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2. The challenges and opportunities of offering and integrating training in clinical molecular genetics and clinical cytogenetics: A survey of LGG Fellowship Program Directors.

Author

Deignan, Joshua, Aggarwal, Vimla, Bale, Allen, Bellissimo, Daniel, Booker, Jessica, Cao, Yang, Crooks, Kristy, Deak, Kristen, Del Gaudio, Daniela, Funke, Birgit, Hoppman, Nicole, Horner, Vanessa, Hufnagel, Robert, Jackson-Cook, Colleen, Koduru, Prasad, Leung, Marco, Li, Shibo, Liu, Pengfei, Luo, Minjie, Mao, Rong, Mason-Suares, Heather, Mikhail, Fady, Moore, Stephen, Naeem, Rizwan, Pollard, Laura, Repnikova, Elena, Shao, Lina, Shaw, Brandon, Shetty, Shashirekha, Smolarek, Teresa, Spiteri, Elizabeth, Van Ziffle, Jessica, Vance, Gail, Vnencak-Jones, Cindy, and Williams, Eli

Subjects
ACGME, Cytogenetics, Fellowship, Molecular genetics, Training
Abstract

PURPOSE: The specialty of Laboratory Genetics and Genomics (LGG) was created in 2017 in an effort to reflect the increasing convergence in technologies and approaches between clinical molecular genetics and clinical cytogenetics. However, there has not yet been any formal evaluation of the merging of these disciplines and the challenges faced by Program Directors (PDs) tasked with ensuring the successful training of laboratory geneticists under the new model. METHODS: An electronic multi-question Qualtrics survey was created and was sent to the PD for each of the Accreditation Council for Graduate Medical Education-accredited LGG fellowship programs at the time. The data were collected, and the responses were aggregated for each question. RESULTS: All of the responding PDs had started training at least 1 LGG fellow. PDs noted challenges with funding, staff shortages, molecular/cytogenetics content integration, limited total training time, increased remote work, increased sendout testing, and a lack of prior cytogenetics knowledge among incoming fellows. CONCLUSION: This survey attempted to assess the challenges that LGG PDs have been facing in offering and integrating clinical molecular genetics and clinical cytogenetics fellowship training. Common challenges between programs were noted, and a set of 6 concluding comments are provided to facilitate future discussion.

Published
2024

7. Efficacy and safety of aldosterone synthase inhibition with and without empagliflozin for chronic kidney disease: a randomised, controlled, phase 2 trial

Author

Tuttle, Katherine R, Hauske, Sibylle J, Canziani, Maria Eugenia, Caramori, Maria Luiza, Cherney, David, Cronin, Lisa, Heerspink, Hiddo J L, Hugo, Christian, Nangaku, Masaomi, Rotter, Ricardo Correa, Silva, Arnold, Shah, Shimoli V, Sun, Zhichao, Urbach, Dorothea, de Zeeuw, Dick, Rossing, Peter, SZETO, Cheuk Chun, Echeverri, Diego, Martin, Edouard, Yee, Ming Li, Wah, William, Wang, Ray, Chacko, Bobby, Swaminathan, Shriram, MacIsaac, Richard, Hashimura, Hikaru, Ward, Glenn, De Vusser, Katrien, Claes, Kathleen, Kuypers, Dirk, Meijers, Björn, Van Craenenbroeck, Amaryllis, Hilbrands, Robert, Debroye, Corinne, Wissing, Karl Martin, Jadoul, Michel, Demoulin, Nathalie, Treille De Grandsaigne, Serge, Beklevic, Ishak, Marcoux, Diane, Liénart, Fabienne, Daper, Claude, De Brouckere, Véronique, Heureux, Mercédès, Felicio, Joao, Felicio, Karem Mileo, Leite, Daniella, Melo, Franciane, Queiroz, Natercia, Souza, Ana Carolina, Vieira, Jocyelle, Franco, Roberto, Mendes, Adriana, Picolli, Giovana, Canani, Luis Henrique, Sartori, Carla, Valenti, Adriana, Eliaschewitz, Freddy, Bona, Renata, Franco, Denise, Ludovico Costa de Castro, Denise, Magalhaes, Vanessa, Oliveira, Marcelo, Sampaio, Célia Regina, Visconti, Guilherme, Halpern, Bruno, Nihei, Camila, Pessoa, Bruna, Seraphim, Carlos, Santos, Daniel, Brito, Claudia, Douverny, Joao, Colella, Marina, Gazeta, Cristina, Vercia, Monique, Watanabe, Renato, Temelkova, Theodora, Kjurkchiev, Dimo, Statkova, Silviya, Popov, Iliya, Radeva, Radosveta, Arabadzhiev, Lachezar, Binova, Mariya, Bosilkov, Aleksandar, Koleva-Stoicheva, Neli, Ivanov, Ivaylo, Ivanova, Zornitsa, Kotseva, Viktoria, Spasov, Petar, Tsvetkov, Ivaylo, Jolly, Shivinder, Bailey, Gordon, Ye, Zhiming, Niu, Jianying, Li, Hongmei, Wu, Qing, Liao, Bing, Hao, Chuanming, Lai, Lingyun, Xu, Yunyu, Zhang, Min, Li, Yiwen, Liu, Bo, Shao, Lina, Chen, Wei, Wu, Haishan, Pirchala, Marian, Skarpova, Iva, Hraskova, Marketa, Soukupova, Simoneta, Veberova, Lucie, Drasnar, Tomas, Falc, Matej, Racz, Blazej, Votocek, Stepan, Weissova, Danica, Syc-Krivanova, Lenka, Slezak, Dagmar, Kantola, Ilkka, Nieminen, Sakari, Anttonen, Milla, Taurio, Jyrki, Lahtela, Jorma, Tsimihodimos, Vasileios, Balafa, Olga, Dounousi, Evangelia, Sakkou, Sissy, Tentolouris, Nikolaos, Siafarikas, Christos, Siami, Evangelia, Doupis, Ioannis, Angelopoulos, Theodoros, Georgoulias, Christodoulos, Pall, Denes, Esze, Regina, Kobling, Tamas, Varadi, Zita, Zsiros, Noemi, Vass, Viktor, Balo, Timea, Csanyi, Erika, Ory, Ivan, Pall, Istvan, Patai, Valentina, Zeak, Zsuzsanna, Takacs, Istvan, Petho, Akos, Szili, Balazs, Koranyi, Laszlo, Bezzegh, Katalin, Pauer, Jozsef, Peterfai, Eva, Konyves, Laszlo, Szoke, Brigitta, Hajdu, Csaba, Kalman, Krisztina, Yadav, Raj, Saxena, Navneet, Bhattacharya, Meenakshi, Sharma, Bal, Thomas, Nihal, K, Felix Jebasingh, Kapoor, Nitin, Kurian, Mathews E., Paul, Jinson, Ramesh, Priyadharshini, Varghese, Sheeba, Shibusawa, Nobuyuki, Nishi, Hiroshi, Noritake, Nobuyasu, Oda, Takashi, Okamoto, Hideki, Kasuga, Hirotake, Hori, Hiroshi, Ito, Yukiko, Mizukoshi, Toshihiro, Ishii, Hideto, Han, Seung Hyeok, Kim, Hyung Woo, Oh, Kook-Hwan, Han, Seung Seok, Han, Sang Youb, Cha, Dae Ryong, Cha, Jin Joo, Kwon, Soon-Kil, Cho, Hyunjeong, Kim, Hye-Young, Kim, Sun Moon, Lee, Jung Pyo, Lee, Jeonghwan, Lee, Li Yuan, Chang, Meng Lee, Laang, Shian Tuck, Tan, Zhao Zhi, Ahmad Rosdi, Hajar, Mohammad Ismail, Siti Hafizah, Simatherai, Devamalar, Tay, Ju Fan, Wong, Eddie, Fook Sem, Yakob, Suryati, Abdul Sukur, Noorhafini, Anuar, Amalina, Md. Rasid, Syaliza, Mushaddik, Irma Liyana, Mustafar, Ruslinda, Abu Shamsi, Muhammad Yusuf, Fong, Voon Ken, Kamaruzaman, Lydia, Mohd, Rozita, Wan Daud, Wan Rohaslizan, Wan Hassan, Wan Hasnul Halimi, Ab Hamid, Suhaidarwani, Abdullah, Muhammad Nabil, Yusoff, Mohd Yusran, Ramanathan, G R Letchuman, Lee, Kim Yen, Wan Ismail, Wan Fadhilah, Morales Villegas, Enrique, Ramirez Baez, Rubria, Vital Lopez, Jorge, Arias Delgadillo, Cristhian, Herrera Marmolejo, Marisol, Parra Perez, Rosa, Alpizar Salazar, Melchor, Flores Montealegre, Ana, Galvan Magaña, Jose, Gutierrez Tlapale, Minerva, Reyes Munguia, Daniela, Witczak, Bartlomiej, Gøransson, Lasse, Strand Thorsen, Inga, Caringal, Clodoaido, Villardo, Mario, Toledo, Ronaldo, Dijamco, Emerlinda Fausto, De Asis, Norman Cornelio, Kuizon, Angelica, Catindig, Elizabeth Ann, Perez, Ronald, Aquitania, Grace, Pableo, Jimrie David, Sanchez, Jay Karlou, Czernecka, Ewa, Cegiel, Aleksandra, Knychas, Dorota, Ochnio, Malgorzata, Kuligowska-Jakubowska, Monika, Cesarz, Marek, Kowalewska-Celejewska, Milena, Masajtis-Zagajewska, Anna, Jankowski, Lukasz, Ojrzanowski, Marcin, Olszewska-Jander, Magdalena, Skokowska, Ewa, Giermakowska-Samek, Malgorzata, Luchowska, Elzbieta, Patkowska, Renata, Sekulska, Marzenna, Marczuk-Krynicka, Dorota, Marciniak, Andrzej, Barwijuk, Michal, Myslicki, Marcin, Siek, Michal, Wronska, Danuta, Tomsia-Goncerz, Jadwiga, Wronski, Krzysztof, Junik, Roman, Dzialak, Szymon, Kurlapska, Ewelina, Malecha, Wieslaw, Suwala, Szymon, Branco, Patrícia, Birne, Rita, Raposo, João, Ferreira, Marta, Alexandrino, Henrique, Alves, Helena, Correia, Sara, Oliveira, Maria João, Ramalho, Diogo, Tavares, Patricia, Coetzee, Kathleen, Blignaut, Sue, Viljoen, Winifred, Potgieter, Elsje, Malherbe, Elmien, Ortiz Arduán, Alberto, Goma Garcés, Elena, Pérez, María, Santamaría, Rafael, López López, Isabel, Pendón de Mier, Victoria, Rodelo Haad, Cristian, Marques, María, Domènech, Esther, Portoles, Josep Maria, Soler, María José, Agraz, Irene, Azancot, María Antonieta, Bermejo, Sheila, Bolufer, Mónica, López, Marina, Ramos, Natalia, Toapanta, Néstor, Cigarrán Guldris, Secundino, Primo, Juan Carlos, Pérez, Luis Enrique, Rebollido Fernández, María, Holmer, Helene, Bruchfeld, Annette, Rofors, Justus, Tengmark, Bengt-Olov, Wuerzner, Gregoire, Leanizbarrutia, Garazi, Ozturk, Savas, Guler, Nurana, Safak, Seda, Lee, Keung, Campbell, Stephen, Siddiqui, Imran, Abbasi, Nadia, Tahir, Faiza, Azizad, Masoud, Jackson, Timothy, Everhart, Brian, Oliver, Michael, Rust, William, Sniezek, Matthew, Arif, Ahmed, Syed, Mohammed, Bhasin, Nitin, Bien, Michael, Gallego, Claudio, Jamal, Aamir, Moghadam, Mojtaba, Rizvi, Abid, Rizvi, Amna, Rizvi, Syed, Wong, Christopher, Lucas, Kathryn, Buery, Andrea, Chang, Ku-Lang, Presswood, Claire, Smith, Justin, Doshi, Ankur, Parikh, Manish, Wallace, Jeannine, Krishna, Arvind, Daugherty, Heidi, Fearday, Aaron, Keller, Christopher, Meng, Jerry, Nielsen, Alexandra, Rovner, Sergio, Almeida, Javier, Marranzini, Benito, Selby, Lisa, Yablon, Zachary, Jean-Louis, Daphne, Kotzker, Wayne, Perez, Chabely, Richards, Marc, Rosario, Reinaldo, Marcus, Roy, Okechukwu, Chike, Ross, Dennis, Gromala, Rachel, Reed, Matthew, Weber, Lisa, Nazeer, Imran, Kumar, Prashant, Mir, Muhammad, Shea, Heidi, Hart, Amanda, Wiebel, Jaime, Kooienga, Laura, Newsome, Britt, Suyumova, Irina, Alvarez, German, Bireddy, Venkata, Lansang, Maria, Mandry, Jose, Freire, Maria, Herrera Albornoz, Oscarina, Desai, Anant, Gandhi, Dayan, Rajan, Sibu, Raymond, Louis, Posada, Jorge, Garcia-Mayol, Luis, Gutierrez-Alsina, Rodolfo, Fernandez, Juan, Bruce, Kendaling, Cuellar, Juan, Ranz y Alvarez, Maria, Bartolacci, Ines, Pautasso, Mauro, Stoppa, Daniela, Riella, Miguel, Barbosa, Maria, Harcsa, Eleonora, Gulati, Yuvraj, Savalia, Denish, Khetan, Prakash, Sinha, Dhananjay, R, Niranjan, K, Srinivas, Pazos, Fabiola, Gacutan-Liwag, Aretha, Duszynska, Malgorzata, Antkowiak-Piatyszek, Karolina, Konieczny, Grzegorz, Sidorowicz-Bialynicka, Anna, Ciesiolkiewicz-Wojcik, Agnieszka, Dwojak, Marek, Szymkowiak, Katarzyna, Gorczyca-Siudak, Daria, Janik-Palazzolo, Marzena, Siudak, Lukasz, Opiela, Jaroslaw, Iwanow, Dariusz, Solkiewicz, Monika, Sipinska-Surzynska, Malgorzata, Olszanecka - Glinianowicz, Magdalena, Rozmilowska, Izabela, Trokis, Julian, Prozesky, Hans, Burgess, Lesley, Cyster, Henry, Jordaan, Jurie, Mohamed, Hawa, Naude, Christina, Sitsila, Thembie, Mehta, Arvind, Mocherla, Bharat, Lee, Sungchun, Boren, Kenneth, Rudolph, Lance, Benjamin, Sabrina, Sugimoto, Danny, Hammoud, Jamal, Bakleh, Muhammad, Hashish, Yaseen, Da Costa, Jonathan, Gold, Marina, Majul, Claudio, Buscema, Juan, Gatto, Maria, Lombardi, Facundo, Paez, Olga, Puleio, Pablo, Alvarisqueta, Andrés, Pajon, Vanessa, Suarez, Gabriel, Hernandez Gauna, Adrian, Pereyra, Alejandro, Reig, Moira, Gelersztein, Elizabeth, Campestri, Gina, Gonzalez Santos, Maria, Sambresqui, Julieta, Catalano, Gustavo, Igarzabal, Cecilia, Vallejos, Augusto, Escobari, Claudio, Marchetto, Rocio, Chahin, Mariano, Aguilera, Andrea, Comes, Ana, Rodriguez Segade, Silvia, Baccaro, Claudia, Larrieu Lacoste, María Verónica, Saurral, Ruben, Cristino, Alberto, Dran, Dario, Koretzky, Martin, Ponti, Juan, Porto, Alejandro, Tenaglia, Yasmin, Maldonado, Natacha, Bertollo, Natalia, Van Perdeck, Verónica, Lopau, Kai, Wanner, Christoph, Berfelo, Florieke, Contzen, Christel, Arbi, Abdulwahab, Lee-Barkey, Young Hee, Maciejewska, Aleksandra, Arelin, Katrin, Haller, Hermann, Kaufeld, Jessica, Schmidt-Ott, Kai, Heinrichs, Sven, Krüger, Thilo, Gebauer, Chris, Paliege, Alexander, Henkel, Elena, Axthelm, Christoph, Derwahl, Karl-Michael, Trevisan, Roberto, Bellante, Rosalia, Borrella, Nicolò, Corsi, Anna, Gesualdo, Loreto, Ardillo, Teodora, Ficarella, Maria, Fikry, Sameh, Mazza, Giuseppe, Poirier, Lysane, Bajaj, Harpreet, Hatziagelaki, Erifili, Katopodis, Sokratis, Katsoudas, Spiros, Yamaura, Shuichi, Shikano, Tsutomu, Tosaki, Takahiro, Miho, Otoya, Tachibana, Naoki, Yumita, Wataru, Kado, Hiroshi, Villarreal Martinez, Jesus, Soto Miranda, Ernesto, Gonzalez Rodriguez, David, Panelo, Araceli, Santos, Telma, Martins, Ana, Mateus, Catarina, Teixeira e Costa, Fernando, Barreto, Sara, Silva Costa, Joana, Ferrer, Francisco, Silva, Joana, Awad, Ahmed, Khaleel, Shatha, Lustig, Ryan, Maharjan, Gajendra, Moya, Jaynier, Johnsingh, Amit, Acosta, Idalia, Newman, George, Buckle, Anita, and Hendon, Kendra

Published
2024
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8. The challenges and opportunities of offering and integrating training in clinical molecular genetics and clinical cytogenetics: A survey of LGG Fellowship Program Directors

Author

Deignan, Joshua L., Aggarwal, Vimla, Bale, Allen E., Bellissimo, Daniel B., Booker, Jessica K., Cao, Yang, Crooks, Kristy R., Deak, Kristen L., Del Gaudio, Daniela, Funke, Birgit, Hoppman, Nicole L., Horner, Vanessa, Hufnagel, Robert B., Jackson-Cook, Colleen, Koduru, Prasad, Leung, Marco L., Li, Shibo, Liu, Pengfei, Luo, Minjie, Mao, Rong, Mason-Suares, Heather, Mikhail, Fady M., Moore, Stephen R., Naeem, Rizwan C., Pollard, Laura M., Repnikova, Elena A., Shao, Lina, Shaw, Brandon M., Shetty, Shashirekha, Smolarek, Teresa A., Spiteri, Elizabeth, Van Ziffle, Jessica, Vance, Gail H., Vnencak-Jones, Cindy L., and Williams, Eli S.

Published
2024
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13. TRIM63 is a sensitive and specific biomarker for MiT family aberration-associated renal cell carcinoma

Author

Wang, Xiao-Ming, Zhang, Yuping, Mannan, Rahul, Skala, Stephanie L., Rangaswamy, Roshni, Chinnaiyan, Anya, Su, Fengyun, Cao, Xuhong, Zelenka-Wang, Sylvia, McMurry, Lisa, Xiao, Hong, Spratt, Daniel E., Sangoi, Ankur R., Shao, Lina, Betz, Bryan L., Brown, Noah, Tickoo, Satish K., McKenney, Jesse K., Argani, Pedram, Gupta, Sounak, Reuter, Victor E., Chinnaiyan, Arul M., Dhanasekaran, Saravana M., and Mehra, Rohit

Published
2021
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15. Identification of hub lncRNAs in head and neck cancer based on weighted gene co‐expression network analysis and experiments

Author

Shao Lina

Subjects
head and neck cancer, risk score prognostic model, The Cancer Genome Atlas, WGCNA, Biology (General), QH301-705.5
Abstract

Head and neck squamous cell carcinoma (HNSCC) ranks as the sixth most common cancer among systemic malignant tumors, with 600 000 new cases occurring every year worldwide. Since HNSCC has high heterogeneity and complex pathogenesis, no effective prognostic indicator has yet been identified. Here, we aimed to identify a lncRNA signature associated with the prognosis of HNSCC as a potential new biomarker. LncRNA expression data were downloaded from The Cancer Genome Atlas database. A polygenic risk score model was constructed by using Lasso–Cox regression analysis. Weighted gene co‐expression network analysis (WGCNA) was applied to analyze the co‐expression modules of lncRNAs associated with the prognosis of HNSCC. The robustness of the signature was validated in testing and external cohorts. Polymerase chain reaction was performed to detect the expression levels of identified lncRNAs in cancer and adjacent tissues. We constructed an 8‐lncRNA signature (LINC00567, LINC00996, MTOR‐AS1, PRKG1‐AS1, RAB11B‐AS1, RPS6KA2‐AS1, SH3BP5‐AS1, ZNF451‐AS1) that could be used as an independent prognostic factor of HNSCC. The signature showed strong robustness and had stable prediction performance in different cohorts. WGCNA results showed that modules related to risk score mainly participated in biological processes such as blood vessel development, positive regulation of catabolic processes, and regulation of growth. The prognostic risk score model based on lncRNA for HNSCC may help clinicians conduct individualized treatment plans.

Published
2021
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19. Genetic reduction of cilium length by targeting intraflagellar transport 88 protein impedes kidney and liver cyst formation in mouse models of autosomal polycystic kidney disease

Author

Shao, Lina, El-Jouni, Wassim, Kong, Fanwu, Ramesh, Janani, Kumar, Radhe Shantha, Shen, Xiaogang, Ren, Jingjing, Devendra, Shruti, Dorschel, Arianna, Wu, Maoqing, Barrera, Ivan, Tabari, Azadeh, Hu, Kang, Haque, Nadeem, Yambayev, Ilyas, Li, Shiqi, Kumar, Amresh, Behera, Tapas Ranjan, McDonough, Gregory, Furuichi, Masahito, Xifaras, Michael, Lu, Tzongshi, Alhayaza, Rami Mohammad, Miyabayashi, Koji, Fan, Qiuling, Ajay, Amrendra K., and Zhou, Jing

Published
2020
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23. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

Author

Zheng, Siyuan, Cherniack, Andrew D, Dewal, Ninad, Moffitt, Richard A, Danilova, Ludmila, Murray, Bradley A, Lerario, Antonio M, Else, Tobias, Knijnenburg, Theo A, Ciriello, Giovanni, Kim, Seungchan, Assie, Guillaume, Morozova, Olena, Akbani, Rehan, Shih, Juliann, Hoadley, Katherine A, Choueiri, Toni K, Waldmann, Jens, Mete, Ozgur, Robertson, A Gordon, Wu, Hsin-Ta, Raphael, Benjamin J, Shao, Lina, Meyerson, Matthew, Demeure, Michael J, Beuschlein, Felix, Gill, Anthony J, Sidhu, Stan B, Almeida, Madson Q, Fragoso, Maria CBV, Cope, Leslie M, Kebebew, Electron, Habra, Mouhammed A, Whitsett, Timothy G, Bussey, Kimberly J, Rainey, William E, L., Sylvia, Bertherat, Jérôme, Fassnacht, Martin, Wheeler, David A, Network, The Cancer Genome Atlas Research, Verhaak, Roel GW, Giordano, Thomas J, Hammer, Gary D, Assié, Guillaume, Wu, Hsin-Tu, Almeida, Madson, Fragoso, Maria Candida Barisson, Habra, Mouhammed Amir, Benz, Christopher, Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Butterfield, Yaron SN, Carlsen, Rebecca, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A, Jones, Steven JM, Kasaian, Katayoon, Lee, Darlene, Li, Haiyan I, Lim, Lynette, Ma, Yussanne, and Marra, Marco A

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Human Genome, Cancer, Rare Diseases, Biotechnology, Clinical Research, Adolescent, Adrenal Cortex Neoplasms, Adrenocortical Carcinoma, Adult, Aged, Aged, 80 and over, Child, DNA Methylation, Disease-Free Survival, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Genetic Predisposition to Disease, Genome, Human, Genomics, Humans, Male, Middle Aged, Mutation, Outcome Assessment, Health Care, Prognosis, Young Adult, Cancer Genome Atlas Research Network, Neurosciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

We describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers.

Published
2016

25. Plasma D-dimer levels are associated with disease progression in diabetic nephropathy: a two-center cohort study

Author

Yu, Yedong, primary, Zhu, Caifeng, additional, Lin, Yi, additional, Qian, Qian, additional, Shen, Xiaogang, additional, Zou, Wenli, additional, Wang, Minmin, additional, Gong, Jianguang, additional, Chen, Maosheng, additional, Liu, Lin, additional, Yu, Rizhen, additional, Shen, Quanquan, additional, Shao, Lina, additional, and Zhu, Bin, additional

Published
2023
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27. Detection of 6 TFEB-amplified renal cell carcinomas and 25 renal cell carcinomas with MITF translocations: systematic morphologic analysis of 85 cases evaluated by clinical TFE3 and TFEB FISH assays

Author

Skala, Stephanie L, Xiao, Hong, Udager, Aaron M, Dhanasekaran, Saravana M, Shukla, Sudhanshu, Zhang, Yang, Landau, Carrie, Shao, Lina, Roulston, Diane, Wang, Lisha, Siddiqui, Javed, Cao, Xuhong, Magi-Galluzzi, Cristina, Zhang, Miao, Osunkoya, Adeboye O, Smith, Steven C, McKenney, Jesse K, Betz, Bryan L, Myers, Jeffrey L, Chinnaiyan, Arul M, Tomlins, Scott A, and Mehra, Rohit

Published
2018
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28. Technical laboratory standards for interpretation and reporting of acquired copy-number abnormalities and copy-neutral loss of heterozygosity in neoplastic disorders: a joint consensus recommendation from the American College of Medical Genetics and Genomics (ACMG) and the Cancer Genomics Consortium (CGC)

Author

Mikhail, Fady M., Biegel, Jaclyn A., Cooley, Linda D., Dubuc, Adrian M., Hirsch, Betsy, Horner, Vanessa L., Newman, Scott, Shao, Lina, Wolff, Daynna J., and Raca, Gordana

Published
2019
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33. Lessons from 801 clinical TFE3/TFEB fluorescence in situ hybridization assays performed on renal cell carcinoma suspicious for MiTF family aberrations.

Author

Wang, Xiao-Ming, Shao, Lina, Xiao, Hong, Myers, Jeffrey L, Pantanowitz, Liron, Skala, Stephanie L, Udager, Aaron M, Vaishampayan, Ulka, Mannan, Rahul, Dhanasekaran, Saravana M, Chinnaiyan, Arul M, Betz, Bryan L, Brown, Noah, and Mehra, Rohit

Subjects
*FLUORESCENCE in situ hybridization, *RENAL cell carcinoma, *KIDNEY tumors, *CHROMOSOMAL rearrangement, *PROGRESSION-free survival, *NUCLEIC acid hybridization
Abstract

Objectives Fluorescence in situ hybridization (FISH) assays for the detection of chromosomal rearrangements involving TFE3 and TFEB are considered the gold standard for the diagnosis of MiTF family altered renal cell carcinoma (MiTF-RCC). We reviewed 801 clinical TFE3 / TFEB FISH assays performed at our tertiary-level institution between 2014 and 2023 on kidney tumors suspicious at the morphologic or biomarker level for MiTF aberrations. Methods We summarized and analyzed clinical information, TFE3 / TFEB FISH results, and available biomarker staining results in a cohort of 453 consecutive kidney tumor cases suspicious for MiTF-RCC. Results In total, 61 of 434 (14%) kidney tumors were confirmed for TFE3 translocation; 10 of 367 cases (2.7%) were confirmed for TFEB translocation. Since TFEB amplification interpretation was implemented in our service line, 20 of 306 cases (6.5%) were diagnosed with TFEB amplification. Importantly, TFE3 and TFEB rearrangements were never co-detected within the same kidney tumor. Patients with TFEB amplification were significantly older (P <.001) than patients with TFE3 or TFEB translocation. Kidney tumors with TFEB amplification were seen to be at least 3 times as common as those with TFEB translocation. Conclusions Clinical TFE3 / TFEB FISH assays successfully identified and confirmed rare MiTF-RCC with TFE3 and TFEB rearrangements. Although morphologic and biomarker features associated with a kidney tumor may be suggestive of MiTF-RCC, clinical TFE3 / TFEB FISH assays are crucial for a confirmation and definitive subclassification of patients with MiTF-RCC. [ABSTRACT FROM AUTHOR]

Published
2023
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42. Isolation and Molecular Characterization of Atypical Porcine Pestivirus Emerging in China.

Author

Song, Hao, Gao, Xiaowei, Fu, Yanhui, Li, Jing, Fan, Gaocheng, Shao, Lina, Zhang, Jiaoer, Qiu, Hua-Ji, and Luo, Yuzi

Subjects
WHOLE genome sequencing, TRANSMISSION electron microscopy, VACCINE development, PIGLETS, SEQUENCE analysis
Abstract

Atypical porcine pestivirus (APPV) is a recently discovered and very divergent species of the genus Pestivirus within the family Flaviviridae, which causes congenital tremor (CT) in newborn piglets. In this study, an APPV epidemiological investigation was conducted by studying 975 swine samples (562 tissue and 413 serum samples) collected from different parts of China from 2017 to 2021. The results revealed that the overall positive rate of the APPV genome was 7.08% (69/975), among which 50.7% (35/69) of the samples tested positive for one or more other common swine viruses, especially porcine circovirus type 2 (PCV2) with a coinfection rate of 36.2% (25/69). Subsequently, a novel APPV strain, named China/HLJ491/2017, was isolated in porcine kidney (PK)-15 cells for the first time from a weaned piglet that was infected with both APPV and PCV2. The new APPV isolate was confirmed by RT-PCR, sequencing, immunofluorescence assay, and transmission electron microscopy. After clearing PCV2, a pure APPV strain was obtained and further stably propagated in PK-15 cells for more than 30 passages. Full genome sequencing and phylogenetic analysis showed that the China/HLJ491/2017 strain was classified as genotype 2, sharing 80.8 to 97.6% of its nucleotide identity with previously published APPV strains. In conclusion, this study enhanced our knowledge of this new pestivirus and the successful isolation of the APPV strain provides critical material for the investigation of the biological and pathogenic properties of this emerging virus, as well as the development of vaccines and diagnostic reagents. [ABSTRACT FROM AUTHOR]

Published
2023
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