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1. Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects

Author

Vrijenhoek, T., Kraaijeveld, K., Elferink, M., Ligt, J. de, Kranendonk, E., Santen, G., Nijman, IJ, Butler, D., Claes, G., Costessi, A., Dorlijn, W., Eyndhoven, W. van, Halley, D.J., Hout, M.C. van den, Hove, S. van, Johansson, L.F., Jongbloed, J.D., Kamps, R., Kockx, C.E., Koning, B. de, Kriek, M., Deprez, R.L., Lunstroo, H., Mannens, M., Mook, O.R., Nelen, M.R., Ploem, C., Rijnen, M., Saris, J.J., Sinke, R., Sistermans, E., Slegtenhorst, M. van, Sleutels, F., Stoep, N. van der, Tienhoven, M. van, Vermaat, M., Vogel, M., Waisfisz, Q., Weiss, J.M., Wijngaard, A. van den, Workum, W. van, IJntema, H., Zwaag, B. van der, van, I.W.F., Dunnen, J.T. den, Veltman, J.A., Hennekam, R., Cuppen, E., Vrijenhoek, T., Kraaijeveld, K., Elferink, M., Ligt, J. de, Kranendonk, E., Santen, G., Nijman, IJ, Butler, D., Claes, G., Costessi, A., Dorlijn, W., Eyndhoven, W. van, Halley, D.J., Hout, M.C. van den, Hove, S. van, Johansson, L.F., Jongbloed, J.D., Kamps, R., Kockx, C.E., Koning, B. de, Kriek, M., Deprez, R.L., Lunstroo, H., Mannens, M., Mook, O.R., Nelen, M.R., Ploem, C., Rijnen, M., Saris, J.J., Sinke, R., Sistermans, E., Slegtenhorst, M. van, Sleutels, F., Stoep, N. van der, Tienhoven, M. van, Vermaat, M., Vogel, M., Waisfisz, Q., Weiss, J.M., Wijngaard, A. van den, Workum, W. van, IJntema, H., Zwaag, B. van der, van, I.W.F., Dunnen, J.T. den, Veltman, J.A., Hennekam, R., and Cuppen, E.

Abstract

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Published
2015

2. Next-generation sequencing-based genome diagnostics across clinical genetics centers: Implementation choices and their effects

Author

Vrijenhoek, T. (T.), Kraaijeveld, K. (Ken), Elferink, M.G. (Martin), Ligt, J. (Joep) de, Kranendonk, E. (Elcke), Santen, G.W.E. (Gijs), Nijman, I.J. (Isaac ), Butler, D. (Derek), Claes, G. (Godelieve), Costessi, A. (Adalberto), Dorlijn, W. (Wim), Van Eyndhoven, W. (Winfried), Halley, D.J.J. (Dicky), Van Den Hout, M.C.G.N. (Mirjam C.G.N.), Van Hove, S. (Steven), Johansson, L.F. (Lennart F.), Jongbloed, J.D.H. (Jan), Kamps, R. (Rick), Kockx, C. (Christel), De Koning, B. (Bart), Kriek, N. (Nadia), Lekanne Dit Deprez, R.H., Lunstroo, H. (Hans), Mannens, M.M.A.M. (Marcel), Mook, O. (Olaf), Nelen, M.R. (Marcel), Ploem, C. (Corrette), Rijnen, M. (Marco), Saris, J.J. (Jasper), Sinke, R.J. (Richard J), Sistermans, E. (Erik), Slegtenhorst, M.A. (Marjon) van, Sleutels, F. (Frank), Stoep, N. (Nienke) van der, Tienhoven, M. (Marianne) van, Vermaat, M. (Martijn), Vogel, M.J. (Maartje), Waisfisz, Q. (Quinten), Weiss, J.M. (Janneke), Wijngaard, A. (Arthur) van den, Workum, W. (W) van, Ijntema, H. (Helger), Zwaag, B. (Bert) van der, IJcken, W.F.J. (Wilfred) van, Dunnen, J.T. (Johan) den, Veltman, J.A. (Joris), Hennekam, R.C.M. (Raoul), Cuppen, E. (Edwin), Vrijenhoek, T. (T.), Kraaijeveld, K. (Ken), Elferink, M.G. (Martin), Ligt, J. (Joep) de, Kranendonk, E. (Elcke), Santen, G.W.E. (Gijs), Nijman, I.J. (Isaac ), Butler, D. (Derek), Claes, G. (Godelieve), Costessi, A. (Adalberto), Dorlijn, W. (Wim), Van Eyndhoven, W. (Winfried), Halley, D.J.J. (Dicky), Van Den Hout, M.C.G.N. (Mirjam C.G.N.), Van Hove, S. (Steven), Johansson, L.F. (Lennart F.), Jongbloed, J.D.H. (Jan), Kamps, R. (Rick), Kockx, C. (Christel), De Koning, B. (Bart), Kriek, N. (Nadia), Lekanne Dit Deprez, R.H., Lunstroo, H. (Hans), Mannens, M.M.A.M. (Marcel), Mook, O. (Olaf), Nelen, M.R. (Marcel), Ploem, C. (Corrette), Rijnen, M. (Marco), Saris, J.J. (Jasper), Sinke, R.J. (Richard J), Sistermans, E. (Erik), Slegtenhorst, M.A. (Marjon) van, Sleutels, F. (Frank), Stoep, N. (Nienke) van der, Tienhoven, M. (Marianne) van, Vermaat, M. (Martijn), Vogel, M.J. (Maartje), Waisfisz, Q. (Quinten), Weiss, J.M. (Janneke), Wijngaard, A. (Arthur) van den, Workum, W. (W) van, Ijntema, H. (Helger), Zwaag, B. (Bert) van der, IJcken, W.F.J. (Wilfred) van, Dunnen, J.T. (Johan) den, Veltman, J.A. (Joris), Hennekam, R.C.M. (Raoul), and Cuppen, E. (Edwin)

Abstract

Implementation of next-generation DNA sequencing (NGS) technology into routine diagnostic genome care requires strategic choices. Instead of theoretical discussions on the consequences of such choices, we compared NGS-based diagnostic practices in eight clinical genetic centers in the Netherlands, based on genetic testing of nine pre-selected patients with cardiomyopathy. We highlight critical implementation choices, including the specific contributions of laboratory and medical specialists, bioinformaticians and researchers to diagnostic genome care, and how these affect interpretation and reporting of variants. Reported pathogenic mutations were consistent for all but one patient. Of the two centers that were inconsistent in their diagnosis, one reported to have found 'no causal variant', thereby underdiagnosing this patient. The other provided an alternative diagnosis, identifying another variant as causal than the other centers. Ethical and legal analysis showed that informed consent procedures in all centers were generally adequate for diagnostic NGS applications that target a limited set of genes, but not for exome- and genome-based diagnosis. We propose changes to further improve and align these procedures, taking into account the blurring boundary between diagnostics and research, and specific counseling options for exome- and genome-based diagnostics. We conclude that alternative diagnoses may infer a certain level of 'greediness' to come to a positive diagnosis in interpreting sequencing results. Moreover, there is an increasing interdependence of clinic, diagnostics and research departments for comprehensive diagnostic genome care. Therefore, we invite clinical geneticists, physicians, researchers, bioinformatics experts and patients to reconsider their role and position in future diagnostic genome care.

Published
2015
Full Text
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3. Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects

Author

Vrijenhoek, T, Kraaijeveld, K, Elferink, M, de Ligt, J, Kranendonk, E, Santen, G, Nijman, IJ, Butler, D, Claes, G, Costessi, A, Dorlijn, W, van Eyndhoven, W, Halley, Dicky, Van den Hout - van Vroonhoven, Mirjam, van Hove, S, Johansson, LF, Jongbloed, JDH, Kamps, R, Kockx, Christel, de Koning, B, Kriek, M, Deprez, RLD, Lunstroo, H, Mannens, M, Mook, OR, Nelen, M, Ploem, C, Rijnen, M, Saris, Jasper, Sinke, R, Sistermans, E, van Slegtenhorst, Marjon, Sleutels, Frank, van der Stoep, N, Tienhoven, Marianne, Vermaat, M, Vogel, M, Waisfisz, Q, Weiss, JM, van den Wijngaard, A, van Workum, W, Ijntema, H, Van der Zwaag, B, van Ijcken, Wilfred, den Dunnen, J, Veltman, JA, Hennekam, R, Cuppen, E, Vrijenhoek, T, Kraaijeveld, K, Elferink, M, de Ligt, J, Kranendonk, E, Santen, G, Nijman, IJ, Butler, D, Claes, G, Costessi, A, Dorlijn, W, van Eyndhoven, W, Halley, Dicky, Van den Hout - van Vroonhoven, Mirjam, van Hove, S, Johansson, LF, Jongbloed, JDH, Kamps, R, Kockx, Christel, de Koning, B, Kriek, M, Deprez, RLD, Lunstroo, H, Mannens, M, Mook, OR, Nelen, M, Ploem, C, Rijnen, M, Saris, Jasper, Sinke, R, Sistermans, E, van Slegtenhorst, Marjon, Sleutels, Frank, van der Stoep, N, Tienhoven, Marianne, Vermaat, M, Vogel, M, Waisfisz, Q, Weiss, JM, van den Wijngaard, A, van Workum, W, Ijntema, H, Van der Zwaag, B, van Ijcken, Wilfred, den Dunnen, J, Veltman, JA, Hennekam, R, and Cuppen, E

Abstract

Implementation of next-generation DNA sequencing (NGS) technology into routine diagnostic genome care requires strategic choices. Instead of theoretical discussions on the consequences of such choices, we compared NGS-based diagnostic practices in eight clinical genetic centers in the Netherlands, based on genetic testing of nine pre-selected patients with cardiomyopathy. We highlight critical implementation choices, including the specific contributions of laboratory and medical specialists, bioinformaticians and researchers to diagnostic genome care, and how these affect interpretation and reporting of variants. Reported pathogenic mutations were consistent for all but one patient. Of the two centers that were inconsistent in their diagnosis, one reported to have found 'no causal variant', thereby underdiagnosing this patient. The other provided an alternative diagnosis, identifying another variant as causal than the other centers. Ethical and legal analysis showed that informed consent procedures in all centers were generally adequate for diagnostic NGS applications that target a limited set of genes, but not for exome-and genome-based diagnosis. We propose changes to further improve and align these procedures, taking into account the blurring boundary between diagnostics and research, and specific counseling options for exome- and genome-based diagnostics. We conclude that alternative diagnoses may infer a certain level of 'greediness' to come to a positive diagnosis in interpreting sequencing results. Moreover, there is an increasing interdependence of clinic, diagnostics and research departments for comprehensive diagnostic genome care. Therefore, we invite clinical geneticists, physicians, researchers, bioinformatics experts and patients to reconsider their role and position in future diagnostic genome care.

Published
2015

4. Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects.

Author

Vrijenhoek T, Kraaijeveld K, Elferink M, de Ligt J, Kranendonk E, Santen G, Nijman IJ, Butler D, Claes G, Costessi A, Dorlijn W, van Eyndhoven W, Halley DJ, van den Hout MC, van Hove S, Johansson LF, Jongbloed JD, Kamps R, Kockx CE, de Koning B, Kriek M, Deprez RL, Lunstroo H, Mannens M, Mook OR, Nelen M, Ploem C, Rijnen M, Saris JJ, Sinke R, Sistermans E, van Slegtenhorst M, Sleutels F, van der Stoep N, van Tienhoven M, Vermaat M, Vogel M, Waisfisz Q, Weiss JM, van den Wijngaard A, van Workum W, Ijntema H, van der Zwaag B, van IJcken WF, den Dunnen JT, Veltman JA, Hennekam R, and Cuppen E

Published
2015
Full Text
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