Meta-analysis of human genome-microbiome association studies: The MiBioGen consortium initiative

Jun Wang; Alexander Kurilshikov; Djawad Radjabzadeh; Williams Turpin; Kenneth Croitoru; Marc Jan Bonder; Matthew A. Jackson; Carolina Medina-Gomez; Fabian Frost; Georg Homuth; Malte Rühlemann; David Hughes; Han Na Kim; Tim D. Spector; Jordana T. Bell; Claire J. Steves; Nicolas Timpson; Andre Franke; Cisca Wijmenga; Katie Meyer; Tim Kacprowski; Lude Franke; Andrew D. Paterson; Jeroen Raes; Robert Kraaij; Alexandra Zhernakova; Tarun Ahluwalia; Elad Barkan; Larbi Bedrani; Hans Bisgaard; Michael Boehnke; Klaus Bønnelykke; Dorret I. Boomsma; Kenneth Croitoru; Gareth E. Davies; Eco de Geus; Frauke Degenhardt; Mauro D’amato; Erik A. Ehli; Osvaldo Espin-Garcia; Casey T. Finnicum; Myriam Fornage; Fabian Frost; Jingyuan Fu; Femke A. Heinsen; Georg Homuth; Richard Ijzerman; Matthew A. Jackson; Leon Eyrich Jessen; Daisy Jonkers; Tim Kacprowski; Hyung Lae Kim; Robert Kraaij; Markku Laakso; Lenore Launer; Markus M. Lerch; Kreete Lüll; Aldons J. Lusis; Massimo Mangino; Julia Mayerle; Hamdi Mbarek; Maria Carolina Medina; Katie Meyer; Karen L. Mohlke; Elin Org; Andrew Paterson; Haydeh Payami; Djawad Radjabzadeh; Jeroen Raes; Daphna Rothschild; Malte Rühle-Mann; Serena Sanna; Eran Segal; Shiraz Shah; Michelle Smith; Jakob Stokholm; Joanna W. Szopinska; Jonathan Thorsen; Nicolas Timpson; Williams Turpin; André G. Uit-Terlinden; Alejandro Arias Vasquez; Henry Völzke; Urmo Vosa; Zachary Wallen; Jun Wang; Frank Ulrich Weiss; Omer Weissbrod; Cisca Wijmenga; Gonneke Willemsen; Wei Xu; Yeojun Yun

doi:https://doi.org/10.1186/s40168-018-0479-3

Meta-analysis of human genome-microbiome association studies: The MiBioGen consortium initiative

Jun Wang, Alexander Kurilshikov, Djawad Radjabzadeh, Williams Turpin, Kenneth Croitoru, Marc Jan Bonder, Matthew A. Jackson, Carolina Medina-Gomez, Fabian Frost, Georg Homuth, Malte Rühlemann, David Hughes, Han Na Kim, Tim D. Spector, Jordana T. Bell, Claire J. Steves, Nicolas Timpson, Andre Franke, Cisca Wijmenga, Katie MeyerTim Kacprowski, Lude Franke, Andrew D. Paterson, Jeroen Raes, Robert Kraaij, Alexandra Zhernakova, Tarun Ahluwalia, Elad Barkan, Larbi Bedrani, Hans Bisgaard, Michael Boehnke, Klaus Bønnelykke, Dorret I. Boomsma, Kenneth Croitoru, Gareth E. Davies, Eco de Geus, Frauke Degenhardt, Mauro D’amato, Erik A. Ehli, Osvaldo Espin-Garcia, Casey T. Finnicum, Myriam Fornage, Fabian Frost, Jingyuan Fu, Femke A. Heinsen, Georg Homuth, Richard Ijzerman, Matthew A. Jackson, Leon Eyrich Jessen, Daisy Jonkers, Tim Kacprowski, Hyung Lae Kim, Robert Kraaij, Markku Laakso, Lenore Launer, Markus M. Lerch, Kreete Lüll, Aldons J. Lusis, Massimo Mangino, Julia Mayerle, Hamdi Mbarek, Maria Carolina Medina, Katie Meyer, Karen L. Mohlke, Elin Org, Andrew Paterson, Haydeh Payami, Djawad Radjabzadeh, Jeroen Raes, Daphna Rothschild, Malte Rühle-Mann, Serena Sanna, Eran Segal, Shiraz Shah, Michelle Smith, Jakob Stokholm, Joanna W. Szopinska, Jonathan Thorsen, Nicolas Timpson, Williams Turpin, André G. Uit-Terlinden, Alejandro Arias Vasquez, Henry Völzke, Urmo Vosa, Zachary Wallen, Jun Wang, Frank Ulrich Weiss, Omer Weissbrod, Cisca Wijmenga, Gonneke Willemsen, Wei Xu, Yeojun Yun

Department of Computer Science and Applied Mathematics

Weizmann Institute of Science

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

Abstract

Background: In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces underlying the observed variation, including the human genetic variants that shape human microbiota. Several preliminary genome-wide association studies (GWAS) have been completed, but more are necessary to achieve a fuller picture. Results: Here, we announce the MiBioGen consortium initiative, which has assembled 18 population-level cohorts and some 19,000 participants. Its aim is to generate new knowledge for the rapidly developing field of microbiota research. Each cohort has surveyed the gut microbiome via 16S rRNA sequencing and genotyped their participants with full-genome SNP arrays. We have standardized the analytical pipelines for both the microbiota phenotypes and genotypes, and all the data have been processed using identical approaches. Our analysis of microbiome composition shows that we can reduce the potential artifacts introduced by technical differences in generating microbiota data. We are now in the process of benchmarking the association tests and performing meta-analyses of genome-wide associations. All pipeline and summary statistics results will be shared using public data repositories. Conclusion: We present the largest consortium to date devoted to microbiota-GWAS. We have adapted our analytical pipelines to suit multi-cohort analyses and expect to gain insight into host-microbiota cross-talk at the genome-wide level. And, as an open consortium, we invite more cohorts to join us (by contacting one of the corresponding authors) and to follow the analytical pipeline we have developed.

Original language	English
Article number	101
Journal	Microbiome
Volume	6
Issue number	1
DOIs	https://doi.org/10.1186/s40168-018-0479-3
State	Published - 8 Jun 2018

All Science Journal Classification (ASJC) codes

Microbiology
Microbiology (medical)

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https://doi.org/10.1186/s40168-018-0479-3License: CC BY

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Wang, J., Kurilshikov, A., Radjabzadeh, D., Turpin, W., Croitoru, K., Bonder, M. J., Jackson, M. A., Medina-Gomez, C., Frost, F., Homuth, G., Rühlemann, M., Hughes, D., Kim, H. N., Spector, T. D., Bell, J. T., Steves, C. J., Timpson, N., Franke, A., Wijmenga, C., ... Yun, Y. (2018). Meta-analysis of human genome-microbiome association studies: The MiBioGen consortium initiative. Microbiome, 6(1), Article 101. https://doi.org/10.1186/s40168-018-0479-3

@article{39a1d61ff4494c2787035ec74927d064,

title = "Meta-analysis of human genome-microbiome association studies: The MiBioGen consortium initiative",

abstract = "Background: In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces underlying the observed variation, including the human genetic variants that shape human microbiota. Several preliminary genome-wide association studies (GWAS) have been completed, but more are necessary to achieve a fuller picture. Results: Here, we announce the MiBioGen consortium initiative, which has assembled 18 population-level cohorts and some 19,000 participants. Its aim is to generate new knowledge for the rapidly developing field of microbiota research. Each cohort has surveyed the gut microbiome via 16S rRNA sequencing and genotyped their participants with full-genome SNP arrays. We have standardized the analytical pipelines for both the microbiota phenotypes and genotypes, and all the data have been processed using identical approaches. Our analysis of microbiome composition shows that we can reduce the potential artifacts introduced by technical differences in generating microbiota data. We are now in the process of benchmarking the association tests and performing meta-analyses of genome-wide associations. All pipeline and summary statistics results will be shared using public data repositories. Conclusion: We present the largest consortium to date devoted to microbiota-GWAS. We have adapted our analytical pipelines to suit multi-cohort analyses and expect to gain insight into host-microbiota cross-talk at the genome-wide level. And, as an open consortium, we invite more cohorts to join us (by contacting one of the corresponding authors) and to follow the analytical pipeline we have developed.",

author = "Jun Wang and Alexander Kurilshikov and Djawad Radjabzadeh and Williams Turpin and Kenneth Croitoru and Bonder, {Marc Jan} and Jackson, {Matthew A.} and Carolina Medina-Gomez and Fabian Frost and Georg Homuth and Malte R{\"u}hlemann and David Hughes and Kim, {Han Na} and Spector, {Tim D.} and Bell, {Jordana T.} and Steves, {Claire J.} and Nicolas Timpson and Andre Franke and Cisca Wijmenga and Katie Meyer and Tim Kacprowski and Lude Franke and Paterson, {Andrew D.} and Jeroen Raes and Robert Kraaij and Alexandra Zhernakova and Tarun Ahluwalia and Elad Barkan and Larbi Bedrani and Hans Bisgaard and Michael Boehnke and Klaus B{\o}nnelykke and Boomsma, {Dorret I.} and Kenneth Croitoru and Davies, {Gareth E.} and Geus, {Eco de} and Frauke Degenhardt and Mauro D{\textquoteright}amato and Ehli, {Erik A.} and Osvaldo Espin-Garcia and Finnicum, {Casey T.} and Myriam Fornage and Fabian Frost and Jingyuan Fu and Heinsen, {Femke A.} and Georg Homuth and Richard Ijzerman and Jackson, {Matthew A.} and Jessen, {Leon Eyrich} and Daisy Jonkers and Tim Kacprowski and Kim, {Hyung Lae} and Robert Kraaij and Markku Laakso and Lenore Launer and Lerch, {Markus M.} and Kreete L{\"u}ll and Lusis, {Aldons J.} and Massimo Mangino and Julia Mayerle and Hamdi Mbarek and Medina, {Maria Carolina} and Katie Meyer and Mohlke, {Karen L.} and Elin Org and Andrew Paterson and Haydeh Payami and Djawad Radjabzadeh and Jeroen Raes and Daphna Rothschild and Malte R{\"u}hle-Mann and Serena Sanna and Eran Segal and Shiraz Shah and Michelle Smith and Jakob Stokholm and Szopinska, {Joanna W.} and Jonathan Thorsen and Nicolas Timpson and Williams Turpin and Uit-Terlinden, {Andr{\'e} G.} and Vasquez, {Alejandro Arias} and Henry V{\"o}lzke and Urmo Vosa and Zachary Wallen and Jun Wang and Weiss, {Frank Ulrich} and Omer Weissbrod and Cisca Wijmenga and Gonneke Willemsen and Wei Xu and Yeojun Yun",

note = "Publisher Copyright: {\textcopyright} 2018 The Author(s).",

year = "2018",

month = jun,

day = "8",

doi = "https://doi.org/10.1186/s40168-018-0479-3",

language = "الإنجليزيّة",

volume = "6",

journal = "Microbiome",

issn = "2049-2618",

publisher = "BioMed Central Ltd.",

number = "1",

}

Wang, J, Kurilshikov, A, Radjabzadeh, D, Turpin, W, Croitoru, K, Bonder, MJ, Jackson, MA, Medina-Gomez, C, Frost, F, Homuth, G, Rühlemann, M, Hughes, D, Kim, HN, Spector, TD, Bell, JT, Steves, CJ, Timpson, N, Franke, A, Wijmenga, C, Meyer, K, Kacprowski, T, Franke, L, Paterson, AD, Raes, J, Kraaij, R, Zhernakova, A, Ahluwalia, T, Barkan, E, Bedrani, L, Bisgaard, H, Boehnke, M, Bønnelykke, K, Boomsma, DI, Croitoru, K, Davies, GE, Geus, ED, Degenhardt, F, D’amato, M, Ehli, EA, Espin-Garcia, O, Finnicum, CT, Fornage, M, Frost, F, Fu, J, Heinsen, FA, Homuth, G, Ijzerman, R, Jackson, MA, Jessen, LE, Jonkers, D, Kacprowski, T, Kim, HL, Kraaij, R, Laakso, M, Launer, L, Lerch, MM, Lüll, K, Lusis, AJ, Mangino, M, Mayerle, J, Mbarek, H, Medina, MC, Meyer, K, Mohlke, KL, Org, E, Paterson, A, Payami, H, Radjabzadeh, D, Raes, J, Rothschild, D, Rühle-Mann, M, Sanna, S, Segal, E, Shah, S, Smith, M, Stokholm, J, Szopinska, JW, Thorsen, J, Timpson, N, Turpin, W, Uit-Terlinden, AG, Vasquez, AA, Völzke, H, Vosa, U, Wallen, Z, Wang, J, Weiss, FU, Weissbrod, O, Wijmenga, C, Willemsen, G, Xu, W & Yun, Y 2018, 'Meta-analysis of human genome-microbiome association studies: The MiBioGen consortium initiative', Microbiome, vol. 6, no. 1, 101. https://doi.org/10.1186/s40168-018-0479-3

TY - JOUR

T1 - Meta-analysis of human genome-microbiome association studies

T2 - The MiBioGen consortium initiative

AU - Wang, Jun

AU - Kurilshikov, Alexander

AU - Radjabzadeh, Djawad

AU - Turpin, Williams

AU - Croitoru, Kenneth

AU - Bonder, Marc Jan

AU - Jackson, Matthew A.

AU - Medina-Gomez, Carolina

AU - Frost, Fabian

AU - Homuth, Georg

AU - Rühlemann, Malte

AU - Hughes, David

AU - Kim, Han Na

AU - Spector, Tim D.

AU - Bell, Jordana T.

AU - Steves, Claire J.

AU - Timpson, Nicolas

AU - Franke, Andre

AU - Wijmenga, Cisca

AU - Meyer, Katie

AU - Kacprowski, Tim

AU - Franke, Lude

AU - Paterson, Andrew D.

AU - Raes, Jeroen

AU - Kraaij, Robert

AU - Zhernakova, Alexandra

AU - Ahluwalia, Tarun

AU - Barkan, Elad

AU - Bedrani, Larbi

AU - Bisgaard, Hans

AU - Boehnke, Michael

AU - Bønnelykke, Klaus

AU - Boomsma, Dorret I.

AU - Croitoru, Kenneth

AU - Davies, Gareth E.

AU - Geus, Eco de

AU - Degenhardt, Frauke

AU - D’amato, Mauro

AU - Ehli, Erik A.

AU - Espin-Garcia, Osvaldo

AU - Finnicum, Casey T.

AU - Fornage, Myriam

AU - Frost, Fabian

AU - Fu, Jingyuan

AU - Heinsen, Femke A.

AU - Homuth, Georg

AU - Ijzerman, Richard

AU - Jackson, Matthew A.

AU - Jessen, Leon Eyrich

AU - Jonkers, Daisy

AU - Kacprowski, Tim

AU - Kim, Hyung Lae

AU - Kraaij, Robert

AU - Laakso, Markku

AU - Launer, Lenore

AU - Lerch, Markus M.

AU - Lüll, Kreete

AU - Lusis, Aldons J.

AU - Mangino, Massimo

AU - Mayerle, Julia

AU - Mbarek, Hamdi

AU - Medina, Maria Carolina

AU - Meyer, Katie

AU - Mohlke, Karen L.

AU - Org, Elin

AU - Paterson, Andrew

AU - Payami, Haydeh

AU - Radjabzadeh, Djawad

AU - Raes, Jeroen

AU - Rothschild, Daphna

AU - Rühle-Mann, Malte

AU - Sanna, Serena

AU - Segal, Eran

AU - Shah, Shiraz

AU - Smith, Michelle

AU - Stokholm, Jakob

AU - Szopinska, Joanna W.

AU - Thorsen, Jonathan

AU - Timpson, Nicolas

AU - Turpin, Williams

AU - Uit-Terlinden, André G.

AU - Vasquez, Alejandro Arias

AU - Völzke, Henry

AU - Vosa, Urmo

AU - Wallen, Zachary

AU - Wang, Jun

AU - Weiss, Frank Ulrich

AU - Weissbrod, Omer

AU - Wijmenga, Cisca

AU - Willemsen, Gonneke

AU - Xu, Wei

AU - Yun, Yeojun

PY - 2018/6/8

Y1 - 2018/6/8

N2 - Background: In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces underlying the observed variation, including the human genetic variants that shape human microbiota. Several preliminary genome-wide association studies (GWAS) have been completed, but more are necessary to achieve a fuller picture. Results: Here, we announce the MiBioGen consortium initiative, which has assembled 18 population-level cohorts and some 19,000 participants. Its aim is to generate new knowledge for the rapidly developing field of microbiota research. Each cohort has surveyed the gut microbiome via 16S rRNA sequencing and genotyped their participants with full-genome SNP arrays. We have standardized the analytical pipelines for both the microbiota phenotypes and genotypes, and all the data have been processed using identical approaches. Our analysis of microbiome composition shows that we can reduce the potential artifacts introduced by technical differences in generating microbiota data. We are now in the process of benchmarking the association tests and performing meta-analyses of genome-wide associations. All pipeline and summary statistics results will be shared using public data repositories. Conclusion: We present the largest consortium to date devoted to microbiota-GWAS. We have adapted our analytical pipelines to suit multi-cohort analyses and expect to gain insight into host-microbiota cross-talk at the genome-wide level. And, as an open consortium, we invite more cohorts to join us (by contacting one of the corresponding authors) and to follow the analytical pipeline we have developed.

AB - Background: In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces underlying the observed variation, including the human genetic variants that shape human microbiota. Several preliminary genome-wide association studies (GWAS) have been completed, but more are necessary to achieve a fuller picture. Results: Here, we announce the MiBioGen consortium initiative, which has assembled 18 population-level cohorts and some 19,000 participants. Its aim is to generate new knowledge for the rapidly developing field of microbiota research. Each cohort has surveyed the gut microbiome via 16S rRNA sequencing and genotyped their participants with full-genome SNP arrays. We have standardized the analytical pipelines for both the microbiota phenotypes and genotypes, and all the data have been processed using identical approaches. Our analysis of microbiome composition shows that we can reduce the potential artifacts introduced by technical differences in generating microbiota data. We are now in the process of benchmarking the association tests and performing meta-analyses of genome-wide associations. All pipeline and summary statistics results will be shared using public data repositories. Conclusion: We present the largest consortium to date devoted to microbiota-GWAS. We have adapted our analytical pipelines to suit multi-cohort analyses and expect to gain insight into host-microbiota cross-talk at the genome-wide level. And, as an open consortium, we invite more cohorts to join us (by contacting one of the corresponding authors) and to follow the analytical pipeline we have developed.

UR - http://www.scopus.com/inward/record.url?scp=85048287255&partnerID=8YFLogxK

U2 - https://doi.org/10.1186/s40168-018-0479-3

DO - https://doi.org/10.1186/s40168-018-0479-3

M3 - مقالة

C2 - 29880062

SN - 2049-2618

VL - 6

JO - Microbiome

JF - Microbiome

IS - 1

M1 - 101

ER -

Meta-analysis of human genome-microbiome association studies: The MiBioGen consortium initiative

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