A vast resource of allelic expression data spanning human tissues

Stephane E. Castel; François Aguet; Pejman Mohammadi; François Aguet; Shankara Anand; Kristin G. Ardlie; Stacey Gabriel; Gad A. Getz; Aaron Graubert; Kane Hadley; Robert E. Handsaker; Katherine H. Huang; Seva Kashin; Xiao Li; Daniel G. MacArthur; Samuel R. Meier; Jared L. Nedzel; Duyen T. Nguyen; Ayellet V. Segrè; Ellen Todres; François Aguet; Shankara Anand; Kristin G. Ardlie; Brunilda Balliu; Alvaro N. Barbeira; Alexis Battle; Rodrigo Bonazzola; Andrew Brown; Christopher D. Brown; Stephane E. Castel; Donald F. Conrad; Daniel J. Cotter; Nancy Cox; Sayantan Das; Olivia M. De Goede; Emmanouil T. Dermitzakis; Jonah Einson; Barbara E. Engelhardt; Eleazar Eskin; Tiffany Y. Eulalio; Nicole M. Ferraro; Elise D. Flynn; Laure Fresard; Eric R. Gamazon; Diego Garrido-Martín; Nicole R. Gay; Gad A. Getz; Michael J. Gloudemans; Aaron Graubert; Roderic Guigó; Kane Hadley; Andrew R. Hame; Robert E. Handsaker; Yuan He; Paul J. Hoffman; Farhad Hormozdiari; Lei Hou; Katherine H. Huang; Hae Kyung Im; Brian Jo; Silva Kasela; Seva Kashin; Manolis Kellis; Sarah Kim-Hellmuth; Alan Kwong; Tuuli Lappalainen; Xiao Li; Xin Li; Yanyu Liang; Daniel G. MacArthur; Serghei Mangul; Samuel R. Meier; Pejman Mohammadi; Stephen B. Montgomery; Manuel Muñoz-Aguirre; Daniel C. Nachun; Jared L. Nedzel; Duyen T. Nguyen; Andrew B. Nobel; Meritxell Oliva; Yo Son Park; Yongjin Park; Princy Parsana; Abhiram S. Rao; Ferran Reverter; John M. Rouhana; Chiara Sabatti; Ashis Saha; Ayellet V. Segrè; Andrew D. Skol; Matthew Stephens; Barbara E. Stranger; Benjamin J. Strober; Nicole A. Teran; Ellen Todres; Ana Viñuela; Gao Wang; Xiaoquan Wen; Fred Wright; Valentin Wucher; Yuxin Zou; Pedro G. Ferreira; Gen Li; Marta Melé; Esti Yeger-Lotem; Mary E. Barcus; Debra Bradbury; Tanya Krubit; Jeffrey A. McLean; Liqun Qi; Karna Robinson; Nancy V. Roche; Anna M. Smith; Leslie Sobin; David E. Tabor; Anita Undale; Jason Bridge; Lori E. Brigham; Barbara A. Foster; Bryan M. Gillard; Richard Hasz; Marcus Hunter; Christopher Johns; Mark Johnson; Ellen Karasik; Gene Kopen; William F. Leinweber; Alisa McDonald; Michael T. Moser; Kevin Myer; Kimberley D. Ramsey; Brian Roe; Saboor Shad; Jeffrey A. Thomas; Gary Walters; Michael Washington; Joseph Wheeler; Scott D. Jewell; Daniel C. Rohrer; Dana R. Valley; David A. Davis; Deborah C. Mash; Mary E. Barcus; Philip A. Branton; Leslie Sobin; Laura K. Barker; Heather M. Gardiner; Maghboeba Mosavel; Laura A. Siminoff; Paul Flicek; Maximilian Haeussler; Thomas Juettemann; W. James Kent; Christopher M. Lee; Conner C. Powell; Kate R. Rosenbloom; Magali Ruffier; Dan Sheppard; Kieron Taylor; Stephen J. Trevanion; Daniel R. Zerbino; Nathan S. Abell; Joshua Akey; Lin Chen; Kathryn Demanelis; Jennifer A. Doherty; Andrew P. Feinberg; Kasper D. Hansen; Peter F. Hickey; Lei Hou; Farzana Jasmine; Lihua Jiang; Rajinder Kaul; Manolis Kellis; Muhammad G. Kibriya; Jin Billy Li; Qin Li; Shin Lin; Sandra E. Linder; Stephen B. Montgomery; Meritxell Oliva; Yongjin Park; Brandon L. Pierce; Lindsay F. Rizzardi; Andrew D. Skol; Kevin S. Smith; Michael Snyder; John Stamatoyannopoulos; Barbara E. Stranger; Hua Tang; Meng Wang; Philip A. Branton; Latarsha J. Carithers; Ping Guan; Susan E. Koester; A. Roger Little; Helen M. Moore; Concepcion R. Nierras; Abhi K. Rao; Jimmie B. Vaught; Simona Volpi; Kristin G. Ardlie; Tuuli Lappalainen

doi:10.1186/s13059-020-02122-z

A vast resource of allelic expression data spanning human tissues

Stephane E. Castel, François Aguet, Pejman Mohammadi, François Aguet, Shankara Anand, Kristin G. Ardlie, Stacey Gabriel, Gad A. Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen TodresFrançois Aguet, Shankara Anand, Kristin G. Ardlie, Brunilda Balliu, Alvaro N. Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Donald F. Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Olivia M. De Goede, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Elise D. Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Gad A. Getz, Michael J. Gloudemans, Aaron Graubert, Roderic Guigó, Kane Hadley, Andrew R. Hame, Robert E. Handsaker, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Katherine H. Huang, Hae Kyung Im, Brian Jo, Silva Kasela, Seva Kashin, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xiao Li, Xin Li, Yanyu Liang, Daniel G. MacArthur, Serghei Mangul, Samuel R. Meier, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel C. Nachun, Jared L. Nedzel, Duyen T. Nguyen, Andrew B. Nobel, Meritxell Oliva, Yo Son Park, Yongjin Park, Princy Parsana, Abhiram S. Rao, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Ayellet V. Segrè, Andrew D. Skol, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ellen Todres, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, Leslie Sobin, David E. Tabor, Anita Undale, Jason Bridge, Lori E. Brigham, Barbara A. Foster, Bryan M. Gillard, Richard Hasz, Marcus Hunter, Christopher Johns, Mark Johnson, Ellen Karasik, Gene Kopen, William F. Leinweber, Alisa McDonald, Michael T. Moser, Kevin Myer, Kimberley D. Ramsey, Brian Roe, Saboor Shad, Jeffrey A. Thomas, Gary Walters, Michael Washington, Joseph Wheeler, Scott D. Jewell, Daniel C. Rohrer, Dana R. Valley, David A. Davis, Deborah C. Mash, Mary E. Barcus, Philip A. Branton, Leslie Sobin, Laura K. Barker, Heather M. Gardiner, Maghboeba Mosavel, Laura A. Siminoff, Paul Flicek, Maximilian Haeussler, Thomas Juettemann, W. James Kent, Christopher M. Lee, Conner C. Powell, Kate R. Rosenbloom, Magali Ruffier, Dan Sheppard, Kieron Taylor, Stephen J. Trevanion, Daniel R. Zerbino, Nathan S. Abell, Joshua Akey, Lin Chen, Kathryn Demanelis, Jennifer A. Doherty, Andrew P. Feinberg, Kasper D. Hansen, Peter F. Hickey, Lei Hou, Farzana Jasmine, Lihua Jiang, Rajinder Kaul, Manolis Kellis, Muhammad G. Kibriya, Jin Billy Li, Qin Li, Shin Lin, Sandra E. Linder, Stephen B. Montgomery, Meritxell Oliva, Yongjin Park, Brandon L. Pierce, Lindsay F. Rizzardi, Andrew D. Skol, Kevin S. Smith, Michael Snyder, John Stamatoyannopoulos, Barbara E. Stranger, Hua Tang, Meng Wang, Philip A. Branton, Latarsha J. Carithers, Ping Guan, Susan E. Koester, A. Roger Little, Helen M. Moore, Concepcion R. Nierras, Abhi K. Rao, Jimmie B. Vaught, Simona Volpi, Kristin G. Ardlie, Tuuli Lappalainen

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

35 Scopus citations

Abstract

Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.

Original language	English (US)
Article number	234
Journal	Genome biology
Volume	21
Issue number	1
DOIs	https://doi.org/10.1186/s13059-020-02122-z
State	Published - Sep 11 2020

Keywords

ASE
Allelic expression
Functional genomics
GTEx
Genomics
Regulatory variation
eQTL

ASJC Scopus subject areas

Genetics
Ecology, Evolution, Behavior and Systematics
Cell Biology

Access to Document

10.1186/s13059-020-02122-z

Cite this

Castel, S. E., Aguet, F., Mohammadi, P., Aguet, F., Anand, S., Ardlie, K. G., Gabriel, S., Getz, G. A., Graubert, A., Hadley, K., Handsaker, R. E., Huang, K. H., Kashin, S., Li, X., MacArthur, D. G., Meier, S. R., Nedzel, J. L., Nguyen, D. T., Segrè, A. V., ... Lappalainen, T. (2020). A vast resource of allelic expression data spanning human tissues. Genome biology, 21(1), Article 234. https://doi.org/10.1186/s13059-020-02122-z

@article{093a1ec5f496425e8f930a519e4e1730,

title = "A vast resource of allelic expression data spanning human tissues",

abstract = "Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.",

keywords = "ASE, Allelic expression, Functional genomics, GTEx, Genomics, Regulatory variation, eQTL",

author = "Castel, {Stephane E.} and Fran{\c c}ois Aguet and Pejman Mohammadi and Fran{\c c}ois Aguet and Shankara Anand and Ardlie, {Kristin G.} and Stacey Gabriel and Getz, {Gad A.} and Aaron Graubert and Kane Hadley and Handsaker, {Robert E.} and Huang, {Katherine H.} and Seva Kashin and Xiao Li and MacArthur, {Daniel G.} and Meier, {Samuel R.} and Nedzel, {Jared L.} and Nguyen, {Duyen T.} and Segr{\`e}, {Ayellet V.} and Ellen Todres and Fran{\c c}ois Aguet and Shankara Anand and Ardlie, {Kristin G.} and Brunilda Balliu and Barbeira, {Alvaro N.} and Alexis Battle and Rodrigo Bonazzola and Andrew Brown and Brown, {Christopher D.} and Castel, {Stephane E.} and Conrad, {Donald F.} and Cotter, {Daniel J.} and Nancy Cox and Sayantan Das and {De Goede}, {Olivia M.} and Dermitzakis, {Emmanouil T.} and Jonah Einson and Engelhardt, {Barbara E.} and Eleazar Eskin and Eulalio, {Tiffany Y.} and Ferraro, {Nicole M.} and Flynn, {Elise D.} and Laure Fresard and Gamazon, {Eric R.} and Diego Garrido-Mart{\'i}n and Gay, {Nicole R.} and Getz, {Gad A.} and Gloudemans, {Michael J.} and Aaron Graubert and Roderic Guig{\'o} and Kane Hadley and Hame, {Andrew R.} and Handsaker, {Robert E.} and Yuan He and Hoffman, {Paul J.} and Farhad Hormozdiari and Lei Hou and Huang, {Katherine H.} and Im, {Hae Kyung} and Brian Jo and Silva Kasela and Seva Kashin and Manolis Kellis and Sarah Kim-Hellmuth and Alan Kwong and Tuuli Lappalainen and Xiao Li and Xin Li and Yanyu Liang and MacArthur, {Daniel G.} and Serghei Mangul and Meier, {Samuel R.} and Pejman Mohammadi and Montgomery, {Stephen B.} and Manuel Mu{\~n}oz-Aguirre and Nachun, {Daniel C.} and Nedzel, {Jared L.} and Nguyen, {Duyen T.} and Nobel, {Andrew B.} and Meritxell Oliva and Park, {Yo Son} and Yongjin Park and Princy Parsana and Rao, {Abhiram S.} and Ferran Reverter and Rouhana, {John M.} and Chiara Sabatti and Ashis Saha and Segr{\`e}, {Ayellet V.} and Skol, {Andrew D.} and Matthew Stephens and Stranger, {Barbara E.} and Strober, {Benjamin J.} and Teran, {Nicole A.} and Ellen Todres and Ana Vi{\~n}uela and Gao Wang and Xiaoquan Wen and Fred Wright and Valentin Wucher and Yuxin Zou and Ferreira, {Pedro G.} and Gen Li and Marta Mel{\'e} and Esti Yeger-Lotem and Barcus, {Mary E.} and Debra Bradbury and Tanya Krubit and McLean, {Jeffrey A.} and Liqun Qi and Karna Robinson and Roche, {Nancy V.} and Smith, {Anna M.} and Leslie Sobin and Tabor, {David E.} and Anita Undale and Jason Bridge and Brigham, {Lori E.} and Foster, {Barbara A.} and Gillard, {Bryan M.} and Richard Hasz and Marcus Hunter and Christopher Johns and Mark Johnson and Ellen Karasik and Gene Kopen and Leinweber, {William F.} and Alisa McDonald and Moser, {Michael T.} and Kevin Myer and Ramsey, {Kimberley D.} and Brian Roe and Saboor Shad and Thomas, {Jeffrey A.} and Gary Walters and Michael Washington and Joseph Wheeler and Jewell, {Scott D.} and Rohrer, {Daniel C.} and Valley, {Dana R.} and Davis, {David A.} and Mash, {Deborah C.} and Barcus, {Mary E.} and Branton, {Philip A.} and Leslie Sobin and Barker, {Laura K.} and Gardiner, {Heather M.} and Maghboeba Mosavel and Siminoff, {Laura A.} and Paul Flicek and Maximilian Haeussler and Thomas Juettemann and Kent, {W. James} and Lee, {Christopher M.} and Powell, {Conner C.} and Rosenbloom, {Kate R.} and Magali Ruffier and Dan Sheppard and Kieron Taylor and Trevanion, {Stephen J.} and Zerbino, {Daniel R.} and Abell, {Nathan S.} and Joshua Akey and Lin Chen and Kathryn Demanelis and Doherty, {Jennifer A.} and Feinberg, {Andrew P.} and Hansen, {Kasper D.} and Hickey, {Peter F.} and Lei Hou and Farzana Jasmine and Lihua Jiang and Rajinder Kaul and Manolis Kellis and Kibriya, {Muhammad G.} and Li, {Jin Billy} and Qin Li and Shin Lin and Linder, {Sandra E.} and Montgomery, {Stephen B.} and Meritxell Oliva and Yongjin Park and Pierce, {Brandon L.} and Rizzardi, {Lindsay F.} and Skol, {Andrew D.} and Smith, {Kevin S.} and Michael Snyder and John Stamatoyannopoulos and Stranger, {Barbara E.} and Hua Tang and Meng Wang and Branton, {Philip A.} and Carithers, {Latarsha J.} and Ping Guan and Koester, {Susan E.} and Little, {A. Roger} and Moore, {Helen M.} and Nierras, {Concepcion R.} and Rao, {Abhi K.} and Vaught, {Jimmie B.} and Simona Volpi and Ardlie, {Kristin G.} and Tuuli Lappalainen",

note = "Funding Information: The GTEx Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health (NIH) and by the National Cancer Institute (NCI), the National Human Genome Research Institute (NHGRI), the National Heart, Lung, and Blood Institute (NHLBI), the National Institute on Drug Abuse (NIDA), the National Institute of Mental Health (NIMH), and the National Institute of Neurological Disorders and Stroke (NINDS). S.E.C. was supported by NHGRI grant 1K99HG009916-01; T.L. and S.E.C. were supported by NIGMS grant R01GM122924 and NIMH grant R01MH101814; T.L. and S.E.C. were supported by NIH contract HHSN2682010000029C; T.L. was supported by NIMH grant R01MH106842 and NIH grants UM1HG008901 and 1U24DK112331. P.M. was supported by the NIH Center for Translational Science Award (CTSA) grants UL1TR002550-01 and 5UL1 TR001114-05. Publisher Copyright: {\textcopyright} 2020 The Author(s).",

year = "2020",

month = sep,

day = "11",

doi = "10.1186/s13059-020-02122-z",

language = "English (US)",

volume = "21",

journal = "Genome biology",

issn = "1474-7596",

publisher = "BioMed Central",

number = "1",

}

Castel, SE, Aguet, F, Mohammadi, P, Aguet, F, Anand, S, Ardlie, KG, Gabriel, S, Getz, GA, Graubert, A, Hadley, K, Handsaker, RE, Huang, KH, Kashin, S, Li, X, MacArthur, DG, Meier, SR, Nedzel, JL, Nguyen, DT, Segrè, AV, Todres, E, Aguet, F, Anand, S, Ardlie, KG, Balliu, B, Barbeira, AN, Battle, A, Bonazzola, R, Brown, A, Brown, CD, Castel, SE, Conrad, DF, Cotter, DJ, Cox, N, Das, S, De Goede, OM, Dermitzakis, ET, Einson, J, Engelhardt, BE, Eskin, E, Eulalio, TY, Ferraro, NM, Flynn, ED, Fresard, L, Gamazon, ER, Garrido-Martín, D, Gay, NR, Getz, GA, Gloudemans, MJ, Graubert, A, Guigó, R, Hadley, K, Hame, AR, Handsaker, RE, He, Y, Hoffman, PJ, Hormozdiari, F, Hou, L, Huang, KH, Im, HK, Jo, B, Kasela, S, Kashin, S, Kellis, M, Kim-Hellmuth, S, Kwong, A, Lappalainen, T, Li, X, Li, X, Liang, Y, MacArthur, DG, Mangul, S, Meier, SR, Mohammadi, P, Montgomery, SB, Muñoz-Aguirre, M, Nachun, DC, Nedzel, JL, Nguyen, DT, Nobel, AB, Oliva, M, Park, YS, Park, Y, Parsana, P, Rao, AS, Reverter, F, Rouhana, JM, Sabatti, C, Saha, A, Segrè, AV, Skol, AD, Stephens, M, Stranger, BE, Strober, BJ, Teran, NA, Todres, E, Viñuela, A, Wang, G, Wen, X, Wright, F, Wucher, V, Zou, Y, Ferreira, PG, Li, G, Melé, M, Yeger-Lotem, E, Barcus, ME, Bradbury, D, Krubit, T, McLean, JA, Qi, L, Robinson, K, Roche, NV, Smith, AM, Sobin, L, Tabor, DE, Undale, A, Bridge, J, Brigham, LE, Foster, BA, Gillard, BM, Hasz, R, Hunter, M, Johns, C, Johnson, M, Karasik, E, Kopen, G, Leinweber, WF, McDonald, A, Moser, MT, Myer, K, Ramsey, KD, Roe, B, Shad, S, Thomas, JA, Walters, G, Washington, M, Wheeler, J, Jewell, SD, Rohrer, DC, Valley, DR, Davis, DA, Mash, DC, Barcus, ME, Branton, PA, Sobin, L, Barker, LK, Gardiner, HM, Mosavel, M, Siminoff, LA, Flicek, P, Haeussler, M, Juettemann, T, Kent, WJ, Lee, CM, Powell, CC, Rosenbloom, KR, Ruffier, M, Sheppard, D, Taylor, K, Trevanion, SJ, Zerbino, DR, Abell, NS, Akey, J, Chen, L, Demanelis, K, Doherty, JA, Feinberg, AP, Hansen, KD, Hickey, PF, Hou, L, Jasmine, F, Jiang, L, Kaul, R, Kellis, M, Kibriya, MG, Li, JB, Li, Q, Lin, S, Linder, SE, Montgomery, SB, Oliva, M, Park, Y, Pierce, BL, Rizzardi, LF, Skol, AD, Smith, KS, Snyder, M, Stamatoyannopoulos, J, Stranger, BE, Tang, H, Wang, M, Branton, PA, Carithers, LJ, Guan, P, Koester, SE, Little, AR, Moore, HM, Nierras, CR, Rao, AK, Vaught, JB, Volpi, S, Ardlie, KG & Lappalainen, T 2020, 'A vast resource of allelic expression data spanning human tissues', Genome biology, vol. 21, no. 1, 234. https://doi.org/10.1186/s13059-020-02122-z

TY - JOUR

T1 - A vast resource of allelic expression data spanning human tissues

AU - Castel, Stephane E.

AU - Aguet, François

AU - Mohammadi, Pejman

AU - Aguet, François

AU - Anand, Shankara

AU - Ardlie, Kristin G.

AU - Gabriel, Stacey

AU - Getz, Gad A.

AU - Graubert, Aaron

AU - Hadley, Kane

AU - Handsaker, Robert E.

AU - Huang, Katherine H.

AU - Kashin, Seva

AU - Li, Xiao

AU - MacArthur, Daniel G.

AU - Meier, Samuel R.

AU - Nedzel, Jared L.

AU - Nguyen, Duyen T.

AU - Segrè, Ayellet V.

AU - Todres, Ellen

AU - Aguet, François

AU - Anand, Shankara

AU - Ardlie, Kristin G.

AU - Balliu, Brunilda

AU - Barbeira, Alvaro N.

AU - Battle, Alexis

AU - Bonazzola, Rodrigo

AU - Brown, Andrew

AU - Brown, Christopher D.

AU - Castel, Stephane E.

AU - Conrad, Donald F.

AU - Cotter, Daniel J.

AU - Cox, Nancy

AU - Das, Sayantan

AU - De Goede, Olivia M.

AU - Dermitzakis, Emmanouil T.

AU - Einson, Jonah

AU - Engelhardt, Barbara E.

AU - Eskin, Eleazar

AU - Eulalio, Tiffany Y.

AU - Ferraro, Nicole M.

AU - Flynn, Elise D.

AU - Fresard, Laure

AU - Gamazon, Eric R.

AU - Garrido-Martín, Diego

AU - Gay, Nicole R.

AU - Getz, Gad A.

AU - Gloudemans, Michael J.

AU - Graubert, Aaron

AU - Guigó, Roderic

AU - Hadley, Kane

AU - Hame, Andrew R.

AU - Handsaker, Robert E.

AU - He, Yuan

AU - Hoffman, Paul J.

AU - Hormozdiari, Farhad

AU - Hou, Lei

AU - Huang, Katherine H.

AU - Im, Hae Kyung

AU - Jo, Brian

AU - Kasela, Silva

AU - Kashin, Seva

AU - Kellis, Manolis

AU - Kim-Hellmuth, Sarah

AU - Kwong, Alan

AU - Lappalainen, Tuuli

AU - Li, Xiao

AU - Li, Xin

AU - Liang, Yanyu

AU - MacArthur, Daniel G.

AU - Mangul, Serghei

AU - Meier, Samuel R.

AU - Mohammadi, Pejman

AU - Montgomery, Stephen B.

AU - Muñoz-Aguirre, Manuel

AU - Nachun, Daniel C.

AU - Nedzel, Jared L.

AU - Nguyen, Duyen T.

AU - Nobel, Andrew B.

AU - Oliva, Meritxell

AU - Park, Yo Son

AU - Park, Yongjin

AU - Parsana, Princy

AU - Rao, Abhiram S.

AU - Reverter, Ferran

AU - Rouhana, John M.

AU - Sabatti, Chiara

AU - Saha, Ashis

AU - Segrè, Ayellet V.

AU - Skol, Andrew D.

AU - Stephens, Matthew

AU - Stranger, Barbara E.

AU - Strober, Benjamin J.

AU - Teran, Nicole A.

AU - Todres, Ellen

AU - Viñuela, Ana

AU - Wang, Gao

AU - Wen, Xiaoquan

AU - Wright, Fred

AU - Wucher, Valentin

AU - Zou, Yuxin

AU - Ferreira, Pedro G.

AU - Li, Gen

AU - Melé, Marta

AU - Yeger-Lotem, Esti

AU - Barcus, Mary E.

AU - Bradbury, Debra

AU - Krubit, Tanya

AU - McLean, Jeffrey A.

AU - Qi, Liqun

AU - Robinson, Karna

AU - Roche, Nancy V.

AU - Smith, Anna M.

AU - Sobin, Leslie

AU - Tabor, David E.

AU - Undale, Anita

AU - Bridge, Jason

AU - Brigham, Lori E.

AU - Foster, Barbara A.

AU - Gillard, Bryan M.

AU - Hasz, Richard

AU - Hunter, Marcus

AU - Johns, Christopher

AU - Johnson, Mark

AU - Karasik, Ellen

AU - Kopen, Gene

AU - Leinweber, William F.

AU - McDonald, Alisa

AU - Moser, Michael T.

AU - Myer, Kevin

AU - Ramsey, Kimberley D.

AU - Roe, Brian

AU - Shad, Saboor

AU - Thomas, Jeffrey A.

AU - Walters, Gary

AU - Washington, Michael

AU - Wheeler, Joseph

AU - Jewell, Scott D.

AU - Rohrer, Daniel C.

AU - Valley, Dana R.

AU - Davis, David A.

AU - Mash, Deborah C.

AU - Barcus, Mary E.

AU - Branton, Philip A.

AU - Sobin, Leslie

AU - Barker, Laura K.

AU - Gardiner, Heather M.

AU - Mosavel, Maghboeba

AU - Siminoff, Laura A.

AU - Flicek, Paul

AU - Haeussler, Maximilian

AU - Juettemann, Thomas

AU - Kent, W. James

AU - Lee, Christopher M.

AU - Powell, Conner C.

AU - Rosenbloom, Kate R.

AU - Ruffier, Magali

AU - Sheppard, Dan

AU - Taylor, Kieron

AU - Trevanion, Stephen J.

AU - Zerbino, Daniel R.

AU - Abell, Nathan S.

AU - Akey, Joshua

AU - Chen, Lin

AU - Demanelis, Kathryn

AU - Doherty, Jennifer A.

AU - Feinberg, Andrew P.

AU - Hansen, Kasper D.

AU - Hickey, Peter F.

AU - Hou, Lei

AU - Jasmine, Farzana

AU - Jiang, Lihua

AU - Kaul, Rajinder

AU - Kellis, Manolis

AU - Kibriya, Muhammad G.

AU - Li, Jin Billy

AU - Li, Qin

AU - Lin, Shin

AU - Linder, Sandra E.

AU - Montgomery, Stephen B.

AU - Oliva, Meritxell

AU - Park, Yongjin

AU - Pierce, Brandon L.

AU - Rizzardi, Lindsay F.

AU - Skol, Andrew D.

AU - Smith, Kevin S.

AU - Snyder, Michael

AU - Stamatoyannopoulos, John

AU - Stranger, Barbara E.

AU - Tang, Hua

AU - Wang, Meng

AU - Branton, Philip A.

AU - Carithers, Latarsha J.

AU - Guan, Ping

AU - Koester, Susan E.

AU - Little, A. Roger

AU - Moore, Helen M.

AU - Nierras, Concepcion R.

AU - Rao, Abhi K.

AU - Vaught, Jimmie B.

AU - Volpi, Simona

AU - Ardlie, Kristin G.

AU - Lappalainen, Tuuli

N1 - Funding Information: The GTEx Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health (NIH) and by the National Cancer Institute (NCI), the National Human Genome Research Institute (NHGRI), the National Heart, Lung, and Blood Institute (NHLBI), the National Institute on Drug Abuse (NIDA), the National Institute of Mental Health (NIMH), and the National Institute of Neurological Disorders and Stroke (NINDS). S.E.C. was supported by NHGRI grant 1K99HG009916-01; T.L. and S.E.C. were supported by NIGMS grant R01GM122924 and NIMH grant R01MH101814; T.L. and S.E.C. were supported by NIH contract HHSN2682010000029C; T.L. was supported by NIMH grant R01MH106842 and NIH grants UM1HG008901 and 1U24DK112331. P.M. was supported by the NIH Center for Translational Science Award (CTSA) grants UL1TR002550-01 and 5UL1 TR001114-05. Publisher Copyright: © 2020 The Author(s).

PY - 2020/9/11

Y1 - 2020/9/11

N2 - Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.

AB - Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.

KW - ASE

KW - Allelic expression

KW - Functional genomics

KW - GTEx

KW - Genomics

KW - Regulatory variation

KW - eQTL

UR - http://www.scopus.com/inward/record.url?scp=85090821242&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85090821242&partnerID=8YFLogxK

U2 - 10.1186/s13059-020-02122-z

DO - 10.1186/s13059-020-02122-z

M3 - Article

C2 - 32912332

AN - SCOPUS:85090821242

SN - 1474-7596

VL - 21

JO - Genome biology

JF - Genome biology

IS - 1

M1 - 234

ER -

A vast resource of allelic expression data spanning human tissues

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