Erratum: Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay (Cell (2016) 165(6) (1519–1529)(S0092867416304214)(10.1016/j.cell.2016.04.027));Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay

Cell

Volumn 165, Issue 6, 2016, Pages 1519-1529

  Tewhey, Ryan ^a,b   Kotliar, Dylan ^a,b   Park, Daniel S ^b   Liu, Brandon ^b   Winnicki, Sarah ^b   Reilly, Steven K ^a,b   Andersen, Kristian G ^a,b   Mikkelsen, Tarjei S ^b   Lander, Eric S ^b   Schaffner, Stephen F ^b   Sabeti, Pardis C ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROSTAGLANDIN E RECEPTOR 4;

ALLELISM; ANKYLOSING SPONDYLITIS; ARTICLE; ASSAY; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HUMAN; MULTIPLEXED REPORTER ASSAY; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; ALLELE; EVALUATION STUDY; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC DISORDER; GENETIC PROCEDURES; GENETIC VARIATION; GENETICS; HEP-G2 CELL LINE; REPORTER GENE; SENSITIVITY AND SPECIFICITY;

ALLELES; GENE EXPRESSION REGULATION; GENE LIBRARY; GENES, REPORTER; GENETIC DISEASES, INBORN; GENETIC TECHNIQUES; GENETIC VARIATION; HEP G2 CELLS; HUMANS; QUANTITATIVE TRAIT LOCI; SENSITIVITY AND SPECIFICITY; SPONDYLITIS, ANKYLOSING;

EID: 84964272066     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2018.02.021     Document Type: Erratum

References (35)

1. G.R. Abecasis, A. Auton, L.D. Brooks, M.A. DePristo, R.M. Durbin, R.E. Handsaker, H.M. Kang, G.T. Marth, G.A. McVean 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes Nature 491 2012 56 65
2. R. Andersson, C. Gebhard, I. Miguel-Escalada, I. Hoof, J. Bornholdt, M. Boyd, Y. Chen, X. Zhao, C. Schmidl, T. Suzuki, et al. FANTOM Consortium An atlas of active enhancers across human cell types and tissues Nature 507 2014 455 461
3. C.D. Arnold, D. Gerlach, C. Stelzer, Ł.M. Boryń, M. Rath, and A. Stark Genome-wide quantitative enhancer activity maps identified by STARR-seq Science 339 2013 1074 1077
4. J.C. Barrett, S. Hansoul, D.L. Nicolae, J.H. Cho, R.H. Duerr, J.D. Rioux, S.R. Brant, M.S. Silverberg, K.D. Taylor, M.M. Barmada, et al. NIDDK IBD Genetics Consortium Belgian-French IBD Consortium Wellcome Trust Case Control Consortium Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease Nat. Genet. 40 2008 955 962
5. M. Claussnitzer, S.N. Dankel, K.-H.H. Kim, G. Quon, W. Meuleman, C. Haugen, V. Glunk, I.S. Sousa, J.L. Beaudry, V. Puviindran, and et al. FTO obesity variant circuitry and adipocyte browning in humans N. Engl. J. Med. 373 2015 895 907
6. G.M. Cooper, and J. Shendure Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data Nat. Rev. Genet. 12 2011 628 640
7. P.L. De Jager, X. Jia, J. Wang, P.I. de Bakker, L. Ottoboni, N.T. Aggarwal, L. Piccio, S. Raychaudhuri, D. Tran, C. Aubin, et al. International MS Genetics Consortium Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci Nat. Genet. 41 2009 776 782
8. T. Dubnicoff, S.A. Valentine, G. Chen, T. Shi, J.A. Lengyel, Z. Paroush, and A.J. Courey Conversion of dorsal from an activator to a repressor by the global corepressor Groucho Genes Dev. 11 1997 2952 2957
9. ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
10. D.M. Evans, C.C. Spencer, J.J. Pointon, Z. Su, D. Harvey, G. Kochan, U. Oppermann, A. Dilthey, M. Pirinen, M.A. Stone, et al. Spondyloarthritis Research Consortium of Canada (SPARCC) Australo-Anglo-American Spondyloarthritis Consortium (TASC) Wellcome Trust Case Control Consortium 2 (WTCCC2) Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility Nat. Genet. 43 2011 761 767
11. K.K. Farh, A. Marson, J. Zhu, M. Kleinewietfeld, W.J. Housley, S. Beik, N. Shoresh, H. Whitton, R.J. Ryan, A.A. Shishkin, and et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants Nature 518 2015 337 343
12. E. Gjoneska, A.R. Pfenning, H. Mathys, G. Quon, A. Kundaje, L.-H.H. Tsai, and M. Kellis Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease Nature 518 2015 365 369
13. R.R. Graham, C. Cotsapas, L. Davies, R. Hackett, C.J. Lessard, J.M. Leon, N.P. Burtt, C. Guiducci, M. Parkin, C. Gates, and et al. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus Nat. Genet. 40 2008 1059 1061
14. S.R. Grossman, K.G. Andersen, I. Shlyakhter, S. Tabrizi, S. Winnicki, A. Yen, D.J. Park, D. Griesemer, E.K. Karlsson, S.H. Wong, et al. 1000 Genomes Project Identifying recent adaptations in large-scale genomic data Cell 152 2013 703 713
15. J.M. Guthridge, R. Lu, H. Sun, C. Sun, G.B. Wiley, N. Dominguez, S.R. Macwana, C.J. Lessard, X. Kim-Howard, B.L. Cobb, and et al. Two functional lupus-associated BLK promoter variants control cell-type- and developmental-stage-specific transcription Am. J. Hum. Genet. 94 2014 586 598
16. M. Gymrek, T. Willems, A. Guilmatre, H. Zeng, B. Markus, S. Georgiev, M.J. Daly, A.L. Price, J.K. Pritchard, A.J. Sharp, and Y. Erlick Abundant contribution of short tandem repeats to gene expression variation in humans Nat. Genet. 48 2015 22 29
17. Y.T. Ip, R. Kraut, M. Levine, and C.A. Rushlow The dorsal morphogen is a sequence-specific DNA-binding protein that interacts with a long-range repression element in Drosophila Cell 64 1991 439 446
18. M. Kasowski, S. Kyriazopoulou-Panagiotopoulou, F. Grubert, J.B. Zaugg, A. Kundaje, Y. Liu, A.P. Boyle, Q.C. Zhang, F. Zakharia, D.V. Spacek, and et al. Extensive variation in chromatin states across humans Science 342 2013 750 752
19. P. Kheradpour, J. Ernst, A. Melnikov, P. Rogov, L. Wang, X. Zhang, J. Alston, T.S. Mikkelsen, and M. Kellis Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay Genome Res. 23 2013 800 811
20. J.C. Kwasnieski, C. Fiore, H.G. Chaudhari, and B.A. Cohen High-throughput functional testing of ENCODE segmentation predictions Genome Res. 24 2014 1595 1602
21. T. Lappalainen, M. Sammeth, M.R. Friedländer, P.A. 't Hoen, J. Monlong, M.A. Rivas, M. Gonzàlez-Porta, N. Kurbatova, T. Griebel, P.G. Ferreira, et al. Geuvadis Consortium Transcriptome and genome sequencing uncovers functional variation in humans Nature 501 2013 506 511
22. M.T. Maurano, R. Humbert, E. Rynes, R.E. Thurman, E. Haugen, H. Wang, A.P. Reynolds, R. Sandstrom, H. Qu, J. Brody, and et al. Systematic localization of common disease-associated variation in regulatory DNA Science 337 2012 1190 1195
23. G. McVicker, B. van de Geijn, J.F. Degner, C.E. Cain, N.E. Banovich, A. Raj, N. Lewellen, M. Myrthil, Y. Gilad, and J.K. Pritchard Identification of genetic variants that affect histone modifications in human cells Science 342 2013 747 749
24. A. Melnikov, A. Murugan, X. Zhang, T. Tesileanu, L. Wang, P. Rogov, S. Feizi, A. Gnirke Jr., C.G. Callan Jr., J.B. Kinney, and et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay Nat. Biotechnol. 30 2012 271 277
25. I. Mogno, J.C. Kwasnieski, and B.A. Cohen Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants Genome Res. 23 2013 1908 1915
26. K. Musunuru, A. Strong, M. Frank-Kamenetsky, N.E. Lee, T. Ahfeldt, K.V. Sachs, X. Li, H. Li, N. Kuperwasser, V.M. Ruda, and et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus Nature 466 2010 714 719
27. D.W. Ow, J.R. DE Wet, D.R. Helinski, S.H. Howell, K.V. Wood, and M. Deluca Transient and stable expression of the firefly luciferase gene in plant cells and transgenic plants Science 234 1986 856 859
28. S.C. Parker, M.L. Stitzel, D.L. Taylor, J.M. Orozco, M.R. Erdos, J.A. Akiyama, K.L. van Bueren, P.S. Chines, N. Narisu, B.L. Black, et al. NISC Comparative Sequencing Program National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program Authors NISC Comparative Sequencing Program Authors Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants Proc. Natl. Acad. Sci. USA 110 2013 17921 17926
29. R.P. Patwardhan, J.B. Hiatt, D.M. Witten, M.J. Kim, R.P. Smith, D. May, C. Lee, J.M. Andrie, S.-I. Lee, G.M. Cooper, and et al. Massively parallel functional dissection of mammalian enhancers in vivo Nat. Biotechnol. 30 2012 265 270
30. M.A. Schaub, A.P. Boyle, A. Kundaje, S. Batzoglou, and M. Snyder Linking disease associations with regulatory information in the human genome Genome Res. 22 2012 1748 1759
31. Y. Shi, E. Seto, L.S. Chang, and T. Shenk Transcriptional repression by YY1, a human GLI-Krüppel-related protein, and relief of repression by adenovirus E1A protein Cell 67 1991 377 388
32. S.A. Tishkoff, F.A. Reed, A. Ranciaro, B.F. Voight, C.C. Babbitt, J.S. Silverman, K. Powell, H.M. Mortensen, J.B. Hirbo, M. Osman, and et al. Convergent adaptation of human lactase persistence in Africa and Europe Nat. Genet. 39 2007 31 40
33. J.C. Ulirsch, S.K. Nandakumar, L. Wang, F.C. Giani, X. Zhang, P. Rogov, A. Melnikov, P. McDonel, R. Do, T.S. Mikkelsen, and V.G. Sankaran Systemic functional dissection of common genetic variation affecting red blood cell traits Cell 165 2016 1530 1545 this issue
34. J.-B.B. Veyrieras, S. Kudaravalli, S.Y. Kim, E.T. Dermitzakis, Y. Gilad, M. Stephens, and J.K. Pritchard High-resolution mapping of expression-QTLs yields insight into human gene regulation PLoS Genet. 4 2008 e1000214
35. C.M. Vockley, C. Guo, W.H. Majoros, M. Nodzenski, D.M. Scholtens, G.M. Hayes, W.L. Lowe, and T.E. Reddy Massively parallel quantification of the regulatory effects of non-coding genetic variation in a human cohort Genome Res. 25 2015 1432 1441 10.1101/gr.190090.115 Published online June 17, 2015