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1. Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies.

Author

Lowther, Chelsea, Valkanas, Elise, Giordano, Jessica, Wang, Harold, Currall, Benjamin, OKeefe, Kathryn, Pierce-Hoffman, Emma, Kurtas, Nehir, Whelan, Christopher, Hao, Stephanie, Weisburd, Ben, Jalili, Vahid, Fu, Jack, Wong, Isaac, Collins, Ryan, Zhao, Xuefang, Austin-Tse, Christina, Evangelista, Emily, Lemire, Gabrielle, Aggarwal, Vimla, Lucente, Diane, Gauthier, Laura, Tolonen, Charlotte, Sahakian, Nareh, Stevens, Christine, An, Joon-Yong, Dong, Shan, MacKenzie, Tippi, Devlin, Bernie, Gilmore, Kelly, Powell, Bradford, Brandt, Alicia, Vetrini, Francesco, DiVito, Michelle, MacArthur, Daniel, Hodge, Jennelle, ODonnell-Luria, Anne, Rehm, Heidi, Vora, Neeta, Levy, Brynn, Brand, Harrison, Wapner, Ronald, Talkowski, Michael, Norton, Mary, and Sanders, Stephan

Subjects
genome sequencing, karyotype, microarray, exome sequencing, structural variant, autism spectrum disorder, structural anomaly, prenatal, first-tier, diagnostic, Female, Pregnancy, Humans, Autism Spectrum Disorder, Pregnancy Trimester, First, Ultrasonography, Prenatal, Chromosome Mapping, Exome
Abstract

Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.

Published
2023

2. Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors

Author

Willim, Jana, Woike, Daniel, Greene, Daniel, Das, Sarada, Pfeifer, Kevin, Yuan, Weimin, Lindsey, Anika, Itani, Omar, Böhme, Amber L., Tibbe, Debora, Hönck, Hans-Hinrich, Hassani Nia, Fatemeh, Zech, Michael, Brunet, Theresa, Faivre, Laurence, Sorlin, Arthur, Vitobello, Antonio, Smol, Thomas, Colson, Cindy, Baranano, Kristin, Schatz, Krista, Bayat, Allan, Schoch, Kelly, Spillmann, Rebecca, Davis, Erica E., Conboy, Erin, Vetrini, Francesco, Platzer, Konrad, Neuser, Sonja, Gburek-Augustat, Janina, Grace, Alexandra Noel, Mitchell, Bailey, Stegmann, Alexander, Sinnema, Margje, Meeks, Naomi, Saunders, Carol, Cadieux-Dion, Maxime, Hoyer, Juliane, Van-Gils, Julien, de Sainte-Agathe, Jean-Madeleine, Thompson, Michelle L., Bebin, E. Martina, Weisz-Hubshman, Monika, Tabet, Anne-Claude, Verloes, Alain, Levy, Jonathan, Latypova, Xenia, Harder, Sönke, Silverman, Gary A., Pak, Stephen C., Schedl, Tim, Freson, Kathleen, Mumford, Andrew, Turro, Ernest, Schlein, Christian, Shashi, Vandana, and Kreienkamp, Hans-Jürgen

Published
2024
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3. HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder

Author

Ambrose, J.C., Arumugam, P., Bevers, R., Bleda, M., Boardman-Pretty, F., Boustred, C.R., Brittain, H., Brown, M.A., Caulfield, M.J., Chan, G.C., Giess, A., Griffin, J.N., Hamblin, A., Henderson, S., Hubbard, T.J.P., Jackson, R., Jones, L.J., Kasperaviciute, D., Kayikci, M., Kousathanas, A., Lahnstein, L., Lakey, A., Leigh, S.E.A., Leong, I.U.S., Lopez, F.J., Maleady-Crowe, F., McEntagart, M., Minneci, F., Mitchell, J., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A.C., O‘Donovan, P., Odhams, C.A., Patch, C., Perez-Gil, D., Pereira, M.B., Pullinger, J., Rahim, T., Rendon, A., Rogers, T., Savage, K., Sawant, K., Scott, R.H., Siddiq, A., Sieghart, A., Smith, S.C., Sosinsky, A., Stuckey, A., Tanguy, M., Taylor Tavares, A.L., Thomas, E.R.A., Thompson, S.R., Tucci, A., Welland, M.J., Williams, E., Witkowska, K., Wood, S.M., Zarowiecki, M., Acosta, Maria T., Adams, David R., Alvarez, Raquel L., Alvey, Justin, Allworth, Aimee, Andrews, Ashley, Ashley, Euan A., Afzali, Ben, Bacino, Carlos A., Bademci, Guney, Balasubramanyam, Ashok, Baldridge, Dustin, Bale, Jim, Bamshad, Michael, Barbouth, Deborah, Bayrak-Toydemir, Pinar, Beck, Anita, Beggs, Alan H., Behrens, Edward, Bejerano, Gill, Bellen, Hugo J., Bennet, Jimmy, Bernstein, Jonathan A., Berry, Gerard T., Bican, Anna, Bivona, Stephanie, Blue, Elizabeth, Bohnsack, John, Bonner, Devon, Botto, Lorenzo, Briere, Lauren C., Brown, Gabrielle, Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Byers, Peter, Byrd, William E., Carey, John, Carrasquillo, Olveen, Cassini, Thomas, Chang, Ta Chen, Chanprasert, Sirisak, Chao, Hsiao-Tuan, Chinn, Ivan, Clark, Gary D., Coakley, Terra R., Cobban, Laurel A., Cogan, Joy D., Coggins, Matthew, Cole, F. Sessions, Colley, Heather A., Cope, Heidi, Corona, Rosario, Craigen, William J., Crouse, Andrew B., Cunningham, Michael, D'Souza, Precilla, Dai, Hongzheng, Dasari, Surendra, Davis, Joie, Dayal, Jyoti G., Delgado, Margaret, Dell'Angelica, Esteban C., Dipple, Katrina, Doherty, Daniel, Dorrani, Naghmeh, Doss, Argenia L., Douine, Emilie D., Earl, Dawn, Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Falk, Marni, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Forghani, Irman, Fu, Jiayu, Gahl, William A., Glass, Ian, Goddard, Page C., Godfrey, Rena A., Grajewski, Alana, Halley, Meghan C., Hamid, Rizwan, Hanchard, Neal, Hassey, Kelly, Hayes, Nichole, High, Frances, Hing, Anne, Hisama, Fuki M., Holm, Ingrid A., Hom, Jason, Horike-Pyne, Martha, Huang, Alden, Huang, Yan, Hutchison, Sarah, Introne, Wendy, Isasi, Rosario, Izumi, Kosuke, Jarvik, Gail P., Jarvik, Jeffrey, Jayadev, Suman, Jean-Marie, Orpa, Jobanputra, Vaidehi, Kaitryn, Emerald, Ketkar, Shamika, Kiley, Dana, Kilich, Gonench, Kobren, Shilpa N., Kohane, Isaac S., Kohler, Jennefer N., Korrick, Susan, Krakow, Deborah, Krasnewich, Donna M., Kravets, Elijah, Lalani, Seema R., Lam, Byron, Lam, Christina, Lanpher, Brendan C., Lanza, Ian R., LeBlanc, Kimberly, Lee, Brendan H., Levitt, Roy, Lewis, Richard A., Liu, Pengfei, Liu, Xue Zhong, Longo, Nicola, Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Maghiro, AudreyStephannie, Mahoney, Rachel, Malicdan, May Christine, Mamounas, Laura A., Manolio, Teri A., Mao, Rong, Marom, Ronit, Marth, Gabor, Martin, Beth A., Martin, Martin G., Martínez-Agosto, Julian A., Marwaha, Shruti, McCauley, Jacob, McConkie-Rosell, Allyn, McCray, Alexa T., McGee, Elisabeth, Might, Matthew, Miller, Danny, Mirzaa, Ghayda, Morava, Eva, Moretti, Paolo, Morimoto, Marie, Mulvihill, John J., Nakano-Okuno, Mariko, Nelson, Stanley F., Nieves-Rodriguez, Shirley, Novacic, Donna, Oglesbee, Devin, Orengo, James P., Pace, Laura, Pak, Stephen, Pallais, J. Carl, Papp, Jeanette C., Parker, Neil H., Petcharet, Leoyklang, Phillips, John A., III, Posey, Jennifer E., Potocki, Lorraine, Swerdzewski, Barbara N., Quinlan, Aaron, Rao, Deepak A., Raper, Anna, Raskind, Wendy, Renteria, Genecee, Reuter, Chloe, Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Rosenthal, Elizabeth, Rossignol, Francis, Ruzhnikov, Maura, Sabaii, Marla, Sacco, Ralph, Sampson, Jacinda B., Saporta, Mario, Schaechter, Judy, Schedl, Timothy, Schoch, Kelly, Scott, Daryl A., Seto, Elaine, Sharma, Prashant, Shashi, Vandana, Shelkowitz, Emily, Sheppeard, Sam, Shin, Jimann, Silverman, Edwin, Sinsheimer, Janet, Sisco, Kathy, Smith, Edward, Smith, Kevin, Solnica-Krezel, Lilianna, Solomon, Ben, Spillmann, Rebecca, Stergachis, Andrew, Stoler, Joan, Sullivan, Kathleen, Sullivan, Jennifer, Sutton, Shirley, Sweetser, David A., Sybert, Virginia, Tabor, Holly K., Tan, Queenie K.-G., Tan, Amelia L., Tarakad, Arjun, Tekin, Mustafa, Telischi, Fred, Thorson, Willa, Tifft, Cynthia, Toro, Camilo, Tran, Alyssa A., Ungar, Rachel A., Urv, Tiina K., Vanderver, Adeline, Velinder, Matt, Viskochil, Dave, Vogel, Tiphanie P., Wahl, Colleen E., Walker, Melissa, Walley, Nicole M., Wambach, Jennifer, Wan, Jijun, Wang, Lee-kai, Wangler, Michael F., Ward, Patricia A., Wegner, Daniel, Weisz, Monika, Wener, Mark, Wenger, Tara, Westerfield, Monte, Wheeler, Matthew T., Whitlock, Jordan, Wolfe, Lynne A., Yamamoto, Shinya, Zhang, Zhe, Zuchner, Stephan, Niggl, Eva, Bouman, Arjan, Hoogenboezem, Remco M., Wallaard, Ilse, Park, Joohyun, Admard, Jakob, Wilke, Martina, Harris-Mostert, Emilio D.R.O., Elgersma, Minetta, Bain, Jennifer, Balasubramanian, Meena, Banka, Siddharth, Benke, Paul J., Bertrand, Miriam, Blesson, Alyssa E., Clayton-Smith, Jill, Ellingford, Jamie M., Gillentine, Madelyn A., Goodloe, Dana H., Haack, Tobias B., Jain, Mahim, Krantz, Ian, Luu, Sharon M., McPheron, Molly, Muss, Candace L., Raible, Sarah E., Robin, Nathaniel H., Spiller, Michael, Starling, Susan, Thiffault, Isabelle, Vetrini, Francesco, Witt, Dennis, Woods, Emily, Zhou, Dihong, Elgersma, Ype, and van Esbroeck, Annelot C.M.

Published
2023
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4. CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels

Author

Yuan, Bo, Wang, Lei, Liu, Pengfei, Shaw, Chad, Dai, Hongzheng, Cooper, Lance, Zhu, Wenmiao, Anderson, Stephanie A., Meng, Linyan, Wang, Xia, Wang, Yue, Xia, Fan, Xiao, Rui, Braxton, Alicia, Peacock, Sandra, Schmitt, Eric, Ward, Patricia A., Vetrini, Francesco, He, Weimin, Chiang, Theodore, Muzny, Donna, Gibbs, Richard A., Beaudet, Arthur L., Breman, Amy M., Smith, Janice, Cheung, Sau Wai, Bacino, Carlos A., Eng, Christine M., Yang, Yaping, Lupski, James R., and Bi, Weimin

Published
2020
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6. A case of MBTPS1‐related disorder due to compound heterozygous variants in MBTPS1 gene: Genotype–phenotype expansion and the emergence of a novel syndrome.

Author

Liaqat, Khurram, Treat, Kayla, Mantcheva, Lili, Nasir, Abdul, Weaver, David D., Conboy, Erin, and Vetrini, Francesco

Abstract

MBTPS1 (NM_003791.4) encodes Site‐1 protease, a serine protease that functions sequentially with Site‐2 protease regulating cholesterol homeostasis and endoplasmic reticulum stress response. MBTPS1 pathogenic variants are associated with spondyloepiphyseal dysplasia, Kondo‐Fu type (MIM:618392; cataract, alopecia, oral mucosal disorder, and psoriasis‐like syndrome, and Silver–Russell‐like syndrome). In this report, we describe a 14‐year‐old female with a complex medical history including white matter volume loss, early‐onset cataracts, retrognathia, laryngomalacia, inguinal hernia, joint hypermobility, feeding dysfunction, and speech delay. Additionally, features of ectodermal dysplasia that she has include decreased sweating, heat intolerance, dysplastic nails, chronically dry skin, and abnormal hair growth issues. Exome sequencing analysis identified compound heterozygous variants in the MBTPS1 gene: c.2255G > T p.(Gly752Val) predicted to affect important function of the protein, which was inherited from the mother, and a splice site variant c.2831 + 5G > T, which was inherited from the father. The RNA‐seq analysis of the splice variant showed skipping of exon 21, predicted to result in frameshifting p.(Ser901fs28*) leading to non‐sense mediated decay. To our knowledge, only eight studies have been published that described the MBPTS1‐related disorders. Interestingly, we observed the features of ectodermal dysplasia in our patient that further expands the phenotypic spectrum of MBTPS1 gene‐related disorders. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Undiagnosed rare disease clinic identifies a novel UBE3A variant in two sisters with Angelman syndrome: The end of a diagnostic odyssey.

Author

Bruns, Rebecca, Liaqat, Khurram, Nasir, Abdul, Treat, Kayla, Murthy, Vinaya S., Mantcheva, Lili, Torres, Wilfredo, Conboy, Erin, and Vetrini, Francesco

Subjects
ANGELMAN syndrome, RARE diseases, DISABILITIES, UBIQUITIN ligases, DEVELOPMENTAL delay, MOVEMENT disorders
Abstract

Angelman syndrome (AS, MIM #105830) is a neurodevelopmental disorder characterized by severe intellectual disability, profound developmental delay, movement or balance problems, an excessively cheerful disposition, and seizures. AS results from inadequate expression of the maternal UBE3A gene (MIM #601623), which encodes an E3 ligase in the ubiquitin‐proteasome pathway. Here we present the case of two sisters with features consistent with AS who had negative methylation analyses. An autism/intellectual disability expanded panel revealed a maternally inherited novel UBE3A (NM_001354506.2) variant c.2443C>T p.(Pro815Ser) in both patients that was initially classified as a variant of uncertain significance. The patients were enrolled in Indiana University's Undiagnosed Rare Disease Clinic (URDC) to further investigate the variant. Additional data, including deep phenotyping, familial segregation analysis, and in silico studies, suggest that the variant is likely pathogenic. 3D modeling studies based on the available crystal structure revealed that the Pro815Ser variant can introduce more flexibility into the protein and alter its enzymatic activity. Recent literature confirms the pathogenic nature of the variant. Reanalysis of the UBE3A variant has heightened existing knowledge of AS and has offered this family an end to their diagnostic odyssey. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Macrocephaly and developmental delay caused by missense variants in RAB5C

Author

Koop, Klaas, primary, Yuan, Weimin, additional, Tessadori, Federico, additional, Rodriguez-Polanco, Wilmer R, additional, Grubbs, Jeremy, additional, Zhang, Bo, additional, Osmond, Matt, additional, Graham, Gail, additional, Sawyer, Sarah, additional, Conboy, Erin, additional, Vetrini, Francesco, additional, Treat, Kayla, additional, Płoski, Rafal, additional, Pienkowski, Victor Murcia, additional, Kłosowska, Anna, additional, Fieg, Elizabeth, additional, Krier, Joel, additional, Mallebranche, Coralie, additional, Alban, Ziegler, additional, Aldinger, Kimberly A, additional, Ritter, Deborah, additional, Macnamara, Ellen, additional, Sullivan, Bonnie, additional, Herriges, John, additional, Alaimo, Joseph T, additional, Helbig, Catherine, additional, Ellis, Colin A, additional, Eyk, Clare, additional, Gecz, Jozef, additional, Farrugia, Daniel, additional, Osei-Owusu, Ikeoluwa, additional, Adès, Lesley, additional, Boogaard, Marie-Jose, additional, Fuchs, Sabine, additional, Bakker, Jeroen, additional, Duran, Karen, additional, Dawson, Zachary D, additional, Lindsey, Anika, additional, Huang, Huiyan, additional, Baldridge, Dustin, additional, Silverman, Gary A, additional, Grant, Barth D, additional, Raizen, David, additional, Network, Undiagnosed Diseases, additional, Haaften, Gijs, additional, Pak, Stephen C, additional, Rehmann, Holger, additional, Schedl, Tim, additional, and van Hasselt, Peter, additional

Published
2023
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9. HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder

Author

Niggl, Eva, primary, Bouman, Arjan, additional, Briere, Lauren C., additional, Hoogenboezem, Remco M., additional, Wallaard, Ilse, additional, Park, Joohyun, additional, Admard, Jakob, additional, Wilke, Martina, additional, Harris-Mostert, Emilio D.R.O., additional, Elgersma, Minetta, additional, Bain, Jennifer, additional, Balasubramanian, Meena, additional, Banka, Siddharth, additional, Benke, Paul J., additional, Bertrand, Miriam, additional, Blesson, Alyssa E., additional, Clayton-Smith, Jill, additional, Ellingford, Jamie M., additional, Gillentine, Madelyn A., additional, Goodloe, Dana H., additional, Haack, Tobias B., additional, Jain, Mahim, additional, Krantz, Ian, additional, Luu, Sharon M., additional, McPheron, Molly, additional, Muss, Candace L., additional, Raible, Sarah E., additional, Robin, Nathaniel H., additional, Spiller, Michael, additional, Starling, Susan, additional, Sweetser, David A., additional, Thiffault, Isabelle, additional, Vetrini, Francesco, additional, Witt, Dennis, additional, Woods, Emily, additional, Zhou, Dihong, additional, Elgersma, Ype, additional, van Esbroeck, Annelot C.M., additional, Ambrose, J.C., additional, Arumugam, P., additional, Bevers, R., additional, Bleda, M., additional, Boardman-Pretty, F., additional, Boustred, C.R., additional, Brittain, H., additional, Brown, M.A., additional, Caulfield, M.J., additional, Chan, G.C., additional, Giess, A., additional, Griffin, J.N., additional, Hamblin, A., additional, Henderson, S., additional, Hubbard, T.J.P., additional, Jackson, R., additional, Jones, L.J., additional, Kasperaviciute, D., additional, Kayikci, M., additional, Kousathanas, A., additional, Lahnstein, L., additional, Lakey, A., additional, Leigh, S.E.A., additional, Leong, I.U.S., additional, Lopez, F.J., additional, Maleady-Crowe, F., additional, McEntagart, M., additional, Minneci, F., additional, Mitchell, J., additional, Moutsianas, L., additional, Mueller, M., additional, Murugaesu, N., additional, Need, A.C., additional, O‘Donovan, P., additional, Odhams, C.A., additional, Patch, C., additional, Perez-Gil, D., additional, Pereira, M.B., additional, Pullinger, J., additional, Rahim, T., additional, Rendon, A., additional, Rogers, T., additional, Savage, K., additional, Sawant, K., additional, Scott, R.H., additional, Siddiq, A., additional, Sieghart, A., additional, Smith, S.C., additional, Sosinsky, A., additional, Stuckey, A., additional, Tanguy, M., additional, Taylor Tavares, A.L., additional, Thomas, E.R.A., additional, Thompson, S.R., additional, Tucci, A., additional, Welland, M.J., additional, Williams, E., additional, Witkowska, K., additional, Wood, S.M., additional, Zarowiecki, M., additional, Acosta, Maria T., additional, Adams, David R., additional, Alvarez, Raquel L., additional, Alvey, Justin, additional, Allworth, Aimee, additional, Andrews, Ashley, additional, Ashley, Euan A., additional, Afzali, Ben, additional, Bacino, Carlos A., additional, Bademci, Guney, additional, Balasubramanyam, Ashok, additional, Baldridge, Dustin, additional, Bale, Jim, additional, Bamshad, Michael, additional, Barbouth, Deborah, additional, Bayrak-Toydemir, Pinar, additional, Beck, Anita, additional, Beggs, Alan H., additional, Behrens, Edward, additional, Bejerano, Gill, additional, Bellen, Hugo J., additional, Bennet, Jimmy, additional, Bernstein, Jonathan A., additional, Berry, Gerard T., additional, Bican, Anna, additional, Bivona, Stephanie, additional, Blue, Elizabeth, additional, Bohnsack, John, additional, Bonner, Devon, additional, Botto, Lorenzo, additional, Brown, Gabrielle, additional, Burke, Elizabeth A., additional, Burrage, Lindsay C., additional, Butte, Manish J., additional, Byers, Peter, additional, Byrd, William E., additional, Carey, John, additional, Carrasquillo, Olveen, additional, Cassini, Thomas, additional, Chang, Ta Chen, additional, Chanprasert, Sirisak, additional, Chao, Hsiao-Tuan, additional, Chinn, Ivan, additional, Clark, Gary D., additional, Coakley, Terra R., additional, Cobban, Laurel A., additional, Cogan, Joy D., additional, Coggins, Matthew, additional, Cole, F. Sessions, additional, Colley, Heather A., additional, Cope, Heidi, additional, Corona, Rosario, additional, Craigen, William J., additional, Crouse, Andrew B., additional, Cunningham, Michael, additional, D'Souza, Precilla, additional, Dai, Hongzheng, additional, Dasari, Surendra, additional, Davis, Joie, additional, Dayal, Jyoti G., additional, Delgado, Margaret, additional, Dell'Angelica, Esteban C., additional, Dipple, Katrina, additional, Doherty, Daniel, additional, Dorrani, Naghmeh, additional, Doss, Argenia L., additional, Douine, Emilie D., additional, Earl, Dawn, additional, Eckstein, David J., additional, Emrick, Lisa T., additional, Eng, Christine M., additional, Falk, Marni, additional, Fieg, Elizabeth L., additional, Fisher, Paul G., additional, Fogel, Brent L., additional, Forghani, Irman, additional, Fu, Jiayu, additional, Gahl, William A., additional, Glass, Ian, additional, Goddard, Page C., additional, Godfrey, Rena A., additional, Grajewski, Alana, additional, Halley, Meghan C., additional, Hamid, Rizwan, additional, Hanchard, Neal, additional, Hassey, Kelly, additional, Hayes, Nichole, additional, High, Frances, additional, Hing, Anne, additional, Hisama, Fuki M., additional, Holm, Ingrid A., additional, Hom, Jason, additional, Horike-Pyne, Martha, additional, Huang, Alden, additional, Huang, Yan, additional, Hutchison, Sarah, additional, Introne, Wendy, additional, Isasi, Rosario, additional, Izumi, Kosuke, additional, Jarvik, Gail P., additional, Jarvik, Jeffrey, additional, Jayadev, Suman, additional, Jean-Marie, Orpa, additional, Jobanputra, Vaidehi, additional, Kaitryn, Emerald, additional, Ketkar, Shamika, additional, Kiley, Dana, additional, Kilich, Gonench, additional, Kobren, Shilpa N., additional, Kohane, Isaac S., additional, Kohler, Jennefer N., additional, Korrick, Susan, additional, Krakow, Deborah, additional, Krasnewich, Donna M., additional, Kravets, Elijah, additional, Lalani, Seema R., additional, Lam, Byron, additional, Lam, Christina, additional, Lanpher, Brendan C., additional, Lanza, Ian R., additional, LeBlanc, Kimberly, additional, Lee, Brendan H., additional, Levitt, Roy, additional, Lewis, Richard A., additional, Liu, Pengfei, additional, Liu, Xue Zhong, additional, Longo, Nicola, additional, Loo, Sandra K., additional, Loscalzo, Joseph, additional, Maas, Richard L., additional, Macnamara, Ellen F., additional, MacRae, Calum A., additional, Maduro, Valerie V., additional, Maghiro, AudreyStephannie, additional, Mahoney, Rachel, additional, Malicdan, May Christine, additional, Mamounas, Laura A., additional, Manolio, Teri A., additional, Mao, Rong, additional, Marom, Ronit, additional, Marth, Gabor, additional, Martin, Beth A., additional, Martin, Martin G., additional, Martínez-Agosto, Julian A., additional, Marwaha, Shruti, additional, McCauley, Jacob, additional, McConkie-Rosell, Allyn, additional, McCray, Alexa T., additional, McGee, Elisabeth, additional, Might, Matthew, additional, Miller, Danny, additional, Mirzaa, Ghayda, additional, Morava, Eva, additional, Moretti, Paolo, additional, Morimoto, Marie, additional, Mulvihill, John J., additional, Nakano-Okuno, Mariko, additional, Nelson, Stanley F., additional, Nieves-Rodriguez, Shirley, additional, Novacic, Donna, additional, Oglesbee, Devin, additional, Orengo, James P., additional, Pace, Laura, additional, Pak, Stephen, additional, Pallais, J. Carl, additional, Papp, Jeanette C., additional, Parker, Neil H., additional, Petcharet, Leoyklang, additional, Phillips, John A., additional, Posey, Jennifer E., additional, Potocki, Lorraine, additional, Swerdzewski, Barbara N., additional, Quinlan, Aaron, additional, Rao, Deepak A., additional, Raper, Anna, additional, Raskind, Wendy, additional, Renteria, Genecee, additional, Reuter, Chloe, additional, Rives, Lynette, additional, Robertson, Amy K., additional, Rodan, Lance H., additional, Rosenfeld, Jill A., additional, Rosenthal, Elizabeth, additional, Rossignol, Francis, additional, Ruzhnikov, Maura, additional, Sabaii, Marla, additional, Sacco, Ralph, additional, Sampson, Jacinda B., additional, Saporta, Mario, additional, Schaechter, Judy, additional, Schedl, Timothy, additional, Schoch, Kelly, additional, Scott, Daryl A., additional, Seto, Elaine, additional, Sharma, Prashant, additional, Shashi, Vandana, additional, Shelkowitz, Emily, additional, Sheppeard, Sam, additional, Shin, Jimann, additional, Silverman, Edwin, additional, Sinsheimer, Janet, additional, Sisco, Kathy, additional, Smith, Edward, additional, Smith, Kevin, additional, Solnica-Krezel, Lilianna, additional, Solomon, Ben, additional, Spillmann, Rebecca, additional, Stergachis, Andrew, additional, Stoler, Joan, additional, Sullivan, Kathleen, additional, Sullivan, Jennifer, additional, Sutton, Shirley, additional, Sybert, Virginia, additional, Tabor, Holly K., additional, Tan, Queenie K.-G., additional, Tan, Amelia L., additional, Tarakad, Arjun, additional, Tekin, Mustafa, additional, Telischi, Fred, additional, Thorson, Willa, additional, Tifft, Cynthia, additional, Toro, Camilo, additional, Tran, Alyssa A., additional, Ungar, Rachel A., additional, Urv, Tiina K., additional, Vanderver, Adeline, additional, Velinder, Matt, additional, Viskochil, Dave, additional, Vogel, Tiphanie P., additional, Wahl, Colleen E., additional, Walker, Melissa, additional, Walley, Nicole M., additional, Wambach, Jennifer, additional, Wan, Jijun, additional, Wang, Lee-kai, additional, Wangler, Michael F., additional, Ward, Patricia A., additional, Wegner, Daniel, additional, Weisz, Monika, additional, Wener, Mark, additional, Wenger, Tara, additional, Westerfield, Monte, additional, Wheeler, Matthew T., additional, Whitlock, Jordan, additional, Wolfe, Lynne A., additional, Yamamoto, Shinya, additional, Zhang, Zhe, additional, and Zuchner, Stephan, additional

Published
2023
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10. P588: De novo and inherited variants in DDX39B cause a novel neurodevelopmental syndrome characterized by hypotonia, epilepsy, and short stature

Author

Booth, Kevin, Jangam, Sharayu, Man Chun Chui, Martin, Treat, Kayla, Graziani, Lorenzo, Soldano, Alessia, White, Kerry, Christensen, Celanie, Lynnes, Ty, Yamamoto, Shinya, Kanca, Oguz, Tsang, Mandy, Lynch, Sally, Mullegama, Sureni, Baptista, Julia, Iancu, Daniela, Joss, Shelag, CY Mak, Christopher, Kwong, Anna, Bellen, Hugo, Conboy, Erin, Sanges, Remo, Wangler, Michael F., Hon-Yin Chung, Brian, and Vetrini, Francesco

Published
2024
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13. Macrocephaly and developmental delay caused by missense variants in RAB5C

Author

Metabole ziekten patientenzorg, Cancer, Genetica Groep Van Haaften, Child Health, Infection & Immunity, Koop, Klaas, Yuan, Weimin, Tessadori, Federico, Rodriguez-Polanco, Wilmer R, Grubbs, Jeremy, Zhang, Bo, Osmond, Matt, Graham, Gail, Sawyer, Sarah, Conboy, Erin, Vetrini, Francesco, Treat, Kayla, Płoski, Rafal, Pienkowski, Victor Murcia, Kłosowska, Anna, Fieg, Elizabeth, Krier, Joel, Mallebranche, Coralie, Alban, Ziegler, Aldinger, Kimberly A, Ritter, Deborah, Macnamara, Ellen, Sullivan, Bonnie, Herriges, John, Alaimo, Joseph T, Helbig, Catherine, Ellis, Colin A, Eyk, Clare, Gecz, Jozef, Farrugia, Daniel, Osei-Owusu, Ikeoluwa, Adès, Lesley, Boogaard, Marie-Jose, Fuchs, Sabine, Bakker, Jeroen, Duran, Karen, Dawson, Zachary D, Lindsey, Anika, Huang, Huiyan, Baldridge, Dustin, Silverman, Gary A, Grant, Barth D, Raizen, David, Network, Undiagnosed Diseases, Haaften, Gijs, Pak, Stephen C, Rehmann, Holger, Schedl, Tim, van Hasselt, Peter, Metabole ziekten patientenzorg, Cancer, Genetica Groep Van Haaften, Child Health, Infection & Immunity, Koop, Klaas, Yuan, Weimin, Tessadori, Federico, Rodriguez-Polanco, Wilmer R, Grubbs, Jeremy, Zhang, Bo, Osmond, Matt, Graham, Gail, Sawyer, Sarah, Conboy, Erin, Vetrini, Francesco, Treat, Kayla, Płoski, Rafal, Pienkowski, Victor Murcia, Kłosowska, Anna, Fieg, Elizabeth, Krier, Joel, Mallebranche, Coralie, Alban, Ziegler, Aldinger, Kimberly A, Ritter, Deborah, Macnamara, Ellen, Sullivan, Bonnie, Herriges, John, Alaimo, Joseph T, Helbig, Catherine, Ellis, Colin A, Eyk, Clare, Gecz, Jozef, Farrugia, Daniel, Osei-Owusu, Ikeoluwa, Adès, Lesley, Boogaard, Marie-Jose, Fuchs, Sabine, Bakker, Jeroen, Duran, Karen, Dawson, Zachary D, Lindsey, Anika, Huang, Huiyan, Baldridge, Dustin, Silverman, Gary A, Grant, Barth D, Raizen, David, Network, Undiagnosed Diseases, Haaften, Gijs, Pak, Stephen C, Rehmann, Holger, Schedl, Tim, and van Hasselt, Peter

Published
2023

14. Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases

Author

Dharmadhikari, Avinash V., Ghosh, Rajarshi, Yuan, Bo, Liu, Pengfei, Dai, Hongzheng, Al Masri, Sami, Scull, Jennifer, Posey, Jennifer E., Jiang, Allen H., He, Weimin, Vetrini, Francesco, Braxton, Alicia A., Ward, Patricia, Chiang, Theodore, Qu, Chunjing, Gu, Shen, Shaw, Chad A., Smith, Janice L., Lalani, Seema, Stankiewicz, Pawel, Cheung, Sau-Wai, Bacino, Carlos A., Patel, Ankita, Breman, Amy M., Wang, Xia, Meng, Linyan, Xiao, Rui, Xia, Fan, Muzny, Donna, Gibbs, Richard A., Beaudet, Arthur L., Eng, Christine M., Lupski, James R., Yang, Yaping, and Bi, Weimin

Published
2019
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15. Correction to: De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith–Magenis syndrome

Author

Vetrini, Francesco, McKee, Shane, Rosenfeld, Jill A., Suri, Mohnish, Lewis, Andrea M., Nugent, Kimberly Margaret, Roeder, Elizabeth, Littlejohn, Rebecca O., Holder, Sue, Zhu, Wenmiao, Alaimo, Joseph T., Graham, Brett, Harris, Jill M., Gibson, James B., Pastore, Matthew, McBride, Kim L., Komara, Makanko, Al-Gazali, Lihadh, Al Shamsi, Aisha, Fanning, Elizabeth A., Wierenga, Klaas J., Scott, Daryl A., Ben-Neriah, Ziva, Meiner, Vardiella, Cassuto, Hanoch, Elpeleg, Orly, Lloyd Holder Jr, J., Burrage, Lindsay C., Seaver, Laurie H., Van Maldergem, Lionel, Mahida, Sonal, Soul, Janet S., Marlatt, Margaret, Matyakhina, Ludmila, Vogt, Julie, Gold, June-Anne, Park, Soo-Mi, Varghese, Vinod, Lampe, Anne K., Kumar, Ajith, Lees, Melissa, Holder-Espinasse, Muriel, McConnell, Vivienne, Bernhard, Birgitta, Blair, Ed, Harrison, Victoria, The DDD study, Muzny, Donna M., Gibbs, Richard A., Elsea, Sarah H., Posey, Jennifer E., Bi, Weimin, Lalani, Seema, Xia, Fan, Yang, Yaping, Eng, Christine M., Lupski, James R., and Liu, Pengfei

Published
2019
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16. De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith–Magenis syndrome

Author

Vetrini, Francesco, McKee, Shane, Rosenfeld, Jill A., Suri, Mohnish, Lewis, Andrea M., Nugent, Kimberly Margaret, Roeder, Elizabeth, Littlejohn, Rebecca O., Holder, Sue, Zhu, Wenmiao, Alaimo, Joseph T., Graham, Brett, Harris, Jill M., Gibson, James B., Pastore, Matthew, McBride, Kim L., Komara, Makanko, Al-Gazali, Lihadh, Al Shamsi, Aisha, Fanning, Elizabeth A., Wierenga, Klaas J., Scott, Daryl A., Ben-Neriah, Ziva, Meiner, Vardiella, Cassuto, Hanoch, Elpeleg, Orly, Holder, Jr, J. Lloyd, Burrage, Lindsay C., Seaver, Laurie H., Van Maldergem, Lionel, Mahida, Sonal, Soul, Janet S., Marlatt, Margaret, Matyakhina, Ludmila, Vogt, Julie, Gold, June-Anne, Park, Soo-Mi, Varghese, Vinod, Lampe, Anne K., Kumar, Ajith, Lees, Melissa, Holder-Espinasse, Muriel, McConnell, Vivienne, Bernhard, Birgitta, Blair, Ed, Harrison, Victoria, The DDD study, Muzny, Donna M., Gibbs, Richard A., Elsea, Sarah H., Posey, Jennifer E., Bi, Weimin, Lalani, Seema, Xia, Fan, Yang, Yaping, Eng, Christine M., Lupski, James R., and Liu, Pengfei

Published
2019
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17. P433: A novel deep intronic variant in DYNC2H1 characterized through exome reanalysis in a neonate with short-rib thoracic dysplasia type III

Author

Buchh, Muqsit, primary, Gillespie, Patrick, additional, Treat, Kayla, additional, Abreu, Marco, additional, Schwantes-An, Tae-Hwi, additional, Helm, Benjamin, additional, Fang, Fang, additional, Xuei, Xaoling, additional, Mantcheva, Lili, additional, Suhrie, Kristen, additional, Graham, Brett, additional, Conboy, Erin, additional, and Vetrini, Francesco, additional

Published
2023
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19. Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features

Author

Zhang, Jing, Gambin, Tomasz, Yuan, Bo, Szafranski, Przemyslaw, Rosenfeld, Jill A., Balwi, Mohammed Al, Alswaid, Abdulrahman, Al-Gazali, Lihadh, Shamsi, Aisha M. Al, Komara, Makanko, Ali, Bassam R., Roeder, Elizabeth, McAuley, Laura, Roy, Daniel S., Manchester, David K., Magoulas, Pilar, King, Lauren E., Hannig, Vickie, Bonneau, Dominique, Denommé-Pichon, Anne-Sophie, Charif, Majida, Besnard, Thomas, Bézieau, Stéphane, Cogné, Benjamin, Andrieux, Joris, Zhu, Wenmiao, He, Weimin, Vetrini, Francesco, Ward, Patricia A., Cheung, Sau Wai, Bi, Weimin, Eng, Christine M., Lupski, James R., Yang, Yaping, Patel, Ankita, Lalani, Seema R., Xia, Fan, and Stankiewicz, Paweł

Published
2017
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20. Characterization of a novel deep-intronic variant inDYNC2H1identified by whole-exome sequencing in a patient with a lethal form of a short-rib thoracic dysplasia type III

Author

Buchh, Muqsit, primary, Gillespie, Patrick J., additional, Treat, Kayla, additional, Abreu, Marco A., additional, Schwantes-An, Tae-Hwi Linus, additional, Helm, Benjamin M., additional, Fang, Fang, additional, Xuei, Xiaoling, additional, Mantcheva, Lili, additional, Suhrie, Kristen R., additional, Graham, Brett H., additional, Conboy, Erin, additional, and Vetrini, Francesco, additional

Published
2022
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21. Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder

Author

Normand, Elizabeth A., Braxton, Alicia, Nassef, Salma, Ward, Patricia A., Vetrini, Francesco, He, Weimin, Patel, Vipulkumar, Qu, Chunjing, Westerfield, Lauren E., Stover, Samantha, Dharmadhikari, Avinash V., Muzny, Donna M., Gibbs, Richard A., Dai, Hongzheng, Meng, Linyan, Wang, Xia, Xiao, Rui, Liu, Pengfei, Bi, Weimin, Xia, Fan, Walkiewicz, Magdalena, Van den Veyver, Ignatia B., Eng, Christine M., and Yang, Yaping

Published
2018
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22. Erratum to: Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features

Author

Zhang, Jing, Gambin, Tomasz, Yuan, Bo, Szafranski, Przemyslaw, Rosenfeld, Jill A., Balwi, Mohammed Al, Alswaid, Abdulrahman, Al-Gazali, Lihadh, Shamsi, Aisha M. Al, Komara, Makanko, Ali, Bassam R., Roeder, Elizabeth, McAuley, Laura, Roy, Daniel S., Manchester, David K., Magoulas, Pilar, King, Lauren E., Hannig, Vickie, Bonneau, Dominique, Denommé-Pichon, Anne-Sophie, Charif, Majida, Besnard, Thomas, Bézieau, Stéphane, Cogné, Benjamin, Andrieux, Joris, Zhu, Wenmiao, He, Weimin, Vetrini, Francesco, Ward, Patricia A., Cheung, Sau Wai, Bi, Weimin, Eng, Christine M., Lupski, James R., Yang, Yaping, Patel, Ankita, Lalani, Seema R., Xia, Fan, and Stankiewicz, Paweł

Published
2017
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24. eP410: De novo missense variants in DDX39B cause a novel syndrome characterized by neurodevelopmental delay, short stature and congenital hypotonia

Author

Treat, Kayla, primary, Jangam, Sharayu, additional, Yamamoto, Shinya, additional, White, Kerry, additional, Kanca, Oguz, additional, Christensen, Celanie, additional, Lynch, Sally, additional, Baptista, Julia, additional, Tsang, Mandy HY., additional, Jay, Kristy, additional, Chung, Brian HY., additional, Yuen, Liz YP., additional, Chui, Martin MC., additional, Bellen, Hugo, additional, Wangler, Michael, additional, Conboy, Erin, additional, and Vetrini, Francesco, additional

Published
2022
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26. TFEB Links Autophagy to Lysosomal Biogenesis

Author

Settembre, Carmine, Di Malta, Chiara, Polito, Vinicia Assunta, Arencibia, Moises Garcia, Vetrini, Francesco, Erdin, Serkan, Erdin, Serpil Uckac, Huynh, Tuong, Medina, Diego, Colella, Pasqualina, Sardiello, Marco, Rubinsztein, David C., and Ballabio, Andrea

Published
2011
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29. Characterization of a novel deep-intronic variant in DYNC2H1 identified by whole-exome sequencing in a patient with a lethal form of a short-rib thoracic dysplasia type III.

Author

Buchh, Muqsit, Gillespie, Patrick J., Treat, Kayla, Abreu, Marco A., Schwantes-An, Tae-Hwi Linus, Helm, Benjamin M., Fang Fang, Xiaoling Xuei, Mantcheva, Lili, Suhrie, Kristen R., Graham, Brett H., Conboy, Erin, and Vetrini, Francesco

Subjects
EXOMES, DYSPLASIA, NEONATAL intensive care, PRENATAL diagnosis, HYDRONEPHROSIS, PATENT foramen ovale
Abstract

Biallelic pathogenic variants in DYNC2H1 are the cause of short-rib thoracic dysplasia type III with or without polydactyly (OMIM #613091), a skeletal ciliopathy characterized by thoracic hypoplasia due to short ribs. In this report, we review the case of a patient who was admitted to the Neonatal Intensive Care Unit (NICU) of Indiana University Health (IUH) for respiratory support after experiencing respiratory distress secondary to a small, narrow chest causing restrictive lung disease. Additional phenotypic features include postaxial polydactyly, short proximal long bones, and ambiguous genitalia were noted. Exome sequencing (ES) revealed a maternally inherited likely pathogenic variant c.10322C > T p.(Leu3448Pro) in the DYNC2H1 gene. However, therewas no variant found on the paternal allele. Microarray analysis to detect deletion or duplication in DYNC2H1 was normal. Therefore, there was insufficient evidence to establish a molecular diagnosis. To further explore the data and perform additional investigations, the patient was subsequently enrolled in the Undiagnosed Rare Disease Clinic (URDC) at Indiana University School of Medicine (IUSM). The investigators at the URDC performed a reanalysis of the ES raw data, which revealed a paternally inherited DYNC2H1 deep-intronic variant c.10606-14A >Gpredicted to create a strong cryptic acceptor splice site. Additionally, the RNA sequencing of fibroblasts demonstrated partial intron retention predicted to cause a premature stop codon and nonsense- mediated mRNA decay (NMD). Droplet digital RT-PCR (RT-ddPCR) showed a drastic reduction by 74% of DYNCH2H1 mRNA levels. As a result, the intronic variant was subsequently reclassified as likely pathogenic resulting in a definitive clinical and genetic diagnosis for this patient. Reanalysis of ES and fibroblast mRNA experiments confirmed the pathogenicity of the splicing variants to supplement critical information not revealed in original ES or CMA reports. The NICU and URDC collaboration ended the diagnostic odyssey for this family; furthermore, its importance is emphasized by the possibility of prenatally diagnosing the mother's current pregnancy. [ABSTRACT FROM AUTHOR]

Published
2022
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30. Gene transfer of master autophagy regulator TFEB results in clearance of toxic protein and correction of hepatic disease in alpha‐1‐anti‐trypsin deficiency

Author

Pastore, Nunzia, Blomenkamp, Keith, Annunziata, Fabio, Piccolo, Pasquale, Mithbaokar, Pratibha, Maria Sepe, Rosa, Vetrini, Francesco, Palmer, Donna, Ng, Philip, Polishchuk, Elena, Iacobacci, Simona, Polishchuk, Roman, Teckman, Jeffrey, Ballabio, Andrea, and Brunetti‐Pierri, Nicola

Published
2013
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31. Characterization of Reference Materials with an Association for Molecular Pathology Pharmacogenetics Working Group Tier 2 Status: CYP2C9, CYP2C19, VKORC1, CYP2C Cluster Variant, and GGCX

Author

Pratt, Victoria M., primary, Turner, Amy, additional, Broeckel, Ulrich, additional, Dawson, D. Brian, additional, Gaedigk, Andrea, additional, Lynnes, Ty C., additional, Medeiros, Elizabeth B., additional, Moyer, Ann M., additional, Requesens, Deborah, additional, Vetrini, Francesco, additional, and Kalman, Lisa V., additional

Published
2021
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33. Prospective Molecular Characterization of Multiple Myeloma Patient Samples Identifies High-Risk Patients and Informs Treatment Sequences through Resistance Mechanisms to Immunotherapies

Author

Pham, Phillip, Sudha, Parvathi, Wang, Lin, Niu, Wen, Morgan, Cameron, Ligocki, Cameron, Al-Azzawi, Ramzi, Ly, Reynold, Vetrini, Francesco, Czader, Magdalena, Tayeh, Marwan, Abu Zaid, Mohammad, Lee, Kelvin P., Suvannasankha, Attaya, Abonour, Rafat, and Walker, Brian A.

Published
2023
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34. Further evidence of involvement of ITSN1 in autosomal dominant neurodevelopmental disorder.

Author

Liaqat, Khurram, Treat, Kayla, Wilson, Theodore E., Conboy, Erin, and Vetrini, Francesco

Subjects
NEURAL development, GUANINE nucleotide exchange factors, NUCLEOTIDE sequencing, AUTISM spectrum disorders
Abstract

This article discusses a case study of a 5-year-old male with autism spectrum disorder (ASD) and other neurodevelopmental disorders. The study identified a de novo pathogenic variant in the ITSN1 gene, which is associated with autosomal dominant neurodevelopmental disorders. The article highlights the importance of next-generation sequencing in understanding Mendelian neurodevelopmental conditions. The findings expand the genetic and phenotypic spectrum of autosomal dominant neurodevelopmental disorders and contribute to the limited clinical data available for ITSN1-related disorders. The study was funded by the Indiana University Grand Challenge Precision Health Initiative, and the authors declare no conflicts of interest. [Extracted from the article]

Published
2024
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35. Familial Autonomic Ganglionopathy Caused by Rare CHRNA3 Genetic Variants

Author

Shibao, Cyndya A., primary, Joos, Karen, additional, Phillips, John A., additional, Cogan, Joy, additional, Newman, John H., additional, Hamid, Rizwan, additional, Meiler, Jens, additional, Capra, John, additional, Sheehan, Jonathan, additional, Vetrini, Francesco, additional, Yang, Yaping, additional, Black, Bonnie, additional, Diedrich, André, additional, Roberston, David, additional, and Biaggioni, Italo, additional

Published
2021
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38. Characterization of Reference Materials for Spinal Muscular Atrophy Genetic Testing: A Genetic Testing Reference Materials Coordination Program Collaborative Project

Author

Prior, Thomas W., Bayrak-Toydemir, Pinar, Lynnes, Ty C., Mao, Rong, Metcalf, James D., Muralidharan, Kasinathan, Iwata-Otsubo, Aiko, Pham, Ha T., Pratt, Victoria M., Qureshi, Shumaila, Requesens, Deborah, Shen, Junqing, Vetrini, Francesco, and Kalman, Lisa

Subjects
DNA Copy Number Variations, Genotyping Techniques, Genetic Carrier Screening, Gene Dosage, Infant, Newborn, Genetic Counseling, Real-Time Polymerase Chain Reaction, Survival of Motor Neuron 1 Protein, Article, Cell Line, Muscular Atrophy, Spinal, Survival of Motor Neuron 2 Protein, Neonatal Screening, Phenotype, Humans, Alleles
Abstract

Spinal muscular atrophy (SMA) is an autosomal recessive disorder predominately caused by bi-allelic loss of the SMN1 gene. Increased copies of SMN2, a low functioning nearly identical paralog, are associated with a less severe phenotype. SMA was recently recommended for inclusion in newborn screening. Clinical laboratories must accurately measure SMN1 and SMN2 copy number to identify SMA patients and carriers, and to identify individuals likely to benefit from therapeutic interventions. Having publicly available and appropriately characterized reference materials with various combinations of SMN1 and SMN2 copy number variants is critical to assure accurate SMA clinical testing. To address this need, the CDC-based Genetic Testing Reference Materials Coordination Program, in collaboration with members of the genetic testing community and the Coriell Institute for Medical Research, has characterized 15 SMA reference materials derived from publicly available cell lines. DNA samples were distributed to four volunteer testing laboratories for genotyping using three different methods. The characterized samples had zero to four copies of SMN1 and zero to five copies SMN2. The samples also contained clinically important allele combinations (eg, zero copies SMN1, three copies SMN2), and several had markers indicative of an SMA carrier. These and other reference materials characterized by the Genetic Testing Reference Materials Coordination Program are available from the Coriell Institute and are proposed to support the quality of clinical laboratory testing.

Published
2020

39. Characterization of Reference Materials for Spinal Muscular Atrophy Genetic Testing

Author

Prior, Thomas W., primary, Bayrak-Toydemir, Pinar, additional, Lynnes, Ty C., additional, Mao, Rong, additional, Metcalf, James D., additional, Muralidharan, Kasinathan, additional, Iwata-Otsubo, Aiko, additional, Pham, Ha T., additional, Pratt, Victoria M., additional, Qureshi, Shumaila, additional, Requesens, Deborah, additional, Shen, Junqing, additional, Vetrini, Francesco, additional, and Kalman, Lisa, additional

Published
2021
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40. BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms

Author

Barish, Scott, primary, Barakat, Tahsin Stefan, additional, Michel, Brittany C., additional, Mashtalir, Nazar, additional, Phillips, Jennifer B., additional, Valencia, Alfredo M., additional, Ugur, Berrak, additional, Wegner, Jeremy, additional, Scott, Tiana M., additional, Bostwick, Brett, additional, Murdock, David R., additional, Dai, Hongzheng, additional, Perenthaler, Elena, additional, Nikoncuk, Anita, additional, van Slegtenhorst, Marjon, additional, Brooks, Alice S., additional, Keren, Boris, additional, Nava, Caroline, additional, Mignot, Cyril, additional, Douglas, Jessica, additional, Rodan, Lance, additional, Nowak, Catherine, additional, Ellard, Sian, additional, Stals, Karen, additional, Lynch, Sally Ann, additional, Faoucher, Marie, additional, Lesca, Gaetan, additional, Edery, Patrick, additional, Engleman, Kendra L., additional, Zhou, Dihong, additional, Thiffault, Isabelle, additional, Herriges, John, additional, Gass, Jennifer, additional, Louie, Raymond J., additional, Stolerman, Elliot, additional, Washington, Camerun, additional, Vetrini, Francesco, additional, Otsubo, Aiko, additional, Pratt, Victoria M., additional, Conboy, Erin, additional, Treat, Kayla, additional, Shannon, Nora, additional, Camacho, Jose, additional, Wakeling, Emma, additional, Yuan, Bo, additional, Chen, Chun-An, additional, Rosenfeld, Jill A., additional, Westerfield, Monte, additional, Wangler, Michael, additional, Yamamoto, Shinya, additional, Kadoch, Cigall, additional, Scott, Daryl A., additional, and Bellen, Hugo J., additional

Published
2020
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43. Systematic evaluation of genome sequencing for the assessment of fetal structural anomalies

Author

Lowther, Chelsea, primary, Valkanas, Elise, additional, Giordano, Jessica L., additional, Wang, Harold Z., additional, Currall, Benjamin B., additional, O’Keefe, Kathryn, additional, Pierce-Hoffman, Emma, additional, Kurtas, Nehir E., additional, Whelan, Christopher W., additional, Hao, Stephanie P., additional, Weisburd, Ben, additional, Jalili, Vahid, additional, Fu, Jack, additional, Wong, Isaac, additional, Collins, Ryan L., additional, Zhao, Xuefang, additional, Austin-Tse, Christina A., additional, Evangelista, Emily, additional, Lemire, Gabrielle, additional, Aggarwal, Vimla S., additional, Lucente, Diane, additional, Gauthier, Laura D., additional, Tolonen, Charlotte, additional, Sahakian, Nareh, additional, Stevens, Christine, additional, An, Joon-Yong, additional, Dong, Shan, additional, Norton, Mary E., additional, MacKenzie, Tippi, additional, Devlin, Bernie, additional, Gilmore, Kelly, additional, Powell, Bradford C., additional, Brandt, Alicia, additional, Vetrini, Francesco, additional, DiVito, Michelle, additional, Sanders, Stephan J., additional, MacArthur, Daniel G., additional, Hodge, Jennelle C., additional, O’Donnell-Luria, Anne, additional, Rehm, Heidi L., additional, Vora, Neeta L., additional, Levy, Brynn, additional, Brand, Harrison, additional, Wapner, Ronald J., additional, and Talkowski, Michael E., additional

Published
2020
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45. Complex Compound Inheritance of Lethal Lung Developmental Disorders due to Disruption of the TBX-FGF Pathway

Author

Karolak, Justyna A, Vincent, Marie, Deutsch, Gail, Gambin, Tomasz, Cogné, Benjamin, Pichon, Olivier, Vetrini, Francesco, Mefford, Heather C, Dines, Jennifer N, Golden-Grant, Katie, Dipple, Katrina, Freed, Amanda S, Leppig, Kathleen A, Dishop, Megan, Mowat, David, Bennetts, Bruce, Gifford, Andrew J, Weber, Martin A, Lee, Anna F, Boerkoel, Cornelius F, Bartell, Tina M, Ward-Melver, Catherine, Besnard, Thomas, Petit, Florence, Bache, Iben, Tümer, Zeynep, Denis-Musquer, Marie, Joubert, Madeleine, Martinovic, Jelena, Bénéteau, Claire, Molin, Arnaud, Carles, Dominique, André, Gwenaelle, Bieth, Eric, Chassaing, Nicolas, Devisme, Louise, Chalabreysse, Lara, Pasquier, Laurent, Secq, Véronique, Don, Massimiliano, Orsaria, Maria, Missirian, Chantal, Mortreux, Jérémie, Sanlaville, Damien, Pons, Linda, Küry, Sébastien, Bézieau, Stéphane, Liet, Jean-Michel, Joram, Nicolas, Bihouée, Tiphaine, Scott, Daryl A, Brown, Chester W, Scaglia, Fernando, Tsai, Anne Chun-Hui, Grange, Dorothy K, Phillips, John A, Pfotenhauer, Jean P, Jhangiani, Shalini N, Gonzaga-Jauregui, Claudia G, Chung, Wendy K, Schauer, Galen M, Lipson, Mark H, Mercer, Catherine L, van Haeringen, Arie, Liu, Qian, Popek, Edwina, Coban Akdemir, Zeynep H, Lupski, James R, Szafranski, Przemyslaw, Isidor, Bertrand, Le Caignec, Cedric, Stankiewicz, Paweł, Karolak, Justyna A, Vincent, Marie, Deutsch, Gail, Gambin, Tomasz, Cogné, Benjamin, Pichon, Olivier, Vetrini, Francesco, Mefford, Heather C, Dines, Jennifer N, Golden-Grant, Katie, Dipple, Katrina, Freed, Amanda S, Leppig, Kathleen A, Dishop, Megan, Mowat, David, Bennetts, Bruce, Gifford, Andrew J, Weber, Martin A, Lee, Anna F, Boerkoel, Cornelius F, Bartell, Tina M, Ward-Melver, Catherine, Besnard, Thomas, Petit, Florence, Bache, Iben, Tümer, Zeynep, Denis-Musquer, Marie, Joubert, Madeleine, Martinovic, Jelena, Bénéteau, Claire, Molin, Arnaud, Carles, Dominique, André, Gwenaelle, Bieth, Eric, Chassaing, Nicolas, Devisme, Louise, Chalabreysse, Lara, Pasquier, Laurent, Secq, Véronique, Don, Massimiliano, Orsaria, Maria, Missirian, Chantal, Mortreux, Jérémie, Sanlaville, Damien, Pons, Linda, Küry, Sébastien, Bézieau, Stéphane, Liet, Jean-Michel, Joram, Nicolas, Bihouée, Tiphaine, Scott, Daryl A, Brown, Chester W, Scaglia, Fernando, Tsai, Anne Chun-Hui, Grange, Dorothy K, Phillips, John A, Pfotenhauer, Jean P, Jhangiani, Shalini N, Gonzaga-Jauregui, Claudia G, Chung, Wendy K, Schauer, Galen M, Lipson, Mark H, Mercer, Catherine L, van Haeringen, Arie, Liu, Qian, Popek, Edwina, Coban Akdemir, Zeynep H, Lupski, James R, Szafranski, Przemyslaw, Isidor, Bertrand, Le Caignec, Cedric, and Stankiewicz, Paweł

Abstract

Primary defects in lung branching morphogenesis, resulting in neonatal lethal pulmonary hypoplasias, are incompletely understood. To elucidate the pathogenetics of human lung development, we studied a unique collection of samples obtained from deceased individuals with clinically and histopathologically diagnosed interstitial neonatal lung disorders: acinar dysplasia (n = 14), congenital alveolar dysplasia (n = 2), and other lethal lung hypoplasias (n = 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n = 8 and n = 2, respectively) or FGF10 (n = 2 and n = 2, respectively) in 16/26 (61%) individuals. In addition to TBX4, the overlapping ∼2 Mb recurrent and nonrecurrent deletions at 17q23.1q23.2 identified in seven individuals with lung hypoplasia also remove a lung-specific enhancer region. Individuals with coding variants involving either TBX4 or FGF10 also harbored at least one non-coding SNV in the predicted lung-specific enhancer region, which was absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. The occurrence of rare coding variants involving TBX4 or FGF10 with the putative hypomorphic non-coding SNVs implies a complex compound inheritance of these pulmonary hypoplasias. Moreover, they support the importance of TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling in human lung organogenesis and help to explain the histopathological continuum observed in these rare lethal developmental disorders of the lung.

Published
2019

46. Additional file 1: of Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder

Author

Normand, Elizabeth, Braxton, Alicia, Nassef, Salma, Ward, Patricia, Vetrini, Francesco, Weimin He, Vipulkumar Patel, Chunjing Qu, Westerfield, Lauren, Stover, Samantha, Dharmadhikari, Avinash, Muzny, Donna, Gibbs, Richard, Hongzheng Dai, Linyan Meng, Wang, Xia, Xiao, Rui, Pengfei Liu, Weimin Bi, Xia, Fan, Walkiewicz, Magdalena, Veyver, Ignatia Van Den, Eng, Christine, and Yaping Yang

Abstract

Figure S1. Comparison of proband versus trio exome workflows. Figure S2. Fetal sample types received and culturing time prior to prenatal exome sequencing. Figure S3. Referring practices. Table S1. Quality metrics of exome sequencing data of the fetal and parental samples. Table S2. Excluded samples without a final report. Table S3. Incidental findings reported for prenatal exome tests. Table S4. Reported fetal phenotypes. Table S5. Pairwise statistical analysis of diagnostic rate based on number of affected organ systems, corrected for multiple comparisons. Table S6. Regions of absence of heterozygosity (AOH) in cases with homozygous variants underlying the molecular diagnosis. Table S7. Pregnancy outcomes for locally referred cases. (PDF 8142 kb)

Published
2018
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47. An unusual cause for Coffin–Lowry syndrome: Three brothers with a novel microduplication in RPS6KA3

Author

Castelluccio, Valerie J., primary, Vetrini, Francesco, additional, Lynnes, Ty, additional, Jones, Julie, additional, Holloway, Lynda, additional, Belonis, Alyce, additional, Breman, Amy M., additional, Graham, Brett H., additional, Sapp, Katherine, additional, Wilson, Theodore, additional, Schwartz, Charles E., additional, Pratt, Victoria M., additional, and Weaver, David D., additional

Published
2019
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48. Abstract P176: Familial Autonomic Ganglionopathy Caused by Rare CHRNA3 Genetic Variants. Novel Genetic Cause of Neurogenic Orthostatic Hypotension

Author

Shibao, Cyndya A, primary, Phillips, John, additional, Cogan, Joy D, additional, Newman, John H, additional, Hamid, Rizwan, additional, Meiler, Jens, additional, Capra, John A, additional, Sheehan, Jonathan, additional, Yan, Yaping, additional, Vetrini, Francesco, additional, Black, Bonnie, additional, Joos, Karen, additional, Robertson, David, additional, and Biaggioni, Italo, additional

Published
2019
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49. Reanalysis of Clinical Exome Sequencing Data

Author

Liu, Pengfei, primary, Meng, Linyan, additional, Normand, Elizabeth A., additional, Xia, Fan, additional, Song, Xiaofei, additional, Ghazi, Andrew, additional, Rosenfeld, Jill, additional, Magoulas, Pilar L., additional, Braxton, Alicia, additional, Ward, Patricia, additional, Dai, Hongzheng, additional, Yuan, Bo, additional, Bi, Weimin, additional, Xiao, Rui, additional, Wang, Xia, additional, Chiang, Theodore, additional, Vetrini, Francesco, additional, He, Weimin, additional, Cheng, Hanyin, additional, Dong, Jie, additional, Gijavanekar, Charul, additional, Benke, Paul J., additional, Bernstein, Jonathan A., additional, Eble, Tanya, additional, Eroglu, Yasemen, additional, Erwin, Deanna, additional, Escobar, Luis, additional, Gibson, James B., additional, Gripp, Karen, additional, Kleppe, Soledad, additional, Koenig, Mary K., additional, Lewis, Andrea M., additional, Natowicz, Marvin, additional, Mancias, Pedro, additional, Minor, LaKeesha, additional, Scaglia, Fernando, additional, Schaaf, Christian P., additional, Streff, Haley, additional, Vernon, Hilary, additional, Uhles, Crescenda L., additional, Zackai, Elaine H., additional, Wu, Nan, additional, Sutton, V. Reid, additional, Beaudet, Arthur L., additional, Muzny, Donna, additional, Gibbs, Richard A., additional, Posey, Jennifer E., additional, Lalani, Seema, additional, Shaw, Chad, additional, Eng, Christine M., additional, Lupski, James R., additional, and Yang, Yaping, additional

Published
2019
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50. Cover Image, Volume 40, Issue 3

Author

Rehman, Atteeq U., primary, Najafi, Maryam, additional, Kambouris, Marios, additional, Al-Gazali, Lihadh, additional, Makrythanasis, Periklis, additional, Rad, Abolfazl, additional, Maroofian, Reza, additional, Rajab, Anna, additional, Stark, Zornitza, additional, Hunter, Jill V., additional, Bakey, Zeineb, additional, Tokita, Mari J., additional, He, Weimin, additional, Vetrini, Francesco, additional, Petersen, Andrea, additional, Santoni, Federico A., additional, Hamamy, Hanan, additional, Wu, Kaman, additional, Al-Jasmi, Fatma, additional, Helmstädter, Martin, additional, Arnold, Sebastian J., additional, Xia, Fan, additional, Richmond, Christopher, additional, Liu, Pengfei, additional, Karimiani, Ehsan Ghayoor, additional, Karami Madani, GholamReza, additional, Lunke, Sebastian, additional, El-Shanti, Hatem, additional, Eng, Christine M., additional, Antonarakis, Stylianos E., additional, Hertecant, Jozef, additional, Walkiewicz, Magdalena, additional, Yang, Yaping, additional, and Schmidts, Miriam, additional

Published
2019
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