11 results on '"Walden, Kellie K."'
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2. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases
- Author
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Genetica, Genetica Klinische Genetica, Circulatory Health, Kerkhof, Jennifer, Rastin, Cassandra, Levy, Michael A., Relator, Raissa, McConkey, Haley, Demain, Leigh, Dominguez-Garrido, Elena, Kaat, Laura Donker, Houge, Sofia Douzgou, DuPont, Barbara R., Fee, Timothy, Fletcher, Robin S., Gokhale, David, Haukanes, Bjørn Ivar, Henneman, Peter, Hilton, Sarah, Hilton, Benjamin A., Jenkinson, Sarah, Lee, Jennifer A., Louie, Raymond J., Motazacker, M. Mahdi, Rzasa, Jessica, Stevenson, Roger E., Plomp, Astrid, van der Laan, Liselot, van der Smagt, Jasper, Walden, Kellie K., Banka, Siddharth, Mannens, Marcel, Skinner, Steven A., Friez, Michael J., Campbell, Christopher, Tedder, Matthew L., Alders, Marielle, Sadikovic, Bekim, Genetica, Genetica Klinische Genetica, Circulatory Health, Kerkhof, Jennifer, Rastin, Cassandra, Levy, Michael A., Relator, Raissa, McConkey, Haley, Demain, Leigh, Dominguez-Garrido, Elena, Kaat, Laura Donker, Houge, Sofia Douzgou, DuPont, Barbara R., Fee, Timothy, Fletcher, Robin S., Gokhale, David, Haukanes, Bjørn Ivar, Henneman, Peter, Hilton, Sarah, Hilton, Benjamin A., Jenkinson, Sarah, Lee, Jennifer A., Louie, Raymond J., Motazacker, M. Mahdi, Rzasa, Jessica, Stevenson, Roger E., Plomp, Astrid, van der Laan, Liselot, van der Smagt, Jasper, Walden, Kellie K., Banka, Siddharth, Mannens, Marcel, Skinner, Steven A., Friez, Michael J., Campbell, Christopher, Tedder, Matthew L., Alders, Marielle, and Sadikovic, Bekim
- Published
- 2024
3. Functional correlation of genome‐wide DNA methylation profiles in genetic neurodevelopmental disorders
- Author
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Levy, Michael A., primary, Relator, Raissa, additional, McConkey, Haley, additional, Pranckeviciene, Erinija, additional, Kerkhof, Jennifer, additional, Barat‐Houari, Mouna, additional, Bargiacchi, Sara, additional, Biamino, Elisa, additional, Palomares Bralo, María, additional, Cappuccio, Gerarda, additional, Ciolfi, Andrea, additional, Clarke, Angus, additional, DuPont, Barbara R., additional, Elting, Mariet W., additional, Faivre, Laurence, additional, Fee, Timothy, additional, Ferilli, Marco, additional, Fletcher, Robin S., additional, Cherick, Florian, additional, Foroutan, Aidin, additional, Friez, Michael J., additional, Gervasini, Cristina, additional, Haghshenas, Sadegheh, additional, Hilton, Benjamin A., additional, Jenkins, Zandra, additional, Kaur, Simranpreet, additional, Lewis, Suzanne, additional, Louie, Raymond J., additional, Maitz, Silvia, additional, Milani, Donatella, additional, Morgan, Angela T., additional, Oegema, Renske, additional, Østergaard, Elsebet, additional, Pallares, Nathalie R., additional, Piccione, Maria, additional, Plomp, Astrid S., additional, Poulton, Cathryn, additional, Reilly, Jack, additional, Rius, Rocio, additional, Robertson, Stephen, additional, Rooney, Kathleen, additional, Rousseau, Justine, additional, Santen, Gijs W. E., additional, Santos‐Simarro, Fernando, additional, Schijns, Josephine, additional, Squeo, Gabriella M., additional, John, Miya St, additional, Thauvin‐Robinet, Christel, additional, Traficante, Giovanna, additional, van der Sluijs, Pleuntje J., additional, Vergano, Samantha A., additional, Vos, Niels, additional, Walden, Kellie K., additional, Azmanov, Dimitar, additional, Balci, Tugce B., additional, Banka, Siddharth, additional, Gecz, Jozef, additional, Henneman, Peter, additional, Lee, Jennifer A., additional, Mannens, Marcel M. A. M., additional, Roscioli, Tony, additional, Siu, Victoria, additional, Amor, David J., additional, Baynam, Gareth, additional, Bend, Eric G., additional, Boycott, Kym, additional, Brunetti‐Pierri, Nicola, additional, Campeau, Philippe M., additional, Campion, Dominique, additional, Christodoulou, John, additional, Dyment, David, additional, Esber, Natacha, additional, Fahrner, Jill A., additional, Fleming, Mark D., additional, Genevieve, David, additional, Heron, Delphine, additional, Husson, Thomas, additional, Kernohan, Kristin D., additional, McNeill, Alisdair, additional, Menke, Leonie A., additional, Merla, Giuseppe, additional, Prontera, Paolo, additional, Rockman‐Greenberg, Cheryl, additional, Schwartz, Charles, additional, Skinner, Steven A., additional, Stevenson, Roger E., additional, Vincent, Marie, additional, Vitobello, Antonio, additional, Tartaglia, Marco, additional, Alders, Marielle, additional, Tedder, Matthew L., additional, and Sadikovic, Bekim, additional
- Published
- 2022
- Full Text
- View/download PDF
4. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders
- Author
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Levy, Michael A., McConkey, Haley, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R., Elting, Mariet W., Faivre, Laurence, Fee, Timothy, Fletcher, Robin S., Cherik, Florian, Foroutan, Aidin, Friez, Michael J., Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A., Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J., Maitz, Silvia, Milani, Donatella, Morgan, Angela T., Oegema, Renske, Ostergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Pizzi, Simone, Plomp, Astrid S., Poulton, Cathryn, Reilly, Jack, Relator, Raissa, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W. E., Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, St John, Miya, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J., Vergano, Samantha A., Vos, Niels, Walden, Kellie K., Azmanov, Dimitar, Balci, Tugce, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A., Mannens, Marcel M. A. M., Roscioli, Tony, Siu, Victoria, Amor, David J., Baynam, Gareth, Bend, Eric G., Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M., Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A., Fleming, Mark D., Genevieve, David, Kerrnohan, Kristin D., McNeill, Alisdair, Menke, Leonie A., Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A., Stevenson, Roger E., Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L., Sadikovic, Bekim, Levy, Michael A., McConkey, Haley, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R., Elting, Mariet W., Faivre, Laurence, Fee, Timothy, Fletcher, Robin S., Cherik, Florian, Foroutan, Aidin, Friez, Michael J., Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A., Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J., Maitz, Silvia, Milani, Donatella, Morgan, Angela T., Oegema, Renske, Ostergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Pizzi, Simone, Plomp, Astrid S., Poulton, Cathryn, Reilly, Jack, Relator, Raissa, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W. E., Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, St John, Miya, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J., Vergano, Samantha A., Vos, Niels, Walden, Kellie K., Azmanov, Dimitar, Balci, Tugce, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A., Mannens, Marcel M. A. M., Roscioli, Tony, Siu, Victoria, Amor, David J., Baynam, Gareth, Bend, Eric G., Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M., Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A., Fleming, Mark D., Genevieve, David, Kerrnohan, Kristin D., McNeill, Alisdair, Menke, Leonie A., Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A., Stevenson, Roger E., Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L., and Sadikovic, Bekim
- Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
- Published
- 2022
5. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders
- Author
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Levy, Michael A., Relator, Raissa, McConkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Palomares Bralo, María, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R., Elting, Mariet W., Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S., Cherick, Florian, Foroutan, Aidin, Friez, Michael J., Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A., Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J., Maitz, Silvia, Milani, Donatella, Morgan, Angela T., Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie R., Piccione, Maria, Plomp, Astrid S., Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W.E., Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella M., John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J., Vergano, Samantha A., Vos, Niels, Walden, Kellie K., Azmanov, Dimitar, Balci, Tugce B., Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A., Mannens, Marcel M.A.M., Roscioli, Tony, Siu, Victoria, Amor, David J., Baynam, Gareth, Bend, Eric G., Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M., Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A., Fleming, Mark D., Genevieve, David, Heron, Delphine, Husson, Thomas, Kernohan, Kristin D., McNeill, Alisdair, Menke, Leonie A., Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A., Stevenson, Roger E., Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L., Sadikovic, Bekim, Levy, Michael A., Relator, Raissa, McConkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Palomares Bralo, María, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R., Elting, Mariet W., Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S., Cherick, Florian, Foroutan, Aidin, Friez, Michael J., Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A., Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J., Maitz, Silvia, Milani, Donatella, Morgan, Angela T., Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie R., Piccione, Maria, Plomp, Astrid S., Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W.E., Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella M., John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J., Vergano, Samantha A., Vos, Niels, Walden, Kellie K., Azmanov, Dimitar, Balci, Tugce B., Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A., Mannens, Marcel M.A.M., Roscioli, Tony, Siu, Victoria, Amor, David J., Baynam, Gareth, Bend, Eric G., Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M., Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A., Fleming, Mark D., Genevieve, David, Heron, Delphine, Husson, Thomas, Kernohan, Kristin D., McNeill, Alisdair, Menke, Leonie A., Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A., Stevenson, Roger E., Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L., and Sadikovic, Bekim
- Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive, and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes, which can share significant overlap among different conditions. In this study, we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders.
- Published
- 2022
6. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders
- Author
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Genetica Klinische Genetica, Brain, Child Health, Levy, Michael A, Relator, Raissa, McConkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Bralo, María Palomares, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R, Elting, Mariet W, Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S, Cherick, Florian, Foroutan, Aidin, Friez, Michael J, Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A, Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J, Maitz, Silvia, Milani, Donatella, Morgan, Angela T, Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Plomp, Astrid S, Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W E, Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J, Vergano, Samantha A, Vos, Niels, Walden, Kellie K, Azmanov, Dimitar, Balci, Tugce B, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A, Mannens, Marcel M A M, Roscioli, Tony, Siu, Victoria, Amor, David J, Baynam, Gareth, Bend, Eric G, Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M, Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A, Fleming, Mark D, Genevieve, David, Heron, Delphine, Husson, Thomas, Kernohan, Kristin D, McNeill, Alisdair, Menke, Leonie A, Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A, Stevenson, Roger E, Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L, Sadikovic, Bekim, Genetica Klinische Genetica, Brain, Child Health, Levy, Michael A, Relator, Raissa, McConkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Bralo, María Palomares, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angus, DuPont, Barbara R, Elting, Mariet W, Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S, Cherick, Florian, Foroutan, Aidin, Friez, Michael J, Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A, Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J, Maitz, Silvia, Milani, Donatella, Morgan, Angela T, Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Plomp, Astrid S, Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W E, Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J, Vergano, Samantha A, Vos, Niels, Walden, Kellie K, Azmanov, Dimitar, Balci, Tugce B, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A, Mannens, Marcel M A M, Roscioli, Tony, Siu, Victoria, Amor, David J, Baynam, Gareth, Bend, Eric G, Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M, Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A, Fleming, Mark D, Genevieve, David, Heron, Delphine, Husson, Thomas, Kernohan, Kristin D, McNeill, Alisdair, Menke, Leonie A, Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charles, Skinner, Steven A, Stevenson, Roger E, Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L, and Sadikovic, Bekim
- Published
- 2022
7. Making the case for global carrier screening for Tay-Sachs disease
- Author
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Michl, Emma, primary, Tan, Wen-Hann, additional, Gonzalez, Efren, additional, Eichler, Florian, additional, Walden, Kellie K., additional, Fletcher, Robin, additional, Pollard, Laura, additional, Yang, Edward, additional, and Al-Hertani, Walla, additional
- Published
- 2022
- Full Text
- View/download PDF
8. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders
- Author
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Levy, Michael A., primary, McConkey, Haley, additional, Kerkhof, Jennifer, additional, Barat-Houari, Mouna, additional, Bargiacchi, Sara, additional, Biamino, Elisa, additional, Bralo, María Palomares, additional, Cappuccio, Gerarda, additional, Ciolfi, Andrea, additional, Clarke, Angus, additional, DuPont, Barbara R., additional, Elting, Mariet W., additional, Faivre, Laurence, additional, Fee, Timothy, additional, Fletcher, Robin S., additional, Cherik, Florian, additional, Foroutan, Aidin, additional, Friez, Michael J., additional, Gervasini, Cristina, additional, Haghshenas, Sadegheh, additional, Hilton, Benjamin A., additional, Jenkins, Zandra, additional, Kaur, Simranpreet, additional, Lewis, Suzanne, additional, Louie, Raymond J., additional, Maitz, Silvia, additional, Milani, Donatella, additional, Morgan, Angela T., additional, Oegema, Renske, additional, Østergaard, Elsebet, additional, Pallares, Nathalie Ruiz, additional, Piccione, Maria, additional, Pizzi, Simone, additional, Plomp, Astrid S., additional, Poulton, Cathryn, additional, Reilly, Jack, additional, Relator, Raissa, additional, Rius, Rocio, additional, Robertson, Stephen, additional, Rooney, Kathleen, additional, Rousseau, Justine, additional, Santen, Gijs W.E., additional, Santos-Simarro, Fernando, additional, Schijns, Josephine, additional, Squeo, Gabriella Maria, additional, St John, Miya, additional, Thauvin-Robinet, Christel, additional, Traficante, Giovanna, additional, van der Sluijs, Pleuntje J., additional, Vergano, Samantha A., additional, Vos, Niels, additional, Walden, Kellie K., additional, Azmanov, Dimitar, additional, Balci, Tugce, additional, Banka, Siddharth, additional, Gecz, Jozef, additional, Henneman, Peter, additional, Lee, Jennifer A., additional, Mannens, Marcel M.A.M., additional, Roscioli, Tony, additional, Siu, Victoria, additional, Amor, David J., additional, Baynam, Gareth, additional, Bend, Eric G., additional, Boycott, Kym, additional, Brunetti-Pierri, Nicola, additional, Campeau, Philippe M., additional, Christodoulou, John, additional, Dyment, David, additional, Esber, Natacha, additional, Fahrner, Jill A., additional, Fleming, Mark D., additional, Genevieve, David, additional, Kerrnohan, Kristin D., additional, McNeill, Alisdair, additional, Menke, Leonie A., additional, Merla, Giuseppe, additional, Prontera, Paolo, additional, Rockman-Greenberg, Cheryl, additional, Schwartz, Charles, additional, Skinner, Steven A., additional, Stevenson, Roger E., additional, Vitobello, Antonio, additional, Tartaglia, Marco, additional, Alders, Marielle, additional, Tedder, Matthew L., additional, and Sadikovic, Bekim, additional
- Published
- 2022
- Full Text
- View/download PDF
9. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders
- Author
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Michael A. Levy, Raissa Relator, Haley McConkey, Erinija Pranckeviciene, Jennifer Kerkhof, Mouna Barat‐Houari, Sara Bargiacchi, Elisa Biamino, María Palomares Bralo, Gerarda Cappuccio, Andrea Ciolfi, Angus Clarke, Barbara R. DuPont, Mariet W. Elting, Laurence Faivre, Timothy Fee, Marco Ferilli, Robin S. Fletcher, Florian Cherick, Aidin Foroutan, Michael J. Friez, Cristina Gervasini, Sadegheh Haghshenas, Benjamin A. Hilton, Zandra Jenkins, Simranpreet Kaur, Suzanne Lewis, Raymond J. Louie, Silvia Maitz, Donatella Milani, Angela T. Morgan, Renske Oegema, Elsebet Østergaard, Nathalie R. Pallares, Maria Piccione, Astrid S. Plomp, Cathryn Poulton, Jack Reilly, Rocio Rius, Stephen Robertson, Kathleen Rooney, Justine Rousseau, Gijs W. E. Santen, Fernando Santos‐Simarro, Josephine Schijns, Gabriella M. Squeo, Miya St John, Christel Thauvin‐Robinet, Giovanna Traficante, Pleuntje J. van der Sluijs, Samantha A. Vergano, Niels Vos, Kellie K. Walden, Dimitar Azmanov, Tugce B. Balci, Siddharth Banka, Jozef Gecz, Peter Henneman, Jennifer A. Lee, Marcel M. A. M. Mannens, Tony Roscioli, Victoria Siu, David J. Amor, Gareth Baynam, Eric G. Bend, Kym Boycott, Nicola Brunetti‐Pierri, Philippe M. Campeau, Dominique Campion, John Christodoulou, David Dyment, Natacha Esber, Jill A. Fahrner, Mark D. Fleming, David Genevieve, Delphine Heron, Thomas Husson, Kristin D. Kernohan, Alisdair McNeill, Leonie A. Menke, Giuseppe Merla, Paolo Prontera, Cheryl Rockman‐Greenberg, Charles Schwartz, Steven A. Skinner, Roger E. Stevenson, Marie Vincent, Antonio Vitobello, Marco Tartaglia, Marielle Alders, Matthew L. Tedder, Bekim Sadikovic, Human genetics, Amsterdam Reproduction & Development (AR&D), Pediatrics, Levy M.A., Relator R., McConkey H., Pranckeviciene E., Kerkhof J., Barat-Houari M., Bargiacchi S., Biamino E., Palomares Bralo M., Cappuccio G., Ciolfi A., Clarke A., DuPont B.R., Elting M.W., Faivre L., Fee T., Ferilli M., Fletcher R.S., Cherick F., Foroutan A., Friez M.J., Gervasini C., Haghshenas S., Hilton B.A., Jenkins Z., Kaur S., Lewis S., Louie R.J., Maitz S., Milani D., Morgan A.T., Oegema R., Ostergaard E., Pallares N.R., Piccione M., Plomp A.S., Poulton C., Reilly J., Rius R., Robertson S., Rooney K., Rousseau J., Santen G.W.E., Santos-Simarro F., Schijns J., Squeo G.M., John M.S., Thauvin-Robinet C., Traficante G., van der Sluijs P.J., Vergano S.A., Vos N., Walden K.K., Azmanov D., Balci T.B., Banka S., Gecz J., Henneman P., Lee J.A., Mannens M.M.A.M., Roscioli T., Siu V., Amor D.J., Baynam G., Bend E.G., Boycott K., Brunetti-Pierri N., Campeau P.M., Campion D., Christodoulou J., Dyment D., Esber N., Fahrner J.A., Fleming M.D., Genevieve D., Heron D., Husson T., Kernohan K.D., McNeill A., Menke L.A., Merla G., Prontera P., Rockman-Greenberg C., Schwartz C., Skinner S.A., Stevenson R.E., Vincent M., Vitobello A., Tartaglia M., Alders M., Tedder M.L., Sadikovic B., Levy, Michael A, Relator, Raissa, Mcconkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Bralo, María Palomare, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angu, Dupont, Barbara R, Elting, Mariet W, Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S, Cherick, Florian, Foroutan, Aidin, Friez, Michael J, Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A, Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J, Maitz, Silvia, Milani, Donatella, Morgan, Angela T, Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Plomp, Astrid S, Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W E, Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J, Vergano, Samantha A, Vos, Niel, Walden, Kellie K, Azmanov, Dimitar, Balci, Tugce B, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A, Mannens, Marcel M A M, Roscioli, Tony, Siu, Victoria, Amor, David J, Baynam, Gareth, Bend, Eric G, Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M, Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A, Fleming, Mark D, Genevieve, David, Heron, Delphine, Husson, Thoma, Kernohan, Kristin D, Mcneill, Alisdair, Menke, Leonie A, Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charle, Skinner, Steven A, Stevenson, Roger E, Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L, Sadikovic, Bekim, Human Genetics, General Paediatrics, Graduate School, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, ARD - Amsterdam Reproduction and Development, ANS - Cellular & Molecular Mechanisms, ANS - Complex Trait Genetics, and ACS - Pulmonary hypertension & thrombosis
- Subjects
DNA methylation ,clinical diagnostics ,Syndrome ,DNA methylation, clinical diagnostics, episignatures, neurodevelopmental syndromes ,neurodevelopmental syndromes ,Epigenesis, Genetic ,Neurodevelopmental Disorders ,Genetics ,Humans ,CpG Islands ,DNA, Intergenic ,episignatures ,Episignature ,Genetics (clinical) - Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
- Published
- 2022
10. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders
- Author
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Michael A. Levy, Haley McConkey, Jennifer Kerkhof, Mouna Barat-Houari, Sara Bargiacchi, Elisa Biamino, María Palomares Bralo, Gerarda Cappuccio, Andrea Ciolfi, Angus Clarke, Barbara R. DuPont, Mariet W. Elting, Laurence Faivre, Timothy Fee, Robin S. Fletcher, Florian Cherik, Aidin Foroutan, Michael J. Friez, Cristina Gervasini, Sadegheh Haghshenas, Benjamin A. Hilton, Zandra Jenkins, Simranpreet Kaur, Suzanne Lewis, Raymond J. Louie, Silvia Maitz, Donatella Milani, Angela T. Morgan, Renske Oegema, Elsebet Østergaard, Nathalie Ruiz Pallares, Maria Piccione, Simone Pizzi, Astrid S. Plomp, Cathryn Poulton, Jack Reilly, Raissa Relator, Rocio Rius, Stephen Robertson, Kathleen Rooney, Justine Rousseau, Gijs W.E. Santen, Fernando Santos-Simarro, Josephine Schijns, Gabriella Maria Squeo, Miya St John, Christel Thauvin-Robinet, Giovanna Traficante, Pleuntje J. van der Sluijs, Samantha A. Vergano, Niels Vos, Kellie K. Walden, Dimitar Azmanov, Tugce Balci, Siddharth Banka, Jozef Gecz, Peter Henneman, Jennifer A. Lee, Marcel M.A.M. Mannens, Tony Roscioli, Victoria Siu, David J. Amor, Gareth Baynam, Eric G. Bend, Kym Boycott, Nicola Brunetti-Pierri, Philippe M. Campeau, John Christodoulou, David Dyment, Natacha Esber, Jill A. Fahrner, Mark D. Fleming, David Genevieve, Kristin D. Kerrnohan, Alisdair McNeill, Leonie A. Menke, Giuseppe Merla, Paolo Prontera, Cheryl Rockman-Greenberg, Charles Schwartz, Steven A. Skinner, Roger E. Stevenson, Antonio Vitobello, Marco Tartaglia, Marielle Alders, Matthew L. Tedder, Bekim Sadikovic, Levy, Michael A, Mcconkey, Haley, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Bralo, María Palomare, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angu, Dupont, Barbara R, Elting, Mariet W, Faivre, Laurence, Fee, Timothy, Fletcher, Robin S, Cherik, Florian, Foroutan, Aidin, Friez, Michael J, Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A, Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J, Maitz, Silvia, Milani, Donatella, Morgan, Angela T, Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Pizzi, Simone, Plomp, Astrid S, Poulton, Cathryn, Reilly, Jack, Relator, Raissa, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W E, Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, St John, Miya, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J, Vergano, Samantha A, Vos, Niel, Walden, Kellie K, Azmanov, Dimitar, Balci, Tugce, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A, Mannens, Marcel M A M, Roscioli, Tony, Siu, Victoria, Amor, David J, Baynam, Gareth, Bend, Eric G, Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A, Fleming, Mark D, Genevieve, David, Kerrnohan, Kristin D, Mcneill, Alisdair, Menke, Leonie A, Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charle, Skinner, Steven A, Stevenson, Roger E, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L, Sadikovic, Bekim, Human Genetics, General Paediatrics, Graduate School, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Reproduction & Development (AR&D), ACS - Pulmonary hypertension & thrombosis, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, and Amsterdam Neuroscience - Complex Trait Genetics
- Subjects
Clinical diagnostic ,INTELLECTUAL DISABILITY ,COMPLEX ,DNA methylation ,MUTATIONS ,SIGNATURE ,Neurodevelopmental disorders ,Epigenetic ,QH426-470 ,VARIANTS ,Article ,DOMAIN ,Clinical diagnostics ,Genetics ,Molecular Medicine ,Epigenetics ,Episignatures ,COFFIN-SIRIS ,Episignature ,Genetics (clinical) - Abstract
Summary: Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
- Published
- 2022
11. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders.
- Author
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Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, and Sadikovic B
- Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions., Competing Interests: The authors declare no competing interests., (© 2021 The Author(s).)
- Published
- 2021
- Full Text
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