JT, Buil, A, Dermitzakis, ET, Dimas, AS, Durbin, R, Glass, D, Hassanali, N, Ingle, C, Knowles, D, Krestyaninova, M, Lindgren, CM, Lowe, CE, Meduri, E, Di Meglio, P, Min, JL, Montgomery, SB, Nestle, FO, Nica, AC, Nisbet, J, O'Rahilly, S, Parts, L, Potter, S, Sandling, J, Sekowska, M, Shin, SY, Small, KS, Soranzo, N, Surdulescu, G, Travers, ME, Tsaprouni, L, Tsoka, S, Wilk, A, Yang, TP & Zondervan, KT 2015, 'Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants', Nature Communications, vol. 6, 7211. https://doi.org/10.1038/ncomms8211

TY - JOUR

T1 - Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

AU - Allum, Fiona

AU - Shao, Xiaojian

AU - Guénard, Frédéric

AU - Simon, Marie Michelle

AU - Busche, Stephan

AU - Caron, Maxime

AU - Lambourne, John

AU - Lessard, Julie

AU - Tandre, Karolina

AU - Hedman, Åsa K.

AU - Kwan, Tony

AU - Ge, Bing

AU - Rönnblom, Lars

AU - McCarthy, Mark I.

AU - Deloukas, Panos

AU - Richmond, Todd

AU - Burgess, Daniel

AU - Spector, Timothy D.

AU - Tchernof, André

AU - Marceau, Simon

AU - Lathrop, Mark

AU - Vohl, Marie Claude

AU - Pastinen, Tomi

AU - Grundberg, Elin

AU - Ahmadi, Kourosh R.

AU - Ainali, Chrysanthi

AU - Barrett, Amy

AU - Bataille, Veronique

AU - Bell, Jordana T.

AU - Buil, Alfonso

AU - Dermitzakis, Emmanouil T.

AU - Dimas, Antigone S.

AU - Durbin, Richard

AU - Glass, Daniel

AU - Hassanali, Neelam

AU - Ingle, Catherine

AU - Knowles, David

AU - Krestyaninova, Maria

AU - Lindgren, Cecilia M.

AU - Lowe, Christopher E.

AU - Meduri, Eshwar

AU - Di Meglio, Paola

AU - Min, Josine L.

AU - Montgomery, Stephen B.

AU - Nestle, Frank O.

AU - Nica, Alexandra C.

AU - Nisbet, James

AU - O'Rahilly, Stephen

AU - Parts, Leopold

AU - Potter, Simon

AU - Sandling, Johanna

AU - Sekowska, Magdalena

AU - Shin, So Youn

AU - Small, Kerrin S.

AU - Soranzo, Nicole

AU - Surdulescu, Gabriela

AU - Travers, Mary E.

AU - Tsaprouni, Loukia

AU - Tsoka, Sophia

AU - Wilk, Alicja

AU - Yang, Tsun Po

AU - Zondervan, Krina T.

N1 - Funding Information: We thank J. Wendt (Roche NimbleGen) for useful input on the experiments. We also thank W. Cheung, M. Turgeon and C. Greenwood at McGill University for bioinformatics and statistical support. This work was supported by a Canadian Institute of Health Research (CIHR) team grant awarded to E.G., A.T., M.C.V. and M.L. (TEC-128093) and the CIHR funded Epigeneome Mapping Centre at McGill University (EP1-120608) awarded to T.P. and M.L., and the Swedish Research Council, Knut and Alice Wallenberg Foundation and the Torsten Söderberg Foundation awarded to L.R. F.A. holds studentship from The Research Institute of the McGill University Health Center (MUHC). F.G. is a recipient of a research fellowship award from the Heart and Stroke Foundation of Canada. A.T. is the director of a Research Chair in Bariatric and Metabolic Surgery. M.C.V. is the recipient of the Canada Research Chair in Genomics Applied to Nutrition and Health (Tier 1). E.G. and T.P. are recipients of a Canada Research Chair Tier 2 award. The MuTHER Study was funded by a programme grant from the Wellcome Trust (081917/Z/07/Z) and core funding for the Wellcome Trust Centre for Human Genetics (090532). TwinsUK was funded by the Wellcome Trust; European Community’s Seventh Framework Programme (FP7/2007-2013). The study also receives support from the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London. T.D.S. is a holder of an ERC Advanced Principal Investigator award. SNP genotyping was performed by The Wellcome Trust Sanger Institute and National Eye Institute via NIH/CIDR. Finally, we thank the NIH Roadmap Epigenomics Consortium and the Mapping Centers (http://nihroadmap.nih.gov/epigenomics/) for the production of publicly available reference epigenomes. Specifically, we thank the mapping centre at MGH/BROAD for generation of human adipose reference epigenomes used in this study. Publisher Copyright: © 2015 Macmillan Publishers Limited. All rights reserved.

PY - 2015/5/29

Y1 - 2015/5/29

UR - https://www.scopus.com/pages/publications/84931274676

UR - https://www.scopus.com/inward/citedby.url?scp=84931274676&partnerID=8YFLogxK

U2 - 10.1038/ncomms8211

DO - 10.1038/ncomms8211

M3 - Article

C2 - 26021296

AN - SCOPUS:84931274676

VL - 6

JO - Nature Communications

JF - Nature Communications

M1 - 7211

ER -

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

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