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2. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study

Author

McDonagh, Ellen M, Rueda, Antonio, Polychronopoulos, Dimitris, Chan, Georgia, Angus-Leppan, Heather, Bhatia, Kailash P, Davison, James E, Festenstein, Richard, Fratta, Pietro, Giunti, Paola, Howard, Robin, Venkata, Laxmi, Laurá, Matilde, McEntagart, Meriel, Menzies, Lara, Morris, Huw, Reilly, Mary M, Robinson, Robert, Rosser, Elisabeth, Faravelli, Francesca, Schrag, Anette, Schott, Jonathan M, Warner, Thomas T, Wood, Nicholas W, Bourn, David, Eggleton, Kelly, Labrum, Robyn, Twiss, Philip, Abbs, Stephen, Santos, Liana, Almheiri, Ghareesa, Sheikh, Isabella, Vandrovcova, Jana, Patch, Christine, Taylor Tavares, Ana Lisa, Hyder, Zerin, Need, Anna, Brittain, Helen, Baple, Emma, Moutsianas, Loukas, Deshpande, Viraj, Perry, Denise L, Ajay, Subramanian S., Chawla, Aditi, Rajan, Vani, Oprych, Kathryn, Chinnery, Patrick F, Douglas, Angela, Wilson, Gill, Ellard, Sian, Temple, I Karen, Mumford, Andrew, McMullan, Dom, Naresh, Kikkeri, Flinter, Frances A, Taylor, Jenny C, Greenhalgh, Lynn, Newman, William, Brennan, Paul, Sayer, John A, Raymond, F Lucy, Chitty, Lyn S, Ambrose, John C., Arumugam, Prabhu, Bleda, Marta, Boardman-Pretty, Freya, Boissiere, Jeanne M., Boustred, Christopher R., Craig, Clare E.H., de Burca, Anna, Devereau, Andrew, Elgar, Greg, Foulger, Rebecca E., Furió-Tarí, Pedro, Hackett, Joanne, Halai, Dina, Hamblin, Angela, Henderson, Shirley, Holman, James, Hubbard, Tim J.P., Jackson, Rob, Jones, Louise J., Kayikci, Melis, Lahnstein, Lea, Lawson, Kay, Leigh, Sarah E.A., Leong, Ivonne U.S., Lopez, Javier F., Maleady-Crowe, Fiona, Mason, Joanne, Mueller, Michael, Murugaesu, Nirupa, Odhams, Chris A., Perez-Gil, Daniel, Pullinger, John, Rahim, Tahrima, Riesgo-Ferreiro, Pablo, Rogers, Tim, Ryten, Mina, Savage, Kevin, Sawant, Kushmita, Siddiq, Afshan, Sieghart, Alexander, Smedley, Damian, Sosinsky, Alona, Spooner, William, Stevens, Helen E., Stuckey, Alexander, Sultana, Razvan, Thompson, Simon R., Tregidgo, Carolyn, Walsh, Emma, Watters, Sarah A., Welland, Matthew J., Williams, Eleanor, Witkowska, Katarzyna, Wood, Suzanne M., Zarowiecki, Magdalena, Ibañez, Kristina, Polke, James, Hagelstrom, R Tanner, Dolzhenko, Egor, Pasko, Dorota, Thomas, Ellen Rachel Amy, Daugherty, Louise C, Kasperaviciute, Dalia, Smith, Katherine R, Deans, Zandra C, Hill, Sue, Fowler, Tom, Scott, Richard H, Hardy, John, Houlden, Henry, Rendon, Augusto, Caulfield, Mark J, Eberle, Michael A, Taft, Ryan J, and Tucci, Arianna

Published
2022
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5. Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease

Author

Gross, Andrew M., Ajay, Subramanian S., Rajan, Vani, Brown, Carolyn, Bluske, Krista, Burns, Nicole J., Chawla, Aditi, Coffey, Alison J., Malhotra, Alka, Scocchia, Alicia, Thorpe, Erin, Dzidic, Natasa, Hovanes, Karine, Sahoo, Trilochan, Dolzhenko, Egor, Lajoie, Bryan, Khouzam, Amirah, Chowdhury, Shimul, Belmont, John, Roller, Eric, Ivakhno, Sergii, Tanner, Stephen, McEachern, Julia, Hambuch, Tina, Eberle, Michael, Hagelstrom, R. Tanner, Bentley, David R., Perry, Denise L., and Taft, Ryan J.

Published
2019
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6. Genome sequencing detects a balanced pericentric inversion with breakpoints that impact the DMD and upstream region of POU3F4 genes.

Author

Chandrasekhar, Anjana, Mroczkowski, Henry J., Urraca, Nora, Gross, Andrew, Bluske, Krista, Thorpe, Erin, Hagelstrom, R. Tanner, Schonberg, Steven A., Perry, Denise L., Taft, Ryan J., and Kesari, Akanchha

Abstract

We describe a family with two maternal half‐brothers both of whom presented with muscular dystrophy, autism spectrum disorder, developmental delay, and sensorineural hearing loss. The elder brother had onset of features at ~3 months of age, followed by clinical confirmation of muscular dystrophy at 3 years. Skeletal biopsy staining at 4.7 years showed an absence of dystrophin protein which prompted extensive molecular testing over 4 years that included gene panels, targeted single‐gene assays, arrays, and karyotyping, all of which failed to identify a clinically significant variant in the DMD gene. At 10 years of age, clinical whole‐genome sequencing (cWGS) was performed, which revealed a novel hemizygous ~50.7 Mb balanced pericentric inversion on chromosome X that disrupts the DMD gene in both siblings, consistent with the muscular dystrophy phenotype. This inversion also impacts the upstream regulatory region of POU3F4, structural rearrangements which are known to cause hearing loss. The unaffected mother is a heterozygous carrier for the pericentric inversion. This finding illustrates the ability of cWGS to detect a wide breadth of disease‐causing genomic variations including large genomic rearrangements. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Inactivation of AMMECR1 is associated with growth, bone, and heart alterations

Author

Moysés‐Oliveira, Mariana, Giannuzzi, Giuliana, Fish, Richard J., Rosenfeld, Jill A., Petit, Florence, Soares, Maria de Fatima, Kulikowski, Leslie Domenici, Di‐Battista, Adriana, Zamariolli, Malú, Xia, Fan, Liehr, Thomas, Kosyakova, Nadezda, Carvalheira, Gianna, Parker, Michael, Seaby, Eleanor G., Ennis, Sarah, Gilbert, Rodney D., Hagelstrom, R. Tanner, Cremona, Maria L., Li, Wenhui L., Malhotra, Alka, Chandrasekhar, Anjana, Perry, Denise L., Taft, Ryan J., McCarrier, Julie, Basel, Donald G., Andrieux, Joris, Stumpp, Taiza, Antunes, Fernanda, Pereira, Gustavo José, Neerman‐Arbez, Marguerite, Meloni, Vera Ayres, Drummond‐Borg, Margaret, Melaragno, Maria Isabel, and Reymond, Alexandre

Published
2018
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10. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study

Author

Ibañez, Kristina, primary, Polke, James, additional, Hagelstrom, R Tanner, additional, Dolzhenko, Egor, additional, Pasko, Dorota, additional, Thomas, Ellen Rachel Amy, additional, Daugherty, Louise C, additional, Kasperaviciute, Dalia, additional, Smith, Katherine R, additional, Deans, Zandra C, additional, Hill, Sue, additional, Fowler, Tom, additional, Scott, Richard H, additional, Hardy, John, additional, Chinnery, Patrick F, additional, Houlden, Henry, additional, Rendon, Augusto, additional, Caulfield, Mark J, additional, Eberle, Michael A, additional, Taft, Ryan J, additional, Tucci, Arianna, additional, McDonagh, Ellen M, additional, Rueda, Antonio, additional, Polychronopoulos, Dimitris, additional, Chan, Georgia, additional, Angus-Leppan, Heather, additional, Bhatia, Kailash P, additional, Davison, James E, additional, Festenstein, Richard, additional, Fratta, Pietro, additional, Giunti, Paola, additional, Howard, Robin, additional, Venkata, Laxmi, additional, Laurá, Matilde, additional, McEntagart, Meriel, additional, Menzies, Lara, additional, Morris, Huw, additional, Reilly, Mary M, additional, Robinson, Robert, additional, Rosser, Elisabeth, additional, Faravelli, Francesca, additional, Schrag, Anette, additional, Schott, Jonathan M, additional, Warner, Thomas T, additional, Wood, Nicholas W, additional, Bourn, David, additional, Eggleton, Kelly, additional, Labrum, Robyn, additional, Twiss, Philip, additional, Abbs, Stephen, additional, Santos, Liana, additional, Almheiri, Ghareesa, additional, Sheikh, Isabella, additional, Vandrovcova, Jana, additional, Patch, Christine, additional, Taylor Tavares, Ana Lisa, additional, Hyder, Zerin, additional, Need, Anna, additional, Brittain, Helen, additional, Baple, Emma, additional, Moutsianas, Loukas, additional, Deshpande, Viraj, additional, Perry, Denise L, additional, Ajay, Subramanian S., additional, Chawla, Aditi, additional, Rajan, Vani, additional, Oprych, Kathryn, additional, Douglas, Angela, additional, Wilson, Gill, additional, Ellard, Sian, additional, Temple, I Karen, additional, Mumford, Andrew, additional, McMullan, Dom, additional, Naresh, Kikkeri, additional, Flinter, Frances A, additional, Taylor, Jenny C, additional, Greenhalgh, Lynn, additional, Newman, William, additional, Brennan, Paul, additional, Sayer, John A, additional, Raymond, F Lucy, additional, Chitty, Lyn S, additional, Ambrose, John C., additional, Arumugam, Prabhu, additional, Bleda, Marta, additional, Boardman-Pretty, Freya, additional, Boissiere, Jeanne M., additional, Boustred, Christopher R., additional, Craig, Clare E.H., additional, de Burca, Anna, additional, Devereau, Andrew, additional, Elgar, Greg, additional, Foulger, Rebecca E., additional, Furió-Tarí, Pedro, additional, Hackett, Joanne, additional, Halai, Dina, additional, Hamblin, Angela, additional, Henderson, Shirley, additional, Holman, James, additional, Hubbard, Tim J.P., additional, Jackson, Rob, additional, Jones, Louise J., additional, Kayikci, Melis, additional, Lahnstein, Lea, additional, Lawson, Kay, additional, Leigh, Sarah E.A., additional, Leong, Ivonne U.S., additional, Lopez, Javier F., additional, Maleady-Crowe, Fiona, additional, Mason, Joanne, additional, Mueller, Michael, additional, Murugaesu, Nirupa, additional, Odhams, Chris A., additional, Perez-Gil, Daniel, additional, Pullinger, John, additional, Rahim, Tahrima, additional, Riesgo-Ferreiro, Pablo, additional, Rogers, Tim, additional, Ryten, Mina, additional, Savage, Kevin, additional, Sawant, Kushmita, additional, Siddiq, Afshan, additional, Sieghart, Alexander, additional, Smedley, Damian, additional, Sosinsky, Alona, additional, Spooner, William, additional, Stevens, Helen E., additional, Stuckey, Alexander, additional, Sultana, Razvan, additional, Thompson, Simon R., additional, Tregidgo, Carolyn, additional, Walsh, Emma, additional, Watters, Sarah A., additional, Welland, Matthew J., additional, Williams, Eleanor, additional, Witkowska, Katarzyna, additional, Wood, Suzanne M., additional, and Zarowiecki, Magdalena, additional

Published
2022
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11. SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females

Author

Radio, Francesca Clementina, Pang, Kaifang, Ciolfi, Andrea, Levy, Michael A., Hernández-García, Andrés, Pedace, Lucia, Pantaleoni, Francesca, Liu, Zhandong, de Boer, Elke, Jackson, Adam, Bruselles, Alessandro, McConkey, Haley, Stellacci, Emilia, Lo Cicero, Stefania, Motta, Marialetizia, Carrozzo, Rosalba, Dentici, Maria Lisa, McWalter, Kirsty, Desai, Megha, Monaghan, Kristin G., Telegrafi, Aida, Philippe, Christophe, Vitobello, Antonio, Au, Margaret, Grand, Katheryn, Sanchez-Lara, Pedro A., Baez, Joanne, Lindstrom, Kristin, Kulch, Peggy, Sebastian, Jessica, Madan-Khetarpal, Suneeta, Roadhouse, Chelsea, MacKenzie, Jennifer J., Monteleone, Berrin, Saunders, Carol J., Jean Cuevas, July K., Cross, Laura, Zhou, Dihong, Hartley, Taila, Sawyer, Sarah L., Monteiro, Fabíola Paoli, Secches, Tania Vertemati, Kok, Fernando, Schultz-Rogers, Laura E., Macke, Erica L., Morava, Eva, Klee, Eric W., Kemppainen, Jennifer, Iascone, Maria, Selicorni, Angelo, Tenconi, Romano, Amor, David J., Pais, Lynn, Gallacher, Lyndon, Turnpenny, Peter D., Stals, Karen, Ellard, Sian, Cabet, Sara, Lesca, Gaetan, Pascal, Joset, Steindl, Katharina, Ravid, Sarit, Weiss, Karin, Castle, Alison M.R., Carter, Melissa T., Kalsner, Louisa, de Vries, Bert B.A., van Bon, Bregje W., Wevers, Marijke R., Pfundt, Rolph, Stegmann, Alexander P.A., Kerr, Bronwyn, Kingston, Helen M., Chandler, Kate E., Sheehan, Willow, Elias, Abdallah F., Shinde, Deepali N., Towne, Meghan C., Robin, Nathaniel H., Goodloe, Dana, Vanderver, Adeline, Sherbini, Omar, Bluske, Krista, Hagelstrom, R. Tanner, Zanus, Caterina, Faletra, Flavio, Musante, Luciana, Kurtz-Nelson, Evangeline C., Earl, Rachel K., Anderlid, Britt-Marie, Morin, Gilles, van Slegtenhorst, Marjon, Diderich, Karin E.M., Brooks, Alice S., Gribnau, Joost, Boers, Ruben G., Finestra, Teresa Robert, Carter, Lauren B., Rauch, Anita, Gasparini, Paolo, Boycott, Kym M., Barakat, Tahsin Stefan, Graham, John M., Jr., Faivre, Laurence, Banka, Siddharth, Wang, Tianyun, Eichler, Evan E., Priolo, Manuela, Dallapiccola, Bruno, Vissers, Lisenka E.L.M., Sadikovic, Bekim, Scott, Daryl A., Holder, Jimmy Lloyd, Jr., and Tartaglia, Marco

Published
2021
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12. A case series of challenging molecular diagnoses identified by clinical whole genome sequencing

Author

Schlachetzki, Zinayida, primary, Chandrasekhar, Anjana, additional, Clause, Amanda, additional, Brown, Carolyn, additional, Schmidt, Sarah, additional, Burns, Nicole, additional, Gross, Andrew, additional, Mroczkowski, Henry Joel, additional, Vanderver, Adeline, additional, Hagelstrom, R. Tanner, additional, Belmont, John, additional, Perry, Denise, additional, and Taft, Ryan, additional

Published
2021
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14. Genome sequencing identifies three molecular diagnoses including a mosaic variant in the COL2A1 gene in an individual with Pol III-related leukodystrophy and Feingold syndrome.

Author

Muirhead, Kayla J., Clause, Amanda R., Schlachetzki, Zinayida, Dubbs, Holly, Perry, Denise L., Hagelstrom, R. Tanner, Taft, Ryan J., and Vanderver, Adeline

Subjects
DNA sequencing, LEUKODYSTROPHY, MOLECULAR diagnosis, MOSAICISM, SINGLE nucleotide polymorphisms, GENETIC counseling
Abstract

Undiagnosed genetic disease imposes a significant burden on families and health-care resources, especially in cases with a complex phenotype. Here we present a child with suspected leukodystrophy in the context of additional features, including hearing loss, clinodactyly, rotated thumbs, tapered fingers, and simplified palmar crease. Trio genome sequencing (GS) identified three molecular diagnoses in this individual: compound heterozygous missense variants associated with polymerase III (Pol III)-related leukodystrophy, a 4-Mb de novo copy-number loss including the MYCN gene associated with Feingold syndrome, and a mosaic single-nucleotide variant associated with COL2A1-related disorders. These variants fully account for the individual's features, but also illustrate the potential for superimposed and unclear contributions of multiple diagnoses to an individual's overall presentation. This report demonstrates the advantage of GS in detection of multiple variant types, including low-level mosaic variants, and emphasizes the need for comprehensive genetic analysis and detailed clinical phenotyping to provide individuals and their families with the maximum benefit for clinical care and genetic counseling. [ABSTRACT FROM AUTHOR]

Published
2021
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15. Effect of Whole-Genome Sequencing on the Clinical Management of Acutely Ill Infants With Suspected Genetic Disease: A Randomized Clinical Trial

Author

Krantz, Ian D., Medne, Livija, Weatherly, Jamila M., Wild, K. Taylor, Biswas, Sawona, Devkota, Batsal, Hartman, Tiffiney, Brunelli, Luca, Fishler, Kristen P., Abdul-Rahman, Omar, Euteneuer, Joshua C., Hoover, Denise, Dimmock, David, Cleary, John, Farnaes, Lauge, Knight, Jason, Schwarz, Adam J., Vargas-Shiraishi, Ofelia M., Wigby, Kristin, Zadeh, Neda, Shinawi, Marwan, Wambach, Jennifer A., Baldridge, Dustin, Cole, F. Sessions, Wegner, Daniel J., Urraca, Nora, Holtrop, Shannon, Mostafavi, Roya, Mroczkowski, Henry J., Pivnick, Eniko K., Ward, Jewell C., Talati, Ajay, Brown, Chester W., Belmont, John W., Ortega, Julia L., Robinson, Keisha D., Brocklehurst, W. Tyler, Perry, Denise L., Ajay, Subramanian S., Hagelstrom, R. Tanner, Bennett, Maren, Rajan, Vani, and Taft, Ryan J.

Abstract

IMPORTANCE: Whole-genome sequencing (WGS) shows promise as a first-line genetic test for acutely ill infants, but widespread adoption and implementation requires evidence of an effect on clinical management. OBJECTIVE: To determine the effect of WGS on clinical management in a racially and ethnically diverse and geographically distributed population of acutely ill infants in the US. DESIGN, SETTING, AND PARTICIPANTS: This randomized, time-delayed clinical trial enrolled participants from September 11, 2017, to April 30, 2019, with an observation period extending to July 2, 2019. The study was conducted at 5 US academic medical centers and affiliated children’s hospitals. Participants included infants aged between 0 and 120 days who were admitted to an intensive care unit with a suspected genetic disease. Data were analyzed from January 14 to August 20, 2020. INTERVENTIONS: Patients were randomized to receive clinical WGS results 15 days (early) or 60 days (delayed) after enrollment, with the observation period extending to 90 days. Usual care was continued throughout the study. MAIN OUTCOMES AND MEASURES: The main outcome was the difference in the proportion of infants in the early and delayed groups who received a change of management (COM) 60 days after enrollment. Additional outcome measures included WGS diagnostic efficacy, within-group COM at 90 days, length of hospital stay, and mortality. RESULTS: A total of 354 infants were randomized to the early (n = 176) or delayed (n = 178) arms. The mean participant age was 15 days (IQR, 7-32 days); 201 participants (56.8%) were boys; 19 (5.4%) were Asian; 47 (13.3%) were Black; 250 (70.6%) were White; and 38 (10.7%) were of other race. At 60 days, twice as many infants in the early group vs the delayed group received a COM (34 of 161 [21.1%; 95% CI, 15.1%-28.2%] vs 17 of 165 [10.3%; 95% CI, 6.1%-16.0%]; P = .009; odds ratio, 2.3; 95% CI, 1.22-4.32) and a molecular diagnosis (55 of 176 [31.0%; 95% CI, 24.5%-38.7%] vs 27 of 178 [15.0%; 95% CI, 10.2%-21.3%]; P < .001). At 90 days, the delayed group showed a doubling of COM (to 45 of 161 [28.0%; 95% CI, 21.2%-35.6%]) and diagnostic efficacy (to 56 of 178 [31.0%; 95% CI, 24.7%-38.8%]). The most frequent COMs across the observation window were subspecialty referrals (39 of 354; 11%), surgery or other invasive procedures (17 of 354; 4%), condition-specific medications (9 of 354; 2%), or other supportive alterations in medication (12 of 354; 3%). No differences in length of stay or survival were observed. CONCLUSIONS AND RELEVANCE: In this randomized clinical trial, for acutely ill infants in an intensive care unit, introduction of WGS was associated with a significant increase in focused clinical management compared with usual care. Access to first-line WGS may reduce health care disparities by enabling diagnostic equity. These data support WGS adoption and implementation in this population. TRAIL REGISTRATION: ClinicalTrials.gov Identifier: NCT03290469

Published
2021
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19. Copy number variants in clinical WGS: deployment and interpretation for rare and undiagnosed disease

Author

Gross, Andrew M, primary, Ajay, Subramanian S., additional, Rajan, Vani, additional, Brown, Carolyn, additional, Bluske, Krista, additional, Burns, Nicole, additional, Chawla, Aditi, additional, Coffey, Alison J, additional, Malhotra, Alka, additional, Scocchia, Alicia, additional, Thorpe, Erin, additional, Dzidic, Natasa, additional, Hovanes, Karine, additional, Sahoo, Trilochan, additional, Dolzhenko, Egor, additional, Lajoie, Bryan, additional, Khouzam, Amirah, additional, Chowdhury, Shimul, additional, Belmont, John, additional, Roller, Eric, additional, Ivakhno, Sergii, additional, Tanner, Stephen, additional, McEachern, Julia, additional, Hambuch, Tina, additional, Eberle, Michael, additional, Hagelstrom, R Tanner, additional, Bentley, David R, additional, Perry, Denise L, additional, and Taft, Ryan J, additional

Published
2018
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20. Inactivation of AMMECR1 is associated with growth, bone, and heart alterations

Author

Moysés-Oliveira, Mariana, primary, Giannuzzi, Giuliana, additional, Fish, Richard J., additional, Rosenfeld, Jill A., additional, Petit, Florence, additional, Soares, Maria de Fatima, additional, Kulikowski, Leslie Domenici, additional, Di-Battista, Adriana, additional, Zamariolli, Malú, additional, Xia, Fan, additional, Liehr, Thomas, additional, Kosyakova, Nadezda, additional, Carvalheira, Gianna, additional, Parker, Michael, additional, Seaby, Eleanor G., additional, Ennis, Sarah, additional, Gilbert, Rodney D., additional, Hagelstrom, R. Tanner, additional, Cremona, Maria L., additional, Li, Wenhui L., additional, Malhotra, Alka, additional, Chandrasekhar, Anjana, additional, Perry, Denise L., additional, Taft, Ryan J., additional, McCarrier, Julie, additional, Basel, Donald G., additional, Andrieux, Joris, additional, Stumpp, Taiza, additional, Antunes, Fernanda, additional, Pereira, Gustavo José, additional, Neerman-Arbez, Marguerite, additional, Meloni, Vera Ayres, additional, Drummond-Borg, Margaret, additional, Melaragno, Maria Isabel, additional, and Reymond, Alexandre, additional

Published
2017
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23. NCCN Guidelines Insights: Chronic Myeloid Leukemia, Version 1.2017

Author

Pallera, Arnel, primary, Altman, Jessica K., additional, Berman, Ellin, additional, Abboud, Camille N., additional, Bhatnagar, Bhavana, additional, Curtin, Peter, additional, DeAngelo, Daniel J., additional, Gotlib, Jason, additional, Hagelstrom, R. Tanner, additional, Hobbs, Gabriela, additional, Jagasia, Madan, additional, Kantarjian, Hagop M., additional, Kropf, Patricia, additional, Metheny, Leland, additional, Moore, Joseph O., additional, Ontiveros, Evelena, additional, Purev, Enkhtsetseg, additional, Quiery, Albert, additional, Reddy, Vishnu V.B., additional, Rose, Michal G., additional, Shah, Neil P., additional, Smith, B. Douglas, additional, Snyder, David S., additional, Sweet, Kendra L., additional, Tibes, Raoul, additional, Yang, David T., additional, Gregory, Kristina, additional, Sundar, Hema, additional, Deininger, Michael, additional, and Radich, Jerald P., additional

Published
2016
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24. Evaluation of the Clinical Utility of Sanger Sequencing Following Next Generation Sequence Analysis

Author

Sanmann, Jennifer N., primary, Nelson, Marilu, additional, Rief, Emily J., additional, Rivera, Kara C., additional, Roberts, Evan M., additional, Carstens, Julie M., additional, Evans, Jacquelynn J., additional, Kaspar, Erin E., additional, Williamson, Janet E., additional, Barbar, Rachel L., additional, Bishay, Danielle L., additional, Starr, Lois J., additional, Dave, Bhavana J., additional, and Hagelstrom, R. Tanner, additional

Published
2016
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26. Inactivation of <italic>AMMECR1</italic> is associated with growth, bone, and heart alterations.

Author

Moysés‐Oliveira, Mariana, Giannuzzi, Giuliana, Fish, Richard J., Rosenfeld, Jill A., Petit, Florence, Soares, Maria de Fatima, Kulikowski, Leslie Domenici, Di‐Battista, Adriana, Zamariolli, Malú, Xia, Fan, Liehr, Thomas, Kosyakova, Nadezda, Carvalheira, Gianna, Parker, Michael, Seaby, Eleanor G., Ennis, Sarah, Gilbert, Rodney D., Hagelstrom, R. Tanner, Cremona, Maria L., and Li, Wenhui L.

Abstract

Abstract: We report five individuals with loss‐of‐function of the X‐linked AMMECR1: a girl with a balanced X‐autosome translocation and inactivation of the normal X‐chromosome; two boys with maternally inherited and de novo nonsense variants; and two half‐brothers with maternally inherited microdeletion variants. They present with short stature, cardiac and skeletal abnormalities, and hearing loss. Variants of unknown significance in AMMECR1 in four male patients from two families with partially overlapping phenotypes were previously reported. AMMECR1 is coexpressed with genes implicated in cell cycle regulation, five of which were previously associated with growth and bone alterations. Our knockdown of the zebrafish orthologous gene resulted in phenotypes reminiscent of patients’ features. The increased transcript and encoded protein levels of AMMECR1L, an AMMECR1 paralog, in the t(X;9) patient's cells indicate a possible partial compensatory mechanism. AMMECR1 and AMMECR1L proteins dimerize and localize to the nucleus as suggested by their nucleic acid‐binding RAGNYA folds. Our results suggest that AMMECR1 is potentially involved in cell cycle control and linked to a new syndrome with growth, bone, heart, and kidney alterations with or without elliptocytosis. [ABSTRACT FROM AUTHOR]

Published
2018
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29. A Novel Partial Duplication of ZEB2and Review of ZEB2Involvement in Mowat-Wilson Syndrome

Author

Baxter, Adrianne L., Vivian, Jay L., Hagelstrom, R. Tanner, Hossain, Waheeda, Golden, Wendy L., Wassman, E. Robert, Vanzo, Rena J., and Butler, Merlin G.

Abstract

Mowat-Wilson syndrome is a rare genetic condition characterized by intellectual disability, structural anomalies, and dysmorphic features. It is caused by haploinsufficiency of the ZEB2gene in chromosome 2q22.3. Over 180 distinct mutations in ZEB2have been reported, including nonsense and missense point mutations, deletions, and large chromosomal rearrangements. We report on a 14-year-old female with a clinical diagnosis of Mowat-Wilson syndrome. Chromosomal microarray identified a novel de novo 69-kb duplication containing exons 1 and 2 of the ZEB2gene. Sequence analysis identified no other variants in this gene. This is the first report of a partial duplication of the ZEB2gene resulting in Mowat-Wilson syndrome.

Published
2017
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32. RNAi phenotype profiling of kinases identifiespotential therapeutic targets in Ewing¿s sarcoma.

Author

Arora, Shilpi, Gonzales, Irma M., Hagelstrom, R Tanner, Beaudry, Christian, Choudhary, Ashish, Sima, Chao, Tibes, Raoul, Mousses, Spyro, and Azorsa, David O.

Subjects
EWING'S sarcoma, OSTEOSARCOMA, PHENOTYPES, GENETICS, CANCER
Abstract

Background: Ewing's sarcomas are aggressive musculoskeletal tumors occurring most frequently in the long and flat bones as a solitary lesion mostly during the teen-age years of life. With current treatments, significant number of patients relapse and survival is poor for those with metastatic disease. As part of novel target discovery in Ewing's sarcoma, we applied RNAi mediated phenotypic profiling to identify kinase targets involved in growth and survival of Ewing's sarcoma cells. Results: Four Ewing's sarcoma cell lines TC-32, TC-71, SK-ES-1 and RD-ES were tested in high throughput-RNAi screens using a siRNA library targeting 572 kinases. Knockdown of 25 siRNAs reduced the growth of all four Ewing's sarcoma cell lines in replicate screens. Of these, 16 siRNA were specific and reduced proliferation of Ewing's sarcoma cells as compared to normal fibroblasts. Secondary validation and preliminary mechanistic studies highlighted the kinases STK10 and TNK2 as having important roles in growth and survival of Ewing's sarcoma cells. Furthermore, knockdown of STK10 and TNK2 by siRNA showed increased apoptosis. Conclusion: In summary, RNAi-based phenotypic profiling proved to be a powerful gene target discovery strategy, leading to successful identification and validation of STK10 and TNK2 as two novel potential therapeutic targets for Ewing's sarcoma. [ABSTRACT FROM AUTHOR]

Published
2010
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