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3. The GALAH Survey: Scientific Motivation

Author

De Silva, G. M., Freeman, K. C., Bland-Hawthorn, J., Martell, S., de Boer, E. Wylie, Asplund, M., Keller, S., Sharma, S., Zucker, D. B., Zwitter, T., Anguiano, B., Bacigalupo, C., Bayliss, D., Beavis, M. A., Bergemann, M., Campbell, S., Cannon, R., Carollo, D., Casagrande, L., Casey, A. R., Da Costa, G., D'Orazi, V., Dotter, A., Duong, L., Heger, A., Ireland, M. J., Kafle, P. R., Kos, J., Lattanzio, J., Lewis, G. F., Lin, J., Lind, K., Munari, U., Nataf, D. M., O'Toole, S., Parker, Q. A., Reid, W., Schlesinger, K. J., Sheinis, A., Simpson, J. D., Stello, D., Ting, Y-S., Traven, G., Watson, F., Wittenmyer, R., Yong, D., and Zerjal, M.

Subjects
Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics
Abstract

The GALAH survey is a large high-resolution spectroscopic survey using the newly commissioned HERMES spectrograph on the Anglo-Australian Telescope. The HERMES spectrograph provides high-resolution (R ~28,000) spectra in four passbands for 392 stars simultaneously over a 2 degree field of view. The goal of the survey is to unravel the formation and evolutionary history of the Milky Way, using fossil remnants of ancient star formation events which have been disrupted and are now dispersed throughout the Galaxy. Chemical tagging seeks to identify such dispersed remnants solely from their common and unique chemical signatures; these groups are unidentifiable from their spatial, photometric or kinematic properties. To carry out chemical tagging, the GALAH survey will acquire spectra for a million stars down to V~14. The HERMES spectra of FGK stars contain absorption lines from 29 elements including light proton-capture elements, alpha-elements, odd-Z elements, iron-peak elements and n-capture elements from the light and heavy s-process and the r-process. This paper describes the motivation and planned execution of the GALAH survey, and presents some results on the first-light performance of HERMES., Comment: 16 pages, 7 figures

Published
2015
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7. The RAdial Velocity Experiment (RAVE): Fourth data release

Author

Kordopatis, G., Gilmore, G., Steinmetz, M., Boeche, C., Seabroke, G. M., Siebert, A., Zwitter, T., Binney, J., de Laverny, P., Recio-Blanco, A., Williams, M. E. K., Piffl, T., Enke, H., Roeser, S., Bijaoui, A., Wyse, R. F. G., Freeman, K., Munari, U., Carillo, I., Anguiano, B., Burton, D., Campbell, R., Cass, C. J. P., Fiegert, K., Hartley, M., Parker, Q. A., Reid, W., Ritter, A., Russell, K. S., Stupart, M., Watson, F. G., Bienayme, O., Bland-Hawthorn, J., Gerhard, O., Gibson, B. K., Grebel, E. K., Helmi, A., Navarro, J. F., Conrad, C., Famaey, B., Faure, C., Just, A., Kos, J., Matijevic, G., McMillan, P. J., Minchev, I., Scholz, R., Sharma, S., Siviero, A., de Boer, E. Wylie, and Zerjal, M.

Subjects
Astrophysics - Astrophysics of Galaxies, Astrophysics - Solar and Stellar Astrophysics
Abstract

We present the stellar atmospheric parameters (effective temperature, surface gravity, overall metallicity), radial velocities, individual abundances and distances determined for 425 561 stars, which constitute the fourth public data release of the RAdial Velocity Experiment (RAVE). The stellar atmospheric parameters are computed using a new pipeline, based on the algorithms of MATISSE and DEGAS. The spectral degeneracies and the 2MASS photometric information are now better taken into consideration, improving the parameter determination compared to the previous RAVE data releases. The individual abundances for six elements (magnesium, aluminum, silicon, titanium, iron and nickel) are also given, based on a special-purpose pipeline which is also improved compared to that available for the RAVE DR3 and Chemical DR1 data releases. Together with photometric information and proper motions, these data can be retrieved from the RAVE collaboration website and the Vizier database., Comment: 40 pages, 36 figures, accepted in AJ

Published
2013
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8. ARGOS IV: The Kinematics of the Milky Way Bulge

Author

Ness, M., Freeman, K., Athanassoula, E., Wylie-de-Boer, E., Bland-Hawthorn, J., Asplund, M., Lewis, G. F, Yong, D., Lane, R. R., Kiss, L. L, and Ibata, R.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

We present the kinematic results from our ARGOS spectroscopic survey of the Galactic bulge of the Milky Way. Our aim is to understand the formation of the Galactic bulge. We examine the kinematics of about 17,400 stars in the bulge located within 3.5 kpc of the Galactic centre, identified from the 28,000 star ARGOS survey. We aim to determine if the formation of the bulge has been internally driven from disk instabilities as suggested by its boxy shape, or if mergers have played a significant role as expected from Lambda CDM simulations. From our velocity measurements across latitudes b = -5 deg, -7.5 deg and -10 deg we find the bulge to be a cylindrically rotating system that transitions smoothly out into the disk. Within the bulge, we find a kinematically distinct metal-poor population ([Fe/H] < -1.0) that is not rotating cylindrically. The 5% of our stars with [Fe/H] < -1.0 are a slowly rotating spheroidal population, which we believe are stars of the metal weak thick disk and halo which presently lie in the inner Galaxy. The kinematics of the two bulge components that we identified in ARGOS paper III (mean [Fe/H] = -0.25 and [Fe/H] = +0.15, respectively) demonstrate that they are likely to share a common formation origin and are distinct from the more metal poor populations of the thick disk and halo which are colocated inside the bulge. We do not exclude an underlying merger generated bulge component but our results favour bulge formation from instabilities in the early thin disk., Comment: Accepted MNRAS 25 March 2013, 12 pages, 11 figures

Published
2013
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9. ARGOS III: Stellar Populations in the Galactic Bulge of the Milky Way

Author

Ness, M., Freeman, K., Athanassoula, E., de Boer, E. Wylie, Hawthorn, J. Bland, Asplund, M., Lewis, G. F., Yong, D., Lane, R. R., and Kiss, L. L.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

We present the metallicity results from the ARGOS spectroscopic survey of the Galactic bulge. Our aim is to understand the formation of the Galactic bulge: did it form via mergers, as expected from Lambda CDM theory, or from disk instabilities, as suggested by its boxy/peanut shape, or both? We have obtained spectra for 28,000 stars at a spectral resolution of R = 11,000. From these spectra, we have determined stellar parameters and distances to an accuracy of < 1.5 kpc. The stars in the inner Galaxy span a large range in [Fe/H], -2.8 < [Fe/H] < +0.6. From the spatial distribution of the red clump stars as a function of [Fe/H] (Ness et al. 2012a), we propose that the stars with [Fe/H] > -0.5 are part of the boxy/peanut bar/bulge. We associate the lower metallicity stars ([Fe/H] < -0.5) with the thick disk, which may be puffed up in the inner region, and with the inner regions of the metal-weak thick disk and inner halo. For the bulge stars with [Fe/H] > -0.5, we find two discrete populations; (i) stars with [Fe/H] ~ -0.25 which provide a roughly constant fraction of the stars in the latitude interval b = -5 deg to -10 deg, and (ii) a kinematically colder, more metal-rich population with mean [Fe/H] ~ +0.15 which is more prominent closer to the plane. The changing ratio of these components with latitude appears as a vertical abundance gradient of the bulge. We attribute both of these bulge components to instability-driven bar/bulge formation from the thin disk. We do not exclude a weak underlying classical merger-generated bulge component, but see no obvious kinematic association of any of our bulge stars with such a classical bulge component. [abridged], Comment: Accepted MNRAS, 21 pages, 20 figures, 6 tables

Published
2012
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10. ARGOS II: The Galactic Bulge Survey

Author

Freeman, K., Ness, M., de Boer, E. Wylie, Athanassoula, E., Hawthorn, J. Bland, Asplund, M., Lewis, G., Yong, D., Lane, R., Kiss, L., and Ibata, R.

Subjects
Astrophysics - Galaxy Astrophysics
Abstract

We describe the motivation, field locations and stellar selection for the ARGOS spectroscopic survey of 28,000 stars in the bulge and inner disk of the Milky Way galaxy across latitudes of b = -5 deg to -10 deg. The primary goal of this survey is to constrain the formation processes of the bulge and establish whether it is predominantly a merger or instability remnant. From the spectra (R = 11,000), we have measured radial velocities and determined stellar parameters, including metallicities and [alpha/Fe] ratios. Distances were estimated from the derived stellar parameters and about 14,000 stars are red giants within 3.5 kpc of the Galactic centre. In this paper, we present the observations and analysis methods. Subsequent papers (III and IV) will discuss the stellar metallicity distribution and kinematics of the Galactic bulge and inner disk, and the implications for the formation of the bulge., Comment: accepted MNRAS, 13 pages, 10 figures; Monthly Notices of the Royal Astronomical Society 2012

Published
2012
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11. The origin of the split red clump in the Galactic bulge of the Milky Way

Author

Ness, M., Freeman, K., Athanassoula, E., Wylie-de-Boer, E., Bland-Hawthorn, J., Lewis, G. F., Yong, D., Asplund, M., Lane, R. R., Kiss, L. L, and Ibata, R.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

Near the minor axis of the Galactic bulge, at latitudes b < -5 degrees, the red giant clump stars are split into two components along the line of sight. We investigate this split using the three fields from the ARGOS survey that lie on the minor axis at (l,b) = (0,-5), (0,-7.5), (0,-10) degrees. The separation is evident for stars with [Fe/H] > -0.5 in the two higher-latitude fields, but not in the field at b = -5 degrees. Stars with [Fe/H] < -0.5 do not show the split. We compare the spatial distribution and kinematics of the clump stars with predictions from an evolutionary N-body model of a bulge that grew from a disk via bar-related instabilities. The density distribution of the peanut-shaped model is depressed near its minor axis. This produces a bimodal distribution of stars along the line of sight through the bulge near its minor axis, very much as seen in our observations. The observed and modelled kinematics of the two groups of stars are also similar. We conclude that the split red clump of the bulge is probably a generic feature of boxy/peanut bulges that grew from disks, and that the disk from which the bulge grew had relatively few stars with [Fe/H] < -0.5, Comment: 12 pages, 9 figures, accepted for publication in ApJ

Published
2012
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12. The Radial Velocity Experiment (RAVE): second data release

Author

Zwitter, T., Siebert, A., Munari, U., Freeman, K. C., Siviero, A., Watson, F. G., Fulbright, J. P., Wyse, R. F. G., Campbell, R., Seabroke, G. M., Williams, M., Steinmetz, M., Bienayme, O., Gilmore, G., Grebel, E. K., Helmi, A., Navarro, J. F., Anguiano, B., Boeche, C., Burton, D., Cass, P., Dawe, J., Fiegert, K., Hartley, M., Russell, K., Veltz, L., Bailin, J., Binney, J., Bland-Hawthorn, J., Brown, A., Dehnen, W., Evans, N. W., Fiorentin, P. Re, Fiorucci, M., Gerhard, O., Gibson, B., Kelz, A., Kujken, K., Matijevic, G., Minchev, I., Parker, Q. A., Penarrubia, J., Quillen, A., Read, M. A., Reid, W., Roeser, S., Ruchti, G., Scholz, R. -D., Smith, M. C., Sordo, R., Tolstoi, E., Tomasella, L., Vidrih, S., and de Boer, E. Wylie

Subjects
Astrophysics
Abstract

We present the second data release of the Radial Velocity Experiment (RAVE), an ambitious spectroscopic survey to measure radial velocities (RVs) and stellar atmosphere parameters of up to one million stars using the 6dF multi-object spectrograph on the 1.2-m UK Schmidt Telescope of the Anglo-Australian Observatory (AAO). It is obtaining medium resolution spectra (median R=7,500) in the Ca-triplet region (8,410--8,795 \AA) for southern hemisphere stars in the magnitude range 9

Published
2008
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13. s- and r-process element abundances in the CMD of 47 Tucanae using the Robert Stobie Spectrograph on SALT

Author

Worley, C. C., Cottrell, P. L., and de Boer, E. C. Wylie

Subjects
Astrophysics
Abstract

A recent study by Wylie et al 2006 has revealed that s-process element abundances are enhanced relative to iron in both red giant branch and asymptotic giant branch stars of 47 Tucanae. A more detailed investigation into s-process element abundances throughout the colour-magnitude diagram of 47 Tucanae is vital in order to determine whether the observed enhancements are intrinsic to the cluster. This paper explores this possibility through observational and theoretical means. The visibility of s- and r-process element lines in synthetic spectra of giant and dwarf stars throughout the colour magnitude diagram of 47 Tucanae has been explored. It was determined that a resolving power of 10 000 was sufficient to observe s-process element abundance variations in globular cluster giant branch stars. These synthetic results were compared with the spectra of eleven 47 Tucanae giant branch stars observed during the performance verification of the Robert Stobie Spectrograph on the Southern African Large Telescope. Three s-process elements, Zr, Ba, Nd, and one r-process element, Eu, were investigated. No abundance variations were found such that [X/Fe] = 0.0 +/- 0.5 dex. It was concluded that this resolving power, R ~ 5000, was not sufficient to obtain exact abundances but upper limits on the s-process element abundances could be determined., Comment: 7 pages, 11 figures

Published
2008
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16. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author

Denomme-Pichon A. -S., Bruel A. -L., Duffourd Y., Safraou H., Thauvin-Robinet C., Tran Mau-Them F., Philippe C., Vitobello A., Jean-Marcais N., Moutton S., Thevenon J., Faivre L., Matalonga L., de Boer E., Gilissen C., Hoischen A., Kleefstra T., Pfundt R., de Vries B. B. A., Willemsen M. H., Vissers L. E. L. M., Jackson A., Banka S., Clayton-Smith J., Benetti E., Fallerini C., Renieri A., Ciolfi A., Dallapiccola B., Pizzi S., Radio F. C., Tartaglia M., Ellwanger K., Graessner H., Haack T. B., Zurek B., Havlovicova M., Macek M., Ryba L., Schwarz M., Votypka P., Lopez-Martin E., Posada M., Mencarelli M. A., Rooryck C., Trimouille A., Verloes A., Abbott K. M., Kerstjens M., Martin E. L., Maystadt I., Morleo M., Nigro V., Pinelli M., Riess O., Agathe J. -M. D. S., Santen G. W. E., Thauvin C., Torella A., Vissers L., Zguro K., Boer E. D., Cohen E., Danis D., Gao F., Horvath R., Johari M., Johanson L., Li S., Morsy H., Nelson I., Paramonov I., te Paske I. B. A. W., Robinson P., Savarese M., Steyaert W., Topf A., van der Velde J. K., Vandrovcova J., Ossowski S., Demidov G., Sturm M., Schulze-Hentrich J. M., Schule R., Xu J., Kessler C., Wayand M., Synofzik M., Wilke C., Traschutz A., Schols L., Hengel H., Lerche H., Kegele J., Heutink P., Brunner H., Scheffer H., Hoogerbrugge N., 't Hoen P. A. C., Sablauskas K., de Voer R. M., Kamsteeg E. -J., van de Warrenburg B., van Os N., Paske I. T., Janssen E., Steehouwer M., Yaldiz B., Brookes A. J., Veal C., Gibson S., Maddi V., Mehtarizadeh M., Riaz U., Warren G., Dizjikan F. Y., Shorter T., Straub V., Bettolo C. M., Manera J. D., Hambleton S., Engelhardt K., Alexander E., Peyron C., Pelissier A., Beltran S., Gut I. G., Laurie S., Piscia D., Papakonstantinou A., Bullich G., Corvo A., Fernandez-Callejo M., Hernandez C., Pico D., Lochmuller H., Gumus G., Bros-Facer V., Rath A., Hanauer M., Lagorce D., Hongnat O., Chahdil M., Lebreton E., Stevanin G., Durr A., Davoine C. -S., Guillot-Noel L., Heinzmann A., Coarelli G., Bonne G., Evangelista T., Allamand V., Ben Yaou R., Metay C., Eymard B., Atalaia A., Stojkovic T., Turnovec M., Thomasova D., Kremlikova R. P., Frankova V., Liskova P., Dolezalova P., Parkinson H., Keane T., Freeberg M., Thomas C., Spalding D., Robert G., Costa A., Patch C., Hanna M., Houlden H., Reilly M., Efthymiou S., Cali E., Magrinelli F., Sisodiya S. M., Rohrer J., Muntoni F., Zaharieva I., Sarkozy A., Timmerman V., Baets J., de Vries G., De Winter J., Beijer D., de Jonghe P., Van de Vondel L., De Ridder W., Weckhuysen S., Mutarelli M., Varavallo A., Banfi S., Musacchia F., Piluso G., Ferlini A., Selvatici R., Gualandi F., Bigoni S., Rossi R., Neri M., Aretz S., Spier I., Sommer A. K., Peters S., Oliveira C., Pelaez J. G., Matos A. R., Jose C. S., Ferreira M., Gullo I., Fernandes S., Garrido L., Ferreira P., Carneiro F., Swertz M. A., Johansson L., van der Vries G., Neerincx P. B., Ruvolo D., Kerstjens Frederikse W. S., Zonneveld-Huijssoon E., Roelofs-Prins D., van Gijn M., Kohler S., Metcalfe A., Drunat S., Heron D., Mignot C., Keren B., Lacombe D., Capella G., Valle L., Holinski-Feder E., Laner A., Steinke-Lange V., Cilio M. -R., Carpancea E., Depondt C., Lederer D., Sznajer Y., Duerinckx S., Mary S., Macaya A., Cazurro-Gutierrez A., Perez-Duenas B., Munell F., Jarava C. F., Maso L. B., Marce-Grau A., Colobran R., Hackman P., Udd B., Hemelsoet D., Dermaut B., Schuermans N., Poppe B., Verdin H., Osorio A. N., Depienne C., Roos A., Cordts I., Deschauer M., Striano P., Zara F., Riva A., Iacomino M., Uva P., Scala M., Scudieri P., Basak A. N., Claeys K., Boztug K., Haimel M., W. E G., Ruivenkamp C. A. L., Natera de Benito D., Thompson R., Polavarapu K., Grimbacher B., Zaganas I., Kokosali E., Lambros M., Evangeliou A., Spilioti M., Kapaki E., Bourbouli M., Balicza P., Molnar M. J., De la Paz M. P., Sanchez E. B., Delgado B. M., Alonso Garcia de la Rosa F. J., Schrock E., Rump A., Mei D., Vetro A., Balestrini S., Guerrini R., Chinnery P. F., Ratnaike T., Schon K., Maver A., Peterlin B., Munchau A., Lohmann K., Herzog R., Pauly M., May P., Beeson D., Cossins J., Furini S., Afenjar A., Goldenberg A., Masurel A., Phan A., Dieux-Coeslier A., Fargeot A., Guerrot A. -M., Toutain A., Molin A., Sorlin A., Putoux A., Jouret B., Laudier B., Demeer B., Doray B., Bonniaud B., Isidor B., Gilbert-Dussardier B., Leheup B., Reversade B., Paul C., Vincent-Delorme C., Neiva C., Poirsier C., Quelin C., Chiaverini C., Coubes C., Francannet C., Colson C., Desplantes C., Wells C., Goizet C., Sanlaville D., Amram D., Lehalle D., Genevieve D., Gaillard D., Zivi E., Sarrazin E., Steichen E., Schaefer E., Lacaze E., Jacquemin E., Bongers E., Kilic E., Colin E., Giuliano F., Prieur F., Laffargue F., Morice-Picard F., Petit F., Cartault F., Feillet F., Baujat G., Morin G., Diene G., Journel H., Perthus I., Lespinasse J., Alessandri J. -L., Amiel J., Martinovic J., Delanne J., Albuisson J., Lambert L., Perrin L., Ousager L. B., Van Maldergem L., Pinson L., Ruaud L., Samimi M., Bournez M., Bonnet-Dupeyron M. N., Vincent M., Jacquemont M. -L., Cordier-Alex M. -P., Gerard-Blanluet M., Willems M., Spodenkiewicz M., Doco-Fenzy M., Rossi M., Renaud M., Fradin M., Mathieu M., Holder-Espinasse M. H., Houcinat N., Hanna N., Leperrier N., Chassaing N., Philip N., Boute O., Van Kien P. K., Parent P., Bitoun P., Sarda P., Vabres P., Jouk P. -S., Touraine R., El Chehadeh S., Whalen S., Marlin S., Passemard S., Grotto S., Bellanger S. A., Blesson S., Nambot S., Naudion S., Lyonnet S., Odent S., Attie-Bitach T., Busa T., Drouin-Garraud V., Layet V., Bizaoui V., Cusin V., Capri Y., Alembik Y., Unión Europea. Comisión Europea. H2020, Unión Europea. Comisión Europea. 7 Programa Marco, Instituto de Salud Carlos III, Instituto Nacional de Bioinformatica (España), Ministry of Health (República Checa), Ministry of Education, Youth and Sports (República Checa), Denomme-Pichon, A. -S., Bruel, A. -L., Duffourd, Y., Safraou, H., Thauvin-Robinet, C., Tran Mau-Them, F., Philippe, C., Vitobello, A., Jean-Marcais, N., Moutton, S., Thevenon, J., Faivre, L., Matalonga, L., de Boer, E., Gilissen, C., Hoischen, A., Kleefstra, T., Pfundt, R., de Vries, B. B. A., Willemsen, M. H., Vissers, L. E. L. M., Jackson, A., Banka, S., Clayton-Smith, J., Benetti, E., Fallerini, C., Renieri, A., Ciolfi, A., Dallapiccola, B., Pizzi, S., Radio, F. C., Tartaglia, M., Ellwanger, K., Graessner, H., Haack, T. B., Zurek, B., Havlovicova, M., Macek, M., Ryba, L., Schwarz, M., Votypka, P., Lopez-Martin, E., Posada, M., Mencarelli, M. A., Rooryck, C., Trimouille, A., Verloes, A., Abbott, K. M., Kerstjens, M., Martin, E. L., Maystadt, I., Morleo, M., Nigro, V., Pinelli, M., Riess, O., Agathe, J. -M. D. S., Santen, G. W. E., Thauvin, C., Torella, A., Vissers, L., Zguro, K., Boer, E. D., Cohen, E., Danis, D., Gao, F., Horvath, R., Johari, M., Johanson, L., Li, S., Morsy, H., Nelson, I., Paramonov, I., te Paske, I. B. A. W., Robinson, P., Savarese, M., Steyaert, W., Topf, A., van der Velde, J. K., Vandrovcova, J., Ossowski, S., Demidov, G., Sturm, M., Schulze-Hentrich, J. M., Schule, R., Xu, J., Kessler, C., Wayand, M., Synofzik, M., Wilke, C., Traschutz, A., Schols, L., Hengel, H., Lerche, H., Kegele, J., Heutink, P., Brunner, H., Scheffer, H., Hoogerbrugge, N., 't Hoen, P. A. C., Sablauskas, K., de Voer, R. M., Kamsteeg, E. -J., van de Warrenburg, B., van Os, N., Paske, I. T., Janssen, E., Steehouwer, M., Yaldiz, B., Brookes, A. J., Veal, C., Gibson, S., Maddi, V., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Straub, V., Bettolo, C. M., Manera, J. D., Hambleton, S., Engelhardt, K., Alexander, E., Peyron, C., Pelissier, A., Beltran, S., Gut, I. G., Laurie, S., Piscia, D., Papakonstantinou, A., Bullich, G., Corvo, A., Fernandez-Callejo, M., Hernandez, C., Pico, D., Lochmuller, H., Gumus, G., Bros-Facer, V., Rath, A., Hanauer, M., Lagorce, D., Hongnat, O., Chahdil, M., Lebreton, E., Stevanin, G., Durr, A., Davoine, C. -S., Guillot-Noel, L., Heinzmann, A., Coarelli, G., Bonne, G., Evangelista, T., Allamand, V., Ben Yaou, R., Metay, C., Eymard, B., Atalaia, A., Stojkovic, T., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Liskova, P., Dolezalova, P., Parkinson, H., Keane, T., Freeberg, M., Thomas, C., Spalding, D., Robert, G., Costa, A., Patch, C., Hanna, M., Houlden, H., Reilly, M., Efthymiou, S., Cali, E., Magrinelli, F., Sisodiya, S. M., Rohrer, J., Muntoni, F., Zaharieva, I., Sarkozy, A., Timmerman, V., Baets, J., de Vries, G., De Winter, J., Beijer, D., de Jonghe, P., Van de Vondel, L., De Ridder, W., Weckhuysen, S., Mutarelli, M., Varavallo, A., Banfi, S., Musacchia, F., Piluso, G., Ferlini, A., Selvatici, R., Gualandi, F., Bigoni, S., Rossi, R., Neri, M., Aretz, S., Spier, I., Sommer, A. K., Peters, S., Oliveira, C., Pelaez, J. G., Matos, A. R., Jose, C. S., Ferreira, M., Gullo, I., Fernandes, S., Garrido, L., Ferreira, P., Carneiro, F., Swertz, M. A., Johansson, L., van der Vries, G., Neerincx, P. B., Ruvolo, D., Kerstjens Frederikse, W. S., Zonneveld-Huijssoon, E., Roelofs-Prins, D., van Gijn, M., Kohler, S., Metcalfe, A., Drunat, S., Heron, D., Mignot, C., Keren, B., Lacombe, D., Capella, G., Valle, L., Holinski-Feder, E., Laner, A., Steinke-Lange, V., Cilio, M. -R., Carpancea, E., Depondt, C., Lederer, D., Sznajer, Y., Duerinckx, S., Mary, S., Macaya, A., Cazurro-Gutierrez, A., Perez-Duenas, B., Munell, F., Jarava, C. F., Maso, L. B., Marce-Grau, A., Colobran, R., Hackman, P., Udd, B., Hemelsoet, D., Dermaut, B., Schuermans, N., Poppe, B., Verdin, H., Osorio, A. N., Depienne, C., Roos, A., Cordts, I., Deschauer, M., Striano, P., Zara, F., Riva, A., Iacomino, M., Uva, P., Scala, M., Scudieri, P., Basak, A. N., Claeys, K., Boztug, K., Haimel, M., W. E, G., Ruivenkamp, C. A. L., Natera de Benito, D., Thompson, R., Polavarapu, K., Grimbacher, B., Zaganas, I., Kokosali, E., Lambros, M., Evangeliou, A., Spilioti, M., Kapaki, E., Bourbouli, M., Balicza, P., Molnar, M. J., De la Paz, M. P., Sanchez, E. B., Delgado, B. M., Alonso Garcia de la Rosa, F. J., Schrock, E., Rump, A., Mei, D., Vetro, A., Balestrini, S., Guerrini, R., Chinnery, P. F., Ratnaike, T., Schon, K., Maver, A., Peterlin, B., Munchau, A., Lohmann, K., Herzog, R., Pauly, M., May, P., Beeson, D., Cossins, J., Furini, S., Afenjar, A., Goldenberg, A., Masurel, A., Phan, A., Dieux-Coeslier, A., Fargeot, A., Guerrot, A. -M., Toutain, A., Molin, A., Sorlin, A., Putoux, A., Jouret, B., Laudier, B., Demeer, B., Doray, B., Bonniaud, B., Isidor, B., Gilbert-Dussardier, B., Leheup, B., Reversade, B., Paul, C., Vincent-Delorme, C., Neiva, C., Poirsier, C., Quelin, C., Chiaverini, C., Coubes, C., Francannet, C., Colson, C., Desplantes, C., Wells, C., Goizet, C., Sanlaville, D., Amram, D., Lehalle, D., Genevieve, D., Gaillard, D., Zivi, E., Sarrazin, E., Steichen, E., Schaefer, E., Lacaze, E., Jacquemin, E., Bongers, E., Kilic, E., Colin, E., Giuliano, F., Prieur, F., Laffargue, F., Morice-Picard, F., Petit, F., Cartault, F., Feillet, F., Baujat, G., Morin, G., Diene, G., Journel, H., Perthus, I., Lespinasse, J., Alessandri, J. -L., Amiel, J., Martinovic, J., Delanne, J., Albuisson, J., Lambert, L., Perrin, L., Ousager, L. B., Van Maldergem, L., Pinson, L., Ruaud, L., Samimi, M., Bournez, M., Bonnet-Dupeyron, M. N., Vincent, M., Jacquemont, M. -L., Cordier-Alex, M. -P., Gerard-Blanluet, M., Willems, M., Spodenkiewicz, M., Doco-Fenzy, M., Rossi, M., Renaud, M., Fradin, M., Mathieu, M., Holder-Espinasse, M. H., Houcinat, N., Hanna, N., Leperrier, N., Chassaing, N., Philip, N., Boute, O., Van Kien, P. K., Parent, P., Bitoun, P., Sarda, P., Vabres, P., Jouk, P. -S., Touraine, R., El Chehadeh, S., Whalen, S., Marlin, S., Passemard, S., Grotto, S., Bellanger, S. A., Blesson, S., Nambot, S., Naudion, S., Lyonnet, S., Odent, S., Attie-Bitach, T., Busa, T., Drouin-Garraud, V., Layet, V., Bizaoui, V., Cusin, V., Capri, Y., Alembik, Y., and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]

Subjects
Exome reanalysis, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Multidisciplinaire, généralités & autres [D99] [Sciences de la santé humaine], Developmental disorder, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Biology and Life Sciences, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], ClinVar, Rare diseases, All institutes and research themes of the Radboud University Medical Center, Medicine and Health Sciences, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], Multidisciplinary, general & others [D99] [Human health sciences], Exome reanalysi, Genetics (clinical)
Abstract

Purpose: Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the "ClinVar low-hanging fruit" reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods: Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results: We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion: The "ClinVar low-hanging fruit" analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement number 779257. Data were analyzed using the RD-Connect Genome-Phenome Analysis Platform, which received funding from the EU projects RD-Connect, Solve-RD, and European Joint Programme on Rare Diseases (grant numbers FP7 305444, H2020 779257, H2020 825575), Instituto de Salud Carlos III (grant numbers PT13/0001/0044, PT17/0009/0019; Instituto Nacional de Bioinformática), and ELIXIR Implementation Studies. The collaborations in this study were facilitated by the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies, one of the 24 European Reference Networks approved by the European Reference Network Board of Member States, cofunded by the European Commission. This project was supported by the Czech Ministry of Health (number 00064203) and by the Czech Ministry of Education, Youth and Sports (number - LM2018132) to M.M. Sí

Published
2023

18. A complex structural variant near SOX3 causes X-linked split-hand/foot malformation

Author

de Boer, E. (Elke), Marcelis, C. (Carlo), Neveling, K. (Kornelia), van Beusekom, E. (Ellen), Hoischen, A. (Alexander), Klein, W. M. (Willemijn M.), de Leeuw, N. (Nicole), Mantere, T. (Tuomo), Melo, U. S. (Uirá S.), van Reeuwijk, J. (Jeroen), Smeets, D. (Dominique), Spielmann, M. (Malte), Kleefstra, T. (Tjitske), van Bokhoven, H. (Hans), Vissers, L. E. (Lisenka E. L. M.), de Boer, E. (Elke), Marcelis, C. (Carlo), Neveling, K. (Kornelia), van Beusekom, E. (Ellen), Hoischen, A. (Alexander), Klein, W. M. (Willemijn M.), de Leeuw, N. (Nicole), Mantere, T. (Tuomo), Melo, U. S. (Uirá S.), van Reeuwijk, J. (Jeroen), Smeets, D. (Dominique), Spielmann, M. (Malte), Kleefstra, T. (Tjitske), van Bokhoven, H. (Hans), and Vissers, L. E. (Lisenka E. L. M.)

Abstract

Summary Split-hand/foot malformation (SHFM) is a congenital limb defect most typically presenting with median clefts in hands and/or feet, that can occur in a syndromic context as well as in isolated form. SHFM is caused by failure to maintain normal apical ectodermal ridge function during limb development. Although several genes and contiguous gene syndromes are implicated in the monogenic etiology of isolated SHFM, the disorder remains genetically unexplained for many families and associated genetic loci. We describe a family with isolated X-linked SHFM, for which the causative variant could be detected after a diagnostic journey of 20 years. We combined well-established approaches including microarray-based copy number variant analysis and fluorescence in situ hybridization coupled with optical genome mapping and whole genome sequencing. This strategy identified a complex structural variant (SV) comprising a 165-kb gain of 15q26.3 material ([GRCh37/hg19] chr15:99795320-99960362dup) inserted in inverted position at the site of a 38-kb deletion on Xq27.1 ([GRCh37/hg19] chrX:139481061-139518989del). In silico analysis suggested that the SV disrupts the regulatory framework on the X chromosome and may lead to SOX3 misexpression. We hypothesize that SOX3 dysregulation in the developing limb disturbed the fine balance between morphogens required for maintaining AER function, resulting in SHFM in this family.

Published
2023

22. P1530: PERITRANFUSIONAL C1-INHIBITOR IN PATIENTS WITH SEVERE COMPLEMENT-MEDIATED AUTOIMMUNE HEMOLYTIC ANEMIA: AN OPEN LABEL PHASE 2 TRIAL.

Author

de Boer, E. C. W., primary, Jalink, M., additional, Delvasto-Nuñes, L., additional, Meulenbroek, E. M., additional, Baas, I., additional, Janssen, S. R., additional, Dijkman, E. E., additional, Gelderman, K. A., additional, Wouters, D., additional, Engel, M. D., additional, de Haas, M., additional, Kersten, M.-J., additional, Jongerius, I., additional, Zeerleder, S., additional, and Vos, J. M., additional

Published
2022
Full Text
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27. Correction: A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis (European Journal of Human Genetics, (2021), 29, 9, (1359-1368), 10.1038/s41431-021-00900-2)

Author

de Boer E., Ockeloen C. W., Matalonga L., Horvath R., Cohen E., Cuesta I., Danis D., Denomme-Pichon A. -S., Duffourd Y., Gilissen C., Johari M., Laurie S., Li S., Nelson I., Peters S., Paramonov I., Prasanth S., Robinson P., Sablauskas K., Savarese M., Steyaert W., Topf A., van der Velde J. K., Vitobello A., Rodenburg R. J., Coenen M. J. H., Janssen M., Henssen D., Banka S., Benetti E., Casari G., Ciolfi A., Clayton-Smith J., Dallapiccola B., Faivre L., Haack T. B., Hammarsjo A., Havlovicova M., Hoischen A., Hugon A., Jackson A., Kleefstra T., Lindstrand A., Lopez-Martin E., Macek M., Nigro V., Nordgren A., Pettersson M., Pinelli M., Pizzi S., Posada M., Radio F. C., Renieri A., Rooryck C., Ryba L., Schwarz M., Tartaglia M., Thauvin C., Torella A., Verloes A., Vissers L., Vyshka K., Zurek B., Trimouille A., Vissers L. E. L. M., de Boer, E., Ockeloen, C. W., Matalonga, L., Horvath, R., Cohen, E., Cuesta, I., Danis, D., Denomme-Pichon, A. -S., Duffourd, Y., Gilissen, C., Johari, M., Laurie, S., Li, S., Nelson, I., Peters, S., Paramonov, I., Prasanth, S., Robinson, P., Sablauskas, K., Savarese, M., Steyaert, W., Topf, A., van der Velde, J. K., Vitobello, A., Rodenburg, R. J., Coenen, M. J. H., Janssen, M., Henssen, D., Banka, S., Benetti, E., Casari, G., Ciolfi, A., Clayton-Smith, J., Dallapiccola, B., Faivre, L., Haack, T. B., Hammarsjo, A., Havlovicova, M., Hoischen, A., Hugon, A., Jackson, A., Kleefstra, T., Lindstrand, A., Lopez-Martin, E., Macek, M., Nigro, V., Nordgren, A., Pettersson, M., Pinelli, M., Pizzi, S., Posada, M., Radio, F. C., Renieri, A., Rooryck, C., Ryba, L., Schwarz, M., Tartaglia, M., Thauvin, C., Torella, A., Verloes, A., Vissers, L., Vyshka, K., Zurek, B., Trimouille, A., and Vissers, L. E. L. M.

Abstract

In the original publication of the article, consortium author lists were missing in the article. The details are as below.

Published
2021

28. Correction: Solving unsolved rare neurological diseases—a Solve-RD viewpoint (European Journal of Human Genetics, (2021), 29, 9, (1332-1336), 10.1038/s41431-021-00901-1)

Author

Schule R., Timmann D., Erasmus C. E., Reichbauer J., Wayand M., Baets J., Balicza P., Chinnery P., Durr A., Haack T., Hengel H., Horvath R., Houlden H., Kamsteeg E. -J., Kamsteeg C., Lohmann K., Macaya A., Marce-Grau A., Maver A., Molnar J., Munchau A., Peterlin B., Riess O., Schols L., Stevanin G., Synofzik M., Timmerman V., van de Warrenburg B., van Os N., Vandrovcova J., Wilke C., Bevot A., Zuchner S., Beltran S., Laurie S., Matalonga L., Graessner H., Zurek B., Ellwanger K., Ossowski S., Demidov G., Sturm M., Schulze-Hentrich J. M., Heutink P., Brunner H., Scheffer H., Hoogerbrugge N., Hoischen A., 't Hoen P. A. C., Vissers L. E. L. M., Gilissen C., Steyaert W., Sablauskas K., de Voer R. M., Janssen E., de Boer E., Steehouwer M., Yaldiz B., Kleefstra T., Brookes A. J., Veal C., Gibson S., Wadsley M., Mehtarizadeh M., Riaz U., Warren G., Dizjikan F. Y., Shorter T., Topf A., Straub V., Bettolo C. M., Specht S., Clayton-Smith J., Banka S., Alexander E., Jackson A., Faivre L., Thauvin C., Vitobello A., Denomme-Pichon A. -S., Duffourd Y., Tisserant E., Bruel A. -L., Peyron C., Pelissier A., Gut I. G., Piscia D., Papakonstantinou A., Bullich G., Corvo A., Garcia C., Fernandez-Callejo M., Hernandez C., Pico D., Paramonov I., Lochmuller H., Gumus G., Bros-Facer V., Rath A., Hanauer M., Olry A., Lagorce D., Havrylenko S., Izem K., Rigour F., Davoine C. -S., Guillot-Noel L., Heinzmann A., Coarelli G., Bonne G., Evangelista T., Allamand V., Nelson I., Yaou R. B., Metay C., Eymard B., Cohen E., Atalaia A., Stojkovic T., Macek M., Turnovec M., Thomasova D., Kremlikova R. P., Frankova V., Havlovicova M., Kremlik V., Parkinson H., Keane T., Spalding D., Senf A., Robinson P., Danis D., Robert G., Costa A., Patch C., Hanna M., Reilly M., Muntoni F., Zaharieva I., Sarkozy A., de Jonghe P., Nigro V., Banfi S., Torella A., Musacchia F., Piluso G., Ferlini A., Selvatici R., Rossi R., Neri M., Aretz S., Spier I., Sommer A. K., Peters S., Oliveira C., Pelaez J. G., Matos A. R., Jose C. S., Ferreira M., Gullo I., Fernandes S., Garrido L., Ferreira P., Carneiro F., Swertz M. A., Johansson L., van der Velde J. K., van der Vries G., Neerincx P. B., Roelofs-Prins D., Kohler S., Metcalfe A., Verloes A., Drunat S., Rooryck C., Trimouille A., Castello R., Morleo M., Pinelli M., Varavallo A., De la Paz M. P., Sanchez E. B., Martin E. L., Delgado B. M., de la Rosa F. J. A. G., Ciolfi A., Dallapiccola B., Pizzi S., Radio F. C., Tartaglia M., Renieri A., Benetti E., Molnar M. J., Herzog R., Pauly M., Osorio A. N., de Benito D. N., Thompson R., Polavarapu K., Beeson D., Cossins J., Cruz P. M. R., Hackman P., Johari M., Savarese M., Udd B., Capella G., Valle L., Holinski-Feder E., Laner A., Steinke-Lange V., Schrock E., Rump A., Schule, R., Timmann, D., Erasmus, C. E., Reichbauer, J., Wayand, M., Baets, J., Balicza, P., Chinnery, P., Durr, A., Haack, T., Hengel, H., Horvath, R., Houlden, H., Kamsteeg, E. -J., Kamsteeg, C., Lohmann, K., Macaya, A., Marce-Grau, A., Maver, A., Molnar, J., Munchau, A., Peterlin, B., Riess, O., Schols, L., Stevanin, G., Synofzik, M., Timmerman, V., van de Warrenburg, B., van Os, N., Vandrovcova, J., Wilke, C., Bevot, A., Zuchner, S., Beltran, S., Laurie, S., Matalonga, L., Graessner, H., Zurek, B., Ellwanger, K., Ossowski, S., Demidov, G., Sturm, M., Schulze-Hentrich, J. M., Heutink, P., Brunner, H., Scheffer, H., Hoogerbrugge, N., Hoischen, A., 't Hoen, P. A. C., Vissers, L. E. L. M., Gilissen, C., Steyaert, W., Sablauskas, K., de Voer, R. M., Janssen, E., de Boer, E., Steehouwer, M., Yaldiz, B., Kleefstra, T., Brookes, A. J., Veal, C., Gibson, S., Wadsley, M., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Topf, A., Straub, V., Bettolo, C. M., Specht, S., Clayton-Smith, J., Banka, S., Alexander, E., Jackson, A., Faivre, L., Thauvin, C., Vitobello, A., Denomme-Pichon, A. -S., Duffourd, Y., Tisserant, E., Bruel, A. -L., Peyron, C., Pelissier, A., Gut, I. G., Piscia, D., Papakonstantinou, A., Bullich, G., Corvo, A., Garcia, C., Fernandez-Callejo, M., Hernandez, C., Pico, D., Paramonov, I., Lochmuller, H., Gumus, G., Bros-Facer, V., Rath, A., Hanauer, M., Olry, A., Lagorce, D., Havrylenko, S., Izem, K., Rigour, F., Davoine, C. -S., Guillot-Noel, L., Heinzmann, A., Coarelli, G., Bonne, G., Evangelista, T., Allamand, V., Nelson, I., Yaou, R. B., Metay, C., Eymard, B., Cohen, E., Atalaia, A., Stojkovic, T., Macek, M., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Havlovicova, M., Kremlik, V., Parkinson, H., Keane, T., Spalding, D., Senf, A., Robinson, P., Danis, D., Robert, G., Costa, A., Patch, C., Hanna, M., Reilly, M., Muntoni, F., Zaharieva, I., Sarkozy, A., de Jonghe, P., Nigro, V., Banfi, S., Torella, A., Musacchia, F., Piluso, G., Ferlini, A., Selvatici, R., Rossi, R., Neri, M., Aretz, S., Spier, I., Sommer, A. K., Peters, S., Oliveira, C., Pelaez, J. G., Matos, A. R., Jose, C. S., Ferreira, M., Gullo, I., Fernandes, S., Garrido, L., Ferreira, P., Carneiro, F., Swertz, M. A., Johansson, L., van der Velde, J. K., van der Vries, G., Neerincx, P. B., Roelofs-Prins, D., Kohler, S., Metcalfe, A., Verloes, A., Drunat, S., Rooryck, C., Trimouille, A., Castello, R., Morleo, M., Pinelli, M., Varavallo, A., De la Paz, M. P., Sanchez, E. B., Martin, E. L., Delgado, B. M., de la Rosa, F. J. A. G., Ciolfi, A., Dallapiccola, B., Pizzi, S., Radio, F. C., Tartaglia, M., Renieri, A., Benetti, E., Molnar, M. J., Herzog, R., Pauly, M., Osorio, A. N., de Benito, D. N., Thompson, R., Polavarapu, K., Beeson, D., Cossins, J., Cruz, P. M. R., Hackman, P., Johari, M., Savarese, M., Udd, B., Capella, G., Valle, L., Holinski-Feder, E., Laner, A., Steinke-Lange, V., Schrock, E., and Rump, A.

Abstract

In the original publication of the article, consortium author lists were missing in the article. The details are given below

Published
2021

35. Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome

Author

Dyment, D. A. (David A.), O'Donnell-Luria, A. (Anne), Agrawal, P. B. (Pankaj B.), Coban Akdemir, Z. (Zeynep), Aleck, K. A. (Kyrieckos A.), Antaki, D. (Danny), Al Sharhan, H. (Hind), Au, P. B. (Ping-Yee B.), Aydin, H. (Hatip), Beggs, A. H. (Alan H.), Bilguvar, K. (Kaya), Boerwinkle, E. (Eric), Brand, H. (Harrison), Brownstein, C. A. (Catherine A.), Buyske, S. (Steve), Chodirker, B. (Bernard), Choi, J. (Jungmin), Chudley, A. E. (Albert E.), Clericuzio, C. L. (Carol L.), Cox, G. F. (Gerald F.), Curry, C. (Cynthia), De Boer, E. (Elke), De Vries, B. B. (Bert B. A.), Dunn, K. (Kathryn), Dutmer, C. M. (Cullen M.), England, E. M. (Eleina M.), Fahrner, J. A. (Jill A.), Geckinli, B. B. (Bilgen B.), Genetti, C. A. (Casie A.), Gezdirici, A. (Alper), Gibson, W. T. (William T.), Gleeson, J. G. (Joseph G.), Greenberg, C. R. (Cheryl R.), Hall, A. (April), Hamosh, A. (Ada), Hartley, T. (Taila), Jhangiani, S. N. (Shalini N.), Karaca, E. (Ender), Kernohan, K. (Kristin), Lauzon, J. L. (Julie L.), Lewis, M. E. (M. E. Suzanne), Lowry, R. B. (R. Brian), López-Giráldez, F. (Francesc), Matise, T. C. (Tara C.), McEvoy-Venneri, J. (Jennifer), McInnes, B. (Brenda), Mhanni, A. (Aziz), Garcia Minaur, S. (Sixto), Moilanen, J. (Jukka), Nguyen, A. (An), Nowaczyk, M. J. (Malgorzata J. M.), Posey, J. E. (Jennifer E.), Õunap, K. (Katrin), Pehlivan, D. (Davut), Pajusalu, S. (Sander), Penney, L. S. (Lynette S.), Poterba, T. (Timothy), Prontera, P. (Paolo), Rodovalho Doriqui, M. J. (Maria Juliana), Sawyer, S. L. (Sarah L.), Sobreira, N. (Nara), Stanley, V. (Valentina), Torun, D. (Deniz), Wargowski, D. (David), Witmer, P. D. (P. Dane), Wong, I. (Isaac), Xing, J. (Jinchuan), Zaki, M. S. (Maha S.), Zhang, Y. (Yeting), C. C. (Care4Rare Consortium), C. F. (Centers For Mendelian Genomics), Boycott, K. M. (Kym M.), Bamshad, M. J. (Michael J.), Nickerson, D. A. (Deborah A.), Blue, E. E. (Elizabeth E.), and Innes, A. M. (A. Micheil)

Subjects
genetic heterogeneity, genome sequencing, Dubowitz syndrome, exome sequencing, microarray
Abstract

Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported with Dubowitz or a “Dubowitz-like” condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome-wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy-number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next-generation sequencing. Overall, the DubS-like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype.

Published
2021

36. Lessons learned during implementation of MR-guided High-Intensity Focused Ultrasound treatment of uterine fibroids

Author

DV&B-MT-Medisch, Anneveldt, K J, Verpalen, I M, Nijholt, I M, Dijkstra, J R, van den Hoed, R D, Van't Veer-Ten Kate, M, de Boer, E, van Osch, J A C, Heijman, E, Naber, H R, Ista, E, Franx, A, Veersema, S, Huirne, J A F, Schutte, J M, Boomsma, M F, DV&B-MT-Medisch, Anneveldt, K J, Verpalen, I M, Nijholt, I M, Dijkstra, J R, van den Hoed, R D, Van't Veer-Ten Kate, M, de Boer, E, van Osch, J A C, Heijman, E, Naber, H R, Ista, E, Franx, A, Veersema, S, Huirne, J A F, Schutte, J M, and Boomsma, M F

Published
2021

37. Targeted RNA sequencing enables detection of relevant translocations, single nucleotide variants and automatic leukemia classification

Author

Sikkema-Raddatz, B., de Lange, K., de Boer, E. N., Bosga, A., Alimohamed, M. Z., Johansson, L. F., Mulder, A. B., Vellenga, E., van Diemen, C. C., Deelen, P., van den Berg, E., Guided Treatment in Optimal Selected Cancer Patients (GUTS), Stem Cell Aging Leukemia and Lymphoma (SALL), and Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)

Published
2020

47. Correction: A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis

Author

M Pettersson, Yannis Duffourd, Marco Tartaglia, Steven Laurie, Tobias B. Haack, Karolis Sablauskas, Andrea Ciolfi, Antonio Vitobello, Aurélien Trimouille, A Nordgren, E Lopez-Martin, A Hugon, K Vyshka, M Schwarz, M Janssen, S Li, Isabelle Nelson, S Prasanth, Christian Gilissen, Lelm Vissers, Rita Horvath, Simone Pizzi, G Casari, Leslie Matalonga, de, Boer, E, Caroline Rooryck, Siddharth Banka, Michele Pinelli, Mridul Johari, Christel Thauvin, Peter N. Robinson, M Posada, Wouter Steyaert, RJ Rodenburg, Marco Savarese, Jill Clayton-Smith, Ana Töpf, Annalaura Torella, A-S Denomme-Pichon, A Hammarsjo, Milan Macek, A Lindstrand, L Ryba, Elisa Benetti, Enzo Cohen, Birte Zurek, van, der, Velde, Jk, CW Ockeloen, D Henssen, Marketa Havlovicova, Daniel Danis, Francesca Clementina Radio, Bruno Dallapiccola, Mjh Coenen, Ida Paramonov, Tjitske Kleefstra, Laurence Faivre, Lisenka E.L.M. Vissers, I Cuesta, Alessandra Renieri, Alexander Hoischen, Alain Verloes, Adam Jackson, Nigro, and Sophia Peters

Subjects
0303 health sciences, Pediatrics, medicine.medical_specialty, business.industry, 030305 genetics & heredity, medicine.disease, Human genetics, MT-TL1, 03 medical and health sciences, Epilepsy, Intellectual disability, Genetics, Spastic tetraparesis, Medicine, business, Genetics (clinical), Exome sequencing
Published
2021

50. Evidence for 28 genetic disorders discovered by combining healthcare and research data

Author

Kaplanis, J., Samocha, K.E., Wiel, L., Zhang, Z., Arvai, K.J., Eberhardt, R.Y., Gallone, G., Lelieveld, S.H., Martin, H.C., McRae, J.F., Short, P.J., Torene, R.I., de Boer, E., Danecek, P., Gardner, E.J., Huang, N., Lord, J., Martincorena, I., Pfundt, R., Reijnders, M.R.F., Yeung, A., Yntema, H.G., Deciphering Developmental Disorders Study, Vissers, L.E.L.M., Juusola, J., Wright, C.F., Brunner, H.G., Firth, H.V., FitzPatrick, D.R., Barrett, J.C., Hurles, M.E., Gilissen, C., and Retterer, K.

Abstract

De novo mutations in protein-coding genes are a well-established cause of developmental disorders. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations. Here, to identify previously undescribed genes associated with developmental disorders, we integrate healthcare and research exome-sequence data from 31,058 parent–offspring trios of individuals with developmental disorders, and develop a simulation-based statistical test to identify gene-specific enrichment of de novo mutations. We identified 285 genes that were significantly associated with developmental disorders, including 28 that had not previously been robustly associated with developmental disorders. Although we detected more genes associated with developmental disorders, much of the excess of de novo mutations in protein-coding genes remains unaccounted for. Modelling suggests that more than 1,000 genes associated with developmental disorders have not yet been described, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of genes associated with developmental disorders.

Published
2020

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