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7. New faces

Author

Miller, Neil

Published
2013

16. Ophthalmic and Systemic Factors of Acute Nonarteritic Anterior Ischemic Optic Neuropathy in the Quark207 Treatment Trial

Author

Clare, Fraser, Celia, Chen, Neil, Shuey, Stephen, Colley, Wang, Ningli, Dou, Hongliang, Zhong, Yong, Tang, Luosheng, Han, Quanhong, Dirk, Sandner, Maria-Andreea, Gamulescu, Nicole, Eter, Helmut, Wilhelm, Katrin, Lorenz, Santhosh, Krishna G., Ramesh, Kekunnaya, S, Ambika, Kumudini, Sharma, Warkad, Vivekanand Uttamrao, Rohit, Saxena, Mahesh, Kumar S., Dipankar, Das, Atul, Hegade, Shahana, Mazumdar, Sachin, Daighavane, Virender, Sachdeva, Hadas, Kalish, Ainat, Klein, Ruth, Huna-Baron, Hana, Leiba, Nitza, Goldenberg-Cohen, Marina, Shneck, Joshua, Kruger, Pasquale, Ciardella Antonio, Gianni, Virgili, Arturo, Carta, Stefania, Bianchi Marzoli, Tow, Sharon, Fang, Chin Chee, Peter, MacIntosh, Jeffrey, Bennett, Byron, Lam, Bradley, Katz, Zoe, Williams, Michael, Lee, Madhura, Tamhankar, Rudrani, Banik, Michael, Rauser, Marc, Levy, Joyce, Liao Yaping, James, Luu, Michael, Tibbetts, David, Scales, Robert, Lesser, Anil, Patel, Syndee, Givre, Gregory, Van Stavern, Steven, Hamilton, Vivian, Rismondo, Courtney, Francis, Dean, Cestari, Marc, Dinkin, John, Pula, Padmaja, Sudhakar, Steven, Newman, Rosa, Tang, Joseph, Chacko, Sachin, Kedar, Peter, Quiros, Larry, Frohman, Nicholas, Volpe, Patrick, Sibony, John, Chen, Luis, Mejico, Gregory, Kosmorsky, Virgil, Alfaro Daniel, David, Katz, Andrew, Lee, Lindsey, DeLott, Vivek, Patel, Swaraj, Bose, Crandall, Peeler, Bhatti, Tariq, Kupersmith, Mark J., Fraser, Clare L., Morgenstern, Rachelle, Miller, Neil R., Levin, Leonard A., and Jette, Nathalie

Published
2024
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22. Benchmarking challenging small variants with linked and long reads.

Author

Wagner, Justin, Olson, Nathan, Harris, Lindsay, Khan, Ziad, Farek, Jesse, Mahmoud, Medhat, Stankovic, Ana, Kovacevic, Vladimir, Yoo, Byunggil, Miller, Neil, Rosenfeld, Jeffrey, Ni, Bohan, Zarate, Samantha, Kirsche, Melanie, Aganezov, Sergey, Schatz, Michael, Narzisi, Giuseppe, Byrska-Bishop, Marta, Clarke, Wayne, Evani, Uday, Markello, Charles, Shafin, Kishwar, Zhou, Xin, Sidow, Arend, Bansal, Vikas, Ebert, Peter, Marschall, Tobias, Lansdorp, Peter, Hanlon, Vincent, Mattsson, Carl-Adam, Barrio, Alvaro, Fiddes, Ian, Xiao, Chunlin, Fungtammasan, Arkarachai, Chin, Chen-Shan, Wenger, Aaron, Rowell, William, Sedlazeck, Fritz, Carroll, Andrew, Salit, Marc, and Zook, Justin

Abstract

Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use accurate linked and long reads to expand benchmarks in 7 samples to include difficult-to-map regions and segmental duplications that are challenging for short reads. These benchmarks add more than 300,000 SNVs and 50,000 insertions or deletions (indels) and include 16% more exonic variants, many in challenging, clinically relevant genes not covered previously, such as PMS2. For HG002, we include 92% of the autosomal GRCh38 assembly while excluding regions problematic for benchmarking small variants, such as copy number variants, that should not have been in the previous version, which included 85% of GRCh38. It identifies eight times more false negatives in a short read variant call set relative to our previous benchmark. We demonstrate that this benchmark reliably identifies false positives and false negatives across technologies, enabling ongoing methods development.

Published
2022

37. Application of a Deep Learning System to Detect Papilledema on Nonmydriatic Ocular Fundus Photographs in an Emergency Department

Author

Fraser, Clare L., Micieli, Jonathan A., Costello, Fiona, Bénard-Séguin, Étienne, Yang, Hui, Chan, Carmen Kar Mun, Cheung, Carol Y, Chan, Noel CY, Hamann, Steffen, Gohier, Philippe, Vautier, Anaïs, Rougier, Marie-Bénédicte, Chiquet, Christophe, Vignal-Clermont, Catherine, Hage, Rabih, Khanna, Raoul Kanav, Tran, Thi Ha Chau, Lagrèze, Wolf Alexander, Jonas, Jost B, Ambika, Selvakumar, Fard, Masoud Aghsaei, La Morgia, Chiara, Carbonelli, Michele, Barboni, Piero, Carelli, Valerio, Romagnoli, Martina, Amore, Giulia, Nakamura, Makoto, Fumio, Takano, Petzold, Axel, Wenniger lj, Maillette de Buy, Kho, Richard, Fonseca, Pedro L., Bikbov, Mukharram M., Milea, Dan, Najjar, Raymond P, Ting, Daniel, Tang, Zhiqun, Loo, Jing Liang, Tow, Sharon, Singhal, Shweta, Vasseneix, Caroline, Wong, Tien Yin, Lamoureux, Ecosse, Yu Chen, Ching, Aung, Tin, Schmetterer, Leopold, Sanda, Nicolae, Thuman, Gabriele, Hwang, Jeong-Min, Vanikieti, Kavin, Suwan, Yanin, Padungkiatsagul, Tanyatuth, Yu-Wai-Man, Patrick, Jurkute, Neringa, Hong, Eun Hee, Biousse, Valerie, Newman, Nancy J., Peragallo, Jason H., Datillo, Michael, Kedar, Sachin, Lin, Mung Yan, Patil, Ajay, Aung, Andre, Boyko, Matthew, Alsakran, Wael Abdulraman, Zayani, Amani, Bouthour, Walid, Banc, Ana, Mosley, Rasha, Labella, Fernando, Miller, Neil R., Chen, John J., Mejico, Luis J., Kilangalanga, Janvier Ngoy, Biousse, Valérie, Najjar, Raymond P., Wright, David W., Keadey, Matthew T., Wong, Tien Y., and Bruce, Beau B.

Published
2024
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38. Giant Cell Arteritis and Polymyalgia Rheumatica

Author

Villiger, Peter M., Christ, Lisa, Seitz, Luca, Scholz, Godehard, Tappeiner, Christoph, Muratore, Francesco, Salvarani, Carlo, Mollan, Sue, Quick, Vanessa, Dejaco, Christian, Lee, Michael, Basu, Neil, Miller, Neil, Stone, John H., and Stone, John H., editor

Published
2023
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39. The BONSAI (Brain and Optic Nerve Study with Artificial Intelligence) deep learning system can accurately identify pediatric papilledema on standard ocular fundus photographs

Author

Fraser, Clare L., Micieli, Jonathan A., Costello, Fiona, Étienne Bénard-Séguin, Yang, Hui, Mun Chan, Carmen Kar, Cheung, Carol Y., Chan, Noel CY., Hamann, Steffen, Gohier, Philippe, Vautier, Anaïs, Rougier, Marie-Bénédicte, Chiquet, Christophe, Vignal-Clermont, Catherine, Hage, Rabih, Khanna, Raoul Kanav, Chau Tran, Thi Ha, Lagrèze, Wolf Alexander, Jonas, Jost B., Ambika, Selvakumar, Fard, Masoud Aghsaei, La Morgia, Chiara, Carbonelli, Michele, Barboni, Piero, Carelli, Valerio, Romagnoli, Martina, Amore, Giulia, Nakamura, Makoto, Fumio, Takano, Petzold, Axel, de Buy Wenniger L.J., Maillette, Kho, Richard, Fonseca, Pedro L., Bikbov, Mukharram M., Milea, Dan, Najjar, Raymond P., Ting, Daniel, Tang, Zhiqun, Loo, Jing Liang, Tow, Sharon, Singhal, Shweta, Vasseneix, Caroline, Wong, Tien Yin, Lamoureux, Ecosse, Chen, Ching Yu, Aung, Tin, Schmetterer, Leopold, Sanda, Nicolae, Thuman, Gabriele, Hwang, Jeong-Min, Vanikieti, Kavin, Suwan, Yanin, Padungkiatsagul, Tanyatuth, Yu-Wai-Man, Patrick, Jurkute, Neringa, Hong, Eun Hee, Biousse, Valerie, Newman, Nancy J., Peragallo, Jason H., Datillo, Michael, Kedar, Sachin, Lin, Mung Yan, Patil, Ajay, Aung, Andre, Boyko, Matthew, Alsakran, Wael Abdulraman, Zayani, Amani, Bouthour, Walid, Banc, Ana, Mosley, Rasha, Labella, Fernando, Miller, Neil R., Chen, John J., Mejico, Luis J., Kilangalanga, Janvier Ngoy, Cioplean, Daniela, Dragomir, Mihaela, Chia, Audrey, and Biousse, Valérie

Published
2024
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41. Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes

Author

Cohen, Ana S.A., Farrow, Emily G., Abdelmoity, Ahmed T., Alaimo, Joseph T., Amudhavalli, Shivarajan M., Anderson, John T., Bansal, Lalit, Bartik, Lauren, Baybayan, Primo, Belden, Bradley, Berrios, Courtney D., Biswell, Rebecca L., Buczkowicz, Pawel, Buske, Orion, Chakraborty, Shreyasee, Cheung, Warren A., Coffman, Keith A., Cooper, Ashley M., Cross, Laura A., Curran, Tom, Dang, Thuy Tien T., Elfrink, Mary M., Engleman, Kendra L., Fecske, Erin D., Fieser, Cynthia, Fitzgerald, Keely, Fleming, Emily A., Gadea, Randi N., Gannon, Jennifer L., Gelineau-Morel, Rose N., Gibson, Margaret, Goldstein, Jeffrey, Grundberg, Elin, Halpin, Kelsee, Harvey, Brian S., Heese, Bryce A., Hein, Wendy, Herd, Suzanne M., Hughes, Susan S., Ilyas, Mohammed, Jacobson, Jill, Jenkins, Janda L., Jiang, Shao, Johnston, Jeffrey J., Keeler, Kathryn, Korlach, Jonas, Kussmann, Jennifer, Lambert, Christine, Lawson, Caitlin, Le Pichon, Jean-Baptiste, Leeder, James Steven, Little, Vicki C., Louiselle, Daniel A., Lypka, Michael, McDonald, Brittany D., Miller, Neil, Modrcin, Ann, Nair, Annapoorna, Neal, Shelby H., Oermann, Christopher M., Pacicca, Donna M., Pawar, Kailash, Posey, Nyshele L., Price, Nigel, Puckett, Laura M.B., Quezada, Julio F., Raje, Nikita, Rowell, William J., Rush, Eric T., Sampath, Venkatesh, Saunders, Carol J., Schwager, Caitlin, Schwend, Richard M., Shaffer, Elizabeth, Smail, Craig, Soden, Sarah, Strenk, Meghan E., Sullivan, Bonnie R., Sweeney, Brooke R., Tam-Williams, Jade B., Walter, Adam M., Welsh, Holly, Wenger, Aaron M., Willig, Laurel K., Yan, Yun, Younger, Scott T., Zhou, Dihong, Zion, Tricia N., Thiffault, Isabelle, and Pastinen, Tomi

Published
2022
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42. A Deep Learning Approach for Accurate Discrimination Between Optic Disc Drusen and Papilledema on Fundus Photographs.

Author

Sathianvichitr, Kanchalika, Najjar, Raymond P., Zhiqun, Tang, Fraser, J. Alexander, Yau, Christine W. L., Girard, Michael J. A., Costello, Fiona, Lin, Mung Y., Lagrèze, Wolf A., Vignal-Clermont, Catherine, Fraser, Clare L., Hamann, Steffen, Newman, Nancy J., Biousse, Valérie, Milea, Dan, Petzold, Axel, Gohier, Philippe, Miller, Neil R., Vanikieti, Kavin, and Milea, Leonard

Abstract

Supplemental Digital Content is Available in the Text. Background: Optic disc drusen (ODD) represent an important differential diagnosis of papilledema caused by intracranial hypertension, but their distinction may be difficult in clinical practice. The aim of this study was to train, validate, and test a dedicated deep learning system (DLS) for binary classification of ODD vs papilledema (including various subgroups within each category), on conventional mydriatic digital ocular fundus photographs collected in a large international multiethnic population. Methods: This retrospective study included 4,508 color fundus images in 2,180 patients from 30 neuro-ophthalmology centers (19 countries) participating in the Brain and Optic Nerve Study with Artificial Intelligence (BONSAI) Group. For training and internal validation, we used 857 ODD images and 3,230 papilledema images, in 1,959 patients. External testing was performed on an independent data set (221 patients), including 207 images with ODD (96 visible and 111 buried), provided by 3 centers of the Optic Disc Drusen Studies Consortium, and 214 images of papilledema (92 mild-to-moderate and 122 severe) from a previously validated study. Results: The DLS could accurately distinguish between all ODD and papilledema (all severities included): area under the receiver operating characteristic curve (AUC) 0.97 (95% confidence interval [CI], 0.96–0.98), accuracy 90.5% (95% CI, 88.0%–92.9%), sensitivity 86.0% (95% CI, 82.1%–90.1%), and specificity 94.9% (95% CI, 92.3%–97.6%). The performance of the DLS remained high for discrimination of buried ODD from mild-to-moderate papilledema: AUC 0.93 (95% CI, 0.90–0.96), accuracy 84.2% (95% CI, 80.2%–88.6%), sensitivity 78.4% (95% CI, 72.2%–84.7%), and specificity 91.3% (95% CI, 87.0%–96.4%). Conclusions: A dedicated DLS can accurately distinguish between ODD and papilledema caused by intracranial hypertension, even when considering buried ODD vs mild-to-moderate papilledema. [ABSTRACT FROM AUTHOR]

Published
2024
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43. CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project

Author

Gaedigk, Andrea, Boone, Erin C., Scherer, Steven E., Lee, Seung-been, Numanagić, Ibrahim, Sahinalp, Cenk, Smith, Joshua D., McGee, Sean, Radhakrishnan, Aparna, Qin, Xiang, Wang, Wendy Y., Farrow, Emily G., Gonzaludo, Nina, Halpern, Aaron L., Nickerson, Deborah A., Miller, Neil A., Pratt, Victoria M., and Kalman, Lisa V.

Published
2022
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45. Deep Learning System Outperforms Clinicians in Identifying Optic Disc Abnormalities

Author

Vasseneix, Caroline, Nusinovici, Simon, Xu, Xinxing, Hwang, Jeong-Min, Hamann, Steffen, Chen, John J., Loo, Jing Liang, Milea, Leonard, Tan, Kenneth B.K., Ting, Daniel S.W., Liu, Yong, Newman, Nancy J., Biousse, Valerie, Wong, Tien Ying, Milea, Dan, Najjar, Raymond P., Gohier, Philippe, Miller, Neil, Vanikieti, Kavin, La Morgia, Chiara, Rougier, Marie-Bénédicte, Ambika, Selvakumar, Fonseca, Pedro, Lagrèze, Wolf Alexander, Sanda, Nicolae, Chiquet, Christophe, Yang, Hui, Chan, Carmen K. M., Cheung, Carol Y., Ha Chau, Tran Thi, Jurkute, Neringa, Yu-Wai-Man, Patrick, Kho, Richard, Jonas, Jost B, Vignal-Clermont, Catherine, Kim, Dong Hyun, Yang, Hee Kyung, Aung, Tin, Singhal, Shweta, Tow, Sharon, Nongpiur, Monisha Esther, Perera, Shamira, Narayanaswamy, Arun, Thirugnanam, Umapathi N., Fraser, Clare L., Mejico, Luis J., and Fard, Masoud Aghsaei

Published
2023
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