Author: "van Enckevort, David" - Searchworks@Jio Institute Digital Library Search Results

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1. Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels.

Author: van Leeuwen, Elisabeth M, Karssen, Lennart C, Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, van Enckevort, David J, Huffman, Jennifer E, White, Charles C, Feitosa, Mary F, Bartz, Traci M, Manichaikul, Ani, Joshi, Peter K, Peloso, Gina M, Deelen, Patrick, van Dijk, Freerk, Willemsen, Gonneke, de Geus, Eco J, Milaneschi, Yuri, Penninx, Brenda WJH, Francioli, Laurent C, Menelaou, Androniki, Pulit, Sara L, Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A, Franco, Oscar H, Mateo Leach, Irene, Beekman, Marian, de Craen, Anton JM, Uh, Hae-Won, Trochet, Holly, Hocking, Lynne J, Porteous, David J, Sattar, Naveed, Packard, Chris J, Buckley, Brendan M, Brody, Jennifer A, Bis, Joshua C, Rotter, Jerome I, Mychaleckyj, Josyf C, Campbell, Harry, Duan, Qing, Lange, Leslie A, Wilson, James F, Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F, Rich, Stephen S, Psaty, Bruce M, Borecki, Ingrid B, Kearney, Patricia M, Stott, David J, Adrienne Cupples, L, Genome of The Netherlands Consortium, Jukema, J Wouter, van der Harst, Pim, Sijbrands, Eric J, Hottenga, Jouke-Jan, Uitterlinden, Andre G, Swertz, Morris A, van Ommen, Gert-Jan B, de Bakker, Paul IW, Eline Slagboom, P, Boomsma, Dorret I, Wijmenga, Cisca, and van Duijn, Cornelia M
Subjects: Genome of The Netherlands Consortium, Humans, Cholesterol, ATP-Binding Cassette Transporters, Gene Frequency, Mutation, Missense, Netherlands, Genetic Association Studies, Mutation, Missense
Abstract: Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of The Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value
Published: 2015

2. State-of-the-Art and Future Challenges in the Integration of Biobank Catalogues

Author: Müller, Heimo, Reihs, Robert, Zatloukal, Kurt, Jeanquartier, Fleur, Merino-Martinez, Roxana, van Enckevort, David, Swertz, Morris A., Holzinger, Andreas, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Holzinger, Andreas, editor, Röcker, Carsten, editor, and Ziefle, Martina, editor
Published: 2015
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3. State-of-the-Art and Future Challenges in the Integration of Biobank Catalogues

Author: Müller, Heimo, primary, Reihs, Robert, additional, Zatloukal, Kurt, additional, Jeanquartier, Fleur, additional, Merino-Martinez, Roxana, additional, van Enckevort, David, additional, Swertz, Morris A., additional, and Holzinger, Andreas, additional
Published: 2015
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4. CORBEL Prototype implementation of distributed automated data access request, review and authorization and delivery systems

Author: Linden, Mikael, Boiten, Jan-Willem, Courtot, Melanie, Holub, Petr, van de Geijn, Gert-Jan, van Enckevort, David, Lappalainen, Ilkka, Nyrönen, Tommi, Parkinson, Helen, Reihs, Robert, Senf, Alexander, Spalding, Dylan, Swedlow, Jason, Swertz, Morris, Törnroos, Juha, Kankaanpää, Pasi, and van Iperen, Erik
Subjects: access authorisation, identity authentication, research infrastructures, research data
Abstract: This deliverable describes research infrastructures’ prototypes for granting a researcher an authorisation to access research data encouraging secondary use of data that is already collected. This deliverable further describes prototypes for delivering the decision on the granted access rights to the environment that enforces access control. The goal of this deliverable is to document and disseminate existing approaches in contributing research infrastructures. The main use case in this deliverable is that data access requires authorisation because of its sensitive nature, for instance, if it involves samples from humans. Alternatively, it is possible that the data per se is not sensitive and suited to become public but cannot be shared pending the publication of the research results or filing a patent application. These two use cases are complementary and can be covered by the same technical approaches. Since this deliverable focuses on accessing research data, access to other kinds of assets (such as, instruments, biological samples and computing capacity) is out of scope. Transfer of research data between datacentres (including legal considerations of cross-national transfers) is also not covered in this deliverable. This deliverable first presents the key concepts, then previous work in life sciences and beyond as well as within relevant standards bodies (in particular, Global Alliance for Genomics and Health). Finally eight prototype implementations are presented from the contributing research infrastructures, including ELIXIR services for registered and controlled access, BBMRI-ERIC’s Colorectal cancer cohort and Negotiator, EGA’s work on DUO, BBMRI-NL Podium, SOLVE-RD Analysis Sandbox and LifeCycle Federated cohort analysis using DataShield. Before data access authorisation and delivery can be carried out, a researcher needs to be identified and their identity authenticated to a sufficient level of assurance. Existing approaches to researcher authentication are described here to the extent necessary for data access authorisation.
Published: 2019
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5. Integrated clinical and omics approach to rare diseases : Novel genes and oligogenic inheritance in holoprosencephaly

Author: Kim, Artem, Savary, Clara, Dubourg, Christèle, Carré, Wilfrid, Mouden, Charlotte, Hamdi-Rozé, Houda, Guyodo, Hélène, Douce, Jerome Le, Génin, Emmanuelle, Campion, Dominique, Dartigues, Jean François, Deleuze, Jean François, Lambert, Jean Charles, Redon, Richard, Ludwig, Thomas, Grenier-Boley, Benjamin, Letort, Sébastien, Lindenbaum, Pierre, Meyer, Vincent, Quenez, Olivier, Dina, Christian, Bellenguez, Céline, Charbonnier-Le Clézio, Camille, Giemza, Joanna, Chatel, Stéphanie, Férec, Claude, Le Marec, Hervé, Letenneur, Luc, Nicolas, Gaël, Rouault, Karen, Bacq, Delphine, Boland, Anne, Lechner, Doris, Wijmenga, Cisca, Swertz, Morris A., Eline Slagboom, P., Van Ommen, Gert Jan B., Van Duijn, Cornelia M., Boomsma, Dorret I., De Bakker, Paul I.W., Bovenberg, Jasper A., De Craen, Anton J.M., Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Sujie Cao, Jeremy, Van Dijk, Freerk, Neerincx, Pieter B.T., Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Vermaat, Martijn, Laros, Jeroen F.J., Den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Mathijs Kattenberg, V., Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D.C., Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Pasquier, Laurent, Flori, Elisabeth, Gonzales, Marie, Bénéteau, Claire, Boute, Odile, Attié-Bitach, Tania, Roume, Joelle, Goujon, Louise, Akloul, Linda, Odent, Sylvie, Watrin, Erwan, Dupé, Valérie, De Tayrac, Marie, David, Véronique, Kim, Artem, Savary, Clara, Dubourg, Christèle, Carré, Wilfrid, Mouden, Charlotte, Hamdi-Rozé, Houda, Guyodo, Hélène, Douce, Jerome Le, Génin, Emmanuelle, Campion, Dominique, Dartigues, Jean François, Deleuze, Jean François, Lambert, Jean Charles, Redon, Richard, Ludwig, Thomas, Grenier-Boley, Benjamin, Letort, Sébastien, Lindenbaum, Pierre, Meyer, Vincent, Quenez, Olivier, Dina, Christian, Bellenguez, Céline, Charbonnier-Le Clézio, Camille, Giemza, Joanna, Chatel, Stéphanie, Férec, Claude, Le Marec, Hervé, Letenneur, Luc, Nicolas, Gaël, Rouault, Karen, Bacq, Delphine, Boland, Anne, Lechner, Doris, Wijmenga, Cisca, Swertz, Morris A., Eline Slagboom, P., Van Ommen, Gert Jan B., Van Duijn, Cornelia M., Boomsma, Dorret I., De Bakker, Paul I.W., Bovenberg, Jasper A., De Craen, Anton J.M., Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Sujie Cao, Jeremy, Van Dijk, Freerk, Neerincx, Pieter B.T., Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Vermaat, Martijn, Laros, Jeroen F.J., Den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Mathijs Kattenberg, V., Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D.C., Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Pasquier, Laurent, Flori, Elisabeth, Gonzales, Marie, Bénéteau, Claire, Boute, Odile, Attié-Bitach, Tania, Roume, Joelle, Goujon, Louise, Akloul, Linda, Odent, Sylvie, Watrin, Erwan, Dupé, Valérie, De Tayrac, Marie, and David, Véronique
Published: 2019

6. Integrated clinical and omics approach to rare diseases: Novel genes and oligogenic inheritance in holoprosencephaly

Author: CMM Groep Kaaij, Genetica Klinische Genetica, Cancer, CMM Groep De Ridder, Child Health, CMM Groep Kloosterman, CMM USEQ Facility, Hubrecht Institute with UMC, Kim, Artem, Savary, Clara, Dubourg, Christèle, Carré, Wilfrid, Mouden, Charlotte, Hamdi-Rozé, Houda, Guyodo, Hélène, Douce, Jerome Le, Génin, Emmanuelle, Campion, Dominique, Dartigues, Jean François, Deleuze, Jean François, Lambert, Jean Charles, Redon, Richard, Ludwig, Thomas, Grenier-Boley, Benjamin, Letort, Sébastien, Lindenbaum, Pierre, Meyer, Vincent, Quenez, Olivier, Dina, Christian, Bellenguez, Céline, Charbonnier-Le Clézio, Camille, Giemza, Joanna, Chatel, Stéphanie, Férec, Claude, Le Marec, Hervé, Letenneur, Luc, Nicolas, Gaël, Rouault, Karen, Bacq, Delphine, Boland, Anne, Lechner, Doris, Wijmenga, Cisca, Swertz, Morris A., Eline Slagboom, P., Van Ommen, Gert Jan B., Van Duijn, Cornelia M., Boomsma, Dorret I., De Bakker, Paul I.W., Bovenberg, Jasper A., De Craen, Anton J.M., Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Sujie Cao, Jeremy, Van Dijk, Freerk, Neerincx, Pieter B.T., Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Vermaat, Martijn, Laros, Jeroen F.J., Den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Mathijs Kattenberg, V., Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D.C., Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Pasquier, Laurent, Flori, Elisabeth, Gonzales, Marie, Bénéteau, Claire, Boute, Odile, Attié-Bitach, Tania, Roume, Joelle, Goujon, Louise, Akloul, Linda, Odent, Sylvie, Watrin, Erwan, Dupé, Valérie, De Tayrac, Marie, David, Véronique, CMM Groep Kaaij, Genetica Klinische Genetica, Cancer, CMM Groep De Ridder, Child Health, CMM Groep Kloosterman, CMM USEQ Facility, Hubrecht Institute with UMC, Kim, Artem, Savary, Clara, Dubourg, Christèle, Carré, Wilfrid, Mouden, Charlotte, Hamdi-Rozé, Houda, Guyodo, Hélène, Douce, Jerome Le, Génin, Emmanuelle, Campion, Dominique, Dartigues, Jean François, Deleuze, Jean François, Lambert, Jean Charles, Redon, Richard, Ludwig, Thomas, Grenier-Boley, Benjamin, Letort, Sébastien, Lindenbaum, Pierre, Meyer, Vincent, Quenez, Olivier, Dina, Christian, Bellenguez, Céline, Charbonnier-Le Clézio, Camille, Giemza, Joanna, Chatel, Stéphanie, Férec, Claude, Le Marec, Hervé, Letenneur, Luc, Nicolas, Gaël, Rouault, Karen, Bacq, Delphine, Boland, Anne, Lechner, Doris, Wijmenga, Cisca, Swertz, Morris A., Eline Slagboom, P., Van Ommen, Gert Jan B., Van Duijn, Cornelia M., Boomsma, Dorret I., De Bakker, Paul I.W., Bovenberg, Jasper A., De Craen, Anton J.M., Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Sujie Cao, Jeremy, Van Dijk, Freerk, Neerincx, Pieter B.T., Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Vermaat, Martijn, Laros, Jeroen F.J., Den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Mathijs Kattenberg, V., Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D.C., Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Pasquier, Laurent, Flori, Elisabeth, Gonzales, Marie, Bénéteau, Claire, Boute, Odile, Attié-Bitach, Tania, Roume, Joelle, Goujon, Louise, Akloul, Linda, Odent, Sylvie, Watrin, Erwan, Dupé, Valérie, De Tayrac, Marie, and David, Véronique
Published: 2019

7. WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene

Author: Nersisyan, Lilit, Nikoghosyan, Maria, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Elbers, Clara C., Kloosterman, Wigard P., van Setten, Jessica, Nijman, Isaac J., Renkens, Ivo, de Bakker, Paul I. W., van Dijk, Freerk, Neerincx, Pieter B. T., Deelen, Patrick, Kanterakis, Alexandros, Dijkstra, Martijn, Byelas, Heorhiy, van der Velde, K. Joeri, Platteel, Mathieu, Swertz, Morris A., Wijmenga, Cisca, Palamara, Pier Francesco, Pe'er, Itsik, Ye, Kai, Lameijer, Eric-Wubbo, Moed, Matthijs H., Beekman, Marian, de Craen, Anton J. M., Suchiman, H. Eka D., Slagboom, P. Eline, Guryev, Victor, Abdellaoui, Abdel, Hottenga, Jouke Jan, Kattenberg, Mathijs, Willemsen, Gonneke, Boomsma, Dorret I., van Leeuwen, Elisabeth M., Karssen, Lennart C., Amin, Najaf, Rivadeneira, Fernando, Isaacs, Aaron, Hofman, Albert, Uitterlinden, Andre G., van Duijn, Cornelia M., van Oven, Mannis, Kayser, Manfred, Vermaat, Martijn, Laros, Jeroen F. J., den Dunnen, Johan T., van Enckevort, David, Mei, Hailiang, Li, Mingkun, Stoneking, Mark, van Schaik, Barbera D. C., Bot, Jan, Marschall, Tobias, Schonhuth, Alexander, Hehir-Kwa, Jayne Y., Handsaker, Robert E., Polak, Paz, Sohail, Mashaal, Vuzman, Dana, Estrada, Karol, McCarroll, Steven A., Sunyaev, Shamil R., Hormozdiari, Fereydoun, Koval, Vyacheslav, Medina-Gomez, Carolina, Oostra, Ben, Veldink, Jan H., van den Berg, Leonard H., Pitts, Steven J., Potluri, Shobha, Sundar, Purnima, Cox, David R., de Knijff, Peter, Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Wang, Jun, Li, Ning, Cao, Sujie, Bovenberg, Jasper A., van Ommen, Gert-Jan B., Arakelyan, Arsen, Nersisyan, Lilit, Nikoghosyan, Maria, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Elbers, Clara C., Kloosterman, Wigard P., van Setten, Jessica, Nijman, Isaac J., Renkens, Ivo, de Bakker, Paul I. W., van Dijk, Freerk, Neerincx, Pieter B. T., Deelen, Patrick, Kanterakis, Alexandros, Dijkstra, Martijn, Byelas, Heorhiy, van der Velde, K. Joeri, Platteel, Mathieu, Swertz, Morris A., Wijmenga, Cisca, Palamara, Pier Francesco, Pe'er, Itsik, Ye, Kai, Lameijer, Eric-Wubbo, Moed, Matthijs H., Beekman, Marian, de Craen, Anton J. M., Suchiman, H. Eka D., Slagboom, P. Eline, Guryev, Victor, Abdellaoui, Abdel, Hottenga, Jouke Jan, Kattenberg, Mathijs, Willemsen, Gonneke, Boomsma, Dorret I., van Leeuwen, Elisabeth M., Karssen, Lennart C., Amin, Najaf, Rivadeneira, Fernando, Isaacs, Aaron, Hofman, Albert, Uitterlinden, Andre G., van Duijn, Cornelia M., van Oven, Mannis, Kayser, Manfred, Vermaat, Martijn, Laros, Jeroen F. J., den Dunnen, Johan T., van Enckevort, David, Mei, Hailiang, Li, Mingkun, Stoneking, Mark, van Schaik, Barbera D. C., Bot, Jan, Marschall, Tobias, Schonhuth, Alexander, Hehir-Kwa, Jayne Y., Handsaker, Robert E., Polak, Paz, Sohail, Mashaal, Vuzman, Dana, Estrada, Karol, McCarroll, Steven A., Sunyaev, Shamil R., Hormozdiari, Fereydoun, Koval, Vyacheslav, Medina-Gomez, Carolina, Oostra, Ben, Veldink, Jan H., van den Berg, Leonard H., Pitts, Steven J., Potluri, Shobha, Sundar, Purnima, Cox, David R., de Knijff, Peter, Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Wang, Jun, Li, Ning, Cao, Sujie, Bovenberg, Jasper A., van Ommen, Gert-Jan B., and Arakelyan, Arsen
Published: 2019

8. Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck

Author: Li, Mingkun, Rothwell, Rebecca, Vermaat, Martijn, Wachsmuth, Manja, Schröder, Roland, Laros, Jeroen F J, Van Oven, Mannis, De Bakker, Paul I W, Bovenberg, Jasper A., Van Duijn, Cornelia M., Van Ommen, Gert Jan B, Slagboom, P. Eline, Swertz, Morris A., Wijmenga, Cisca, Kayser, Manfred, Boomsma, Dorret I., Zöllner, Sebastian, De Knijff, Peter, Stoneking, Mark, De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Van Dijk, Freerk, Neerincx, Pieter B T, Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Den Dunnen, Johan T., Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Genetic Identification, Epidemiology, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Biological Psychology, EMGO+ - Quality of Care, and Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep
Subjects: Male, Netherlands Twin Register (NTR), 0301 basic medicine, LEVEL, Inheritance Patterns, Twins, Twin Study, POINT MUTATIONS, Genome, Gene Frequency, Paternal mtDNA transmission, Genetics(clinical), Non-U.S. Gov't, Genetics (clinical), Netherlands, Genetics, Research Support, Non-U.S. Gov't, PURIFYING SELECTION, MITOCHONDRIAL-DNA MUTATIONS, RANDOM GENETIC DRIFT, HUMAN-DISEASE, Heteroplasmy, Female, Mitochondrial DNA, TISSUES, OOCYTES, Biology, Research Support, INHERITANCE, DNA, Mitochondrial, White People, Genetic Heterogeneity, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Journal Article, Humans, Family, Selection, Genetic, Allele, Allele frequency, Alleles, Models, Statistical, Polymorphism, Genetic, Models, Genetic, Research, Twin study, Minor allele frequency, 030104 developmental biology, Mutation, MELAS SYNDROME
Abstract: Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies.
Published: 2016

9. Privacy-Preserving Linkage of Genomic and Clinical Data Sets

Author: Baker, Dixie B., primary, Knoppers, Bartha M., additional, Phillips, Mark, additional, van Enckevort, David, additional, Kaufmann, Petra, additional, Lochmuller, Hanns, additional, and Taruscio, Domenica, additional
Published: 2019
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10. Recommendations for Improving the Quality of Rare Disease Registries

Author: Kodra, Yllka, Weinbach, Jerome, Posada-de-la-Paz, Manuel, Coi, Alessio, Lemonnier, S. Lydie, van Enckevort, David, Roos, Marco, Jacobsen, Annika, Cornet, Ronald, Ahmed, S. Faisal, Bros-Facer, Virginie, Popa, Veronica, Van Meel, Marieke, Renault, Daniel, von Gizycki, Rainald, Santoro, Michele, Landais, Paul, Torreri, Paola, Carta, Claudio, Mascalzoni, Deborah, Gainotti, Sabina, Lopez, Estrella, Ambrosini, Anna, Muller, Heimo, Reis, Robert, Bianchi, Fabrizio, Rubinstein, Yaffa R., Lochmueller, Hanns, Mueller, Heimo, Taruscio, Domenica, Kodra, Yllka, Weinbach, Jerome, Posada-de-la-Paz, Manuel, Coi, Alessio, Lemonnier, S. Lydie, van Enckevort, David, Roos, Marco, Jacobsen, Annika, Cornet, Ronald, Ahmed, S. Faisal, Bros-Facer, Virginie, Popa, Veronica, Van Meel, Marieke, Renault, Daniel, von Gizycki, Rainald, Santoro, Michele, Landais, Paul, Torreri, Paola, Carta, Claudio, Mascalzoni, Deborah, Gainotti, Sabina, Lopez, Estrella, Ambrosini, Anna, Muller, Heimo, Reis, Robert, Bianchi, Fabrizio, Rubinstein, Yaffa R., Lochmueller, Hanns, Mueller, Heimo, and Taruscio, Domenica
Abstract: Rare diseases (RD) patient registries are powerful instruments that help develop clinical research, facilitate the planning of appropriate clinical trials, improve patient care, and support healthcare management. They constitute a key information system that supports the activities of European Reference Networks (ERNs) on rare diseases. A rapid proliferation of RD registries has occurred during the last years and there is a need to develop guidance for the minimum requirements, recommendations and standards necessary to maintain a high-quality registry. In response to these heterogeneities, in the framework of RD-Connect, a European platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research, we report on a list of recommendations, developed by a group of experts, including members of patient organizations, to be used as a framework for improving the quality of RD registries. This list includes aspects of governance, Findable, Accessible, Interoperable and Reusable (FAIR) data and information, infrastructure, documentation, training, and quality audit. The list is intended to be used by established as well as new RD registries. Further work includes the development of a toolkit to enable continuous assessment and improvement of their organizational and data quality.
Published: 2018
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11. CORBEL Review of identifier schemes, standards and interoperability maps and proposed harmonization strategy

Author: Goble, Carol, Parkinson, Helen, Jupp, Simon, Kottmann, Renzo, Boiten, Jan-Willem, Glöckner, Frank Oliver, Williams, Eleanor, Swedlow, Jason, Swertz, Morris, van Enckevort, David, Juty, Nick, and Gaulton, Anna
Subjects: Bio Medical Research Infrastructures, Identifier schemes, Identifier standards, Interoperability
Abstract: This work addresses identifier recommendations and harmonisation in the context of the BMS Research Infrastructures (RIs) participating in CORBEL. We summarise community activities in this space (Appendix 1), provide two checklists for: (i) RI identifier strategy and (ii) identifier harmonisation of common entities and services for identity use cases which span the participating BMS RIs. We use six case studies to guide the work. We also define priorities and document existing services that can be adopted, or extended in support of CORBEL.
Published: 2017
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12. CORBEL Report on models and pilot designs for sustainable scalable cloud-based provision of data access and compute across infrastructures

Author: Swertz, Morris, Kelpin, Fleur, van Enckevort, David, Lappalainen, Ilkka, Linden, Mikael, Nyrönen, Tommi, Holub, Petr, Boiten, Jan-Willem, Molder, Anna Leida, and Parkinson, Helen
Subjects: Cloud-based provision of data, Data access, Data management
Abstract: The mission of CORBEL is to facilitate joint operation of research infrastructures of Europe and to provide access to bioscientific resources in a standardised fashion. Task 3 in Work Package 6 addresses the secure data management and compute needs of service providers dealing with data that needs to be access controlled, for example human identifiable data such as genome sequences and related personal meta-data, and dealing with users acting in different roles. As first deliverable we here report on models and pilot designs for sustainable scalable cloud-based provision of data and compute across infrastructures, providing guidance to BMS infrastructure development. Therefore we have first surveyed use cases and needs of BMS infrastructures and their users. Subsequently we surveyed existing models for the provisioning of data access and compute. Finally, we have shortlisted a series of pilot designs to inform next steps in the joint development across BMS infrastructures and e-infrastructure providers, in particular within deliverable 6.5 of CORBEL but also in ongoing projects EXCELERATE, EGI-engage, BBMRI-ERIC ADOPT, etc.
Published: 2017
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13. A Decentralized IT Architecture for Locating and Negotiating Access to Biobank Samples

Author: Proynova, Rumyana, Alexandre, Diogo, Lablans, Martin, Van Enckevort, David, Mate, Sebastian, Eklund, Niina, Silander, Kaisa, Hummel, Michael, Holub, Petr, Ückert, Frank, Rohrig, Rainer, Sax, Ulrich, Timmer, Antje, and Binder, Harald
Subjects: Biological specimen banks, European research infrastructure, Information storage and retrieval, Decentral search
Abstract: There is a need among researchers for the easy discoverability of biobank samples. Currently, there is no uniform way for finding samples and negotiate access. Instead, researchers have to communicate with each biobank separately. We present the architecture for the BBMRI-CS IT platform, whose goal is to facilitate sample location and access. We chose a decentral approach, which allows for strong data protection and provides the high flexibility needed in the highly heterogeneous landscape of European biobanks. This is the first implementation of a decentral search in the biobank field. With the addition of a Negotiator component, it also allows for easy communication and a follow-through of the lengthy approval process for accessing samples.
Published: 2017

14. MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians

Author: van der Velde, K Joeri, primary, Imhann, Floris, additional, Charbon, Bart, additional, Pang, Chao, additional, van Enckevort, David, additional, Slofstra, Mariska, additional, Barbieri, Ruggero, additional, Alberts, Rudi, additional, Hendriksen, Dennis, additional, Kelpin, Fleur, additional, de Haan, Mark, additional, de Boer, Tommy, additional, Haakma, Sido, additional, Stroomberg, Connor, additional, Scholtens, Salome, additional, van de Geijn, Gert-Jan, additional, Festen, Eleonora A M, additional, Weersma, Rinse K, additional, and Swertz, Morris A, additional
Published: 2018
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15. Recommendations for Improving the Quality of Rare Disease Registries

Author: Kodra, Yllka, primary, Weinbach, Jérôme, additional, Posada-de-la-Paz, Manuel, additional, Coi, Alessio, additional, Lemonnier, S., additional, van Enckevort, David, additional, Roos, Marco, additional, Jacobsen, Annika, additional, Cornet, Ronald, additional, Ahmed, S., additional, Bros-Facer, Virginie, additional, Popa, Veronica, additional, Van Meel, Marieke, additional, Renault, Daniel, additional, von Gizycki, Rainald, additional, Santoro, Michele, additional, Landais, Paul, additional, Torreri, Paola, additional, Carta, Claudio, additional, Mascalzoni, Deborah, additional, Gainotti, Sabina, additional, Lopez, Estrella, additional, Ambrosini, Anna, additional, Müller, Heimo, additional, Reis, Robert, additional, Bianchi, Fabrizio, additional, Rubinstein, Yaffa, additional, Lochmüller, Hanns, additional, and Taruscio, Domenica, additional
Published: 2018
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16. MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases

Author: Townend, Gillian S., primary, Ehrhart, Friederike, additional, van Kranen, Henk J., additional, Wilkinson, Mark, additional, Jacobsen, Annika, additional, Roos, Marco, additional, Willighagen, Egon L., additional, van Enckevort, David, additional, Evelo, Chris T., additional, and Curfs, Leopold M. G., additional
Published: 2018
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17. Overview of a suite of middle-ware services for implementing FAIR data principles

Author: Thompson, Mark, Bonino, Luiz, Wilkinson, Mark D., Kaliyaperumal, Rajaram, Burger, Kees, Van Leeuwen, Shamanou, Jacobsen, Annika, Carta, Claudio, Schultes, Erik, Van Enckevort, David, Finkers, Richard, Jansen, Mascha, Mons, Barend, Roos, Marco, Thompson, Mark, Bonino, Luiz, Wilkinson, Mark D., Kaliyaperumal, Rajaram, Burger, Kees, Van Leeuwen, Shamanou, Jacobsen, Annika, Carta, Claudio, Schultes, Erik, Van Enckevort, David, Finkers, Richard, Jansen, Mascha, Mons, Barend, and Roos, Marco
Abstract: Principles of Findable, Accessible, Interoperable, and Reusable data for humansand computers (FAIR)1are widely endorsed by organizations such as the Euro-pean Open Science Cloud, the life science data infrastructure ELIXIR, the NIHvia its commons program, the biobanking infrastructure consortium BBMRI-ERIC, the G20 and the G7. Implementing a data ecosystem based on FAIRprinciples requires guidelines, tools, and training, and FAIR data stewards tohelp apply them. The principles as such do not recommend any particular im-plementation: user communities will have to decide the most appropriate imple-mentation for their domain. Here, we demonstrate the use of a suite of SemanticWeb-based middle-ware services that help communities implement FAIR dataprinciples2. Aiming to facilitate adoption, the services are made to complementexisting data infrastructures, including local and centralised data resources, andthus establish a robust, federated ecosystem of FAIR resources. The servicesare also particularly suited for training data stewards. We demonstrate the ap-plication of the services by rare disease and plant breeding communities wherethe combination of Ontologies, Linked Data, and light-weight FAIR services arebeing explored as the means to implement FAIR data principles.
Published: 2017

18. Report on Web Services based integration of BioMedBridges integration across all appropriate services

Author: Juty, Nick, McMurry, Julie, Jupp, Simon, Burdett, Tony, Jenkinson, Andy, Parkinson, Helen, Chambers, Jon, Morris, Chris, Winn, Martyn, Gormanns, Philipp, Schneltzer, Elida, Bild, Raffael, Krauth, Christian, Kuchinke, Wolfgang, de Bruijn, Freek, Blondé, Ward, Beliën, Jeroen, Klein, Stefan, Vast, Erwin, Hendriksen, Dennis, Charbon, Bart, van Enckevort, David, and Swertz, Morris
Subjects: data interoperability, semantic interoperability, data integration, RDF
Abstract: European e-Infrastructure projects are increasingly turning to Semantic Web[1] (SemWeb) technologies to address data integration challenges. This approach is proving to be a solution to some of the emerging challenges in the life sciences. The BioMedBridges semantic web pilot spans deliverables 4.4, 4.6, 4.7, and 4.8; its goal is to test the suitability of a semantic web approach to the task of integrating research data and to report on our experience of running an RDF-based platform integrating multiple data resources. In order to leverage experience where it exists and minimise the risks inherent in novel technology projects, a three-stage delivery was chosen for the pilot. As summarised below, these three stages are reported in separate deliverables. This deliverable D4.8 reports on the strategy, implementation and lessons learned for the semantic web pilots for BioMedBridges. By following this schedule and aligning partner-specific roadmaps to the blueprint delivered in Phase I (D4.4), the pilot projects were developed synchronously, allowing knowledge to be shared efficiently (Phases 2-3: D4.6-4.8). This enabled infrastructures to collaborate effectively and address common issues as they arose. In support of this effort, a knowledge-exchange workshop ran on the 29-30 April 2014 at TMF, Berlin, Germany. The programme and course materials are available at BioMedBridges website[2] and can be found in D4.7 Appendix 2 (‘Resources’), item 3 (‘SWAT4LS SemWeb training materials’). In December 2013 and December 2014, at SWAT4LS[3] and in May 2015 at an industry workshop, tutorials were delivered demonstrating the queries and analyses the RDF platform makes possible. A training course at the School of Computer Science, University of Manchester in December 2014 delivered a summary of the practicalities of working with and running an RDF platform, which summarised the technological approach and technology experience. All of the SemWeb pilot work was informed by the work of WP3, with respect to the choice and use of ontologies, as well as provision and re-use of identifiers, reflecting the application of standards derived from the use case work packages (e.g. WP7 and WP10). BioMedBridges played a major role at the CRI (Clinical Research Informatics) Day organised by ECRIN: "First CRI Solutions Day" (26-27 May 2014 at Heinrich-Heine University, Düsseldorf, Germany). The presentation about BioMedBridges (S. Suhr) was accompanied by presentations of software tools and hands-on sessions with their developers. Tools developed or employed in BioMedBridges (BBMRI Catalogue, CTIM, tranSMART, MOLGENIS / BiobankConnect, XNAT) and the approaches for data sharing of BioMedBridges could be compared with those of many other Research Infrastructures and EU projects, such as EATRIS, BBMRI, ECRIN, BioSHaRE, TRANSFoRm, EHR4CR, and p-medicine. The first impression of participants at the CRI Solutions Day was that EU projects often seem to cope with similar problems and have developed similar solutions. For example, all domains struggle with the same rigid conditions for data protection and the challenge of semantic interoperability. It was suggested that it might be better to bring projects together and to work jointly on software solutions to common problems. Especially in the area of semantic interoperability and legally compliant data sharing, BioMedBridges has developed generic solutions that may be of help for other projects. A workshop on translational research infrastructure including tools like XNAT, tranSMART, MOLGENIS, OpenClinica and Galaxy and the interfaces between them, co-organised by Dutch representatives of BBMRI, EuroBioImaging, and EATRIS, was held at the OpenBridges symposium (see section 3.2.1.2, Pilots 1 through 3). Materials such as presentations, documentation on discussions relating to the OpenClinica-tranSMART and tranSMART-Galaxy connections, as well as XNAT at the Dutch DTL Programmers Meeting are available elsewhere[4]. Various other outreach and dissemination activities have taken place during the course of BioMedBridges WP4, and are detailed within this report, in the relevant sections. While many of the most refined pilots (below) are centred on the use of RDF, it is not the only appropriate solution for data integration; our experience indicated that certain kinds of data are better suited to different distribution and integration mechanisms. Therefore, this report covers an array of solutions that achieve integration, including RDF-based, as well as those that provide integration points for future efforts; D4.6 included both RDF-based and pilots using alternative methodologies, D4.7 was targeted specifically at judging the suitability and scalability of a purely RDF-centric data integration solution, with other deliverables providing various interfaces to data (REST, widgets, GUIs). Here we summarize our processes, products, and lessons learnt during the execution of this work package. We also describe the further work that has been conducted in the period intervening D4.6 and this report (D4.8), as well as detailing the sustainability of these pilot activities, and lessons learnt throughout the entirety of WP4. [1] https://wiki.dtls.nl/index.php/DTL_Programmers_Meeting [2] http://www.biomedbridges.eu/trainings/knowledge-exchange-workshop-resource-description-framework-rdf [3] http://www.swat4ls.org/workshops/berlin2014/ [4] http://www.w3.org/standards/semanticweb/
Published: 2016
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19. Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data

Author: Zhang, Chao, primary, Bijlard, Jochem, additional, Staiger, Christine, additional, Scollen, Serena, additional, van Enckevort, David, additional, Hoogstrate, Youri, additional, Senf, Alexander, additional, Hiltemann, Saskia, additional, Repo, Susanna, additional, Pipping, Wibo, additional, Bierkens, Mariska, additional, Payralbe, Stefan, additional, Stringer, Bas, additional, Heringa, Jaap, additional, Stubbs, Andrew, additional, Bonino Da Silva Santos, Luiz Olavo, additional, Belien, Jeroen, additional, Weistra, Ward, additional, Azevedo, Rita, additional, van Bochove, Kees, additional, Meijer, Gerrit, additional, Boiten, Jan-Willem, additional, Rambla, Jordi, additional, Fijneman, Remond, additional, Spalding, J. Dylan, additional, and Abeln, Sanne, additional
Published: 2017
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20. BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration

Author: Pang, Chao, primary, Kelpin, Fleur, additional, van Enckevort, David, additional, Eklund, Niina, additional, Silander, Kaisa, additional, Hendriksen, Dennis, additional, de Haan, Mark, additional, Jetten, Jonathan, additional, de Boer, Tommy, additional, Charbon, Bart, additional, Holub, Petr, additional, Hillege, Hans, additional, and Swertz, Morris A, additional
Published: 2017
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21. Integration of EGA secure data access into Galaxy

Author: Hoogstrate, Youri, primary, Zhang, Chao, additional, Senf, Alexander, additional, Bijlard, Jochem, additional, Hiltemann, Saskia, additional, van Enckevort, David, additional, Repo, Susanna, additional, Heringa, Jaap, additional, Jenster, Guido, additional, Fijneman, Remond J.A., additional, Boiten, Jan-Willem, additional, A. Meijer, Gerrit, additional, Stubbs, Andrew, additional, Rambla, Jordi, additional, Spalding, Dylan, additional, and Abeln, Sanne, additional
Published: 2016
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22. BBMRI-ERIC Directory: 515 Biobanks with Over 60 Million Biological Samples

Author: Holub, Petr, primary, Swertz, Morris, additional, Reihs, Robert, additional, van Enckevort, David, additional, Müller, Heimo, additional, and Litton, Jan-Eric, additional
Published: 2016
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23. Characteristics of de novo structural changes in the human genome

Author: Kloosterman, Wigard P., Francioli, Laurent C., Hormozdiari, Fereydoun, Marschall, Tobias, Hehir-Kwa, Jayne Y., Abdellaoui, Abdel, Lameijer, Eric Wubbo, Moed, Matthijs H., Koval, Vyacheslav, Renkens, Ivo, Van Roosmalen, Markus J., Arp, Pascal, Karssen, Lennart C., Coe, Bradley P., Handsaker, Robert E., Suchiman, Eka D., Cuppen, Edwin, Thung, Djie Tjwan, McVey, Mitch, Wendl, Michael C., Uitterlinden, André, Van Duijn, Cornelia M., Swertz, Morris A., Wijmenga, Cisca, Van Ommen, Gert Jan B, Slagboom, P. Eline, Boomsma, Dorret I., Schönhuth, Alexander, Eichler, Evan E., De Bakker, Paul I W, Ye, Kai, Guryev, Victor, Bovenberg, Jasper A., De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Van Dijk, Freerk, Neerincx, Pieter B T, Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Vermaat, Martijn, Laros, Jeroen F J, Den Dunnen, Johan T., De Knijff, Peter, Van Leeuwen, Elisa M., Amin, Najaf, Rivadeneira, Fernando, Estrada, Karol, De Ligt, Joep, Hottenga, Jouke Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, McCarroll, Steven A., Ko, Arthur, Sudmant, Peter, Nijman, Isaac J., Adult Psychiatry, Epidemiology and Data Science, ACS - Amsterdam Cardiovascular Sciences, AII - Amsterdam institute for Infection and Immunity, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, ANS - Amsterdam Neuroscience, CCA -Cancer Center Amsterdam, Biological Psychology, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, Internal Medicine, Epidemiology, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Stem Cell Aging Leukemia and Lymphoma (SALL), and Groningen Research Institute for Asthma and COPD (GRIAC)
Subjects: Male, Netherlands Twin Register (NTR), Mutation rate, INTELLECTUAL DISABILITY, Retrotransposon, Genome of Netherlands Consortium, VARIANTS, Medical and Health Sciences, Genome, 0302 clinical medicine, INDEL Mutation, Mutation Rate, Genetics(clinical), Copy-number variation, Genetics (clinical), Genetics, 0303 health sciences, education.field_of_study, food and beverages, Genomics, Single Nucleotide, Biological Sciences, Female, Sequence Analysis, Human, Retroelements, SEQUENCING DATA, Bioinformatics, Molecular Sequence Data, Population, MUTATION-RATES, POPULATION-SCALE, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Humans, Amino Acid Sequence, Polymorphism, Indel, education, Alleles, 030304 developmental biology, COPY NUMBER VARIATION, INDIVIDUAL HUMAN, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], IDENTIFICATION, Genome, Human, Research, Human Genome, Genetic Variation, Sequence Analysis, DNA, DNA, GENE, Haplotypes, DISCOVERY, Human genome, Sequence Alignment, 030217 neurology & neurosurgery
Abstract: Contains fulltext : 154750.pdf (Publisher’s version ) (Open Access) Small insertions and deletions (indels) and large structural variations (SVs) are major contributors to human genetic diversity and disease. However, mutation rates and characteristics of de novo indels and SVs in the general population have remained largely unexplored. We report 332 validated de novo structural changes identified in whole genomes of 250 families, including complex indels, retrotransposon insertions, and interchromosomal events. These data indicate a mutation rate of 2.94 indels (1-20 bp) and 0.16 SVs (>20 bp) per generation. De novo structural changes affect on average 4.1 kbp of genomic sequence and 29 coding bases per generation, which is 91 and 52 times more nucleotides than de novo substitutions, respectively. This contrasts with the equal genomic footprint of inherited SVs and substitutions. An excess of structural changes originated on paternal haplotypes. Additionally, we observed a nonuniform distribution of de novo SVs across offspring. These results reveal the importance of different mutational mechanisms to changes in human genome structure across generations. 01 juni 2015
Published: 2015

24. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

Author: Pulit, Sara L., Deelen, Patrick, van Enckevort, David J., Leach, Irene Mateo, Peloso, Gina M., Feitosa, Mary F., Isaacs, Aaron, van Dijk, Freerk, Hofman, Albert, Kanterakis, Alexandros, Penninx, Brenda W.J.H., Oostra, Ben A., de Geus, Eco J., Karssen, Lennart C., Willemsen, Gonneke, Postmus, Iris, Mbarek, Hamdi, Huffman, Jennifer E., Bartz, Traci M., van Leeuwen, Elisabeth M., Joshi, Peter K., Medina-Gomez, Carolina, Menelaou, Androniki, White, Charles C., Verweij, Niek, Manichaikul, Ani, Rivadeneira, Fernando, Milaneschi, Yuri, Francioli, Laurent C., Deelen, Joris, Trompet, Stella, and Franco, Oscar H.
Abstract: Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value
Published: 2015
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25. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

Author: Hehir-Kwa, Jayne Y., Marschall, Tobias, Kloosterman, Wigard P., Francioli, Laurent C., Baaijens, Jasmijn A., Dijkstra, Louis J., Abdellaoui, Abdel, Koval, Vyacheslav, Thung, Djie Tjwan, Wardenaar, René, Renkens, Ivo, Coe, Bradley P., Deelen, Patrick, De Ligt, Joep, Lameijer, Eric Wubbo, Van Dijk, Freerk, Hormozdiari, Fereydoun, Uitterlinden, André G., Van Duijn, Cornelia M., Eichler, Evan E., De Bakker, Paul I.W., Swertz, Morris A., Wijmenga, Cisca, Van Ommen, Gert Jan B, Slagboom, P. Eline, Boomsma, Dorret I., Schönhuth, Alexander, Ye, Kai, Guryev, Victor, Bovenberg, Jasper A., De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Neerincx, Pieter B T, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Vermaat, Martijn, Laros, Jeroen F., den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Rivadeneira, Fernando, Estrada, Karol, Hottenga, Jouke-Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, Handsaker, Robert E., McCarroll, Steven A., Ko, Arthur, Sudmant, Peter, Nijman, Isaac J., Hehir-Kwa, Jayne Y., Marschall, Tobias, Kloosterman, Wigard P., Francioli, Laurent C., Baaijens, Jasmijn A., Dijkstra, Louis J., Abdellaoui, Abdel, Koval, Vyacheslav, Thung, Djie Tjwan, Wardenaar, René, Renkens, Ivo, Coe, Bradley P., Deelen, Patrick, De Ligt, Joep, Lameijer, Eric Wubbo, Van Dijk, Freerk, Hormozdiari, Fereydoun, Uitterlinden, André G., Van Duijn, Cornelia M., Eichler, Evan E., De Bakker, Paul I.W., Swertz, Morris A., Wijmenga, Cisca, Van Ommen, Gert Jan B, Slagboom, P. Eline, Boomsma, Dorret I., Schönhuth, Alexander, Ye, Kai, Guryev, Victor, Bovenberg, Jasper A., De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Neerincx, Pieter B T, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Vermaat, Martijn, Laros, Jeroen F., den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Rivadeneira, Fernando, Estrada, Karol, Hottenga, Jouke-Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, Handsaker, Robert E., McCarroll, Steven A., Ko, Arthur, Sudmant, Peter, and Nijman, Isaac J.
Published: 2016

26. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

Author: Genetica, CMM Groep Kloosterman, Child Health, Cancer, CMM Groep Kaaij, CMM Groep Cuppen, CMM Groep De Ridder, Epi Methoden Team 2, Infection & Immunity, Circulatory Health, Hubrecht Institute with UMC, Genetica Medische Informatica, Genetica Sectie Genoomdiagnostiek, Hehir-Kwa, Jayne Y., Marschall, Tobias, Kloosterman, Wigard P., Francioli, Laurent C., Baaijens, Jasmijn A., Dijkstra, Louis J., Abdellaoui, Abdel, Koval, Vyacheslav, Thung, Djie Tjwan, Wardenaar, René, Renkens, Ivo, Coe, Bradley P., Deelen, Patrick, De Ligt, Joep, Lameijer, Eric Wubbo, Van Dijk, Freerk, Hormozdiari, Fereydoun, Uitterlinden, André G., Van Duijn, Cornelia M., Eichler, Evan E., De Bakker, Paul I.W., Swertz, Morris A., Wijmenga, Cisca, Van Ommen, Gert Jan B, Slagboom, P. Eline, Boomsma, Dorret I., Schönhuth, Alexander, Ye, Kai, Guryev, Victor, Bovenberg, Jasper A., De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Neerincx, Pieter B T, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Vermaat, Martijn, Laros, Jeroen F., den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Rivadeneira, Fernando, Estrada, Karol, Hottenga, Jouke-Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, Handsaker, Robert E., McCarroll, Steven A., Ko, Arthur, Sudmant, Peter, Nijman, Isaac J., Genetica, CMM Groep Kloosterman, Child Health, Cancer, CMM Groep Kaaij, CMM Groep Cuppen, CMM Groep De Ridder, Epi Methoden Team 2, Infection & Immunity, Circulatory Health, Hubrecht Institute with UMC, Genetica Medische Informatica, Genetica Sectie Genoomdiagnostiek, Hehir-Kwa, Jayne Y., Marschall, Tobias, Kloosterman, Wigard P., Francioli, Laurent C., Baaijens, Jasmijn A., Dijkstra, Louis J., Abdellaoui, Abdel, Koval, Vyacheslav, Thung, Djie Tjwan, Wardenaar, René, Renkens, Ivo, Coe, Bradley P., Deelen, Patrick, De Ligt, Joep, Lameijer, Eric Wubbo, Van Dijk, Freerk, Hormozdiari, Fereydoun, Uitterlinden, André G., Van Duijn, Cornelia M., Eichler, Evan E., De Bakker, Paul I.W., Swertz, Morris A., Wijmenga, Cisca, Van Ommen, Gert Jan B, Slagboom, P. Eline, Boomsma, Dorret I., Schönhuth, Alexander, Ye, Kai, Guryev, Victor, Bovenberg, Jasper A., De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Neerincx, Pieter B T, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Vermaat, Martijn, Laros, Jeroen F., den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Rivadeneira, Fernando, Estrada, Karol, Hottenga, Jouke-Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, Handsaker, Robert E., McCarroll, Steven A., Ko, Arthur, Sudmant, Peter, and Nijman, Isaac J.
Published: 2016

27. Transmission of human mtDNA heteroplasmy in the genome of the Netherlands families: Support for a variable-size bottleneck

Author: Epidemiology & Health Economics, CMM Groep Kaaij, Brain, Infection & Immunity, Circulatory Health, JC onderzoeksprogramma Methodologie, CMM Groep Cuppen, Cancer, CMM Groep Kloosterman, Child Health, Genetica Medische Informatica, Genetica Sectie Genoomdiagnostiek, Li, Mingkun, Rothwell, Rebecca, Vermaat, Martijn, Wachsmuth, Manja, Schröder, Roland, Laros, Jeroen F J, Van Oven, Mannis, De Bakker, Paul I W, Bovenberg, Jasper A., Van Duijn, Cornelia M., Van Ommen, Gert Jan B, Slagboom, P. Eline, Swertz, Morris A., Wijmenga, Cisca, Kayser, Manfred, Boomsma, Dorret I., Zöllner, Sebastian, De Knijff, Peter, Stoneking, Mark, De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Van Dijk, Freerk, Neerincx, Pieter B T, Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Den Dunnen, Johan T., Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Epidemiology & Health Economics, CMM Groep Kaaij, Brain, Infection & Immunity, Circulatory Health, JC onderzoeksprogramma Methodologie, CMM Groep Cuppen, Cancer, CMM Groep Kloosterman, Child Health, Genetica Medische Informatica, Genetica Sectie Genoomdiagnostiek, Li, Mingkun, Rothwell, Rebecca, Vermaat, Martijn, Wachsmuth, Manja, Schröder, Roland, Laros, Jeroen F J, Van Oven, Mannis, De Bakker, Paul I W, Bovenberg, Jasper A., Van Duijn, Cornelia M., Van Ommen, Gert Jan B, Slagboom, P. Eline, Swertz, Morris A., Wijmenga, Cisca, Kayser, Manfred, Boomsma, Dorret I., Zöllner, Sebastian, De Knijff, Peter, Stoneking, Mark, De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Van Dijk, Freerk, Neerincx, Pieter B T, Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Den Dunnen, Johan T., Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., and Guryev, Victor
Published: 2016

28. Toward Global Biobank Integration by Implementation of the Minimum Information About BIobank Data Sharing (MIABIS 2.0 Core)

Author: Merino-Martinez, Roxana, primary, Norlin, Loreana, additional, van Enckevort, David, additional, Anton, Gabriele, additional, Schuffenhauer, Simone, additional, Silander, Kaisa, additional, Mook, Linda, additional, Holub, Petr, additional, Bild, Raffael, additional, Swertz, Morris, additional, and Litton, Jan-Eric, additional
Published: 2016
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29. MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks

Author: Pang, Chao, primary, van Enckevort, David, additional, de Haan, Mark, additional, Kelpin, Fleur, additional, Jetten, Jonathan, additional, Hendriksen, Dennis, additional, de Boer, Tommy, additional, Charbon, Bart, additional, Winder, Erwin, additional, van der Velde, K. Joeri, additional, Doiron, Dany, additional, Fortier, Isabel, additional, Hillege, Hans, additional, and Swertz, Morris A., additional
Published: 2016
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30. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

Author: Van Leeuwen, Elisabeth M., Karssen, Lennart C., Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, Van Enckevort, David J., Huffman, Jennifer E., White, Charles C., Feitosa, Mary F., Bartz, Traci M., Manichaikul, Ani, Joshi, Peter K., Peloso, Gina M., Deelen, Patrick, Van Dijk, Freerk, Willemsen, Gonneke, De Geus, Eco J., Milaneschi, Yuri, Penninx, Brenda W J H, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A., Franco, Oscar H., Leach, Irene Mateo, Beekman, Marian, De Craen, Anton J M, Uh, Hae Won, Trochet, Holly, Hocking, Lynne J., Porteous, David J., Sattar, Naveed, Packard, Chris J., Buckley, Brendan M., Brody, Jennifer A., Bis, Joshua C., Rotter, Jerome I., Mychaleckyj, Josyf C., Campbell, Harry, Duan, Qing, Lange, Leslie A., Wilson, James F., Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F., Rich, Stephen S., Psaty, Bruce M., Borecki, Ingrid B., Kearney, Patricia M., Stott, David J., Cupples, L. Adrienne, Jukema, J. Wouter, Van Der Harst, Pim, Sijbrands, Eric J., Hottenga, Jouke Jan, Uitterlinden, Andre G., Swertz, Morris A., Van Ommen, Gert Jan B, De Bakker, Paul I W, Eline Slagboom, P., Boomsma, Dorret I., Wijmenga, Cisca, Van Duijn, Cornelia M., Neerincx, Pieter B T, Elbers, Clara C., Palamara, Pier Francesco, Peer, Itsik, Abdellaoui, Abdel, Kloosterman, Wigard P., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F J, Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Veldink, Jan H., Van Den Berg, Leonard H., Byelas, Heorhiy, Den Dunnen, Johan T., Dijkstra, Martijn, Amin, Najaf, Van Der Velde, K. Joeri, Van Setten, Jessica, Kattenberg, Mathijs, Van Schaik, Barbera D C, Bot, Jan, Nijman, Isaäc J., Mei, Hailiang, Koval, Vyacheslav, Ye, Kai, Lameijer, Eric Wubbo, Moed, Matthijs H., Hehir-Kwa, Jayne Y., Handsaker, Robert E., Sunyaev, Shamil R., Sohail, Mashaal, Hormozdiari, Fereydoun, Marschall, Tobias, Schönhuth, Alexander, Guryev, Victor, Suchiman, H. Eka D, Wolffenbuttel, Bruce H., Platteel, Mathieu, Pitts, Steven J., Potluri, Shobha, Cox, David R., Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, Bovenberg, Jasper A., Van Leeuwen, Elisabeth M., Karssen, Lennart C., Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, Van Enckevort, David J., Huffman, Jennifer E., White, Charles C., Feitosa, Mary F., Bartz, Traci M., Manichaikul, Ani, Joshi, Peter K., Peloso, Gina M., Deelen, Patrick, Van Dijk, Freerk, Willemsen, Gonneke, De Geus, Eco J., Milaneschi, Yuri, Penninx, Brenda W J H, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A., Franco, Oscar H., Leach, Irene Mateo, Beekman, Marian, De Craen, Anton J M, Uh, Hae Won, Trochet, Holly, Hocking, Lynne J., Porteous, David J., Sattar, Naveed, Packard, Chris J., Buckley, Brendan M., Brody, Jennifer A., Bis, Joshua C., Rotter, Jerome I., Mychaleckyj, Josyf C., Campbell, Harry, Duan, Qing, Lange, Leslie A., Wilson, James F., Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F., Rich, Stephen S., Psaty, Bruce M., Borecki, Ingrid B., Kearney, Patricia M., Stott, David J., Cupples, L. Adrienne, Jukema, J. Wouter, Van Der Harst, Pim, Sijbrands, Eric J., Hottenga, Jouke Jan, Uitterlinden, Andre G., Swertz, Morris A., Van Ommen, Gert Jan B, De Bakker, Paul I W, Eline Slagboom, P., Boomsma, Dorret I., Wijmenga, Cisca, Van Duijn, Cornelia M., Neerincx, Pieter B T, Elbers, Clara C., Palamara, Pier Francesco, Peer, Itsik, Abdellaoui, Abdel, Kloosterman, Wigard P., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F J, Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Veldink, Jan H., Van Den Berg, Leonard H., Byelas, Heorhiy, Den Dunnen, Johan T., Dijkstra, Martijn, Amin, Najaf, Van Der Velde, K. Joeri, Van Setten, Jessica, Kattenberg, Mathijs, Van Schaik, Barbera D C, Bot, Jan, Nijman, Isaäc J., Mei, Hailiang, Koval, Vyacheslav, Ye, Kai, Lameijer, Eric Wubbo, Moed, Matthijs H., Hehir-Kwa, Jayne Y., Handsaker, Robert E., Sunyaev, Shamil R., Sohail, Mashaal, Hormozdiari, Fereydoun, Marschall, Tobias, Schönhuth, Alexander, Guryev, Victor, Suchiman, H. Eka D, Wolffenbuttel, Bruce H., Platteel, Mathieu, Pitts, Steven J., Potluri, Shobha, Cox, David R., Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, and Bovenberg, Jasper A.
Abstract: Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (∼35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value -4), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted to be deleterious. The frequency of this ABCA6 variant is 3.65-fold increased in the Dutch and its effect (βLDL-C =0.135, βTC =0.140) is estimated to be very similar to those observed for single variants in well-known lipid genes, such as LDLR.
Published: 2015

31. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

Author: CMM Groep Kaaij, CMM Groep Kloosterman, Child Health, Cancer, ZL Neuromusculaire Ziekten Medisch, Experimentele Afd. Cardiologie 1, CMM Groep Cuppen, JC onderzoeksprogramma Methodologie, Van Leeuwen, Elisabeth M., Karssen, Lennart C., Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, Van Enckevort, David J., Huffman, Jennifer E., White, Charles C., Feitosa, Mary F., Bartz, Traci M., Manichaikul, Ani, Joshi, Peter K., Peloso, Gina M., Deelen, Patrick, Van Dijk, Freerk, Willemsen, Gonneke, De Geus, Eco J., Milaneschi, Yuri, Penninx, Brenda W J H, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A., Franco, Oscar H., Leach, Irene Mateo, Beekman, Marian, De Craen, Anton J M, Uh, Hae Won, Trochet, Holly, Hocking, Lynne J., Porteous, David J., Sattar, Naveed, Packard, Chris J., Buckley, Brendan M., Brody, Jennifer A., Bis, Joshua C., Rotter, Jerome I., Mychaleckyj, Josyf C., Campbell, Harry, Duan, Qing, Lange, Leslie A., Wilson, James F., Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F., Rich, Stephen S., Psaty, Bruce M., Borecki, Ingrid B., Kearney, Patricia M., Stott, David J., Cupples, L. Adrienne, Jukema, J. Wouter, Van Der Harst, Pim, Sijbrands, Eric J., Hottenga, Jouke Jan, Uitterlinden, Andre G., Swertz, Morris A., Van Ommen, Gert Jan B, De Bakker, Paul I W, Eline Slagboom, P., Boomsma, Dorret I., Wijmenga, Cisca, Van Duijn, Cornelia M., Neerincx, Pieter B T, Elbers, Clara C., Palamara, Pier Francesco, Peer, Itsik, Abdellaoui, Abdel, Kloosterman, Wigard P., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F J, Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Veldink, Jan H., Van Den Berg, Leonard H., Byelas, Heorhiy, Den Dunnen, Johan T., Dijkstra, Martijn, Amin, Najaf, Van Der Velde, K. Joeri, Van Setten, Jessica, Kattenberg, Mathijs, Van Schaik, Barbera D C, Bot, Jan, Nijman, Isaäc J., Mei, Hailiang, Koval, Vyacheslav, Ye, Kai, Lameijer, Eric Wubbo, Moed, Matthijs H., Hehir-Kwa, Jayne Y., Handsaker, Robert E., Sunyaev, Shamil R., Sohail, Mashaal, Hormozdiari, Fereydoun, Marschall, Tobias, Schönhuth, Alexander, Guryev, Victor, Suchiman, H. Eka D, Wolffenbuttel, Bruce H., Platteel, Mathieu, Pitts, Steven J., Potluri, Shobha, Cox, David R., Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, Bovenberg, Jasper A., de Bakker, Paul I W, CMM Groep Kaaij, CMM Groep Kloosterman, Child Health, Cancer, ZL Neuromusculaire Ziekten Medisch, Experimentele Afd. Cardiologie 1, CMM Groep Cuppen, JC onderzoeksprogramma Methodologie, Van Leeuwen, Elisabeth M., Karssen, Lennart C., Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, Van Enckevort, David J., Huffman, Jennifer E., White, Charles C., Feitosa, Mary F., Bartz, Traci M., Manichaikul, Ani, Joshi, Peter K., Peloso, Gina M., Deelen, Patrick, Van Dijk, Freerk, Willemsen, Gonneke, De Geus, Eco J., Milaneschi, Yuri, Penninx, Brenda W J H, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A., Franco, Oscar H., Leach, Irene Mateo, Beekman, Marian, De Craen, Anton J M, Uh, Hae Won, Trochet, Holly, Hocking, Lynne J., Porteous, David J., Sattar, Naveed, Packard, Chris J., Buckley, Brendan M., Brody, Jennifer A., Bis, Joshua C., Rotter, Jerome I., Mychaleckyj, Josyf C., Campbell, Harry, Duan, Qing, Lange, Leslie A., Wilson, James F., Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F., Rich, Stephen S., Psaty, Bruce M., Borecki, Ingrid B., Kearney, Patricia M., Stott, David J., Cupples, L. Adrienne, Jukema, J. Wouter, Van Der Harst, Pim, Sijbrands, Eric J., Hottenga, Jouke Jan, Uitterlinden, Andre G., Swertz, Morris A., Van Ommen, Gert Jan B, De Bakker, Paul I W, Eline Slagboom, P., Boomsma, Dorret I., Wijmenga, Cisca, Van Duijn, Cornelia M., Neerincx, Pieter B T, Elbers, Clara C., Palamara, Pier Francesco, Peer, Itsik, Abdellaoui, Abdel, Kloosterman, Wigard P., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F J, Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Veldink, Jan H., Van Den Berg, Leonard H., Byelas, Heorhiy, Den Dunnen, Johan T., Dijkstra, Martijn, Amin, Najaf, Van Der Velde, K. Joeri, Van Setten, Jessica, Kattenberg, Mathijs, Van Schaik, Barbera D C, Bot, Jan, Nijman, Isaäc J., Mei, Hailiang, Koval, Vyacheslav, Ye, Kai, Lameijer, Eric Wubbo, Moed, Matthijs H., Hehir-Kwa, Jayne Y., Handsaker, Robert E., Sunyaev, Shamil R., Sohail, Mashaal, Hormozdiari, Fereydoun, Marschall, Tobias, Schönhuth, Alexander, Guryev, Victor, Suchiman, H. Eka D, Wolffenbuttel, Bruce H., Platteel, Mathieu, Pitts, Steven J., Potluri, Shobha, Cox, David R., Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, Bovenberg, Jasper A., and de Bakker, Paul I W
Published: 2015

32. Characteristics of de novo structural changes in the human genome

Author: CMM Groep Kloosterman, Child Health, Cancer, Genetica, CMM Sectie Genomics and Bioinformatics, Hubrecht Institute with UMC, JC onderzoeksprogramma Methodologie, Epi Methoden Team 1, Kloosterman, Wigard P., Francioli, Laurent C., Hormozdiari, Fereydoun, Marschall, Tobias, Hehir-Kwa, Jayne Y., Abdellaoui, Abdel, Lameijer, Eric Wubbo, Moed, Matthijs H., Koval, Vyacheslav, Renkens, Ivo, Van Roosmalen, Markus J., Arp, Pascal, Karssen, Lennart C., Coe, Bradley P., Handsaker, Robert E., Suchiman, Eka D., Cuppen, Edwin, Thung, Djie Tjwan, McVey, Mitch, Wendl, Michael C., Uitterlinden, André, Van Duijn, Cornelia M., Swertz, Morris A., Wijmenga, Cisca, Van Ommen, Gert Jan B, Slagboom, P. Eline, Boomsma, Dorret I., Schönhuth, Alexander, Eichler, Evan E., De Bakker, Paul I W, Ye, Kai, Guryev, Victor, Bovenberg, Jasper A., De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Van Dijk, Freerk, Neerincx, Pieter B T, Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Vermaat, Martijn, Laros, Jeroen F J, Den Dunnen, Johan T., De Knijff, Peter, Van Leeuwen, Elisa M., Amin, Najaf, Rivadeneira, Fernando, Estrada, Karol, De Ligt, Joep, Hottenga, Jouke Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, McCarroll, Steven A., Ko, Arthur, Sudmant, Peter, Nijman, Isaac J., CMM Groep Kloosterman, Child Health, Cancer, Genetica, CMM Sectie Genomics and Bioinformatics, Hubrecht Institute with UMC, JC onderzoeksprogramma Methodologie, Epi Methoden Team 1, Kloosterman, Wigard P., Francioli, Laurent C., Hormozdiari, Fereydoun, Marschall, Tobias, Hehir-Kwa, Jayne Y., Abdellaoui, Abdel, Lameijer, Eric Wubbo, Moed, Matthijs H., Koval, Vyacheslav, Renkens, Ivo, Van Roosmalen, Markus J., Arp, Pascal, Karssen, Lennart C., Coe, Bradley P., Handsaker, Robert E., Suchiman, Eka D., Cuppen, Edwin, Thung, Djie Tjwan, McVey, Mitch, Wendl, Michael C., Uitterlinden, André, Van Duijn, Cornelia M., Swertz, Morris A., Wijmenga, Cisca, Van Ommen, Gert Jan B, Slagboom, P. Eline, Boomsma, Dorret I., Schönhuth, Alexander, Eichler, Evan E., De Bakker, Paul I W, Ye, Kai, Guryev, Victor, Bovenberg, Jasper A., De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Van Dijk, Freerk, Neerincx, Pieter B T, Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Vermaat, Martijn, Laros, Jeroen F J, Den Dunnen, Johan T., De Knijff, Peter, Van Leeuwen, Elisa M., Amin, Najaf, Rivadeneira, Fernando, Estrada, Karol, De Ligt, Joep, Hottenga, Jouke Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, McCarroll, Steven A., Ko, Arthur, Sudmant, Peter, and Nijman, Isaac J.
Published: 2015

33. OSSE Goes FAIR -- Implementation of the FAIR Data Principles for an Open-Source Registry for Rare Diseases.

Author: SCHAAF, Jannik, KADIOGLU, Dennis, GOEBEL, Jens, BEHRENDT, Christian-Alexander, ROOS, Marco, van ENCKEVORT, David, ÜCKERT, Frank, SADIKU, Fatlume, WAGNER, Thomas O. F., and STORF, Holger
Abstract: The Open Source Registry for Rare Diseases (OSSE) provides a concept and a software for the management of registries for patients with rare diseases. A disease is defined as rare if less than 5 out of 10,000 people are affected. Up to date, approximately 6,000 rare diseases are catalogued. Networking and data exchange for research purposes remains challenging due to the paucity of interoperability and due to the fact that small data stocks are stored locally. The so called "Findable, Accessible, Interoperable, Reusable" (FAIR) Data Principles have been developed to improve research in the field of rare diseases. Subsequently, the OSSE architecture was adapted to implement the FAIR Data Principles. Therefore, the socalled FAIR Data Point was integrated into OSSE to provide a description of metadata in a FAIR manner. OSSE relies on the existing metadata repository (MDR), which is used in to define data elements in the system. This is an important step towards unified documentation across multiple registries. The integration and use of new procedures to improve interoperability plays an important role in the context of registries for rare diseases. [ABSTRACT FROM AUTHOR]
Published: 2018
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34. MOLGENIS catalogue

Author: Swertz, Morris, primary, van Enckevort, David, additional, and Pang, Chao, additional
Published: 2015
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35. The Genome of the Netherlands:design, and project goals

Author: Boomsma, Dorret I., Wijmenga, Cisca, Slagboom, Eline P., Swertz, Morris A., Karssen, Lennart C., Abdellaoui, Abdel, Ye, Kai, Guryev, Victor, Vermaat, Martijn, van Dijk, Freerk, Francioli, Laurent C., Hottenga, Jouke Jan, Laros, Jeroen F. J., Li, Qibin, Li, Yingrui, Cao, Hongzhi, Chen, Ruoyan, Du, Yuanping, Li, Ning, Cao, Sujie, van Setten, Jessica, Menelaou, Androniki, Pulit, Sara L., Hehir-Kwa, Jayne Y., Beekman, Marian, Elbers, Clara C., Byelas, Heorhiy, de Craen, Anton J. M., Deelen, Patrick, Dijkstra, Martijn, den Dunnen, Johan T., de Knijff, Peter, Houwing-Duistermaat, Jeanine, Koval, Vyacheslav, Estrada, Karol, Hofman, Albert, Kanterakis, Alexandros, van Enckevort, David, Mai, Hailiang, Kattenberg, Mathijs, van Leeuwen, Elisabeth M., Neerincx, Pieter B. T., Oostra, Ben, Rivadeneira, Fernanodo, Suchiman, Eka H. D., Uitterlinden, Andre G., Willemsen, Gonneke, Wolffenbuttel, Bruce H., Wang, Jun, de Bakker, Paul I. W., van Ommen, Gert-Jan, van Duijn, Cornelia M., Boomsma, Dorret I., Wijmenga, Cisca, Slagboom, Eline P., Swertz, Morris A., Karssen, Lennart C., Abdellaoui, Abdel, Ye, Kai, Guryev, Victor, Vermaat, Martijn, van Dijk, Freerk, Francioli, Laurent C., Hottenga, Jouke Jan, Laros, Jeroen F. J., Li, Qibin, Li, Yingrui, Cao, Hongzhi, Chen, Ruoyan, Du, Yuanping, Li, Ning, Cao, Sujie, van Setten, Jessica, Menelaou, Androniki, Pulit, Sara L., Hehir-Kwa, Jayne Y., Beekman, Marian, Elbers, Clara C., Byelas, Heorhiy, de Craen, Anton J. M., Deelen, Patrick, Dijkstra, Martijn, den Dunnen, Johan T., de Knijff, Peter, Houwing-Duistermaat, Jeanine, Koval, Vyacheslav, Estrada, Karol, Hofman, Albert, Kanterakis, Alexandros, van Enckevort, David, Mai, Hailiang, Kattenberg, Mathijs, van Leeuwen, Elisabeth M., Neerincx, Pieter B. T., Oostra, Ben, Rivadeneira, Fernanodo, Suchiman, Eka H. D., Uitterlinden, Andre G., Willemsen, Gonneke, Wolffenbuttel, Bruce H., Wang, Jun, de Bakker, Paul I. W., van Ommen, Gert-Jan, and van Duijn, Cornelia M.
Published: 2014

36. Whole-genome sequence variation, population structure and demographic history of the Dutch population

Author: Francioli, Laurent C., Menelaou, Andronild, Pulit, Sara L., Van Dijk, Freerk, Palamara, Pier Francesco, Elbers, Clara C., Neerincx, Pieter B. T., Ye, Kai, Guryev, Victor, Kloosterman, Wigard P., Deelen, Patrick, Abdellaoui, Abdel, Van Leeuwen, Elisabeth M., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F. J., Karssen, Lennart C., Kanterakis, Alexandros, Amin, Najaf, Hottenga, Jouke Jan, Lameijer, Eric-Wubbo, Kattenberg, Mathijs, Dijkstra, Martijn, Byelas, Heorhiy, Van Settenl, Jessica, Van Schaik, Barbera D. C., Bot, Jan, Nijman, Isaac J., Renkens, Ivo, Marscha, Tobias, Schonhuth, Alexander, Hehir-Kwa, Jayne Y., Handsaker, Robert E., Polak, Paz, Sohail, Mashaal, Vuzman, Dana, Hormozdiari, Fereydoun, Van Enckevort, David, Mei, Hailiang, Koval, Vyacheslav, Moed, Ma-Tthijs H., Van der Velde, K. Joeri, Rivadeneira, Fernando, Estrada, Karol, Medina-Gomez, Carolina, Isaacs, Aaron, McCarroll, Steven A., Beekrnan, Marian, De Craen, Anton J. M., Suchiman, H. Eka D., Hofman, Albert, Oostra, Ben, Uitterlinden, Andre G., Willemsen, Gonneke, Plattee, Mathieu, Veldink, Jan H., Van den Berg, Leonard H., Pitts, Steven J., Potluri, Shobha, Sundar, Purnima, Cox, David R., Sunyaev, Shamil R., Den Dunnen, Johan T., Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, Bovenberg, Jasper A., Peer, Itsik, Slagboom, P. Eline, Van Duijn, Cornelia M., Boomsma, Dorret I., Van Ommen, Gert-Jan B., De Bakker, Paul I. W., Swertz, Morris A., Wijmenga, Cisca, Francioli, Laurent C., Menelaou, Andronild, Pulit, Sara L., Van Dijk, Freerk, Palamara, Pier Francesco, Elbers, Clara C., Neerincx, Pieter B. T., Ye, Kai, Guryev, Victor, Kloosterman, Wigard P., Deelen, Patrick, Abdellaoui, Abdel, Van Leeuwen, Elisabeth M., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F. J., Karssen, Lennart C., Kanterakis, Alexandros, Amin, Najaf, Hottenga, Jouke Jan, Lameijer, Eric-Wubbo, Kattenberg, Mathijs, Dijkstra, Martijn, Byelas, Heorhiy, Van Settenl, Jessica, Van Schaik, Barbera D. C., Bot, Jan, Nijman, Isaac J., Renkens, Ivo, Marscha, Tobias, Schonhuth, Alexander, Hehir-Kwa, Jayne Y., Handsaker, Robert E., Polak, Paz, Sohail, Mashaal, Vuzman, Dana, Hormozdiari, Fereydoun, Van Enckevort, David, Mei, Hailiang, Koval, Vyacheslav, Moed, Ma-Tthijs H., Van der Velde, K. Joeri, Rivadeneira, Fernando, Estrada, Karol, Medina-Gomez, Carolina, Isaacs, Aaron, McCarroll, Steven A., Beekrnan, Marian, De Craen, Anton J. M., Suchiman, H. Eka D., Hofman, Albert, Oostra, Ben, Uitterlinden, Andre G., Willemsen, Gonneke, Plattee, Mathieu, Veldink, Jan H., Van den Berg, Leonard H., Pitts, Steven J., Potluri, Shobha, Sundar, Purnima, Cox, David R., Sunyaev, Shamil R., Den Dunnen, Johan T., Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, Bovenberg, Jasper A., Peer, Itsik, Slagboom, P. Eline, Van Duijn, Cornelia M., Boomsma, Dorret I., Van Ommen, Gert-Jan B., De Bakker, Paul I. W., Swertz, Morris A., and Wijmenga, Cisca
Published: 2014

37. BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration.

Author: Chao Pang, Kelpin, Fleur, van Enckevort, David, Eklund, Niina, Silander, Kaisa, Hendriksen, Dennis, de Haan, Mark, Jetten, Jonathan, de Boer, Tommy, Charbon, Bart, Holub, Petr, Hillege, Hans, and Swertz, Morris A.
Subjects: BIOBANKS, MEDICAL databases, EPIDEMIOLOGICAL research, MACHINE learning, PUBLIC health, INFORMATION retrieval
Abstract: Motivation: Biobanks are indispensable for large-scale genetic/epidemiological studies, yet it remains difficult for researchers to determine which biobanks contain data matching their research questions. Results: To overcome this, we developed a new matching algorithm that identifies pairs of related data elements between biobanks and research variables with high precision and recall. It integrates lexical comparison, Unified Medical Language System ontology tagging and semantic query expansion. The result is BiobankUniverse, a fast matchmaking service for biobanks and researchers. Biobankers upload their data elements and researchers their desired study variables, BiobankUniverse automatically shortlists matching attributes between them. Users can quickly explore matching potential and search for biobanks/data elements matching their research. They can also curate matches and define personalized data-universes. [ABSTRACT FROM AUTHOR]
Published: 2017
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38. MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.

Author: Chao Pang, van Enckevort, David, de Haan, Mark, Kelpin, Fleur, Jetten, Jonathan, Hendriksen, Dennis, de Boer, Tommy, Charbon, Bart, Winder, Erwin, van der Velde, K. Joeri, Doiron, Dany, Fortier, Isabel, Hillege, Hans, and Swertz, Morris A.
Subjects: *BIOBANKS, *BIOLOGICAL specimens, *ACQUISITION of data, *ONTOLOGY, *PHENOTYPES, *GENETICS
Abstract: Motivation: While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. Results: To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. [ABSTRACT FROM AUTHOR]
Published: 2016
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39. Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'.

Author: Deelen, Patrick, Menelaou, Androniki, van Leeuwen, Elisabeth M, Kanterakis, Alexandros, van Dijk, Freerk, Medina-Gomez, Carolina, Francioli, Laurent C, Hottenga, Jouke Jan, Karssen, Lennart C, Estrada, Karol, Kreiner-Møller, Eskil, Rivadeneira, Fernando, van Setten, Jessica, Gutierrez-Achury, Javier, Westra, Harm-Jan, Franke, Lude, van Enckevort, David, Dijkstra, Martijn, Byelas, Heorhiy, and van Duijn, Cornelia M
Subjects: GENOMES, GENETICS, GENOMICS, GENOTYPES
Abstract: Although genome-wide association studies (GWAS) have identified many common variants associated with complex traits, low-frequency and rare variants have not been interrogated in a comprehensive manner. Imputation from dense reference panels, such as the 1000 Genomes Project (1000G), enables testing of ungenotyped variants for association. Here we present the results of imputation using a large, new population-specific panel: the Genome of The Netherlands (GoNL). We benchmarked the performance of the 1000G and GoNL reference sets by comparing imputation genotypes with 'true' genotypes typed on ImmunoChip in three European populations (Dutch, British, and Italian). GoNL showed significant improvement in the imputation quality for rare variants (MAF 0.05-0.5%) compared with 1000G. In Dutch samples, the mean observed Pearson correlation, r2, increased from 0.61 to 0.71. We also saw improved imputation accuracy for other European populations (in the British samples, r2 improved from 0.58 to 0.65, and in the Italians from 0.43 to 0.47). A combined reference set comprising 1000G and GoNL improved the imputation of rare variants even further. The Italian samples benefitted the most from this combined reference (the mean r2 increased from 0.47 to 0.50). We conclude that the creation of a large population-specific reference is advantageous for imputing rare variants and that a combined reference panel across multiple populations yields the best imputation results. [ABSTRACT FROM AUTHOR]
Published: 2014
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40. A framework for the detection of de novo mutations in family-based sequencing data

Author: Francioli, Laurent C, Cretu-Stancu, Mircea, Garimella, Kiran V, Fromer, Menachem, Kloosterman, Wigard P, Wijmenga, Cisca, Investigator, Principal, Swertz, Morris A, van Duijn, Cornelia M, Boomsma, Dorret I, Slagboom, PEline, van Ommen, Gertjan B, de Bakker, Paul IW, van Dijk, Freerk, Menelaou, Androniki, Neerincx, Pieter BT, Pulit, Sara L, Deelen, Patrick, Elbers, Clara C, Francesco Palamara, Pier, Pe'er, Itsik, Abdellaoui, Abdel, van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen FJ, Stoneking, Mark, de Knijff, Peter, Kayser, Manfred, Veldink, Jan H, van den Berg, Leonard H, Byelas, Heorhiy, den Dunnen, Johan T, Dijkstra, Martijn, Amin, Najaf, van der Velde, K Joeri, Hottenga, Jouke Jan, van Setten, Jessica, van Leeuwen, Elisabeth M, Kanterakis, Alexandros, Kattenberg, Mathijs, Karssen, Lennart C, van Schaik, Barbera DC, Bot, Jan, Nijman, Isaäc J, Renkens, Ivo, van Enckevort, David, Mei, Hailiang, Koval, Vyacheslav, Estrada, Karol, Medina-Gomez, Carolina, Ye, Kai, Lameijer, Eric-Wubbo, Moed, Matthijs H, Hehir-Kwa, Jayne Y, Handsaker, Robert E, McCarroll, Steven A, Sunyaev, Shamil R, Polak, Paz, Vuzman, Dana, Sohail, Mashaal, Hormozdiari, Fereydoun, Marschall, Tobias, Schönhuth, Alexander, Guryev, Victor, Slagboom, P Eline, Beekman, Marian B, de Craen, Anton JM, Suchiman, H Eka D, Hofman, Albert, Oostra, Ben, Isaacs, Aaron, Rivadeneira, Fernando, Uitterlinden, André G, Willemsen, Gonneke, Platteel, Mathieu, Pitts, Steven J, Potluri, Shobha, Sundar, Purnima, Cox, David R, Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, Bovenberg, Jasper A, Brandsma, Margreet, Samocha, Kaitlin E, Neale, Benjamin M, Daly, Mark J, Banks, Eric, and DePristo, Mark A
Abstract: Germline mutation detection from human DNA sequence data is challenging due to the rarity of such events relative to the intrinsic error rates of sequencing technologies and the uneven coverage across the genome. We developed PhaseByTransmission (PBT) to identify de novo single nucleotide variants and short insertions and deletions (indels) from sequence data collected in parent-offspring trios. We compute the joint probability of the data given the genotype likelihoods in the individual family members, the known familial relationships and a prior probability for the mutation rate. Candidate de novo mutations (DNMs) are reported along with their posterior probability, providing a systematic way to prioritize them for validation. Our tool is integrated in the Genome Analysis Toolkit and can be used together with the ReadBackedPhasing module to infer the parental origin of DNMs based on phase-informative reads. Using simulated data, we show that PBT outperforms existing tools, especially in low coverage data and on the X chromosome. We further show that PBT displays high validation rates on empirical parent-offspring sequencing data for whole-exome data from 104 trios and X-chromosome data from 249 parent-offspring families. Finally, we demonstrate an association between father's age at conception and the number of DNMs in female offspring's X chromosome, consistent with previous literature reports.
Published: 2016
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41. MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians.

Author: van der Velde KJ, Imhann F, Charbon B, Pang C, van Enckevort D, Slofstra M, Barbieri R, Alberts R, Hendriksen D, Kelpin F, de Haan M, de Boer T, Haakma S, Stroomberg C, Scholtens S, van de Geijn GJ, Festen EAM, Weersma RK, and Swertz MA
Subjects: Algorithms, Genome, Genomics, Computational Biology, Software
Abstract: Motivation: The volume and complexity of biological data increases rapidly. Many clinical professionals and biomedical researchers without a bioinformatics background are generating big '-omics' data, but do not always have the tools to manage, process or publicly share these data., Results: Here we present MOLGENIS Research, an open-source web-application to collect, manage, analyze, visualize and share large and complex biomedical datasets, without the need for advanced bioinformatics skills., Availability and Implementation: MOLGENIS Research is freely available (open source software). It can be installed from source code (see http://github.com/molgenis), downloaded as a precompiled WAR file (for your own server), setup inside a Docker container (see http://molgenis.github.io), or requested as a Software-as-a-Service subscription. For a public demo instance and complete installation instructions see http://molgenis.org/research., (© The Author(s) 2018. Published by Oxford University Press.)
Published: 2019
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42. A Decentralized IT Architecture for Locating and Negotiating Access to Biobank Samples.

Author: Proynova R, Alexandre D, Lablans M, Van Enckevort D, Mate S, Eklund N, Silander K, Hummel M, Holub P, and Ückert F
Subjects: Access to Information, Biological Specimen Banks, Databases, Factual, Negotiating
Abstract: There is a need among researchers for the easy discoverability of biobank samples. Currently, there is no uniform way for finding samples and negotiate access. Instead, researchers have to communicate with each biobank separately. We present the architecture for the BBMRI-CS IT platform, whose goal is to facilitate sample location and access. We chose a decentral approach, which allows for strong data protection and provides the high flexibility needed in the highly heterogeneous landscape of European biobanks. This is the first implementation of a decentral search in the biobank field. With the addition of a Negotiator component, it also allows for easy communication and a follow-through of the lengthy approval process for accessing samples.
Published: 2017

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