23 results on '"Bryen, Samantha J"'
Search Results
2. SpliceVault predicts the precise nature of variant-associated mis-splicing
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Dawes, Ruebena, Bournazos, Adam M., Bryen, Samantha J., Bommireddipalli, Shobhana, Marchant, Rhett G., Joshi, Himanshu, and Cooper, Sandra T.
- Published
- 2023
- Full Text
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3. Genome Sequencing for Diagnosing Rare Diseases
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Wojcik, Monica H., primary, Lemire, Gabrielle, additional, Berger, Eva, additional, Zaki, Maha S., additional, Wissmann, Mariel, additional, Win, Wathone, additional, White, Susan M., additional, Weisburd, Ben, additional, Wieczorek, Dagmar, additional, Waddell, Leigh B., additional, Verboon, Jeffrey M., additional, VanNoy, Grace E., additional, Töpf, Ana, additional, Tan, Tiong Yang, additional, Syrbe, Steffen, additional, Strehlow, Vincent, additional, Straub, Volker, additional, Stenton, Sarah L., additional, Snow, Hana, additional, Singer-Berk, Moriel, additional, Silver, Josh, additional, Shril, Shirlee, additional, Seaby, Eleanor G., additional, Schneider, Ronen, additional, Sankaran, Vijay G., additional, Sanchis-Juan, Alba, additional, Russell, Kathryn A., additional, Reinson, Karit, additional, Ravenscroft, Gianina, additional, Radtke, Maximilian, additional, Popp, Denny, additional, Polster, Tilman, additional, Platzer, Konrad, additional, Pierce, Eric A., additional, Place, Emily M., additional, Pajusalu, Sander, additional, Pais, Lynn, additional, Õunap, Katrin, additional, Osei-Owusu, Ikeoluwa, additional, Opperman, Henry, additional, Okur, Volkan, additional, Oja, Kaisa Teele, additional, O’Leary, Melanie, additional, O’Heir, Emily, additional, Morel, Chantal F., additional, Merkenschlager, Andreas, additional, Marchant, Rhett G., additional, Mangilog, Brian E., additional, Madden, Jill A., additional, MacArthur, Daniel, additional, Lovgren, Alysia, additional, Lerner-Ellis, Jordan P., additional, Lin, Jasmine, additional, Laing, Nigel, additional, Hildebrandt, Friedhelm, additional, Hentschel, Julia, additional, Groopman, Emily, additional, Goodrich, Julia, additional, Gleeson, Joseph G., additional, Ghaoui, Roula, additional, Genetti, Casie A., additional, Gburek-Augustat, Janina, additional, Gazda, Hanna T., additional, Ganesh, Vijay S., additional, Ganapathi, Mythily, additional, Gallacher, Lyndon, additional, Fu, Jack M., additional, Evangelista, Emily, additional, England, Eleina, additional, Donkervoort, Sandra, additional, DiTroia, Stephanie, additional, Cooper, Sandra T., additional, Chung, Wendy K., additional, Christodoulou, John, additional, Chao, Katherine R., additional, Cato, Liam D., additional, Bujakowska, Kinga M., additional, Bryen, Samantha J., additional, Brand, Harrison, additional, Bönnemann, Carsten G., additional, Beggs, Alan H., additional, Baxter, Samantha M., additional, Bartolomaeus, Tobias, additional, Agrawal, Pankaj B., additional, Talkowski, Michael, additional, Austin-Tse, Christina, additional, Abou Jamra, Rami, additional, Rehm, Heidi L., additional, and O’Donnell-Luria, Anne, additional
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- 2024
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4. Genome and RNA sequencing boost neuromuscular diagnoses to 62% from 34% with exome sequencing alone
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Marchant, Rhett G., primary, Bryen, Samantha J., additional, Bahlo, Melanie, additional, Cairns, Anita, additional, Chao, Katherine R., additional, Corbett, Alastair, additional, Davis, Mark R., additional, Ganesh, Vijay S., additional, Ghaoui, Roula, additional, Jones, Kristi J., additional, Kornberg, Andrew J., additional, Lek, Monkol, additional, Liang, Christina, additional, MacArthur, Daniel G., additional, Oates, Emily C., additional, O'Donnell‐Luria, Anne, additional, O'Grady, Gina L., additional, Osei‐Owusu, Ikeoluwa A., additional, Rafehi, Haloom, additional, Reddel, Stephen W., additional, Roxburgh, Richard H., additional, Ryan, Monique M., additional, Sandaradura, Sarah A., additional, Scott, Liam W., additional, Valkanas, Elise, additional, Weisburd, Ben, additional, Young, Helen, additional, Evesson, Frances J., additional, Waddell, Leigh B., additional, and Cooper, Sandra T., additional
- Published
- 2024
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5. A genetic basis is identified in 74% cases of paediatric hyperCKaemia without weakness presenting to a tertiary paediatric neuromuscular centre
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Wong, Wui-Kwan, Bryen, Samantha J, Bournazos, Adam, Yasa, Joe, Lemckert, Frances, Bommireddipall, Shobhana, Waddell, Leigh B, Menezes, Manoj P, Webster, Richard, Davis, Mark, Liang, Christina, Cooper, Sandra T, and Jones, Kristi J
- Published
- 2022
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6. Pathogenic deep intronic MTM1 variant activates a pseudo-exon encoding a nonsense codon resulting in severe X-linked myotubular myopathy
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Bryen, Samantha J., Oates, Emily C., Evesson, Frances J., Lu, Jessica K., Waddell, Leigh B., Joshi, Himanshu, Ryan, Monique M., Cummings, Beryl B., McLean, Catriona A., MacArthur, Daniel G., Kornberg, Andrew J., and Cooper, Sandra T.
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- 2021
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7. Pathogenic Abnormal Splicing Due to Intronic Deletions that Induce Biophysical Space Constraint for Spliceosome Assembly
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Bryen, Samantha J., Joshi, Himanshu, Evesson, Frances J., Girard, Cyrille, Ghaoui, Roula, Waddell, Leigh B., Testa, Alison C., Cummings, Beryl, Arbuckle, Susan, Graf, Nicole, Webster, Richard, MacArthur, Daniel G., Laing, Nigel G., Davis, Mark R., Lührmann, Reinhard, and Cooper, Sandra T.
- Published
- 2019
- Full Text
- View/download PDF
8. Unique Capabilities of Genome Sequencing for Rare Disease Diagnosis
- Author
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Wojcik, Monica H, primary, Lemire, Gabrielle, additional, Zaki, Maha S, additional, Wissmann, Mariel, additional, Win, Wathone, additional, White, Sue, additional, Weisburd, Ben, additional, Waddell, Leigh B, additional, Verboon, Jeffrey M, additional, VanNoy, Grace E, additional, Topf, Ana, additional, Tan, Tiong Yang, additional, Straub, Volker, additional, Stenton, Sarah L, additional, Snow, Hana, additional, Singer-Berk, Moriel, additional, Silver, Josh, additional, Shril, Shirlee, additional, Seaby, Eleanor G, additional, Schneider, Ronen, additional, Sankaran, Vijay G, additional, Sanchis-Juan, Alba, additional, Russell, Kathryn A, additional, Reinson, Karit, additional, Ravenscroft, Gina, additional, Pierce, Eric A, additional, Place, Emily M, additional, Pajusalu, Sander, additional, Pais, Lynn, additional, Ounap, Katrin, additional, Osei-Owusu, Ikeoluwa, additional, Okur, Volkan, additional, Oja, Kaisa Teele, additional, OLeary, Melanie, additional, OHeir, Emily, additional, Morel, Chantal, additional, Marchant, Rhett G, additional, Mangilog, Brian E, additional, Madden, Jill A, additional, MacArthur, Daniel, additional, Lovgren, Alysia, additional, Lerner-Ellis, Jordan P, additional, Lin, Jasmine, additional, Laing, Nigel, additional, Hildebrandt, Friedhelm, additional, Groopman, Emily, additional, Goodrich, Julia, additional, Gleeson, Joseph G, additional, Ghaoui, Roula, additional, Genetti, Casie A, additional, Gazda, Hanna, additional, Ganesh, Vijay S, additional, Ganapathi, Mythily, additional, Gallacher, Lyndon, additional, Fu, Jack, additional, Evangelista, Emily, additional, England, Eleina, additional, Donkervoort, Sandra, additional, DiTroia, Stephanie, additional, Cooper, Sandra T, additional, Chung, Wendy K, additional, Christodoulou, John, additional, Chao, Katherine R, additional, Cato, Liam D, additional, Bujakowska, Kinga M, additional, Bryen, Samantha J, additional, Brand, Harrison, additional, Bonnemann, Carsten, additional, Beggs, Alan H, additional, Baxter, Samantha M, additional, Agrawal, Pankaj B, additional, Talkowski, Michael, additional, Austin-Tse, Christina, additional, Rehm, Heidi L, additional, and ODonnell-Luria, Anne, additional
- Published
- 2023
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9. Recessive DES cardio/myopathy without myofibrillar aggregates: intronic splice variant silences one allele leaving only missense L190P-desmin
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Riley, Lisa G., Waddell, Leigh B., Ghaoui, Roula, Evesson, Frances J., Cummings, Beryl B., Bryen, Samantha J., Joshi, Himanshu, Wang, Min-Xia, Brammah, Susan, Kritharides, Leonard, Corbett, Alastair, MacArthur, Daniel G., and Cooper, Sandra T.
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- 2019
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10. Connective tissue presentation in two families expands the phenotypic spectrum of PYROXD1 disorders
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Evesson, Frances J, primary, Dziaduch, Gregory, additional, Bryen, Samantha J, additional, Moore, Francesca, additional, Pittman, Sara, additional, Devanapalli, Beena, additional, Waddell, Leigh B, additional, Ryan, Monique M, additional, Menezes, Manoj P, additional, Weihl, Conrad C, additional, Tolun, Adviye Ayper, additional, Zaidman, Craig, additional, Young, Helen, additional, Adès, Lesley C, additional, and Cooper, Sandra T, additional
- Published
- 2023
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11. Compound heterozygous splicing variants expand the genotypic spectrum of EMC1‐related disorders
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Bryen, Samantha J., primary, Zhang, Katharine, additional, Dziaduch, Gregory, additional, Bommireddipalli, Shobhana, additional, Naseri, Take, additional, Reupena, Muagututi'a Sefuiva, additional, Viali, Satupa'itea, additional, Minster, Ryan L., additional, Waddell, Leigh B., additional, Charlton, Amanda, additional, O'Grady, Gina L., additional, Evesson, Frances J., additional, and Cooper, Sandra T., additional
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- 2023
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12. Case report: Adult-onset limb girdle muscular dystrophy in sibling pair due to novel homozygous LAMA2 missense variant
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Katz, Matthew, primary, Waddell, Leigh B., additional, Yuen, Michaela, additional, Bryen, Samantha J., additional, Oates, Emily, additional, Garton, Fleur C., additional, Robertson, Thomas, additional, Henderson, Robert David, additional, Cooper, Sandra T., additional, and McCombe, Pamela A., additional
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- 2023
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13. Prevalence, parameters, and pathogenic mechanisms for splice-altering acceptor variants that disrupt the AG exclusion zone
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Bryen, Samantha J., primary, Yuen, Michaela, additional, Joshi, Himanshu, additional, Dawes, Ruebena, additional, Zhang, Katharine, additional, Lu, Jessica K., additional, Jones, Kristi J., additional, Liang, Christina, additional, Wong, Wui-Kwan, additional, Peduto, Anthony J., additional, Waddell, Leigh B., additional, Evesson, Frances J., additional, and Cooper, Sandra T., additional
- Published
- 2022
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14. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants
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Bournazos, Adam M., primary, Riley, Lisa G., additional, Bommireddipalli, Shobhana, additional, Ades, Lesley, additional, Akesson, Lauren S., additional, Al-Shinnag, Mohammad, additional, Alexander, Stephen I., additional, Archibald, Alison D., additional, Balasubramaniam, Shanti, additional, Berman, Yemima, additional, Beshay, Victoria, additional, Boggs, Kirsten, additional, Bojadzieva, Jasmina, additional, Brown, Natasha J., additional, Bryen, Samantha J., additional, Buckley, Michael F., additional, Chong, Belinda, additional, Davis, Mark R., additional, Dawes, Ruebena, additional, Delatycki, Martin, additional, Donaldson, Liz, additional, Downie, Lilian, additional, Edwards, Caitlin, additional, Edwards, Matthew, additional, Engel, Amanda, additional, Ewans, Lisa J., additional, Faiz, Fathimath, additional, Fennell, Andrew, additional, Field, Michael, additional, Freckmann, Mary-Louise, additional, Gallacher, Lyndon, additional, Gear, Russell, additional, Goel, Himanshu, additional, Goh, Shuxiang, additional, Goodwin, Linda, additional, Hanna, Bernadette, additional, Harraway, James, additional, Higgins, Megan, additional, Ho, Gladys, additional, Hopper, Bruce K., additional, Horton, Ari E., additional, Hunter, Matthew F., additional, Huq, Aamira J., additional, Josephi-Taylor, Sarah, additional, Joshi, Himanshu, additional, Kirk, Edwin, additional, Krzesinski, Emma, additional, Kumar, Kishore R., additional, Lemckert, Frances, additional, Leventer, Richard J., additional, Lindsey-Temple, Suzanna E., additional, Lunke, Sebastian, additional, Ma, Alan, additional, Macaskill, Steven, additional, Mallawaarachchi, Amali, additional, Marty, Melanie, additional, Marum, Justine E., additional, McCarthy, Hugh J., additional, Menezes, Manoj P., additional, McLean, Alison, additional, Milnes, Di, additional, Mohammad, Shekeeb, additional, Mowat, David, additional, Niaz, Aram, additional, Palmer, Elizabeth E., additional, Patel, Chirag, additional, Patel, Shilpan G., additional, Phelan, Dean, additional, Pinner, Jason R., additional, Rajagopalan, Sulekha, additional, Regan, Matthew, additional, Rodgers, Jonathan, additional, Rodrigues, Miriam, additional, Roxburgh, Richard H., additional, Sachdev, Rani, additional, Roscioli, Tony, additional, Samarasekera, Ruvishani, additional, Sandaradura, Sarah A., additional, Savva, Elena, additional, Schindler, Tim, additional, Shah, Margit, additional, Sinnerbrink, Ingrid B., additional, Smith, Janine M., additional, Smith, Richard J., additional, Springer, Amanda, additional, Stark, Zornitza, additional, Strom, Samuel P., additional, Sue, Carolyn M., additional, Tan, Kenneth, additional, Tan, Tiong Y., additional, Tantsis, Esther, additional, Tchan, Michel C., additional, Thompson, Bryony A., additional, Trainer, Alison H., additional, van Spaendonck-Zwarts, Karin, additional, Walsh, Rebecca, additional, Warwick, Linda, additional, White, Stephanie, additional, White, Susan M., additional, Williams, Mark G., additional, Wilson, Meredith J., additional, Wong, Wui Kwan, additional, Wright, Dale C., additional, Yap, Patrick, additional, Yeung, Alison, additional, Young, Helen, additional, Jones, Kristi J., additional, Bennetts, Bruce, additional, Cooper, Sandra T., additional, Abdulrasool, Ghusoon, additional, Al Eryani, Ghamdan, additional, Arts, Peer, additional, Bagnall, Richard, additional, Baker, Naomi L., additional, Barnett, Christopher, additional, Beecroft, Sarah, additional, Berbic, Marina, additional, Black, Michael, additional, Blackburn, Jim, additional, Blombery, Piers, additional, Bournazos, Adam M., additional, Branford, Susan, additional, Breen, Jimmy, additional, Burnett, Leslie, additional, Canson, Daffodil, additional, Cheong, Pak, additional, Chew, Edward, additional, Christodoulou, John, additional, Chung, Seo-Kyung, additional, Clark, Mike, additional, Cliffe, Corrina, additional, Cole, Melissa, additional, Collins, Felicity, additional, Compton, Alison, additional, Cooper, Antony, additional, Corbett, Mark, additional, Cowley, Mark, additional, Dudding, Tracy, additional, Eggers, Stefanie, additional, Eyras, Eduardo, additional, Fernandez, Miriam Fanjul, additional, Fellowes, Andrew, additional, Fleischer, Ron, additional, Folland, Chiara, additional, Fox, Lucy, additional, Gaff, Clara, additional, Galea, Melanie, additional, Ghaoui, Roula, additional, Gornanitis, Ilias, additional, Ha, Thuong, additional, Hayashi, Rippei, additional, Hayes, Ian, additional, Henderson, Alex, additional, Hesson, Luke, additional, Heyer, Erin, additional, Hildebrand, Michael, additional, Hipwell, Michael, additional, Hoskins, Cass, additional, Jackson, Matilda, additional, James, Paul, additional, Wong, Justin Jong-Leong, additional, Kassahn, Karin, additional, Kaub, Peter, additional, Kevin, Lucy, additional, Kumble, Smitha, additional, Kummerfeld, Sarah, additional, Laing, Nigel, additional, Lau, Chiyan, additional, Lee, Eric, additional, Leighton, Sarah, additional, Lundie, Ben, additional, Mayoh, Chelsea, additional, McGaughran, Julie, additional, McPhillips, Mary, additional, Meldrum, Cliff, additional, Middleton, Edwina, additional, Mina, Kym, additional, Nisselle, Amy, additional, Oates, Emily, additional, Oshlack, Alicia, additional, Parasivam, Gayathri, additional, Parsons, Michael, additional, Quinn, Michael, additional, Rasko, John, additional, Ravenscroft, Gina, additional, Ravine, Anja, additional, Recsei, Krista, additional, Rehn, Jacqueline, additional, Robertson, Stephen, additional, Ronan, Anne, additional, Ryland, Georgina, additional, Sadedin, Simon, additional, Schreiber, Andreas, additional, Scott, Hamish, additional, Scott, Rodney, additional, Semsarian, Christopher, additional, Simons, Cas, additional, Singer, Emma, additional, Smyth, Renee, additional, Spurdle, Amanda, additional, Sullivan, Patricia, additional, Sundercombe, Samantha, additional, Thorburn, David, additional, Toubia, John, additional, Trent, Ronald, additional, Tudini, Emma, additional, Voneague, Irina, additional, Waddell, Leigh, additional, Walker, Logan, additional, Wallis, Mathew, additional, Warnock, Nick, additional, Weatheritt, Robert, additional, White, Deborah, additional, Winship, Ingrid, additional, Worgan, Lisa, additional, Wu, Kathy, additional, and Ziolowski, Andrew, additional
- Published
- 2022
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15. WGS and RNA Studies Diagnose Noncoding DMD Variants in Males With High Creatine Kinase
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Waddell, Leigh B., primary, Bryen, Samantha J., additional, Cummings, Beryl B., additional, Bournazos, Adam, additional, Evesson, Frances J., additional, Joshi, Himanshu, additional, Marshall, Jamie L., additional, Tukiainen, Taru, additional, Valkanas, Elise, additional, Weisburd, Ben, additional, Sadedin, Simon, additional, Davis, Mark R., additional, Faiz, Fathimath, additional, Gooding, Rebecca, additional, Sandaradura, Sarah A., additional, O'Grady, Gina L., additional, Tchan, Michel C., additional, Mowat, David R., additional, Oates, Emily C., additional, Farrar, Michelle A., additional, Sampaio, Hugo, additional, Ma, Alan, additional, Neas, Katherine, additional, Wang, Min-Xia, additional, Charlton, Amanda, additional, Chan, Charles, additional, Kenwright, Diane N., additional, Graf, Nicole, additional, Arbuckle, Susan, additional, Clarke, Nigel F., additional, MacArthur, Daniel G., additional, Jones, Kristi J., additional, Lek, Monkol, additional, and Cooper, Sandra T., additional
- Published
- 2021
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16. Pathogenic deep intronic MTM1 variant activates a pseudo-exon encoding a nonsense codon resulting in severe X-linked myotubular myopathy
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Bryen, Samantha J., primary, Oates, Emily C., additional, Evesson, Frances J., additional, Lu, Jessica K., additional, Waddell, Leigh B., additional, Joshi, Himanshu, additional, Ryan, Monique M., additional, Cummings, Beryl B., additional, McLean, Catriona A., additional, MacArthur, Daniel G., additional, Kornberg, Andrew J., additional, and Cooper, Sandra T., additional
- Published
- 2020
- Full Text
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17. Recurrent TTN metatranscript‐only c.39974–11T>G splice variant associated with autosomal recessive arthrogryposis multiplex congenita and myopathy
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Bryen, Samantha J., primary, Ewans, Lisa J., additional, Pinner, Jason, additional, MacLennan, Suzanna C., additional, Donkervoort, Sandra, additional, Castro, Diana, additional, Töpf, Ana, additional, O'Grady, Gina, additional, Cummings, Beryl, additional, Chao, Katherine R., additional, Weisburd, Ben, additional, Francioli, Laurent, additional, Faiz, Fathimath, additional, Bournazos, Adam M., additional, Hu, Ying, additional, Grosmann, Carla, additional, Malicki, Denise M., additional, Doyle, Helen, additional, Witting, Nanna, additional, Vissing, John, additional, Claeys, Kristl G., additional, Urankar, Kathryn, additional, Beleza‐Meireles, Ana, additional, Baptista, Julia, additional, Ellard, Sian, additional, Savarese, Marco, additional, Johari, Mridul, additional, Vihola, Anna, additional, Udd, Bjarne, additional, Majumdar, Anirban, additional, Straub, Volker, additional, Bönnemann, Carsten G., additional, MacArthur, Daniel G., additional, Davis, Mark R., additional, and Cooper, Sandra T., additional
- Published
- 2019
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18. Importance of muscle biopsy to establish pathogenicity of DMD missense and splice variants
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Jones, Hannah F, primary, Bryen, Samantha J, additional, Waddell, Leigh B, additional, Bournazos, Adam, additional, Davis, Mark, additional, Farrar, Michelle A, additional, McLean, Catriona A, additional, Mowat, David R, additional, Sampaio, Hugo, additional, Woodcock, Ian R, additional, Ryan, Monique M, additional, Jones, Kristi J, additional, and Cooper, Sandra T, additional
- Published
- 2019
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19. Translating Technical Innovations for Splicing Diagnostics Into Clinical Genomics
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Bournazos, Adam, primary, Riley, Lisa G., additional, Bryen, Samantha J., additional, Waddell, Leigh B., additional, Davis, Mark R., additional, Bennetts, Bruce, additional, and Cooper, Sandra T., additional
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- 2019
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20. Recurrent TTN metatranscript‐only c.39974–11T>G splice variant associated with autosomal recessive arthrogryposis multiplex congenita and myopathy.
- Author
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Bryen, Samantha J., Ewans, Lisa J., Pinner, Jason, MacLennan, Suzanna C., Donkervoort, Sandra, Castro, Diana, Töpf, Ana, O'Grady, Gina, Cummings, Beryl, Chao, Katherine R., Weisburd, Ben, Francioli, Laurent, Faiz, Fathimath, Bournazos, Adam M., Hu, Ying, Grosmann, Carla, Malicki, Denise M., Doyle, Helen, Witting, Nanna, and Vissing, John
- Abstract
We present eight families with arthrogryposis multiplex congenita and myopathy bearing a TTN intron 213 extended splice‐site variant (NM_001267550.1:c.39974‐11T>G), inherited in trans with a second pathogenic TTN variant. Muscle‐derived RNA studies of three individuals confirmed mis‐splicing induced by the c.39974‐11T>G variant; in‐frame exon 214 skipping or use of a cryptic 3′ splice‐site effecting a frameshift. Confounding interpretation of pathogenicity is the absence of exons 213‐217 within the described skeletal muscle TTN N2A isoform. However, RNA‐sequencing from 365 adult human gastrocnemius samples revealed that 56% specimens predominantly include exons 213‐217 in TTN transcripts (inclusion rate ≥66%). Further, RNA‐sequencing of five fetal muscle samples confirmed that 4/5 specimens predominantly include exons 213‐217 (fifth sample inclusion rate 57%). Contractures improved significantly with age for four individuals, which may be linked to decreased expression of pathogenic fetal transcripts. Our study extends emerging evidence supporting a vital developmental role for TTN isoforms containing metatranscript‐only exons. [ABSTRACT FROM AUTHOR]
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- 2020
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21. Pathogenic deep intronic MTM1variant activates a pseudo-exon encoding a nonsense codon resulting in severe X-linked myotubular myopathy
- Author
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Bryen, Samantha J., Oates, Emily C., Evesson, Frances J., Lu, Jessica K., Waddell, Leigh B., Joshi, Himanshu, Ryan, Monique M., Cummings, Beryl B., McLean, Catriona A., MacArthur, Daniel G., Kornberg, Andrew J., and Cooper, Sandra T.
- Abstract
X-linked myotubular myopathy (XLMTM) is a severe congenital myopathy characterised by generalised weakness and respiratory insufficiency. XLMTM is associated with pathogenic variants in MTM1; a gene encoding the lipid phosphatase myotubularin. Whole genome sequencing (WGS) of an exome-negative male proband with severe hypotonia, respiratory insufficiency and centralised nuclei on muscle biopsy identified a deep intronic MTM1variant NG_008199.1(NM_000252.2):c.1468-577A>G, which strengthened a cryptic 5' splice site (A>G substitution at the +5 position). Muscle RNA sequencing was non-diagnostic due to low read depth. Reverse transcription PCR (RT-PCR) of muscle RNA confirmed the c.1468-577A>G variant activates inclusion of a pseudo-exon encoding a premature stop codon into all detected MTM1transcripts. Western blot analysis establishes deficiency of myotubularin protein, consistent with the severe XLMTM phenotype. We expand the genotypic spectrum of XLMTM and highlight benefits of screening non-coding regions of MTM1in male probands with phenotypically concordant XLMTM who remain undiagnosed following exome sequencing.
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- 2021
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22. Recessive DEScardio/myopathy without myofibrillar aggregates: intronic splice variant silences one allele leaving only missense L190P-desmin
- Author
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Riley, Lisa, Waddell, Leigh, Ghaoui, Roula, Evesson, Frances, Cummings, Beryl, Bryen, Samantha J., Joshi, Himanshu, Wang, Min-Xia, Brammah, Susan, Kritharides, Leonard, Corbett, Alastair, MacArthur, Daniel, and Cooper, Sandra
- Abstract
We establish autosomal recessive DESvariants p.(Leu190Pro) and a deep intronic splice variant causing inclusion of a frameshift-inducing artificial exon/intronic fragment, as the likely cause of myopathy with cardiac involvement in female siblings. Both sisters presented in their twenties with slowly progressive limb girdle weakness, severe systolic dysfunction, and progressive, severe respiratory weakness. Desmin is an intermediate filament protein typically associated with autosomal dominant myofibrillar myopathy with cardiac involvement. However a few rare cases of autosomal recessive desminopathy are reported. In this family, a paternal missense p.(Leu190Pro) variant was viewed unlikely to be causative of autosomal dominant desminopathy, as the father and brothers carrying this variant were clinically unaffected. Clinical fit with a DES-related myopathy encouraged closer scrutiny of all DESvariants, identifying a maternal deep intronic variant within intron-7, predicted to create a cryptic splice site, which segregated with disease. RNA sequencing and studies of muscle cDNA confirmed the deep intronic variant caused aberrant splicing of an artificial exon/intronic fragment into maternal DESmRNA transcripts, encoding a premature termination codon, and potently activating nonsense-mediate decay (92% paternal DEStranscripts, 8% maternal). Western blot showed 60–75% reduction in desmin levels, likely comprised only of missense p.(Leu190Pro) desmin. Biopsy showed fibre size variation with increased central nuclei. Electron microscopy showed extensive myofibrillar disarray, duplication of the basal lamina, but no inclusions or aggregates. This study expands the phenotypic spectrum of recessive DEScardio/myopathy, and emphasizes the continuing importance of muscle biopsy for functional genomics pursuit of ‘tricky’ variants in neuromuscular conditions.
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- 2019
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23. Unique Capabilities of Genome Sequencing for Rare Disease Diagnosis.
- Author
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Wojcik MH, Lemire G, Zaki MS, Wissman M, Win W, White S, Weisburd B, Waddell LB, Verboon JM, VanNoy GE, Töpf A, Tan TY, Straub V, Stenton SL, Snow H, Singer-Berk M, Silver J, Shril S, Seaby EG, Schneider R, Sankaran VG, Sanchis-Juan A, Russell KA, Reinson K, Ravenscroft G, Pierce EA, Place EM, Pajusalu S, Pais L, Õunap K, Osei-Owusu I, Okur V, Oja KT, O'Leary M, O'Heir E, Morel C, Marchant RG, Mangilog BE, Madden JA, MacArthur D, Lovgren A, Lerner-Ellis JP, Lin J, Laing N, Hildebrandt F, Groopman E, Goodrich J, Gleeson JG, Ghaoui R, Genetti CA, Gazda HT, Ganesh VS, Ganapathy M, Gallacher L, Fu J, Evangelista E, England E, Donkervoort S, DiTroia S, Cooper ST, Chung WK, Christodoulou J, Chao KR, Cato LD, Bujakowska KM, Bryen SJ, Brand H, Bonnemann C, Beggs AH, Baxter SM, Agrawal PB, Talkowski M, Austin-Tse C, Rehm HL, and O'Donnell-Luria A
- Abstract
Background: Causal variants underlying rare disorders may remain elusive even after expansive gene panels or exome sequencing (ES). Clinicians and researchers may then turn to genome sequencing (GS), though the added value of this technique and its optimal use remain poorly defined. We therefore investigated the advantages of GS within a phenotypically diverse cohort., Methods: GS was performed for 744 individuals with rare disease who were genetically undiagnosed. Analysis included review of single nucleotide, indel, structural, and mitochondrial variants., Results: We successfully solved 218/744 (29.3%) cases using GS, with most solves involving established disease genes (157/218, 72.0%). Of all solved cases, 148 (67.9%) had previously had non-diagnostic ES. We systematically evaluated the 218 causal variants for features requiring GS to identify and 61/218 (28.0%) met these criteria, representing 8.2% of the entire cohort. These included small structural variants (13), copy neutral inversions and complex rearrangements (8), tandem repeat expansions (6), deep intronic variants (15), and coding variants that may be more easily found using GS related to uniformity of coverage (19)., Conclusion: We describe the diagnostic yield of GS in a large and diverse cohort, illustrating several types of pathogenic variation eluding ES or other techniques. Our results reveal a higher diagnostic yield of GS, supporting the utility of a genome-first approach, with consideration of GS as a secondary or tertiary test when higher-resolution structural variant analysis is needed or there is a strong clinical suspicion for a condition and prior targeted genetic testing has been negative.
- Published
- 2023
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