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1. Erratum to: Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps (Nature Genetics, (2016), 48, 11, (1303-1312), 10.1038/ng.3668)

Author

Iotchkova, V., Huang, J., Morris, J. A., Jain, D., Barbieri, C., Ukovich, Walter, Min, J. L., Chen, L., Astle, W., Cocca, M., Deelen, P., Elding, H., Farmaki, A. -E., Franklin, C. S., Franberg, M., Gaunt, T. R., Hofman, A., Jiang, T., Kleber, M. E., Lachance, G., Luan, J., Malerba, G., Matchan, A., Mead, D., Memari, Y., Ntalla, I., Panoutsopoulou, K., Pazoki, R., Perry, J. R. B., Rivadeneira, F., Sabater-Lleal, M., Sennblad, B., Shin, S. -Y., Southam, L., Traglia, M., van Dijk, F., van Leeuwen, E. M., Zaza, G., Zhang, W., Amin, N., Butterworth, A., Chambers, J. C., Dedoussis, G., Dehghan, A., Franco, O. H., Franke, L., Frontini, M., Gambaro, G., Gasparini, P., Hamsten, A., Isaacs, A., Kooner, J. S., Kooperberg, C., Langenberg, C., Marz, W., Scott, R. A., Swertz, M. A., Toniolo, D., Uitterlinden, A. G., van Duijn, C. M., Watkins, H., Zeggini, E., Maurano, M. T., Timpson, N. J., Reiner, A. P., Auer, P. L., Soranzo, N., Iotchkova, V., Huang, J., Morris, J. A., Jain, D., Barbieri, C., Ukovich, Walter, Min, J. L., Chen, L., Astle, W., Cocca, M., Deelen, P., Elding, H., Farmaki, A. -E., Franklin, C. S., Franberg, M., Gaunt, T. R., Hofman, A., Jiang, T., Kleber, M. E., Lachance, G., Luan, J., Malerba, G., Matchan, A., Mead, D., Memari, Y., Ntalla, I., Panoutsopoulou, K., Pazoki, R., Perry, J. R. B., Rivadeneira, F., Sabater-Lleal, M., Sennblad, B., Shin, S. -Y., Southam, L., Traglia, M., van Dijk, F., van Leeuwen, E. M., Zaza, G., Zhang, W., Amin, N., Butterworth, A., Chambers, J. C., Dedoussis, G., Dehghan, A., Franco, O. H., Franke, L., Frontini, M., Gambaro, G., Gasparini, P., Hamsten, A., Isaacs, A., Kooner, J. S., Kooperberg, C., Langenberg, C., Marz, W., Scott, R. A., Swertz, M. A., Toniolo, D., Uitterlinden, A. G., van Duijn, C. M., Watkins, H., Zeggini, E., Maurano, M. T., Timpson, N. J., Reiner, A. P., Auer, P. L., and Soranzo, N.

Subjects
Author correction
Abstract

In the version of the article published, the surname of author Aaron Isaacs is misspelled as Issacs.

Published
2018

2. A Simplified Approach for Prosthetic Rehabilitation of an Anophtalmic Patient with Chronic Mucoid Discharge Using a Previous Ocular Prosthesis

Author

Memari Y, Fayaz A, and Tadayonfard A

Subjects
lcsh:RK1-715, lcsh:R5-920, genetic structures, Maxillofacial Prosthesis, lcsh:Dentistry, Prosthetic Eye, Custom Ocular Prosthesis, sense organs, lcsh:Medicine (General), eye diseases, Impression
Abstract

The defects of eye, whatever the cause, are associated with significant anatomical deficiency and emotional and psychological disturbance for affected patients. Defect size may range from a small enucleation defect to an extensive exenterated one affecting eye and surrounding soft and hard tissues in maxillofacial complex. A properly fabricated custom ocular or orbital prosthesis could give the patient an optimal normalcy in social and psychological as well as functional aspects. A 68-year-old male patient presented with an enucleation defect in the left eye. After clinical examination, an impression was taken with additional silicon elastomeric impression material using patient’s previous prosthesis as a custom tray. Then, the scleral blank was made from wax and the Iris was attached to it. The external clear acrylic resin was packed and processed. The prosthesis was polished and delivered to patient. Modifying and converting a previously fabricated ocular prosthesis into a newly fabricated well-fitting custom ocular prosthesis can help minimizing clinical adjustments and simplifying laboratory procedures.

Published
2017

3. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Author

Haworth, S, Shapland, CY, Hayward, C, Prins, BP, Felix, JF, Medina-Gomez, C, Rivadeneira, F, Wang, C, Ahluwalia, TS, Vrijheid, M, Guxens, M, Sunyer, J, Tachmazidou, I, Walter, K, Iotchkova, V, Jackson, A, Cleal, L, Huffmann, J, Min, JL, Sass, L, Timmers, PRHJ, Al Turki, S, Anderson, CA, Anney, R, Antony, D, Artigas, MS, Ayub, M, Bala, S, Barrett, JC, Barroso, I, Beales, P, Bentham, J, Bhattacharya, S, Birney, E, Blackwood, D, Bobrow, M, Bochukova, E, Bolton, PF, Bounds, R, Boustred, C, Breen, G, Calissano, M, Carss, K, Charlton, R, Chatterjee, K, Chen, L, Ciampi, A, Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, DA, Cosgrove, C, Cox, T, Craddock, N, Crooks, L, Curran, S, Curtis, D, Daly, A, Danecek, P, Day, INM, Day-Williams, A, Dominiczak, A, Down, T, Du, Y, Dunham, I, Durbin, R, Edkins, S, Ekong, R, Ellis, P, Evans, DM, Farooqi, IS, Fitzpatrick, DR, Flicek, P, Floyd, J, Foley, AR, Franklin, CS, Futema, M, Gallagher, L, Gaunt, TR, Geihs, M, Geschwind, D, Greenwood, CMT, Griffin, H, Grozeva, D, Guo, X, Gurling, H, Hart, D, Hendricks, AE, Holmans, P, Howie, B, Huang, J, Huang, L, Hubbard, T, Humphries, SE, Hurles, ME, Hysi, P, Jackson, DK, Jamshidi, Y, Joyce, C, Karczewski, KJ, Kaye, J, Keane, T, Kemp, JP, Kennedy, K, Kent, A, Keogh, J, Khawaja, F, van Kogelenberg, M, Kolb-Kokocinski, A, Lachance, G, Langford, C, Lawson, D, Lee, I, Lek, M, Li, R, Li, Y, Liang, J, Lin, H, Liu, R, Lonnqvist, J, Lopes, LR, Lopes, M, MacArthur, DG, Mangino, M, Marchini, J, Marenne, G, Maslen, J, Mathieson, I, McCarthy, S, McGuffin, P, McIntosh, AM, McKechanie, AG, McQuillin, A, Memari, Y, Metrustry, S, Migone, N, Mitchison, HM, Moayyeri, A, Morris, A, Morris, J, Muddyman, D, Muntoni, F, Northstone, K, O'Donovan, MC, O'Rahilly, S, Onoufriadis, A, Oualkacha, K, Owen, MJ, Palotie, A, Panoutsopoulou, K, Parker, V, Parr, JR, Paternoster, L, Paunio, T, Payne, F, Payne, SJ, Perry, JRB, Pietilainen, O, Plagnol, V, Pollitt, RC, Porteous, DJ, Povey, S, Quail, MA, Quaye, L, Raymond, FL, Rehnstrom, K, Richards, JB, Ridout, CK, Ring, S, Ritchie, GRS, Roberts, N, Robinson, RL, Savage, DB, Scambler, P, Schiffels, S, Schmidts, M, Schoenmakers, N, Scott, RH, Semple, RK, Serra, E, Sharp, SI, Shaw, A, Shihab, HA, Shin, S-Y, Skuse, D, Small, KS, Smee, C, Smith, BH, Soranzo, N, Southam, L, Spasic-Boskovic, O, Spector, TD, St Clair, D, Stalker, J, Stevens, E, Sun, J, Surdulescu, G, Suvisaari, J, Syrris, P, Taylor, R, Tian, J, Tobin, MD, Valdes, AM, Vandersteen, AM, Vijayarangakannan, P, Visscher, PM, Wain, LV, Walters, JTR, Wang, G, Wang, J, Wang, Y, Ward, K, Wheeler, E, Whyte, T, Williams, HJ, Williamson, KA, Wilson, C, Wilson, SG, Wong, K, Xu, C, Yang, J, Zhang, F, Zhang, P, Zheng, H-F, Smith, GD, Fisher, SE, Wilson, JF, Cole, TJ, Fernandez-Orth, D, Bonnelykke, K, Bisgaard, H, Pennell, CE, Jaddoe, VWV, Dedoussis, G, Timpson, N, Zeggini, E, Vitart, V, St Pourcain, B, UK10K Consortium, Epidemiology, Erasmus MC other, Pediatrics, Internal Medicine, and Child and Adolescent Psychiatry / Psychology

Abstract

Cranial growth and development is a complex process which affects the closely related traits of head circumference (HC) and intracranial volume (ICV). The underlying genetic influences shaping these traits during the transition from childhood to adulthood are little understood, but might include both age-specific genetic factors and low-frequency genetic variation. Here, we model the developmental genetic architecture of HC, showing this is genetically stable and correlated with genetic determinants of ICV. Investigating up to 46,000 children and adults of European descent, we identify association with final HC and/or final ICV + HC at 9 novel common and low-frequency loci, illustrating that genetic variation from a wide allele frequency spectrum contributes to cranial growth. The largest effects are reported for low-frequency variants within TP53, with 0.5 cm wider heads in increaser-allele carriers versus non-carriers during mid-childhood, suggesting a previously unrecognized role of TP53 transcripts in human cranial development.

Published
2019

4. Homozygous loss-of-function variants in European cosmopolitan and isolate populations

Author

Kaiser, V.B., Svinti, V., Prendergast, J.G., Chau, Y.Y., Campbell, A., Patarcic, I., Barroso, I., Joshi, P.K., Hastie, N.D., Miljkovic, A., Taylor, M.S., Enroth, S., Memari, Y., Kolb-Kokocinski, A., Wright, A.F., Gyllensten, U., Durbin, R., Rudan, I., Campbell, H., Polašek, O., Johansson, A., Sauer, S., Porteous, D.J., Fraser, R.M., Drake, C., Vitart, V., Hayward, C., Semple, C.A., and Wilson, J.F.

Subjects
Phenotype, Gene Frequency, Homozygote, Mutation, Humans, Exome, Original Articles, Technology Platforms, Selection, Genetic, White People
Abstract

Homozygous Loss of Function (HLOF) variants provide a valuable window on gene function in humans, as well as an inventory of the human genes that are not essential for survival and reproduction. All humans carry at least a few HLOF variants, but the exact number of inactivated genes that can be tolerated is currently unknown - as are the phenotypic effects of losing function for most human genes. Here, we make use of 1,432 whole exome sequences from five European populations to expand the catalogue of known human HLOF mutations; after stringent filtering of variants in our dataset, we identify a total of 173 HLOF mutations, 76 (44%) of which have not been observed previously. We find that population isolates are particularly well suited to surveys of novel HLOF genes because individuals in such populations carry extensive runs of homozygosity, which we show are enriched for novel, rare HLOF variants. Further, we make use of extensive phenotypic data to show that most HLOFs, ascertained in population-based samples, appear to have little detectable effect on the phenotype. On the contrary, we document several genes directly implicated in disease that seem to tolerate HLOF variants. Overall HLOF genes are enriched for olfactory receptor function and are expressed in testes more often than expected, consistent with reduced purifying selection and incipient pseudogenisation.

Published
2015

5. Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity

Author

Hendricks, A.E. Bochukova, E.G. Marenne, G. Keogh, J.M. Atanassova, N. Bounds, R. Wheeler, E. Mistry, V. Henning, E. Körner, A. Muddyman, D. McCarthy, S. Hinney, A. Hebebrand, J. Scott, R.A. Langenberg, C. Wareham, N.J. Surendran, P. Howson, J.M. Butterworth, A.S. Danesh, J. Nordestgaard, Bø.G. Nielsen, S.F. Afzal, S. Papadia, S. Ashford, S. Garg, S. Millhauser, G.L. Palomino, R.I. Kwasniewska, A. Tachmazidou, I. O'Rahilly, S. Zeggini, E. Barroso, I. Farooqi, I.S. Benzeval, M. Burton, J. Buck, N. Jäckle, A. Kumari, M. Laurie, H. Lynn, P. Pudney, S. Rabe, B. Wolke, D. Overvad, K. Tjønneland, A. Clavel-Chapelon, F. Kaaks, R. Boeing, H. Trichopoulou, A. Ferrari, P. Palli, D. Krogha, V. Panico, S. Tuminoa, R. Matullo, G. Boer, J. Van Der Schouw, Y. Weiderpass, E. Quiros, J.R. Sánchez, M.-J. Navarro, C. Moreno-Iribas, C. Arriola, L. Melander, O. Wennberg, P. Key, T.J. Riboli, E. Turki, S.A. Anderson, C.A. Anney, R. Antony, D. Soler Artigas, M. Ayub, M. Bala, S. Barrett, J.C. Beales, P. Bentham, J. Bhattacharyaa, S. Birney, E. Blackwooda, D. Bobrow, M. Bolton, P.F. Boustred, C. Breen, G. Calissanoa, M. Carss, K. Charlton, R. Chatterjee, K. Chen, L. Ciampia, A. Cirak, S. Clapham, P. Clement, G. Coates, G. Coccaa, M. Collier, D.A. Cosgrove, C. Coxa, T. Craddock, N. Crooks, L. Curran, S. Curtis, D. Daly, A. Danecek, P. Day, I.N.M. Day-Williams, A. Dominiczak, A. Down, T. Du, Y. Dunham, I. Durbin, R. Edkins, S. Ekong, R. Ellis, P. Evansa, D.M. Fitzpatrick, D.R. Flicek, P. Floyd, J. Foley, A.R. Franklin, C.S. Futema, M. Gallagher, L. Gaunt, T.R. Geihs, M. Geschwind, D. Greenwood, C.M.T. Griffin, H. Grozeva, D. Guo, X. Guo, X. Gurling, H. Hart, D. Holmans, P. Howie, B. Huang, J. Huang, L. Hubbard, T. Humphries, S.E. Hurles, M.E. Hysi, P. Iotchkova, V. Jackson, D.K. Jamshidi, Y. Joyce, C. Karczewski, K.J. Kaye, J. Keane, T. Kemp, J.P. Kennedy, K. Kent, A. Khawaja, F. Van Kogelenberg, M. Kolb-Kokocinski, A. Lachance, G. Langford, C. Lawson, D. Lee, I. Lek, M. Li, R. Li, Y. Liang, J. Lin, H. Liu, R. Lönnqvist, J. Lopes, L.R. Lopes, M. MacArthur, D.G. Mangino, M. Marchini, J. Maslen, J. Mathieson, I. McGuffin, P. McIntosh, A.M. McKechanie, A.G. McQuillin, A. Memari, Y. Metrustry, S. Migone, N. Min, J.L. Mitchison, H.M. Moayyeri, A. Morris, A. Morris, J. Muntoni, F. Northstone, K. O'Donovan, M.C. Onoufriadis, A. Oualkacha, K. Owen, M.J. Palotie, A. Panoutsopoulou, K. Parker, V. Parr, J.R. Paternoster, L. Paunio, T. Payne, F. Payne, S.J. Perry, J.R.B. Pietilainen, O. Plagnol, V. Pollitt, R.C. Porteous, D.J. Povey, S. Quail, M.A. Quaye, L. Raymond, F.L. Rehnström, K. Richards, J.B. Ridout, C.K. Ring, S. Ritchie, G.R.S. Roberts, N. Robinson, R.L. Savage, D.B. Scambler, P. Schiffels, S. Schmidts, M. Schoenmakers, N. Scott, R.H. Semple, R.K. Serra, E. Sharp, S.I. Shaw, A. Shihab, H.A. Shin, S.-Y. Skuse, D. Small, K.S. Smee, C. Smith, B.H. Davey Smith, G. Soranzo, N. Southam, L. Spasic-Boskovic, O. Spector, T.D. St Clair, D. St Pourcain, B. Stalker, J. Stevens, E. Sun, J. Surdulescu, G. Suvisaari, J. Syrris, P. Taylor, R. Tian, J. Timpson, N.J. Tobin, M.D. Valdes, A.M. Vandersteen, A.M. Vijayarangakannan, P. Visscher, P.M. Wain, L.V. Walter, K. Walters, J.T.R. Wang, G. Wang, J. Wang, Y. Ward, K. Whyte, T. Williams, H.J. Williamson, K.A. Wilson, C. Wilson, S.G. Wong, K. Xu, C. Yang, J. Zhang, F. Zhang, P. Zheng, H.-F.

Abstract

Obesity is a genetically heterogeneous disorder. Using targeted and whole-exome sequencing, we studied 32 human and 87 rodent obesity genes in 2,548 severely obese children and 1,117 controls. We identified 52 variants contributing to obesity in 2% of cases including multiple novel variants in GNAS, which were sometimes found with accelerated growth rather than short stature as described previously. Nominally significant associations were found for rare functional variants in BBS1, BBS9, GNAS, MKKS, CLOCK and ANGPTL6. The p.S284X variant in ANGPTL6 drives the association signal (rs201622589, MAF∼0.1%, odds ratio = 10.13, p-value = 0.042) and results in complete loss of secretion in cells. Further analysis including additional case-control studies and population controls (N = 260,642) did not support association of this variant with obesity (odds ratio = 2.34, p-value = 2.59 × 10-3), highlighting the challenges of testing rare variant associations and the need for very large sample sizes. Further validation in cohorts with severe obesity and engineering the variants in model organisms will be needed to explore whether human variants in ANGPTL6 and other genes that lead to obesity when deleted in mice, do contribute to obesity. Such studies may yield druggable targets for weight loss therapies. © 2017 The Author(s).

Published
2017

6. A GWAS sequence variant for platelet volume marks an alternative DNM3 promoter in megakaryocytes near a MEIS1 binding site

Author

Nürnberg ST, Rendon A, Smethurst PA, Paul DS, Voss K, Thon JN, Lloyd Jones H, Sambrook JG, Tijssen MR, Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic Canic J, Elling U, Goodall AH, Labrune Y, Lopez LM, Mägi R, Meacham S, Okada Y, Sorice R, Teumer A, Zhang W, Ramirez Solis R, Bis JC, Ellinghaus D, Gögele M, Hottenga JJ, Langenberg C, Kovacs P, F. P, Shin SY, Esko T, Hartiala J, Kanoni S, Murgia F, Parsa A, Stephens J, van der Harst P, van der Schoot C, Allayee H, Attwood A, Balkau B, Bastardot F, Basu S, Baumeister SE, Biino G, Bomba L, Bonnefond A, Cambien F, Chambers JC, Cucca F, Davies G, de Geus EJ, de Boer RA, Döring A, Elliott P, Erdmann J, Feng W, Evans DM, Falchi M, Folsom AR, Frazer IH, Gibson QD, Glazer NL, Hammond C, Hartikainen AL, Heckbert SR, Hengstenberg C, Hersch M, Illig T, Loos RJ, Jolley J, Khaw KT, Kühnel B, Kyrtsonis MC, Lagou V, Lumley T, Mangino M, Maschio A, Mateo Leach I, McKnight B, Memari Y, Mitchell BD, Montgomery GW, Nöthlings U, Nakamura Y, Nauck M, Navis G, Nolte IM, Porteous DJ, Pouta A, Pramstaller PP, Pullat J, Ring SM, Rotter JI, Ruggiero D, Ruokonen A, Sala C, Samani NJ, Sambrook J, Schlessinger D, Schreiber S, Schunkert H, Scott J, Smith NL, Snieder H, Starr JM, Stumvoll M, Takahashi A, Taylor K, Tenesa A, Thein SL, Tönjes A, Uda M, Ulivi S, Wichmann HE, Yang TP, van Veldhuisen DJ, Visscher PM, Völker U, Wiggins KL, Willemsen G, Zhao JH, Zitting P, Bradley JR, Dedoussis GV, Hazen SL, Metspalu A, Pirastu M, Shuldiner AR, van Pelt L, Zwaginga JJ, Boomsma DI, Deary IJ, Franke A, Froguel P, Ganesh SK, Jarvelin MR, Martin NG, Meisinger C, Psaty BM, Spector TD, Wareham NJ, Akkerman JW, Ciullo M, Deloukas P, Greinacher A, Jupe S, Kamatani N, Khadake J, Kooner JS, Penninger J, Prokopenko I, Stemple D, Toniolo D, Wernisch L, Sanna S, Hicks AA, Ferreira MA, Italiano JE Jr, Gottgens B, Soranzo N, Ouwehand WH, PIRASTU, Nicola, D'ADAMO, ADAMO PIO, GASPARINI, PAOLO, Nürnberg, St, Rendon, A, Smethurst, Pa, Paul, D, Voss, K, Thon, Jn, Lloyd Jones, H, Sambrook, Jg, Tijssen, Mr, Gieger, C, Radhakrishnan, A, Cvejic, A, Tang, W, Porcu, E, Pistis, G, Serbanovic Canic, J, Elling, U, Goodall, Ah, Labrune, Y, Lopez, Lm, Mägi, R, Meacham, S, Okada, Y, Pirastu, Nicola, Sorice, R, Teumer, A, Zhang, W, Ramirez Solis, R, Bis, Jc, Ellinghaus, D, Gögele, M, Hottenga, Jj, Langenberg, C, Kovacs, P, F., P, Shin, Sy, Esko, T, Hartiala, J, Kanoni, S, Murgia, F, Parsa, A, Stephens, J, van der Harst, P, van der Schoot, C, Allayee, H, Attwood, A, Balkau, B, Bastardot, F, Basu, S, Baumeister, Se, Biino, G, Bomba, L, Bonnefond, A, Cambien, F, Chambers, Jc, Cucca, F, D'Adamo, ADAMO PIO, Davies, G, de Geus, Ej, de Boer, Ra, Döring, A, Elliott, P, Erdmann, J, Feng, W, Evans, Dm, Falchi, M, Folsom, Ar, Frazer, Ih, Gibson, Qd, Glazer, Nl, Hammond, C, Hartikainen, Al, Heckbert, Sr, Hengstenberg, C, Hersch, M, Illig, T, Loos, Rj, Jolley, J, Khaw, Kt, Kühnel, B, Kyrtsonis, Mc, Lagou, V, Lumley, T, Mangino, M, Maschio, A, Mateo Leach, I, Mcknight, B, Memari, Y, Mitchell, Bd, Montgomery, Gw, Nöthlings, U, Nakamura, Y, Nauck, M, Navis, G, Nolte, Im, Porteous, Dj, Pouta, A, Pramstaller, Pp, Pullat, J, Ring, Sm, Rotter, Ji, Ruggiero, D, Ruokonen, A, Sala, C, Samani, Nj, Sambrook, J, Schlessinger, D, Schreiber, S, Schunkert, H, Scott, J, Smith, Nl, Snieder, H, Starr, Jm, Stumvoll, M, Takahashi, A, Taylor, K, Tenesa, A, Thein, Sl, Tönjes, A, Uda, M, Ulivi, S, Wichmann, He, Yang, Tp, van Veldhuisen, Dj, Visscher, Pm, Völker, U, Wiggins, Kl, Willemsen, G, Zhao, Jh, Zitting, P, Bradley, Jr, Dedoussis, Gv, Gasparini, Paolo, Hazen, Sl, Metspalu, A, Pirastu, M, Shuldiner, Ar, van Pelt, L, Zwaginga, Jj, Boomsma, Di, Deary, Ij, Franke, A, Froguel, P, Ganesh, Sk, Jarvelin, Mr, Martin, Ng, Meisinger, C, Psaty, Bm, Spector, Td, Wareham, Nj, Akkerman, Jw, Ciullo, M, Deloukas, P, Greinacher, A, Jupe, S, Kamatani, N, Khadake, J, Kooner, J, Penninger, J, Prokopenko, I, Stemple, D, Toniolo, D, Wernisch, L, Sanna, S, Hicks, Aa, Ferreira, Ma, Italiano JE, Jr, Gottgens, B, Soranzo, N, Ouwehand, Wh, Biological Psychology, and EMGO+ - Mental Health

Subjects
Netherlands Twin Register (NTR), Transcription, Genetic, Gene Expression, Biochemistry, megakaryocyte, Mice, DNM3 promoter, Transcription (biology), GWAS, Platelet, Thrombopoiesis, Myeloid Ecotropic Viral Integration Site 1 Protein, Promoter Regions, Genetic, Cells, Cultured, Reverse Transcriptase Polymerase Chain Reaction, Hematology, Neoplasm Proteins, Haematopoiesis, Transcription Initiation Site, Megakaryocytes, platelet volume, DNM3, megakaryocytes, MEIS1, Blood Platelets, Chromatin Immunoprecipitation, Immunology, Biology, Polymorphism, Single Nucleotide, MEIS1 binding site, SDG 3 - Good Health and Well-being, Cell Line, Tumor, Animals, Humans, Cell Lineage, Binding site, Gene, Transcription factor, Homeodomain Proteins, Binding Sites, Genome, Human, Platelet Count, Hydrazones, Genetic Variation, Cell Biology, Sequence Analysis, DNA, Platelets and Thrombopoiesis, Molecular biology, Dynamin III
Abstract

We recently identified 68 genomic loci where common sequence variants are associated with platelet count and volume. Platelets are formed in the bone marrow by megakaryocytes, which are derived from hematopoietic stem cells by a process mainly controlled by transcription factors. The homeobox transcription factor MEIS1 is uniquely transcribed in megakaryocytes and not in the other lineage-committed blood cells. By ChIP-seq, we show that 5 of the 68 loci pinpoint a MEIS1 binding event within a group of 252 MK-overexpressed genes. In one such locus in DNM3, regulating platelet volume, the MEIS1 binding site falls within a region acting as an alternative promoter that is solely used in megakaryocytes, where allelic variation dictates different levels of a shorter transcript. The importance of dynamin activity to the latter stages of thrombopoiesis was confirmed by the observation that the inhibitor Dynasore reduced murine proplatelet for-mation in vitro.

Published
2013

7. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Author

Huang, J, Howie, B, Mccarthy, S, Memari, Y, Walter, K, Min, Jl, Danecek, P, Malerba, Giovanni, Trabetti, Elisabetta, Zheng, Hf, Gambaro, G, Richards, Jb, Durbin, R, Timpson, Nj, Marchini, J, Soranzo, N, Al Turki, S, Amuzu, A, Anderson, Ca, Anney, R, Antony, D, Artigas, Ms, Ayub, M, Bala, S, Barrett, Jc, Barroso, I, Beales, P, Benn, M, Bentham, J, Bhattacharya, S, Birney, E, Blackwood, D, Bobrow, M, Bochukova, E, Bolton, Pf, Bounds, R, Boustred, C, Breen, G, Calissano, M, Carss, K, Casas, Jp, Chambers, Jc, Charlton, R, Chatterjee, K, Chen, L, Ciampi, A, Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, Da, Cosgrove, C, Cox, T, Craddock, N, Crooks, L, Curran, S, Curtis, D, Daly, A, Day, In, Day Williams, A, Dedoussis, G, Down, T, Du, Y, van Duijn, Cm, Dunham, I, Edkins, S, Ekong, R, Ellis, P, Evans, Dm, Farooqi, Is, Fitzpatrick, Dr, Flicek, P, Floyd, J, Foley, Ar, Franklin, Cs, Futema, M, Gallagher, L, Gasparini, P, Gaunt, Tr, Geihs, M, Geschwind, D, Greenwood, C, Griffin, H, Grozeva, D, Guo, X, Gurling, H, Hart, D, Hendricks, Ae, Holmans, P, Huang, L, Hubbard, T, Humphries, Se, Hurles, Me, Hysi, P, Iotchkova, V, Isaacs, A, Jackson, Dk, Jamshidi, Y, Johnson, J, Joyce, C, Karczewski, Kj, Kaye, J, Keane, T, Kemp, Jp, Kennedy, K, Kent, A, Keogh, J, Khawaja, F, Kleber, Me, van Kogelenberg, M, Kolb Kokocinski, A, Kooner, Js, Lachance, G, Langenberg, C, Langford, C, Lawson, D, Lee, I, van Leeuwen, Em, Lek, M, Li, R, Li, Y, Liang, J, Lin, H, Liu, R, Lönnqvist, J, Lopes, Lr, Lopes, M, Luan, J, Macarthur, Dg, Mangino, M, Marenne, G, März, W, Maslen, J, Matchan, A, Mathieson, I, Mcguffin, P, Mcintosh, Am, Mckechanie, Ag, Mcquillin, A, Metrustry, S, Migone, N, Mitchison, Hm, Moayyeri, A, Morris, J, Morris, R, Muddyman, D, Muntoni, F, Nordestgaard, Bg, Northstone, K, O'Donovan, Mc, O'Rahilly, S, Onoufriadis, A, Oualkacha, K, Owen, Mj, Palotie, A, Panoutsopoulou, K, Parker, V, Parr, Jr, Paternoster, L, Paunio, T, Payne, F, Payne, Sj, Perry, Jr, Pietilainen, O, Plagnol, V, Pollitt, Rc, Povey, S, Quail, Ma, Quaye, L, Raymond, L, Rehnström, K, Ridout, Ck, Ring, S, Ritchie, Gr, Roberts, N, Robinson, Rl, Savage, Db, Scambler, P, Schiffels, S, Schmidts, M, Schoenmakers, N, Scott, Rh, Scott, Ra, Semple, Rk, Serra, E, Sharp, Si, Shaw, A, Shihab, Ha, Shin, Sy, Skuse, D, Small, Ks, Smee, C, Smith, Gd, Southam, L, Spasic Boskovic, O, Spector, Td, St Clair, D, St Pourcain, B, Stalker, J, Stevens, E, Sun, J, Surdulescu, G, Suvisaari, J, Syrris, P, Tachmazidou, I, Taylor, R, Tian, J, Tobin, Md, Toniolo, D, Traglia, M, Tybjaerg Hansen, A, Valdes, Am, Vandersteen, Am, Varbo, A, Vijayarangakannan, P, Visscher, Pm, Wain, Lv, Walters, Jt, Wang, G, Wang, J, Wang, Y, Ward, K, Wheeler, E, Whincup, P, Whyte, T, Williams, Hj, Williamson, Ka, Wilson, C, Wilson, Sg, Wong, K, Xu, C, Yang, J, Zaza, Gianluigi, Zeggini, E, Zhang, F, Zhang, P, Zhang, W., Clinicum, Department of Psychiatry, Jie, Huang, Bryan, Howie, Shane, Mccarthy, Yasin, Memari, Klaudia, Walter, Josine L., Min, Petr, Danecek, Giovanni, Malerba, Elisabetta, Trabetti, Hou Feng, Zheng, Saeed Al, Turki, Antoinette, Amuzu, Carl A., Anderson, Richard, Anney, Dinu, Antony, María Soler, Artiga, Muhammad, Ayub, Senduran, Bala, Jeffrey C., Barrett, Inês, Barroso, Phil, Beale, Marianne, Benn, Jamie, Bentham, Shoumo, Bhattacharya, Ewan, Birney, Douglas, Blackwood, Martin, Bobrow, Elena, Bochukova, Patrick F., Bolton, Rebecca, Bound, Chris, Boustred, Gerome, Breen, Mattia, Calissano, Keren, Car, Juan Pablo, Casa, John C., Chamber, Ruth, Charlton, Krishna, Chatterjee, Lu, Chen, Antonio, Ciampi, Sebahattin, Cirak, Peter, Clapham, Gail, Clement, Guy, Coate, Cocca, Massimiliano, David A., Collier, Catherine, Cosgrove, Tony, Cox, Nick, Craddock, Lucy, Crook, Sarah, Curran, David, Curti, Allan, Daly, Ian N. M., Day, Aaron Day, William, George, Dedoussi, Thomas, Down, Yuanping, Du, Cornelia M., van Duijn, Ian, Dunham, Sarah, Edkin, Rosemary, Ekong, Peter, Elli, David M., Evan, I., Sadaf Farooqi, David R., Fitzpatrick, Paul, Flicek, James, Floyd, A., Reghan Foley, Christopher S., Franklin, Marta, Futema, Louise, Gallagher, Gasparini, Paolo, Tom R., Gaunt, Matthias, Geih, Daniel, Geschwind, Celia, Greenwood, Heather, Griffin, Detelina, Grozeva, Xiaosen, Guo, Xueqin, Guo, Hugh, Gurling, Deborah, Hart, Audrey E., Hendrick, Peter, Holman, Liren, Huang, Tim, Hubbard, Steve E., Humphrie, Matthew E., Hurle, Pirro, Hysi, Valentina, Iotchkova, Aaron, Isaac, David K., Jackson, Yalda, Jamshidi, Jon, Johnson, Chris, Joyce, Konrad J., Karczewski, Jane, Kaye, Thomas, Keane, John P., Kemp, Karen, Kennedy, Alastair, Kent, Julia, Keogh, Farrah, Khawaja, Marcus E., Kleber, Margriet van, Kogelenberg, Anja Kolb, Kokocinski, Jaspal S., Kooner, Genevieve, Lachance, Claudia, Langenberg, Cordelia, Langford, Daniel, Lawson, Irene, Lee, Elisabeth M., van Leeuwen, Monkol, Lek, Rui, Li, Yingrui, Li, Jieqin, Liang, Hong, Lin, Ryan, Liu, Jouko, Lönnqvist, Luis R., Lope, Margarida, Lope, Jian'An, Luan, Daniel G., Macarthur, Massimo, Mangino, Gaëlle, Marenne, Winfried, März, John, Maslen, Angela, Matchan, Iain, Mathieson, Peter, Mcguffin, Andrew M., Mcintosh, Andrew G., Mckechanie, Andrew, Mcquillin, Sarah, Metrustry, Nicola, Migone, Hannah M., Mitchison, Alireza, Moayyeri, James, Morri, Richard, Morri, Dawn, Muddyman, Francesco, Muntoni, Børge G., Nordestgaard, Kate, Northstone, Michael C., O'Donovan, Stephen, O'Rahilly, Alexandros, Onoufriadi, Karim, Oualkacha, Michael J., Owen, Aarno, Palotie, Kalliope, Panoutsopoulou, Victoria, Parker, Jeremy R., Parr, Lavinia, Paternoster, Tiina, Paunio, Felicity, Payne, Stewart J., Payne, John R. B., Perry, Olli, Pietilainen, Vincent, Plagnol, Rebecca C., Pollitt, Sue, Povey, Michael A., Quail, Lydia, Quaye, Lucy, Raymond, Karola, Rehnström, Cheryl K., Ridout, Susan, Ring, Graham R. S., Ritchie, Nicola, Robert, Rachel L., Robinson, David B., Savage, Peter, Scambler, Stephan, Schiffel, Miriam, Schmidt, Nadia, Schoenmaker, Richard H., Scott, Robert A., Scott, Robert K., Semple, Eva, Serra, Sally I., Sharp, Adam, Shaw, Hashem A., Shihab, So Youn, Shin, David, Skuse, Kerrin S., Small, Carol, Smee, George Davey, Smith, Lorraine, Southam, Olivera Spasic, Boskovic, Timothy D., Spector, David St, Clair, Beate St, Pourcain, Jim, Stalker, Elizabeth, Steven, Jianping, Sun, Gabriela, Surdulescu, Jaana, Suvisaari, Petros, Syrri, Ioanna, Tachmazidou, Rohan, Taylor, Jing, Tian, Martin D., Tobin, Daniela, Toniolo, Michela, Traglia, Anne Tybjaerg, Hansen, Ana M., Valde, Anthony M., Vandersteen, Anette, Varbo, Parthiban, Vijayarangakannan, Peter M., Visscher, Louise V., Wain, James T. R., Walter, Guangbiao, Wang, Jun, Wang, Yu, Wang, Kirsten, Ward, Eleanor, Wheeler, Peter, Whincup, Tamieka, Whyte, Hywel J., William, Kathleen A., Williamson, Crispian, Wilson, Scott G., Wilson, Kim, Wong, Changjiang, Xu, Jian, Yang, Gianluigi, Zaza, Eleftheria, Zeggini, Feng, Zhang, Pingbo, Zhang, Weihua, Zhang, Giovanni, Gambaro, J., Brent Richard, Richard, Durbin, Nicholas J., Timpson, Jonathan, Marchini, and Nicole, Soranzo

Subjects
Computer science, General Physics and Astronomy, Genome-wide association study, 0302 clinical medicine, Gene Frequency, Haplotype, Genetics,Biological sciences, Settore MED/14 - NEFROLOGIA, Aged, 80 and over, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, TWINSUK, Middle Aged, single-nucleotide polymorphism, Whole-genome sequencing, WGS imputation panel, single-nucleotide polymorphism, Biological sciences, Italy, MAP, Adult, Adolescent, Genotype, WGS imputation panel, Population, Single-nucleotide polymorphism, FORMAT, Computational biology, GENOTYPE IMPUTATION, Polymorphism, Single Nucleotide, Article, White People, General Biochemistry, Genetics and Molecular Biology, Young Adult, 03 medical and health sciences, Humans, GENOME-WIDE ASSOCIATION, 1000 Genomes Project, education, Allele frequency, Alleles, Aged, 030304 developmental biology, Whole-genome sequencing, Models, Statistical, Models, Genetic, Genome, Human, Genetic Variation, General Chemistry, United Kingdom, Minor allele frequency, Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11], Haplotypes, 3111 Biomedicine, 030217 neurology & neurosurgery, Imputation (genetics)
Abstract

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants., Imputation uses genotype information from SNP arrays to infer the genotypes of missing markers. Here, the authors show that an imputation reference panel derived from whole-genome sequencing of 3,781 samples from the UK10K project improves the imputation accuracy and coverage of low frequency variants compared to existing methods.

Published
2015

8. The QUaD Galactic Plane Survey. II

Author

Culverhouse, T., Ade, P., Bock, J., Bowden, M., Brown, M. L., Cahill, G., Castro, P. G., Church, S., Friedman, R., Ganga, K., Gear, W. K., Gupta, S., Hinderks, J., Kovac, J., Lange, A. E., Leitch, E., Melhuish, S. J., Memari, Y., Murphy, J. A., Orlando, A., Pryke, C., Schwarz, R., O'Sullivan, C., Piccirillo, L., Rajguru, N., Rusholme, B., Taylor, A. N., Thompson, K. L., Turner, A. H., Wu, E. Y. S., and Zemcov, M.

Published
2011
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9. The QUaD Galactic Plane Survey 1: Maps And Analysis of Diffuse Emission

Author

Culverhouse, T., Ade, P., Bock, J., Bowden, M., Brown, M.L., Cahill, G., Castro, P.G., Church, S., Friedman, R., Ganga, K., Gear, W.K., Gupta, S., Hinderks, J., Kovac, J., Lange, A.E., Leach, S., Melhuish, S.J., Memari, Y., Murphy, J.A., Orlando, A., Schwarz, R., O'Sullivan, C., Piccirillo, L., Pryke, C., Rajguru, N., Rusholme, B., Taylor, A.N., Thompson, K.L., Turner, A.H., Wu, E.Y.S., and Zemcov, M.

Subjects
Experimental Physics, Astrophysics of Galaxies (astro-ph.GA), FOS: Physical sciences, Astrophysics - Astrophysics of Galaxies
Abstract

We present a survey of ~800 square degrees of the galactic plane observed with the QUaD telescope. The primary product of the survey are maps of Stokes I, Q and U parameters at 100 and 150 GHz, with spatial resolution 5 and 3.5 arcminutes respectively. Two regions are covered, spanning approximately 245-295 and 315-5 degrees in galactic longitude l, and -4, Comment: 19 pages, 21 figures, accepted for publication in ApJ; new revision includes tests of spectral line contribution. The maps analyzed in this paper are available for public download at http://find.spa.umn.edu/quad/quad_galactic/

Published
2010

10. Parameter Estimation from Improved Measurements of the CMB from QUaD

Author

QUaD Collaboration, Gupta, S., Ade, P., Bock, J., Bowden, M., Brown, M. L., Cahill, G., Castro, P. G., Church, S., Culverhouse, T., Friedman, R. B., Ganga, K., Gear, W. K., Hinderks, J., Kovac, J., Lange, A. E., Leitch, E., Melhuish, S. J., Memari, Y., Murphy, J. A., Orlando, A., O'Sullivan, C., Piccirillo, L., Pryke, C., Rajguru, N., Rusholme, B., Schwarz, R., Taylor, A. N., Thompson, K. L., Turner, A. H., Wu, E. Y. S., and Zemcov, M.

Subjects
Cosmology and Nongalactic Astrophysics (astro-ph.CO), FOS: Physical sciences, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We evaluate the contribution of cosmic microwave background (CMB) polarization spectra to cosmological parameter constraints. We produce cosmological parameters using high-quality CMB polarization data from the ground-based QUaD experiment and demonstrate for the majority of parameters that there is significant improvement on the constraints obtained from satellite CMB polarization data. We split a multi-experiment CMB dataset into temperature and polarization subsets and show that the best-fit confidence regions for the LCDM 6-parameter cosmological model are consistent with each other, and that polarization data reduces the confidence regions on all parameters. We provide the best limits on parameters from QUaD EE/BB polarization data and we find best-fit parameters from the multi-experiment CMB dataset using the optimal pivot scale of k_p=0.013 Mpc-1 to be {omch2, ombh2, H_0, A_s, n_s, tau}= {0.113, 0.0224, 70.6, 2.29 times 10^-9, 0.960, 0.086}., 7 pages, 5 figures, updated to reflect published version, minor changes to spelling and format

Published
2009

11. Cosmological Parameters from the QUaD CMB Polarization Experiment

Author

Brown, Michael, Castro, P. G., Ade, P., Bock, J., Bowden, M., Brown, M. L., Cahill, G., Church, S., Culverhouse, T., Friedman, R. B., Ganga, K., Gear, W. K., Gupta, S., Hinderks, J., Kovac, J., Lange, A. E., Leitch, E., Melhuish, S. J., Memari, Y., Murphy, J. A., Orlando, A., Pryke, C., Schwarz, R., O'Sullivan, C., Piccirillo, L., Rajguru, N., Rusholme, B., Taylor, A. N., Thompson, K. L., Turner, A. H., Wu, E. Y S, Zemcov, M., APC - Cosmologie, AstroParticule et Cosmologie (APC (UMR_7164)), Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), QUaD, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Physique Corpusculaire et Cosmologie - Collège de France (PCC), and Collège de France (CdF)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS)

Subjects
cosmic microwave background, Cosmology and Nongalactic Astrophysics (astro-ph.CO), Statistical [Methods], Cold dark matter, [SDU.ASTR.CO]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Physics beyond the Standard Model, Cosmological parameters, Cosmic microwave background, FOS: Physical sciences, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics, 01 natural sciences, Cosmology, [PHYS.ASTR.CO]Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Polarization, 0103 physical sciences, cosmological parameters, 010303 astronomy & astrophysics, Physics, methods: statistical, polarization, 010308 nuclear & particles physics, Spectral density, Astronomy and Astrophysics, CMB cold spot, Galaxy, Space and Planetary Science, Neutrino, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

In this paper we present a parameter estimation analysis of the polarization and temperature power spectra from the second and third season of observations with the QUaD experiment. QUaD has for the first time detected multiple acoustic peaks in the E-mode polarization spectrum with high significance. Although QUaD-only parameter constraints are not competitive with previous results for the standard 6-parameter LCDM cosmology, they do allow meaningful polarization-only parameter analyses for the first time. In a standard 6-parameter LCDM analysis we find the QUaD TT power spectrum to be in good agreement with previous results. However, the QUaD polarization data shows some tension with LCDM. The origin of this 1 to 2 sigma tension remains unclear, and may point to new physics, residual systematics or simple random chance. We also combine QUaD with the five-year WMAP data set and the SDSS Luminous Red Galaxies 4th data release power spectrum, and extend our analysis to constrain individual isocurvature mode fractions, constraining cold dark matter density, alpha(cdmi), 8 pages, 5 figures, submitted to ApJ

Published
2009

12. Cosmological Parameters from the QUaD CMB Polarization Experiment

Author

Castro, P.G., Ade, P., Bock, J., Bowden, M.L., Brown, M.L., Cahill, G., Church, S., Culverhouse, T., Friedman, R.B., Ganga, K., Gear, W.K., Gupta, S., Hinderks, J., Kovac, J., Lange, A.E., Leitch, E., Melhuish, S.J., Memari, Y., Murphy, J.A., Orlando, A., Pryke, C., Schwarz, R., O'Sullivan, C., Piccirillo, L., Taylor, A.N., Thompson, K.L., Turner, A.H., Wu, E.Y.S., and Zemcov, M.

Subjects
Experimental Physics, Astrophysics::Cosmology and Extragalactic Astrophysics
Abstract

In this paper, we present a parameter estimation analysis of the polarization and temperature power spectra from the second and third season of observations with the QUaD experiment. QUaD has for the first time detected multiple acoustic peaks in the E-mode polarization spectrum with high significance. Although QUaD-only parameter constraints are not competitive with previous results for the standard six-parameter ΛCDM cosmology, they do allow meaningful polarization-only parameter analyses for the first time. In a standard six-parameter ΛCDM analysis, we find the QUaD TT power spectrum to be in good agreement with previous results. However, the QUaD polarization data show some tension with ΛCDM. The origin of this 1σ–2σ tension remains unclear, and may point to new physics, residual systematics, or simple random chance. We also combine QUaD with the five-year WMAP data set and the SDSS luminous red galaxies 4th data release power spectrum, and extend our analysis to constrain individual isocurvature mode fractions, constraining cold dark matter density, αcdmi < 0.11 (95% confidence limit (CL)), neutrino density, αndi < 0.26 (95% CL), and neutrino velocity, αnvi < 0.23 (95% CL), modes. Our analysis sets a benchmark for future polarization experiments.

Published
2009

13. Improved measurements of the temperature and polarization of the CMB from QUaD

Author

The QUaD Collaboration, Brown, M. L., Ade, P., Bock, J., Bowden, M., Cahill, G., Castro, P. G., Church, S., Culverhouse, T., Friedman, R. B., Ganga, K., Gear, W. K., Gupta, S., Hinderks, J., Kovac, J., Lange, A. E., Leitch, E., Melhuish, S. J., Memari, Y., Murphy, J. A., Orlando, A., O'Sullivan, C., Piccirillo, L., Pryke, C., Rajguru, N., Rusholme, B., Schwarz, R., Taylor, A. N., Thompson, K. L., Turner, A. H., Wu, E. Y. S., and Zemcov, M.

Subjects
Cosmology and Nongalactic Astrophysics (astro-ph.CO), FOS: Physical sciences, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We present an improved analysis of the final dataset from the QUaD experiment. Using an improved technique to remove ground contamination, we double the effective sky area and hence increase the precision of our CMB power spectrum measurements by ~30% versus that previously reported. In addition, we have improved our modeling of the instrument beams and have reduced our absolute calibration uncertainty from 5% to 3.5% in temperature. The robustness of our results is confirmed through extensive jackknife tests and by way of the agreement we find between our two fully independent analysis pipelines. For the standard 6-parameter LCDM model, the addition of QUaD data marginally improves the constraints on a number of cosmological parameters over those obtained from the WMAP experiment alone. The impact of QUaD data is significantly greater for a model extended to include either a running in the scalar spectral index, or a possible tensor component, or both. Adding both the QUaD data and the results from the ACBAR experiment, the uncertainty in the spectral index running is reduced by ~25% compared to WMAP alone, while the upper limit on the tensor-to-scalar ratio is reduced from r < 0.48 to r < 0.33 (95% c.l). This is the strongest limit on tensors to date from the CMB alone. We also use our polarization measurements to place constraints on parity violating interactions to the surface of last scattering, constraining the energy scale of Lorentz violating interactions to < 1.5 x 10^{-43} GeV (68% c.l.). Finally, we place a robust upper limit on the strength of the lensing B-mode signal. Assuming a single flat band power between l = 200 and l = 2000, we constrain the amplitude of B-modes to be < 0.57 micro-K^2 (95% c.l.)., 23 pages, 19 figures, updated to reflect published version

Published
2009

14. QUaD: A High-Resolution Cosmic Microwave Background Polarimeter

Author

Hinderks, J., Ade, P., Bock, J., Bowden, M.L., Cahill, G., Carlstrom, J.E., Castro, P.G., Church, S., Culverhouse, T., Friedman, R., Ganga, K., Gear, W.K., Gupta, S., Harris, J., Haynes, V., Keating, B.G., Kovac, J., Kirby, E., Lange, A.E., Leitch, E., Mallie, O.E., Melhuish, S., Memari, Y., Murphy, A., Orlando, A., Schwarz, R., O'Sullivan, C., Piccirillo, L., Pryke, C., Rajguru, N., Rusholme, B., Taylor, A.N., Thompson, K.L., Tucker, C., Turner, A.H., Wu, E.Y.S., and Zemcov, M.

Subjects
Experimental Physics, Astrophysics::Instrumentation and Methods for Astrophysics, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics::Galaxy Astrophysics
Abstract

We describe the QUaD experiment, a millimeter-wavelength polarimeter designed to observe the cosmic microwave background (CMB) from a site at the South Pole. The experiment comprises a 2.64 m Cassegrain telescope equipped with a cryogenically cooled receiver containing an array of 62 polarization-sensitive bolometers. The focal plane contains pixels at two different frequency bands, 100 GHz and 150 GHz, with angular resolutions of 5 and 3.5, respectively. The high angular resolution allows observation of CMB temperature and polarization anisotropies over a wide range of scales. The instrument commenced operation in early 2005 and collected science data during three successive Austral winter seasons of observation.

Published
2009

15. Small Angular Scale Measurements of the CMB Temperature Power Spectrum from QUaD

Author

QUaD Collaboration, Friedman, R. B., Ade, P., Bock, J., Bowden, M., Brown, M. L., Cahill, G., Castro, P. G., Church, S., Culverhouse, T., Ganga, K., Gear, W. K., Gupta, S., Hinderks, J., Kovac, J., Lange, A. E., Leitch, E., Melhuish, S. J., Memari, Y., Murphy, J. A., Orlando, A., Sullivan, C. O', Piccirillo, L., Pryke, C., Rajguru, N., Rusholme, B., Schwarz, R., Taylor, A. N., Thompson, K. L., Turner, A. H., Wu, E. Y. S., and Zemcov, M.

Subjects
Cosmology and Nongalactic Astrophysics (astro-ph.CO), Astrophysics::Instrumentation and Methods for Astrophysics, FOS: Physical sciences, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We present measurements of the cosmic microwave background (CMB) radiation temperature anisotropy in the multipole range 2000, Comment: 5 pages, 5 figures, updated beam model, full data release available online (see text), accepted to ApJL

Published
2009

16. Second and third season QUaD CMB temperature and polarization power spectra

Author

QUaD collaboration, Pryke, C., Ade, P., Bock, J., Bowden, M., Brown, M. L., Cahill, G., Castro, P. G., Church, S., Culverhouse, T., Friedman, R., Ganga, K., Gear, W. K., Gupta, S., Hinderks, J., Kovac, J., Lange, A. E., Leitch, E., Melhuish, S. J., Memari, Y., Murphy, J. A., Orlando, A., Schwarz, R., O'Sullivan, C., Piccirillo, L., Rajguru, N., Rusholme, B., Taylor, A. N., Thompson, K. L., Turner, A. H., Wu, E. Y. S., Zemcov, M., APC - Cosmologie, AstroParticule et Cosmologie (APC (UMR_7164)), Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), QUaD, Physique Corpusculaire et Cosmologie - Collège de France (PCC), Collège de France (CdF)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Collège de France (CdF)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-AstroParticule et Cosmologie (APC (UMR_7164)), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.ASTR.CO]Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], [SDU.ASTR.CO]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Astrophysics (astro-ph), FOS: Physical sciences, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics
Abstract

We report results from the second and third seasons of observation with the QUaD experiment. Angular power spectra of the Cosmic Microwave Background are derived for both temperature and polarization at both 100 GHz and 150 GHz, and as cross frequency spectra. All spectra are subjected to an extensive set of jackknife tests to probe for possible systematic contamination. For the implemented data cuts and processing technique such contamination is undetectable. We analyze the difference map formed between the 100 and 150 GHz bands and find no evidence of foreground contamination in polarization. The spectra are then combined to form a single set of results which are shown to be consistent with the prevailing LCDM model. The sensitivity of the polarization results is considerably better than that of any previous experiment -- for the first time multiple acoustic peaks are detected in the E-mode power spectrum at high significance., Comment: 24 pages, 23 figures, updated to reflect published version

Published
2008
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17. Parity violation constraints using 2006-2007 QUaD CMB polarization spectra

Author

QUaD Collaboration, Wu, E. Y. S., Ade, P., Bock, J., Bowden, M., Brown, M. L., Cahill, G., Castro, P. G., Church, S., Culverhouse, T., Friedman, R., Ganga, K., Gear, W. K., Gupta, S., Hinderks, J., Kovac, J., Lange, A. E., Leitch, E., Melhuish, S. J., Memari, Y., Murphy, J. A., Orlando, A., Piccirillo, L., Pryke, C., Rajguru, N., Rusholme, B., Schwarz, R., O'Sullivan, C., Taylor, A. N., Thompson, K. L., Turner, A. H., and Zemcov, M.

Subjects
High Energy Physics - Phenomenology, High Energy Physics - Phenomenology (hep-ph), Astrophysics (astro-ph), FOS: Physical sciences, High Energy Physics::Experiment, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics
Abstract

We constrain parity-violating interactions to the surface of last scattering using spectra from the QUaD experiment's second and third seasons of observations by searching for a possible systematic rotation of the polarization directions of CMB photons. We measure the rotation angle due to such a possible "cosmological birefringence" to be 0.55 deg. +/- 0.82 deg. (random) +/- 0.5 deg. (systematic) using QUaD's 100 and 150 GHz TB and EB spectra over the multipole range 200 < l < 2000, consistent with null, and constrain Lorentz violating interactions to < 2^-43 GeV (68% confidence limit). This is the best constraint to date on electrodynamic parity violation on cosmological scales., 4 pages, 2 figures, accepted to Physical Review Letters. Improved method, updated result and clarified language

Published
2008
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18. Polarization Calibration of the QUaD Experiment

Author

Hinderks, J. R., Peter Ade, Bock, J., Bowden, M., Brown, M. L., Cahill, G., Carlstrom, J. E., Castro, P. G., Church, S., Culverhouse, T., Friedman, R., Ganga, K., Gear, W. K., Gupta, S., Harris, J., Haynes, V., Kovac, J., Lange, A. E., Leitch, E., Mallie, O. E., Melhuish, S., Memari, Y., Murphy, A., Orlando, A., Schwarz, R., Sullivan, C. O., Piccirillo, L., Pryke, C., Rajguru, N., Rusholme, B., Taylor, A. N., Thompson, K. L., Tucker, C., Turner, A. H., Wu, E. Y. S., and Zemcov, M.

Subjects
Astrophysics::Instrumentation and Methods for Astrophysics, Astrophysics::Cosmology and Extragalactic Astrophysics
Abstract

We describe the polarization calibration of the QUaD experiment, including determination of the polarization efficiency of the detectors and their orientation angles. QUaD is a millimeter-wavelength polarimeter that observed the Cosmic Microwave Background (CMB) from a site at the South Pole. The experiment comprises a 2.64 m Cassegrain telescope equipped with a cryogenically cooled receiver containing an array of 62 polarization-sensitive bolometers. The focal plane contains pixels at two different frequency bands, 100 GHz and 150 GHz, with angular resolutions of 5prime and 3farcm5, respectively. The high angular resolution allows observation of CMB temperature and polarization anisotropies over a wide range of scales. The instrument commenced operation in early 2005 and collected science data during three successive Austral winter seasons of observation.

19. Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps

Author

Iotchkova, V, Huang, J, Morris, JA, Jain, D, Barbieri, C, Walter, K, Min, JL, Chen, L, Astle, W, Cocca, M, Deelen, P, Elding, H, Farmaki, A-E, Franklin, CS, Franberg, M, Gaunt, TR, Hofman, A, Jiang, T, Kleber, ME, Lachance, G, Luan, J, Malerba, G, Matchan, A, Mead, D, Memari, Y, Ntalla, I, Panoutsopoulou, K, Pazoki, R, Perry, JRB, Rivadeneira, F, Sabater-Lleal, M, Sennblad, B, Shin, S-Y, Southam, L, Traglia, M, Van Dijk, F, Van Leeuwen, EM, Zaza, G, Zhang, W, UK10K Consortium, Amin, N, Butterworth, A, Chambers, JC, Dedoussis, G, Dehghan, A, Franco, OH, Franke, L, Frontini, M, Gambaro, G, Gasparini, P, Hamsten, A, Issacs, A, Kooner, JS, Kooperberg, C, Langenberg, C, Marz, W, Scott, RA, Swertz, MA, Toniolo, D, Uitterlinden, AG, Van Duijn, CM, Watkins, H, Zeggini, E, Maurano, MT, Timpson, NJ, Reiner, AP, Auer, PL, and Soranzo, N

Subjects
Male, Heart Diseases, Genetic Loci, Genome, Human, Quantitative Trait Loci, Genetic Variation, Humans, Female, Genetic Predisposition to Disease, Sequence Analysis, DNA, Hematologic Diseases, 3. Good health, Genome-Wide Association Study
Abstract

Large-scale whole-genome sequence data sets offer novel opportunities to identify genetic variation underlying human traits. Here we apply genotype imputation based on whole-genome sequence data from the UK10K and 1000 Genomes Project into 35,981 study participants of European ancestry, followed by association analysis with 20 quantitative cardiometabolic and hematological traits. We describe 17 new associations, including 6 rare (minor allele frequency (MAF) < 1%) or low-frequency (1% < MAF < 5%) variants with platelet count (PLT), red blood cell indices (MCH and MCV) and HDL cholesterol. Applying fine-mapping analysis to 233 known and new loci associated with the 20 traits, we resolve the associations of 59 loci to credible sets of 20 or fewer variants and describe trait enrichments within regions of predicted regulatory function. These findings improve understanding of the allelic architecture of risk factors for cardiometabolic and hematological diseases and provide additional functional insights with the identification of potentially novel biological targets.

20. Seventy-five genetic loci influencing the human red blood cell

Author

Teresa Nutile, Anna-Liisa Hartikainen, Stavroula Kanoni, Johannes H. Smit, Harm-Jan Westra, Beben Benyamin, Gonneke Willemsen, Clara S. Tang, Maria Dimitriou, Peter Vollenweider, Olle Melander, Inga Prokopenko, W.H. Wilson Tang, John P. Kemp, Tim D. Spector, Evelin Mihailov, Paul F. O'Reilly, Eleonora Porcu, Marcus E. Kleber, Sheila Ulivi, George Dedoussis, Manuela Uda, Matthias Nauck, Brenda W.J.H. Penninx, Daniela Ruggiero, Xinzhong Li, Dirk S. Paul, Niek Verweij, Bernd Genser, Harold Snieder, Willem H. Ouwehand, Ido P. Kema, Miriam F. Moffatt, Carmel Moore, Hilma Holm, Nicola Pirastu, Adamo Pio D'Adamo, Michael Stumvoll, Rossella Sorice, Kay-Tee Khaw, Heather Lloyd-Jones, Federico Murgia, Stephen F. Garner, Jing Hua Zhao, Laura Portas, Abdel Abdellaoui, Ursula Puc, Andres Metspalu, Marleen H. M. de Moor, Isleifur Olafsson, Ruth J. F. Loos, Andres Salumets, François Bastardot, James Scott, Jian Yang, Braxton D. Mitchell, Debora Parracciani, Maria Novatchkova, Panos Deloukas, William O.C.M. Cookson, Lorna M. Lopez, Andrew A. Hicks, Aude Saint-Pierre, Daniel F. Gudbjartsson, Vinicius Tragante, Mario Pirastu, Jacques S. Beckmann, L. Joost van Pelt, Winfried Maerz, Hooman Allayee, Jouke-Jan Hottenga, Kari Stefansson, Debashish Das, Weihua Zhang, Anke Tönjes, Michela Traglia, Stuart Meacham, Antonio Piga, Cornelis A. Albers, Nicholas G. Martin, John C. Chambers, Christa Meisinger, Leo-Pekka Lyytikäinen, Nicole Soranzo, Mika Kähönen, Katrin Voss, Micha Hersch, Claudia Langenberg, Sian Tsung Tan, Sandosh Padmanabhan, Christian X. Weichenberger, J. Gustav Smith, Antony P. Attwood, Claire E. Hastie, Gunnar Engström, Janina S. Ried, Carsten Oliver Schmidt, Pall T. Onundarson, Kathy Miller, Francisco S. Domingues, Stefania Bandinelli, Ulrich Elling, Augusto Rendon, Paul Elliott, Quince Gibson, Tõnu Esko, Robert Sladek, Marina Ciullo, Gerald Wirnsberger, Franco Anni, Antonietta Robino, Serena Sanna, Hein Schepers, Jonathan Stephens, Joban Sehmi, Beverley Balkau, Jennifer G. Sambrook, Lucia Perseu, Ilja M. Nolte, Herman H W Silljé, John M. Starr, Cinzia Sala, Peter P. Pramstaller, David M. Evans, Renzo Galanello, Uwe Völker, Philippe Froguel, Dorret I. Boomsma, Vasiliki Lagou, Gerjan Navis, Christian Gieger, Susan M. Ring, Alexander Teumer, Angela Döring, Ale Algra, Toshiko Tanaka, Bo Hedblad, Anneli Pouta, Unnur Thorsteinsdottir, Bernhard R. Winkelmann, Liming Liang, John Danesh, Paolo Gasparini, Sarah E. Medland, Ian J. Deary, Martin Gögele, Pim van der Harst, Giorgia Girotto, Josef M. Penninger, Jaspal S. Kooner, Patrick Sulem, Thomas Illig, Yasin Memari, Sarah E. Harris, Wiek H. van Gilst, Francesco Cucca, Dirk J. van Veldhuisen, So-Youn Shin, Giorgio Pistis, Olli T. Raitakari, Lude Franke, Folkert W. Asselbergs, Abtehale Al-Hussani, Stanley L. Hazen, Manuel A. R. Ferreira, Aimo Ruokonen, Christian Dina, Aparna Radhakrishnan, Irene Mateo Leach, Nicholas J. Wareham, George Davey Smith, Eric E. Schadt, Alan R. Shuldiner, John Whitfield, Gudmundur I. Eyjolfsson, Eco J. C. de Geus, Grant W. Montgomery, Afshin Parsa, Terho Lehtimäki, Paolo Fortina, Luigi Ferrucci, Andreas Greinacher, Marjo-Riitta Järvelin, Krista Fischer, Fabrice Danjou, Rudolf A. de Boer, Paul I.W. de Bakker, Peter M. Visscher, Anna F. Dominiczak, Ramiro Ramirez-Solis, Jennifer Jolley, Bruce H. R. Wolffenbuttel, Jaana Hartiala, Daniela Toniolo, Bernhard O. Boehm, van der Harst, P, Zhang, W, Mateo Leach, I, Rendon, A, Verweij, N, Sehmi, J, Paul, D, Elling, U, Allayee, H, Li, X, Radhakrishnan, A, Tan, St, Voss, K, Weichenberger, Cx, Albers, Ca, Al Hussani, A, Asselbergs, Fw, Ciullo, M, Danjou, F, Dina, C, Esko, T, Evans, Dm, Franke, L, Gögele, M, Hartiala, J, Hersch, M, Holm, H, Hottenga, Jj, Kanoni, S, Kleber, Me, Lagou, V, Langenberg, C, Lopez, Lm, Lyytikäinen, Lp, Melander, O, Murgia, F, Nolte, Im, O'Reilly, Pf, Padmanabhan, S, Parsa, A, Pirastu, Nicola, Porcu, E, Portas, L, Prokopenko, I, Ried, J, Shin, Sy, Tang, C, Teumer, A, Traglia, Michela, Ulivi, S, Westra, Hj, Yang, J, Zhao, Jh, Anni, F, Abdellaoui, A, Attwood, A, Balkau, B, Bandinelli, S, Bastardot, F, Benyamin, B, Boehm, Bo, Cookson, Wo, Das, D, de Bakker, Pi, de Boer, Ra, de Geus, Ej, de Moor, Mh, Dimitriou, M, Domingues, F, Döring, A, Engström, G, Eyjolfsson, Gi, Ferrucci, L, Fischer, K, Galanello, R, Garner, Sf, Genser, B, Gibson, Qd, Girotto, Giorgia, Gudbjartsson, Df, Harris, Se, Hartikainen, Al, Hastie, Ce, Hedblad, B, Illig, T, Jolley, J, Kähönen, M, Kema, Ip, Kemp, Jp, Liang, L, Lloyd Jones, H, Loos, Rj, Meacham, S, Medland, Se, Meisinger, C, Memari, Y, Mihailov, E, Miller, K, Moffatt, Mf, Nauck, M, Novatchkova, M, Nutile, T, Olafsson, I, Onundarson, Pt, Parracciani, D, Penninx, Bw, Perseu, L, Piga, A, Pistis, G, Pouta, A, Puc, U, Raitakari, O, Ring, Sm, Robino, Antonietta, Ruggiero, D, Ruokonen, A, Saint Pierre, A, Sala, C, Salumets, A, Sambrook, J, Schepers, H, Schmidt, Co, Silljé, Hh, Sladek, R, Smit, Jh, Starr, Jm, Stephens, J, Sulem, P, Tanaka, T, Thorsteinsdottir, U, Tragante, V, van Gilst, Wh, van Pelt, Lj, van Veldhuisen, Dj, Völker, U, Whitfield, Jb, Willemsen, G, Winkelmann, Br, Wirnsberger, G, Algra, A, Cucca, F, D'Adamo, ADAMO PIO, Danesh, J, Deary, Ij, Dominiczak, Af, Elliott, P, Fortina, P, Froguel, P, Gasparini, Paolo, Greinacher, A, Hazen, Sl, Jarvelin, Mr, Khaw, Kt, Lehtimäki, T, Maerz, W, Martin, Ng, Metspalu, A, Mitchell, Bd, Montgomery, Gw, Moore, C, Navis, G, Pirastu, M, Pramstaller, Pp, Ramirez Solis, R, Schadt, E, Scott, J, Shuldiner, Ar, Smith, Gd, Smith, Jg, Snieder, H, Sorice, R, Spector, Td, Stefansson, K, Stumvoll, M, Tang, Wh, Toniolo, D, Tönjes, A, Visscher, Pm, Vollenweider, P, Wareham, Nj, Wolffenbuttel, Bh, Boomsma, Di, Beckmann, J, Dedoussis, Gv, Deloukas, P, Ferreira, Ma, Sanna, S, Uda, M, Hicks, Aa, Penninger, Jm, Gieger, C, Kooner, J, Ouwehand, Wh, Soranzo, N, Chambers, J. C., Psychiatry, EMGO - Mental health, NCA - Anxiety & Depression, Biological Psychology, Neuroscience Campus Amsterdam - Anxiety & Depression, EMGO+ - Mental Health, Van Der Harst, Pim, Zhang, Weihua, Mateo Leach, Irene, Rendon, Augusto, Benyamin, Beben, Chambers, John C, Cardiovascular Centre (CVC), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Life Course Epidemiology (LCE), Guided Treatment in Optimal Selected Cancer Patients (GUTS), Lifestyle Medicine (LM), Stem Cell Aging Leukemia and Lymphoma (SALL), Groningen Kidney Center (GKC), Vascular Ageing Programme (VAP), and Center for Liver, Digestive and Metabolic Diseases (CLDM)

Subjects
Male, Netherlands Twin Register (NTR), Candidate gene, Erythrocytes, PROTEIN, Genome-wide association study, DISEASE, Hemoglobins, Mice, 0302 clinical medicine, Genetics, Genomics, blood, 0303 health sciences, Multidisciplinary, biology, Cell Cycle, COMMON VARIANTS, Genomics, Phenotype, anemia, 3. Good health, Haematopoiesis, DROSOPHILA, Drosophila melanogaster, medicine.anatomical_structure, HEMOGLOBIN LEVELS, Organ Specificity, 030220 oncology & carcinogenesis, Cytokines, Female, RNA Interference, TRAITS, Signal Transduction, EXPRESSION, Polymorphism, Single Nucleotide, Article, Genomic disorders and inherited multi-system disorders DCN MP - Plasticity and memory [IGMD 3], 03 medical and health sciences, SDG 3 - Good Health and Well-being, Genetic, blood, medicine, Animals, Humans, GENOME-WIDE ASSOCIATION, 030304 developmental biology, RECEPTOR, CONSORTIUM, ta3121, hemoglobin, biology.organism_classification, Hematopoiesis, meta-analysis, Red blood cell, Gene Expression Regulation, Genetic Loci, Expression quantitative trait loci, genome-wide association studies, Genome-Wide Association Study
Abstract

Item does not contain fulltext Anaemia is a chief determinant of global ill health, contributing to cognitive impairment, growth retardation and impaired physical capacity. To understand further the genetic factors influencing red blood cells, we carried out a genome-wide association study of haemoglobin concentration and related parameters in up to 135,367 individuals. Here we identify 75 independent genetic loci associated with one or more red blood cell phenotypes at P < 10(-8), which together explain 4-9% of the phenotypic variance per trait. Using expression quantitative trait loci and bioinformatic strategies, we identify 121 candidate genes enriched in functions relevant to red blood cell biology. The candidate genes are expressed preferentially in red blood cell precursors, and 43 have haematopoietic phenotypes in Mus musculus or Drosophila melanogaster. Through open-chromatin and coding-variant analyses we identify potential causal genetic variants at 41 loci. Our findings provide extensive new insights into genetic mechanisms and biological pathways controlling red blood cell formation and function.

Published
2012

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