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1. Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

Author

Viennas, E. (Emmanouil), Komianou, A. (Angeliki), Mizzi, C. (Clint), Stojiljkovic, M. (Maja), Mitropoulou, C. (Christina), Muilu, J. (Juha), Vihinen, M. (Mauno), Grypioti, P. (Panagiota), Papadaki, S. (Styliani), Pavlidis, C. (Cristiana), Zukic, B. (Branka), Katsila, T. (Theodora), Spek, P.J. (Peter) van der, Pavlovic, S. (Sonja), Tzimas, G. (Giannis), Patrinos, G.P. (George), Viennas, E. (Emmanouil), Komianou, A. (Angeliki), Mizzi, C. (Clint), Stojiljkovic, M. (Maja), Mitropoulou, C. (Christina), Muilu, J. (Juha), Vihinen, M. (Mauno), Grypioti, P. (Panagiota), Papadaki, S. (Styliani), Pavlidis, C. (Cristiana), Zukic, B. (Branka), Katsila, T. (Theodora), Spek, P.J. (Peter) van der, Pavlovic, S. (Sonja), Tzimas, G. (Giannis), and Patrinos, G.P. (George)

Abstract

FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leadingmostly tomonogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnicmutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications.

Published
2017
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2. Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

Author

Viennas, E, Komianou, A, Mizzi, Clint, Stojiljkovic, M, Mitropoulou, C, Muilu, J, Vihinen, M, Grypioti, P, Papadaki, S, Pavlidis, C, Zukic, B, Katsila, T, van der Spek, Peter, Pavlovic, S, Tzimas, G, Patrinos, George, Viennas, E, Komianou, A, Mizzi, Clint, Stojiljkovic, M, Mitropoulou, C, Muilu, J, Vihinen, M, Grypioti, P, Papadaki, S, Pavlidis, C, Zukic, B, Katsila, T, van der Spek, Peter, Pavlovic, S, Tzimas, G, and Patrinos, George

Published
2017

3. Standard development at the Human Variome Project

Author

Smith, TD, Vihinen, M, Smith, TD, and Vihinen, M

Abstract

The Human Variome Project (HVP) is a world organization working towards facilitating the collection, curation, interpretation and free and open sharing of genetic variation information. A key component of HVP activities is the development of standards and guidelines. HVP Standards are systems, procedures and technologies that the HVP Consortium has determined must be used by HVP-affiliated data sharing infrastructure and should be used by the broader community. HVP guidelines are considered to be beneficial for HVP affiliated data sharing infrastructure and the broader community to adopt. The HVP also maintains a process for assessing systems, processes and tools that implement HVP Standards and Guidelines. Recommended System Status is an accreditation process designed to encourage the adoption of HVP Standards and Guidelines. Here, we describe the HVP standards development process and discuss the accepted standards, guidelines and recommended systems as well as those under acceptance. Certain HVP Standards and Guidelines are already widely adopted by the community and there are committed users for the others.

Published
2015

4. Planning the human variome project: the Spain report.

Author

Kaput, J., Cotton, R.G., Hardman, L., Watson, M., Aqeel, A.I. Al, Al-Aama, J.Y., Al-Mulla, F., Alonso, S., Aretz, S., Auerbach, A.D., Bapat, B., Bernstein, I.T., Bhak, J., Bleoo, S.L., Blocker, H., Brenner, S.E., Burn, J., Bustamante, M., Calzone, R., Cambon-Thomsen, A., Cargill, M., Carrera, P., Cavedon, L., Cho, Y.S., Chung, Y.J., Claustres, M., Cutting, G., Dalgleish, R., Dunnen, J.T. den, Diaz, C., Dobrowolski, S., Santos, M.R. dos, Ekong, R., Flanagan, S.B., Flicek, P., Furukawa, Y., Genuardi, M., Ghang, H., Golubenko, M.V., Greenblatt, M.S., Hamosh, A., Hancock, J.M., Hardison, R., Harrison, T.M., Hoffmann, R., Horaitis, R., Howard, H.J., Barash, C.I., Izagirre, N., Jung, J., Kojima, T., Laradi, S., Lee, Y.S., Lee, J.Y., Gil-da-Silva-Lopes, V.L., Macrae, F.A., Maglott, D., Marafie, M.J., Marsh, S.G., Matsubara, Y., Messiaen, L.M., Moslein, G., Netea, M.G., Norton, M.L., Oefner, P.J., Oetting, W.S., O'Leary, J.C., Ramirez, A.M. de, Paalman, M.H., Parboosingh, J., Patrinos, G.P., Perozzi, G., Phillips, I.R., Povey, S., Prasad, S., Qi, M., Quin, D.J., Ramesar, R.S., Richards, C.S., Savige, J., Scheible, D.G., Scott, R.J., Seminara, D., Shephard, E.A., Sijmons, R.H., Smith, T.D., Sobrido, M.J., Tanaka, T., Tavtigian, S.V., Taylor, G.R., Teague, J., Topel, T., Ullman-Cullere, M., Utsunomiya, J., Kranen, H.J. van, Vihinen, M., Webb, E., Weber, T.K., Yeager, M., Kaput, J., Cotton, R.G., Hardman, L., Watson, M., Aqeel, A.I. Al, Al-Aama, J.Y., Al-Mulla, F., Alonso, S., Aretz, S., Auerbach, A.D., Bapat, B., Bernstein, I.T., Bhak, J., Bleoo, S.L., Blocker, H., Brenner, S.E., Burn, J., Bustamante, M., Calzone, R., Cambon-Thomsen, A., Cargill, M., Carrera, P., Cavedon, L., Cho, Y.S., Chung, Y.J., Claustres, M., Cutting, G., Dalgleish, R., Dunnen, J.T. den, Diaz, C., Dobrowolski, S., Santos, M.R. dos, Ekong, R., Flanagan, S.B., Flicek, P., Furukawa, Y., Genuardi, M., Ghang, H., Golubenko, M.V., Greenblatt, M.S., Hamosh, A., Hancock, J.M., Hardison, R., Harrison, T.M., Hoffmann, R., Horaitis, R., Howard, H.J., Barash, C.I., Izagirre, N., Jung, J., Kojima, T., Laradi, S., Lee, Y.S., Lee, J.Y., Gil-da-Silva-Lopes, V.L., Macrae, F.A., Maglott, D., Marafie, M.J., Marsh, S.G., Matsubara, Y., Messiaen, L.M., Moslein, G., Netea, M.G., Norton, M.L., Oefner, P.J., Oetting, W.S., O'Leary, J.C., Ramirez, A.M. de, Paalman, M.H., Parboosingh, J., Patrinos, G.P., Perozzi, G., Phillips, I.R., Povey, S., Prasad, S., Qi, M., Quin, D.J., Ramesar, R.S., Richards, C.S., Savige, J., Scheible, D.G., Scott, R.J., Seminara, D., Shephard, E.A., Sijmons, R.H., Smith, T.D., Sobrido, M.J., Tanaka, T., Tavtigian, S.V., Taylor, G.R., Teague, J., Topel, T., Ullman-Cullere, M., Utsunomiya, J., Kranen, H.J. van, Vihinen, M., Webb, E., Weber, T.K., and Yeager, M.

Abstract

Contains fulltext : 81952.pdf (publisher's version ) (Closed access), The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008.

Published
2009

5. Planning the Human Variome Project: The Spain Report

Author

Kaput, J, Cotton, RGH, Hardman, L, Watson, M, Al Aqeel, AI, Al-Aama, JY, Al-Mulla, F, Alonso, S, Aretz, S, Auerbach, AD, Bapat, B, Bernstein, IT, Bhak, J, Bleoo, SL, Bloecker, H, Brenner, SE, Burn, J, Bustamante, M, Calone, R, Cambon-Thomsen, A, Cargill, M, Carrera, P, Cavedon, L, Cho, YS, Chung, Y-J, Claustres, M, Cutting, G, Dalgleish, R, den Dunnen, JT, Diaz, C, Dobrowolski, S, dos Santos, MRN, Ekong, R, Flanagan, SB, Flicek, P, Furukawa, Y, Genuardi, M, Ghang, H, Golubenko, MV, Greenblatt, MS, Hamosh, A, Hancock, JM, Hardison, R, Harrison, TM, Hoffmann, R, Horaitis, R, Howard, HJ, Barash, CI, Izagirre, N, Jung, J, Kojima, T, Laradi, S, Lee, Y-S, Lee, J-Y, Gil-da-Silva-Lopes, VL, Macrae, FA, Maglott, D, Marafie, MJ, Marsh, SGE, Matsubara, Y, Messiaen, LM, Moeslein, G, Netea, MG, Norton, ML, Oefner, PJ, Oetting, WS, O'Leary, JC, Oller de Ramirez, AM, Paalman, MH, Parboosingh, J, Patrinos, GP, Perozzi, G, Phillips, IR, Povey, S, Prasad, S, Qi, M, Quin, DJ, Ramesar, RS, Richards, CS, Savige, J, Scheible, DG, Scott, RJ, Seminara, D, Shephard, EA, Sijmons, RH, Smith, TD, Sobrido, M-J, Tanaka, T, Tavtigian, SV, Taylor, GR, Teague, J, Toepel, T, Ullman-Cullere, M, Utsunomiya, J, van Kranen, HJ, Vihinen, M, Webb, E, Weber, TK, Yeager, M, Yeom, YI, Yim, S-H, Yoo, H-S, Kaput, J, Cotton, RGH, Hardman, L, Watson, M, Al Aqeel, AI, Al-Aama, JY, Al-Mulla, F, Alonso, S, Aretz, S, Auerbach, AD, Bapat, B, Bernstein, IT, Bhak, J, Bleoo, SL, Bloecker, H, Brenner, SE, Burn, J, Bustamante, M, Calone, R, Cambon-Thomsen, A, Cargill, M, Carrera, P, Cavedon, L, Cho, YS, Chung, Y-J, Claustres, M, Cutting, G, Dalgleish, R, den Dunnen, JT, Diaz, C, Dobrowolski, S, dos Santos, MRN, Ekong, R, Flanagan, SB, Flicek, P, Furukawa, Y, Genuardi, M, Ghang, H, Golubenko, MV, Greenblatt, MS, Hamosh, A, Hancock, JM, Hardison, R, Harrison, TM, Hoffmann, R, Horaitis, R, Howard, HJ, Barash, CI, Izagirre, N, Jung, J, Kojima, T, Laradi, S, Lee, Y-S, Lee, J-Y, Gil-da-Silva-Lopes, VL, Macrae, FA, Maglott, D, Marafie, MJ, Marsh, SGE, Matsubara, Y, Messiaen, LM, Moeslein, G, Netea, MG, Norton, ML, Oefner, PJ, Oetting, WS, O'Leary, JC, Oller de Ramirez, AM, Paalman, MH, Parboosingh, J, Patrinos, GP, Perozzi, G, Phillips, IR, Povey, S, Prasad, S, Qi, M, Quin, DJ, Ramesar, RS, Richards, CS, Savige, J, Scheible, DG, Scott, RJ, Seminara, D, Shephard, EA, Sijmons, RH, Smith, TD, Sobrido, M-J, Tanaka, T, Tavtigian, SV, Taylor, GR, Teague, J, Toepel, T, Ullman-Cullere, M, Utsunomiya, J, van Kranen, HJ, Vihinen, M, Webb, E, Weber, TK, Yeager, M, Yeom, YI, Yim, S-H, and Yoo, H-S

Abstract

The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008.

Published
2009

6. Planning the human variome project: the Spain report.

Author

Kaput, J., Cotton, R.G., Hardman, L., Watson, M., Aqeel, A.I. Al, Al-Aama, J.Y., Al-Mulla, F., Alonso, S., Aretz, S., Auerbach, A.D., Bapat, B., Bernstein, I.T., Bhak, J., Bleoo, S.L., Blocker, H., Brenner, S.E., Burn, J., Bustamante, M., Calzone, R., Cambon-Thomsen, A., Cargill, M., Carrera, P., Cavedon, L., Cho, Y.S., Chung, Y.J., Claustres, M., Cutting, G., Dalgleish, R., Dunnen, J.T. den, Diaz, C., Dobrowolski, S., Santos, M.R. dos, Ekong, R., Flanagan, S.B., Flicek, P., Furukawa, Y., Genuardi, M., Ghang, H., Golubenko, M.V., Greenblatt, M.S., Hamosh, A., Hancock, J.M., Hardison, R., Harrison, T.M., Hoffmann, R., Horaitis, R., Howard, H.J., Barash, C.I., Izagirre, N., Jung, J., Kojima, T., Laradi, S., Lee, Y.S., Lee, J.Y., Gil-da-Silva-Lopes, V.L., Macrae, F.A., Maglott, D., Marafie, M.J., Marsh, S.G., Matsubara, Y., Messiaen, L.M., Moslein, G., Netea, M.G., Norton, M.L., Oefner, P.J., Oetting, W.S., O'Leary, J.C., Ramirez, A.M. de, Paalman, M.H., Parboosingh, J., Patrinos, G.P., Perozzi, G., Phillips, I.R., Povey, S., Prasad, S., Qi, M., Quin, D.J., Ramesar, R.S., Richards, C.S., Savige, J., Scheible, D.G., Scott, R.J., Seminara, D., Shephard, E.A., Sijmons, R.H., Smith, T.D., Sobrido, M.J., Tanaka, T., Tavtigian, S.V., Taylor, G.R., Teague, J., Topel, T., Ullman-Cullere, M., Utsunomiya, J., Kranen, H.J. van, Vihinen, M., Webb, E., Weber, T.K., Yeager, M., Kaput, J., Cotton, R.G., Hardman, L., Watson, M., Aqeel, A.I. Al, Al-Aama, J.Y., Al-Mulla, F., Alonso, S., Aretz, S., Auerbach, A.D., Bapat, B., Bernstein, I.T., Bhak, J., Bleoo, S.L., Blocker, H., Brenner, S.E., Burn, J., Bustamante, M., Calzone, R., Cambon-Thomsen, A., Cargill, M., Carrera, P., Cavedon, L., Cho, Y.S., Chung, Y.J., Claustres, M., Cutting, G., Dalgleish, R., Dunnen, J.T. den, Diaz, C., Dobrowolski, S., Santos, M.R. dos, Ekong, R., Flanagan, S.B., Flicek, P., Furukawa, Y., Genuardi, M., Ghang, H., Golubenko, M.V., Greenblatt, M.S., Hamosh, A., Hancock, J.M., Hardison, R., Harrison, T.M., Hoffmann, R., Horaitis, R., Howard, H.J., Barash, C.I., Izagirre, N., Jung, J., Kojima, T., Laradi, S., Lee, Y.S., Lee, J.Y., Gil-da-Silva-Lopes, V.L., Macrae, F.A., Maglott, D., Marafie, M.J., Marsh, S.G., Matsubara, Y., Messiaen, L.M., Moslein, G., Netea, M.G., Norton, M.L., Oefner, P.J., Oetting, W.S., O'Leary, J.C., Ramirez, A.M. de, Paalman, M.H., Parboosingh, J., Patrinos, G.P., Perozzi, G., Phillips, I.R., Povey, S., Prasad, S., Qi, M., Quin, D.J., Ramesar, R.S., Richards, C.S., Savige, J., Scheible, D.G., Scott, R.J., Seminara, D., Shephard, E.A., Sijmons, R.H., Smith, T.D., Sobrido, M.J., Tanaka, T., Tavtigian, S.V., Taylor, G.R., Teague, J., Topel, T., Ullman-Cullere, M., Utsunomiya, J., Kranen, H.J. van, Vihinen, M., Webb, E., Weber, T.K., and Yeager, M.

Abstract

Contains fulltext : 81952.pdf (publisher's version ) (Closed access), The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008.

Published
2009

7. Planning the human variome project: the Spain report.

Author

Kaput, J., Cotton, R.G., Hardman, L., Watson, M., Aqeel, A.I. Al, Al-Aama, J.Y., Al-Mulla, F., Alonso, S., Aretz, S., Auerbach, A.D., Bapat, B., Bernstein, I.T., Bhak, J., Bleoo, S.L., Blocker, H., Brenner, S.E., Burn, J., Bustamante, M., Calzone, R., Cambon-Thomsen, A., Cargill, M., Carrera, P., Cavedon, L., Cho, Y.S., Chung, Y.J., Claustres, M., Cutting, G., Dalgleish, R., Dunnen, J.T. den, Diaz, C., Dobrowolski, S., Santos, M.R. dos, Ekong, R., Flanagan, S.B., Flicek, P., Furukawa, Y., Genuardi, M., Ghang, H., Golubenko, M.V., Greenblatt, M.S., Hamosh, A., Hancock, J.M., Hardison, R., Harrison, T.M., Hoffmann, R., Horaitis, R., Howard, H.J., Barash, C.I., Izagirre, N., Jung, J., Kojima, T., Laradi, S., Lee, Y.S., Lee, J.Y., Gil-da-Silva-Lopes, V.L., Macrae, F.A., Maglott, D., Marafie, M.J., Marsh, S.G., Matsubara, Y., Messiaen, L.M., Moslein, G., Netea, M.G., Norton, M.L., Oefner, P.J., Oetting, W.S., O'Leary, J.C., Ramirez, A.M. de, Paalman, M.H., Parboosingh, J., Patrinos, G.P., Perozzi, G., Phillips, I.R., Povey, S., Prasad, S., Qi, M., Quin, D.J., Ramesar, R.S., Richards, C.S., Savige, J., Scheible, D.G., Scott, R.J., Seminara, D., Shephard, E.A., Sijmons, R.H., Smith, T.D., Sobrido, M.J., Tanaka, T., Tavtigian, S.V., Taylor, G.R., Teague, J., Topel, T., Ullman-Cullere, M., Utsunomiya, J., Kranen, H.J. van, Vihinen, M., Webb, E., Weber, T.K., Yeager, M., Kaput, J., Cotton, R.G., Hardman, L., Watson, M., Aqeel, A.I. Al, Al-Aama, J.Y., Al-Mulla, F., Alonso, S., Aretz, S., Auerbach, A.D., Bapat, B., Bernstein, I.T., Bhak, J., Bleoo, S.L., Blocker, H., Brenner, S.E., Burn, J., Bustamante, M., Calzone, R., Cambon-Thomsen, A., Cargill, M., Carrera, P., Cavedon, L., Cho, Y.S., Chung, Y.J., Claustres, M., Cutting, G., Dalgleish, R., Dunnen, J.T. den, Diaz, C., Dobrowolski, S., Santos, M.R. dos, Ekong, R., Flanagan, S.B., Flicek, P., Furukawa, Y., Genuardi, M., Ghang, H., Golubenko, M.V., Greenblatt, M.S., Hamosh, A., Hancock, J.M., Hardison, R., Harrison, T.M., Hoffmann, R., Horaitis, R., Howard, H.J., Barash, C.I., Izagirre, N., Jung, J., Kojima, T., Laradi, S., Lee, Y.S., Lee, J.Y., Gil-da-Silva-Lopes, V.L., Macrae, F.A., Maglott, D., Marafie, M.J., Marsh, S.G., Matsubara, Y., Messiaen, L.M., Moslein, G., Netea, M.G., Norton, M.L., Oefner, P.J., Oetting, W.S., O'Leary, J.C., Ramirez, A.M. de, Paalman, M.H., Parboosingh, J., Patrinos, G.P., Perozzi, G., Phillips, I.R., Povey, S., Prasad, S., Qi, M., Quin, D.J., Ramesar, R.S., Richards, C.S., Savige, J., Scheible, D.G., Scott, R.J., Seminara, D., Shephard, E.A., Sijmons, R.H., Smith, T.D., Sobrido, M.J., Tanaka, T., Tavtigian, S.V., Taylor, G.R., Teague, J., Topel, T., Ullman-Cullere, M., Utsunomiya, J., Kranen, H.J. van, Vihinen, M., Webb, E., Weber, T.K., and Yeager, M.

Abstract

Contains fulltext : 81952.pdf (publisher's version ) (Closed access), The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008.

Published
2009

8. Planning the Human Variome Project: The Spain Report

Author

Kaput, J, Cotton, R, Hardman, L, Watson, M, Al Aqeel, A, Al-Aama, J, Al-Mulla, F, Alonso, S, Aretz, S, Auerbach, A, Bapat, B, Bernstein, I, Bhak, J, Bleoo, S, Blocker, H, Brenner, S, Burn, J, Bustamante, M, Calone, R, Cambon-Thomsen, A, Cargill, M, Carrera, P, Cavedon, L, Cho, Y, Chung, Y, Claustres, M, Cutting, G, Dalgleish, R, den Dunnen, J, Diaz, C, Dobrowolski, S, dos Santos, M, Ekong, R, Flanagan, S, Flicek, P, Furukawa, Y, Genuardi, Maurizio, Ghang, H, Golubenko, M, Greenblatt, M, Hamosh, A, Hancock, J, Hardison, R, Harrison, T, Hoffmann, R, Horaitis, R, Howard, H, Barash, C, Izagirre, N, Jung, J, Kojima, T, Laradi, S, Lee, Y, Lee, J, Gil-da-Silva-Lopes, V, Macrae, F, Maglott, D, Marafie, M, Marsh, S, Matsubara, Y, Messiaen, L, Moslein, G, Netea, M, Norton, M, Oefner, P, Oetting, W, O'Leary, J, de Ramirez, A, Paalman, M, Parboosingh, J, Patrinos, G, Perozzi, G, Phillips, I, Povey, S, Prasad, S, Qi, M, Quinzani, Dario, Ramesar, R, Richards, C, Savige, J, Scheible, D, Scott, R, Seminara, D, Shephard, E, Sijmons, R, Smith, T, Sobrido, M, Tanaka, T, Tavtigian, S, Taylor, G, Teague, J, Topel, T, Ullman-Cullere, M, Utsunomiya, J, van Kranen, H, Vihinen, M, Webb, E, Weber, Bertram, Yeager, M, Yeom, Y, Yim, S, Yoo, H, Genuardi, M (ORCID:0000-0002-7410-8351), Quin, D, Weber, T, Kaput, J, Cotton, R, Hardman, L, Watson, M, Al Aqeel, A, Al-Aama, J, Al-Mulla, F, Alonso, S, Aretz, S, Auerbach, A, Bapat, B, Bernstein, I, Bhak, J, Bleoo, S, Blocker, H, Brenner, S, Burn, J, Bustamante, M, Calone, R, Cambon-Thomsen, A, Cargill, M, Carrera, P, Cavedon, L, Cho, Y, Chung, Y, Claustres, M, Cutting, G, Dalgleish, R, den Dunnen, J, Diaz, C, Dobrowolski, S, dos Santos, M, Ekong, R, Flanagan, S, Flicek, P, Furukawa, Y, Genuardi, Maurizio, Ghang, H, Golubenko, M, Greenblatt, M, Hamosh, A, Hancock, J, Hardison, R, Harrison, T, Hoffmann, R, Horaitis, R, Howard, H, Barash, C, Izagirre, N, Jung, J, Kojima, T, Laradi, S, Lee, Y, Lee, J, Gil-da-Silva-Lopes, V, Macrae, F, Maglott, D, Marafie, M, Marsh, S, Matsubara, Y, Messiaen, L, Moslein, G, Netea, M, Norton, M, Oefner, P, Oetting, W, O'Leary, J, de Ramirez, A, Paalman, M, Parboosingh, J, Patrinos, G, Perozzi, G, Phillips, I, Povey, S, Prasad, S, Qi, M, Quinzani, Dario, Ramesar, R, Richards, C, Savige, J, Scheible, D, Scott, R, Seminara, D, Shephard, E, Sijmons, R, Smith, T, Sobrido, M, Tanaka, T, Tavtigian, S, Taylor, G, Teague, J, Topel, T, Ullman-Cullere, M, Utsunomiya, J, van Kranen, H, Vihinen, M, Webb, E, Weber, Bertram, Yeager, M, Yeom, Y, Yim, S, Yoo, H, Genuardi, M (ORCID:0000-0002-7410-8351), Quin, D, and Weber, T

Abstract

The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols Spain, in May 2008. Hum Mutat 30, 496-510, 2009. (C) 2009 Wiley-Liss, Inc.

Published
2009

9. The EUROclass trial: Defining subgroups in common variable immunodeficiency

Author

Wehr, C. (Claudia), Kivioja, T. (Teemu), Schmitt, C. (Christian), Ferry, B. (Berne), Witte, T. (Torsten), Eren, E. (Efrem), Vlkova, M. (Marcela), Hernandez, M. (Manuel), Detkova, D. (Drahomira), Bos, P.R. (Philip), Poerksen, G. (Gonke), Bernuth, H. (Horst) von, Baumann, U. (Ulrich), Goldacker, S. (Sigune), Gutenberger, S. (Sylvia), Schlesier, M. (Michael), Bergeron-Van der Cruyssen, F. (Florence), Le Garff, M. (Magali), Debré, P. (Patrice), Jacobs, R. (Roland), Jones, J. (John), Bateman, E. (Elizabeth), Litzman, J. (Jiri), Hagen, P.M. (Martin) van, Plebani, A. (Alessandro), Schmidt, R. (Reinhold), Thon, V. (Vojtech), Quinti, I. (Isabella), Espanol, T. (Teresa), Webster, A.D. (David), Chapel, H. (Helen), Vihinen, M. (Mauno), Oksenhendler, E. (Eric), Peter, H.H., Warnatz, K. (Klaus), Wehr, C. (Claudia), Kivioja, T. (Teemu), Schmitt, C. (Christian), Ferry, B. (Berne), Witte, T. (Torsten), Eren, E. (Efrem), Vlkova, M. (Marcela), Hernandez, M. (Manuel), Detkova, D. (Drahomira), Bos, P.R. (Philip), Poerksen, G. (Gonke), Bernuth, H. (Horst) von, Baumann, U. (Ulrich), Goldacker, S. (Sigune), Gutenberger, S. (Sylvia), Schlesier, M. (Michael), Bergeron-Van der Cruyssen, F. (Florence), Le Garff, M. (Magali), Debré, P. (Patrice), Jacobs, R. (Roland), Jones, J. (John), Bateman, E. (Elizabeth), Litzman, J. (Jiri), Hagen, P.M. (Martin) van, Plebani, A. (Alessandro), Schmidt, R. (Reinhold), Thon, V. (Vojtech), Quinti, I. (Isabella), Espanol, T. (Teresa), Webster, A.D. (David), Chapel, H. (Helen), Vihinen, M. (Mauno), Oksenhendler, E. (Eric), Peter, H.H., and Warnatz, K. (Klaus)

Abstract

The heterogeneity of common variable immunodeficiency (CVID) calls for a classification addressing pathogenic mechanisms as well as clinical relevance. This European multicenter trial was initiated to develop a consensus of 2 existing classification schemes based on flowcytometric B-cell phenotyping and the clinical course. The clinical evaluation of 303 patients with the established diagnosis of CVID demonstrated a significant coincidence of granulomatous disease, autoimmune cytopenia, and splenomegaly. Phenotyping of B-cell subpopulations confirmed a severe reduction of switched memory B cells in most of the patients that was associated with a higher risk for splenomegaly and granulomatous disease. An expansion of CD21lowB cells marked patients with splenomegaly. Lymphadenopathy was significantly linked with transitional B-cell expansion. Based on these findings and pathogenic consideration of B-cell differentiation, we suggest an improved classification for CVID (EUROclass), separating patients with nearly absent B cells (less than 1%), severely reduced switched memory B cells (less than 2%), and expansion of transitional (more th

Published
2008
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10. The Tec family of cytoplasmic tyrosine kinases : mammalian Btk, Bmx, Itk, Tec, Txk and homologs in other species

Author

Smith, C I E, Islam, T C, Mattsson, Pekka T, Mohamed, A J, Nore, B F, Vihinen, M, Smith, C I E, Islam, T C, Mattsson, Pekka T, Mohamed, A J, Nore, B F, and Vihinen, M

Abstract

Cytoplasmic protein-tyrosine kinases (PTKs) are enzymes involved in transducing a vast number of signals in metazoans, The importance of the Tec family of kinases was immediately recognized when, in 1993, mutations in the gene encoding Bruton's tyrosine kinase (Btk) were reported to cause the human disease X-linked agammaglobulinemia (XLA).((1,2)) Since then, additional kinases belonging to this family have been isolated, and the availability of full genome sequences allows identification of all members in selected species enabling phylogenetic considerations. Tec kinases are endowed with Pleckstrin homology (PH) and Tec homology (TH) domains and are involved in diverse biological processes related to the control of survival and differentiation fate, Membrane translocation resulting in the activation of Tec kinases with subsequent Ca2+ release seems to be a general feature, However, nuclear translocation may also be of importance, the purpose of this essay is to characterize members of the Tec family and discuss their involvement in signaling. The three-dimensional structure, expression pattern and evolutionary aspects will also be considered.

Published
2001
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11. Thermal unfolding of small proteins with SH3 domain folding pattern

Author

Knapp, S, Mattson, P T, Christova, P, Berndt, Kurt D, Karshikoff, A, Vihinen, M, Smith, C I E, Ladenstein, R, Knapp, S, Mattson, P T, Christova, P, Berndt, Kurt D, Karshikoff, A, Vihinen, M, Smith, C I E, and Ladenstein, R

Abstract

The thermal unfolding of three SH3 domains of the Tec family of tyrosine kinases was studied by differential scanning calorimetry and CD spectroscopy, The unfolding transition of the three protein domains in the acidic pH region can be described as a reversible two-state process. For all three SH3 domains maximum stability was observed in the pH region 4.5 < pH < 7.0 where these domains unfold at temperatures of 353K (Btk), 342K (Itk), and 344K (Tec), At these temperatures an enthalpy change of 196 kJ/mol, 178 kJ/mol, and 169 kJ/mol was measured for Btk-, Itk-, and Tec-SH3 domains, respectively. The determined changes in heat capacity between the native and the denatured state are in an usual range expected for small proteins. Our analysis revealed that all SH3 domains studied are only weakly stabilized and have free energies of unfolding which do not exceed 12-16 kJ/mol but show quite high melting temperatures. Comparing unfolding free energies measured for eukaryotic SH3 domains with those of the topologically identical Sso7d protein from the hyperthermophile Sulfolobus solfataricus, the increased melting temperature of the thermostable protein is due to a broadening as well as a significant lifting of its stability curve. However, at their physiological temperatures, 310K for mesophilic SH3 domains and 350K for Sso7d, eukaryotic SH3 domains and Sso7d show very similar stabilities. (C) 1998 Wiley-Liss, Inc., Times Cited: 24 Article English Cited References Count: 71 Zk813

Published
1998
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12. Deletion within the Src homology domain 3 of Bruton's tyrosine kinase resulting in X-linked agammaglobulinemia (XLA).

Author

Zhu, Q, Zhu, Q, Zhang, M, Rawlings, DJ, Vihinen, M, Hagemann, T, Saffran, DC, Kwan, SP, Nilsson, L, Smith, CI, Witte, ON, Chen, SH, Ochs, HD, Zhu, Q, Zhu, Q, Zhang, M, Rawlings, DJ, Vihinen, M, Hagemann, T, Saffran, DC, Kwan, SP, Nilsson, L, Smith, CI, Witte, ON, Chen, SH, and Ochs, HD

Abstract

The gene responsible for X-linked agammaglobulinemia (XLA) has been recently identified to code for a cytoplasmic tyrosine kinase (Bruton's agammaglobulinemia tyrosine kinase, BTK), required for normal B cell development. BTK, like many other cytoplasmic tyrosine kinases, contains Src homology domains (SH2 and SH3), and catalytic kinase domain. SH3 domains are important for the targeting of signaling molecules to specific subcellular locations. We have identified a family with XLA whose affected members have a point mutation (g-->a) at the 5' splice site of intron 8, resulting in the skipping of coding exon 8 and loss of 21 amino acids forming the COOH-terminal portion of the BTK SH3 domain. The study of three generations within this kinship, using restriction fragment length polymorphism and DNA analysis, allowed identification of the mutant X chromosome responsible for XLA and the carrier status in this family. BTK mRNA was present in normal amounts in Epstein-Barr virus-induced B lymphoblastoid cell lines established from affected family members. Although the SH3 deletion did not alter BTK protein stability and kinase activity of the truncated BTK protein was normal, the affected patients nevertheless have a severe B cell defect characteristic for XLA. The mutant protein was modeled using the normal BTK SH3 domain. The deletion results in loss of two COOH-terminal beta strands containing several residues critical for the formation of the putative SH3 ligand-binding pocket. We predict that, as a result, one or more crucial SH3 binding proteins fail to interact with BTK, interrupting the cytoplasmic signal transduction process required for B cell differentiation.

Published
1994

13. Deletion within the Src homology domain 3 of Bruton's tyrosine kinase resulting in X-linked agammaglobulinemia (XLA).

Author

Zhu, Q, Zhu, Q, Zhang, M, Rawlings, DJ, Vihinen, M, Hagemann, T, Saffran, DC, Kwan, SP, Nilsson, L, Smith, CI, Witte, ON, Chen, SH, Ochs, HD, Zhu, Q, Zhu, Q, Zhang, M, Rawlings, DJ, Vihinen, M, Hagemann, T, Saffran, DC, Kwan, SP, Nilsson, L, Smith, CI, Witte, ON, Chen, SH, and Ochs, HD

Abstract

The gene responsible for X-linked agammaglobulinemia (XLA) has been recently identified to code for a cytoplasmic tyrosine kinase (Bruton's agammaglobulinemia tyrosine kinase, BTK), required for normal B cell development. BTK, like many other cytoplasmic tyrosine kinases, contains Src homology domains (SH2 and SH3), and catalytic kinase domain. SH3 domains are important for the targeting of signaling molecules to specific subcellular locations. We have identified a family with XLA whose affected members have a point mutation (g-->a) at the 5' splice site of intron 8, resulting in the skipping of coding exon 8 and loss of 21 amino acids forming the COOH-terminal portion of the BTK SH3 domain. The study of three generations within this kinship, using restriction fragment length polymorphism and DNA analysis, allowed identification of the mutant X chromosome responsible for XLA and the carrier status in this family. BTK mRNA was present in normal amounts in Epstein-Barr virus-induced B lymphoblastoid cell lines established from affected family members. Although the SH3 deletion did not alter BTK protein stability and kinase activity of the truncated BTK protein was normal, the affected patients nevertheless have a severe B cell defect characteristic for XLA. The mutant protein was modeled using the normal BTK SH3 domain. The deletion results in loss of two COOH-terminal beta strands containing several residues critical for the formation of the putative SH3 ligand-binding pocket. We predict that, as a result, one or more crucial SH3 binding proteins fail to interact with BTK, interrupting the cytoplasmic signal transduction process required for B cell differentiation.

Published
1994

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