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21 results on '"Fischer, Catherine G."'

1. 3D genomic mapping reveals multifocality of human pancreatic precancers

Author

Braxton, Alicia M., Kiemen, Ashley L., Grahn, Mia P., Forjaz, André, Parksong, Jeeun, Mahesh Babu, Jaanvi, Lai, Jiaying, Zheng, Lily, Niknafs, Noushin, Jiang, Liping, Cheng, Haixia, Song, Qianqian, Reichel, Rebecca, Graham, Sarah, Damanakis, Alexander I., Fischer, Catherine G., Mou, Stephanie, Metz, Cameron, Granger, Julie, Liu, Xiao-Ding, Bachmann, Niklas, Zhu, Yutong, Liu, YunZhou, Almagro-Pérez, Cristina, Jiang, Ann Chenyu, Yoo, Jeonghyun, Kim, Bridgette, Du, Scott, Foster, Eli, Hsu, Jocelyn Y., Rivera, Paula Andreu, Chu, Linda C., Liu, Fengze, Fishman, Elliot K., Yuille, Alan, Roberts, Nicholas J., Thompson, Elizabeth D., Scharpf, Robert B., Cornish, Toby C., Jiao, Yuchen, Karchin, Rachel, Hruban, Ralph H., Wu, Pei-Hsun, Wirtz, Denis, and Wood, Laura D.

Published
2024
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3. Genomic characterization of malignant progression in neoplastic pancreatic cysts

Author

Noë, Michaël, Niknafs, Noushin, Fischer, Catherine G., Hackeng, Wenzel M., Beleva Guthrie, Violeta, Hosoda, Waki, Debeljak, Marija, Papp, Eniko, Adleff, Vilmos, White, James R., Luchini, Claudio, Pea, Antonio, Scarpa, Aldo, Butturini, Giovanni, Zamboni, Giuseppe, Castelli, Paola, Hong, Seung-Mo, Yachida, Shinichi, Hiraoka, Nobuyoshi, Gill, Anthony J., Samra, Jaswinder S., Offerhaus, G. Johan A., Hoorens, Anne, Verheij, Joanne, Jansen, Casper, Adsay, N. Volkan, Jiang, Wei, Winter, Jordan, Albores-Saavedra, Jorge, Terris, Benoit, Thompson, Elizabeth D., Roberts, Nicholas J., Hruban, Ralph H., Karchin, Rachel, Scharpf, Robert B., Brosens, Lodewijk A. A., Velculescu, Victor E., and Wood, Laura D.

Published
2020
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5. Data from Artificial Intelligence-Assisted Serial Analysis of Clinical Cancer Genomics Data Identifies Changing Treatment Recommendations and Therapeutic Targets

Author

Fischer, Catherine G., primary, Pallavajjala, Aparna, primary, Jiang, LiQun, primary, Anagnostou, Valsamo, primary, Tao, Jessica, primary, Adams, Emily, primary, Eshleman, James R., primary, Gocke, Christopher D., primary, Lin, Ming-Tseh, primary, Platz, Elizabeth A., primary, and Xian, Rena R., primary

Published
2023
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6. Supplementary Figure from Artificial Intelligence-Assisted Serial Analysis of Clinical Cancer Genomics Data Identifies Changing Treatment Recommendations and Therapeutic Targets

Author

Fischer, Catherine G., primary, Pallavajjala, Aparna, primary, Jiang, LiQun, primary, Anagnostou, Valsamo, primary, Tao, Jessica, primary, Adams, Emily, primary, Eshleman, James R., primary, Gocke, Christopher D., primary, Lin, Ming-Tseh, primary, Platz, Elizabeth A., primary, and Xian, Rena R., primary

Published
2023
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7. Supplementary Data from Artificial Intelligence-Assisted Serial Analysis of Clinical Cancer Genomics Data Identifies Changing Treatment Recommendations and Therapeutic Targets

Author

Fischer, Catherine G., primary, Pallavajjala, Aparna, primary, Jiang, LiQun, primary, Anagnostou, Valsamo, primary, Tao, Jessica, primary, Adams, Emily, primary, Eshleman, James R., primary, Gocke, Christopher D., primary, Lin, Ming-Tseh, primary, Platz, Elizabeth A., primary, and Xian, Rena R., primary

Published
2023
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8. Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions

Author

Braxton, Alicia M, primary, Kiemen, Ashley L, additional, Grahn, Mia P, additional, Forjaz, André, additional, Babu, Jaanvi Mahesh, additional, Zheng, Lily, additional, Jiang, Liping, additional, Cheng, Haixia, additional, Song, Qianqian, additional, Reichel, Rebecca, additional, Graham, Sarah, additional, Damanakis, Alexander I, additional, Fischer, Catherine G, additional, Mou, Stephanie, additional, Metz, Cameron, additional, Granger, Julie, additional, Liu, Xiao-Ding, additional, Bachmann, Niklas, additional, Almagro-Pérez, Cristina, additional, Jiang, Ann Chenyu, additional, Yoo, Jeonghyun, additional, Kim, Bridgette, additional, Du, Scott, additional, Foster, Eli, additional, Hsu, Jocelyn Y, additional, Rivera, Paula Andreu, additional, Chu, Linda C, additional, Liu, Fengze, additional, Niknafs, Noushin, additional, Fishman, Elliot K, additional, Yuille, Alan, additional, Roberts, Nicholas J, additional, Thompson, Elizabeth D, additional, Scharpf, Robert B, additional, Cornish, Toby C, additional, Jiao, Yuchen, additional, Karchin, Rachel, additional, Hruban, Ralph H, additional, Wu, Pei-Hsun, additional, Wirtz, Denis, additional, and Wood, Laura D, additional

Published
2023
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10. Artificial Intelligence-Assisted Serial Analysis of Clinical Cancer Genomics Data Identifies Changing Treatment Recommendations and Therapeutic Targets

Author

Fischer, Catherine G., primary, Pallavajjala, Aparna, additional, Jiang, LiQun, additional, Anagnostou, Valsamo, additional, Tao, Jessica, additional, Adams, Emily, additional, Eshleman, James R., additional, Gocke, Christopher D., additional, Lin, Ming-Tseh, additional, Platz, Elizabeth A., additional, and Xian, Rena R., additional

Published
2022
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11. Genomic characterization of malignant progression in neoplastic pancreatic cysts

Author

Pathologie Groep Brosens, Cancer, Pathologie Pathologen staf, Noë, Michaël, Niknafs, Noushin, Fischer, Catherine G, Hackeng, Wenzel M, Beleva Guthrie, Violeta, Hosoda, Waki, Debeljak, Marija, Papp, Eniko, Adleff, Vilmos, White, James R, Luchini, Claudio, Pea, Antonio, Scarpa, Aldo, Butturini, Giovanni, Zamboni, Giuseppe, Castelli, Paola, Hong, Seung-Mo, Yachida, Shinichi, Hiraoka, Nobuyoshi, Gill, Anthony J, Samra, Jaswinder S, Offerhaus, G Johan A, Hoorens, Anne, Verheij, Joanne, Jansen, Casper, Adsay, N Volkan, Jiang, Wei, Winter, Jordan, Albores-Saavedra, Jorge, Terris, Benoit, Thompson, Elizabeth D, Roberts, Nicholas J, Hruban, Ralph H, Karchin, Rachel, Scharpf, Robert B, Brosens, Lodewijk A A, Velculescu, Victor E, Wood, Laura D, Pathologie Groep Brosens, Cancer, Pathologie Pathologen staf, Noë, Michaël, Niknafs, Noushin, Fischer, Catherine G, Hackeng, Wenzel M, Beleva Guthrie, Violeta, Hosoda, Waki, Debeljak, Marija, Papp, Eniko, Adleff, Vilmos, White, James R, Luchini, Claudio, Pea, Antonio, Scarpa, Aldo, Butturini, Giovanni, Zamboni, Giuseppe, Castelli, Paola, Hong, Seung-Mo, Yachida, Shinichi, Hiraoka, Nobuyoshi, Gill, Anthony J, Samra, Jaswinder S, Offerhaus, G Johan A, Hoorens, Anne, Verheij, Joanne, Jansen, Casper, Adsay, N Volkan, Jiang, Wei, Winter, Jordan, Albores-Saavedra, Jorge, Terris, Benoit, Thompson, Elizabeth D, Roberts, Nicholas J, Hruban, Ralph H, Karchin, Rachel, Scharpf, Robert B, Brosens, Lodewijk A A, Velculescu, Victor E, and Wood, Laura D

Published
2020

12. Multiregion whole-exome sequencing of intraductal papillary mucinous neoplasms reveals frequent somatic KLF4 mutations predominantly in low-grade regions

Author

Fujikura, Kohei, primary, Hosoda, Waki, additional, Felsenstein, Matthäus, additional, Song, Qianqian, additional, Reiter, Johannes G, additional, Zheng, Lily, additional, Beleva Guthrie, Violeta, additional, Rincon, Natalia, additional, Dal Molin, Marco, additional, Dudley, Jonathan, additional, Cohen, Joshua D, additional, Wang, Pei, additional, Fischer, Catherine G, additional, Braxton, Alicia M, additional, Noë, Michaël, additional, Jongepier, Martine, additional, Fernández-del Castillo, Carlos, additional, Mino-Kenudson, Mari, additional, Schmidt, C Max, additional, Yip-Schneider, Michele T, additional, Lawlor, Rita T, additional, Salvia, Roberto, additional, Roberts, Nicholas J, additional, Thompson, Elizabeth D, additional, Karchin, Rachel, additional, Lennon, Anne Marie, additional, Jiao, Yuchen, additional, and Wood, Laura D, additional

Published
2020
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13. Intraductal Papillary Mucinous Neoplasms Arise From Multiple Independent Clones, Each With Distinct Mutations

Author

Fischer, Catherine G., primary, Beleva Guthrie, Violeta, additional, Braxton, Alicia M., additional, Zheng, Lily, additional, Wang, Pei, additional, Song, Qianqian, additional, Griffin, James F., additional, Chianchiano, Peter E., additional, Hosoda, Waki, additional, Niknafs, Noushin, additional, Springer, Simeon, additional, Dal Molin, Marco, additional, Masica, David, additional, Scharpf, Robert B., additional, Thompson, Elizabeth D., additional, He, Jin, additional, Wolfgang, Christopher L., additional, Hruban, Ralph H., additional, Roberts, Nicholas J., additional, Lennon, Anne Marie, additional, Jiao, Yuchen, additional, Karchin, Rachel, additional, and Wood, Laura D., additional

Published
2019
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14. Single‐cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions

Author

Kuboki, Yuko, primary, Fischer, Catherine G, additional, Beleva Guthrie, Violeta, additional, Huang, Wenjie, additional, Yu, Jun, additional, Chianchiano, Peter, additional, Hosoda, Waki, additional, Zhang, Hao, additional, Zheng, Lily, additional, Shao, Xiaoshan, additional, Thompson, Elizabeth D, additional, Waters, Kevin, additional, Poling, Justin, additional, He, Jin, additional, Weiss, Matthew J, additional, Wolfgang, Christopher L, additional, Goggins, Michael G, additional, Hruban, Ralph H, additional, Roberts, Nicholas J, additional, Karchin, Rachel, additional, and Wood, Laura D, additional

Published
2019
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15. Multiregion whole-exome sequencing of intraductal papillary mucinous neoplasms reveals frequent somatic KLF4 mutations predominantly in low-grade regions.

Author

Fujikura, Kohei, Hosoda, Waki, Felsenstein, Matthäus, Qianqian Song, Reiter, Johannes G., Zheng, Lily, Guthrie, Violeta Beleva, Rincon, Natalia, Dal Molin, Marco, Dudley, Jonathan, Cohen, Joshua D., Pei Wang, Fischer, Catherine G., Braxton, Alicia M., Noë, Michaël, Jongepier, Martine, Fernández-del Castillo, Carlos, Mino-Kenudson, Mari, Schmidt, C. Max, and Yip-Schneider, Michele T.

Subjects
PANCREATIC cysts, PANCREATIC intraepithelial neoplasia, SOMATIC mutation, MEDICAL sciences, CANCER genetics, TUMORS, TUMOR suppressor genes
Published
2021
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16. IPMNs with co-occurring invasive cancers : Neighbours but not always relatives

Author

Felsenstein, Matthäus, Noë, Michaël, Masica, David L., Hosoda, Waki, Chianchiano, Peter, Fischer, Catherine G., Lionheart, Gemma, Brosens, Lodewijk A.A., Pea, Antonio, Yu, Jun, Gemenetzis, Georgios, Groot, Vincent P., Makary, Martin A., He, Jin, Weiss, Matthew J., Cameron, John L., Wolfgang, Christopher L., Hruban, Ralph H., Roberts, Nicholas J., Karchin, Rachel, Goggins, Michael G., Wood, Laura D., Felsenstein, Matthäus, Noë, Michaël, Masica, David L., Hosoda, Waki, Chianchiano, Peter, Fischer, Catherine G., Lionheart, Gemma, Brosens, Lodewijk A.A., Pea, Antonio, Yu, Jun, Gemenetzis, Georgios, Groot, Vincent P., Makary, Martin A., He, Jin, Weiss, Matthew J., Cameron, John L., Wolfgang, Christopher L., Hruban, Ralph H., Roberts, Nicholas J., Karchin, Rachel, Goggins, Michael G., and Wood, Laura D.

Published
2018

17. IPMNs with co-occurring invasive cancers: Neighbours but not always relatives

Author

Pathologie ICT innovatie & ontwikkeling, Pathologie Pathologen staf, Felsenstein, Matthäus, Noë, Michaël, Masica, David L., Hosoda, Waki, Chianchiano, Peter, Fischer, Catherine G., Lionheart, Gemma, Brosens, Lodewijk A.A., Pea, Antonio, Yu, Jun, Gemenetzis, Georgios, Groot, Vincent P., Makary, Martin A., He, Jin, Weiss, Matthew J., Cameron, John L., Wolfgang, Christopher L., Hruban, Ralph H., Roberts, Nicholas J., Karchin, Rachel, Goggins, Michael G., Wood, Laura D., Pathologie ICT innovatie & ontwikkeling, Pathologie Pathologen staf, Felsenstein, Matthäus, Noë, Michaël, Masica, David L., Hosoda, Waki, Chianchiano, Peter, Fischer, Catherine G., Lionheart, Gemma, Brosens, Lodewijk A.A., Pea, Antonio, Yu, Jun, Gemenetzis, Georgios, Groot, Vincent P., Makary, Martin A., He, Jin, Weiss, Matthew J., Cameron, John L., Wolfgang, Christopher L., Hruban, Ralph H., Roberts, Nicholas J., Karchin, Rachel, Goggins, Michael G., and Wood, Laura D.

Published
2018

19. IPMNs with co-occurring invasive cancers: neighbours but not always relatives

Author

Felsenstein, Matthäus, primary, Noë, Michaël, additional, Masica, David L, additional, Hosoda, Waki, additional, Chianchiano, Peter, additional, Fischer, Catherine G, additional, Lionheart, Gemma, additional, Brosens, Lodewijk A A, additional, Pea, Antonio, additional, Yu, Jun, additional, Gemenetzis, Georgios, additional, Groot, Vincent P, additional, Makary, Martin A, additional, He, Jin, additional, Weiss, Matthew J, additional, Cameron, John L, additional, Wolfgang, Christopher L, additional, Hruban, Ralph H, additional, Roberts, Nicholas J, additional, Karchin, Rachel, additional, Goggins, Michael G, additional, and Wood, Laura D, additional

Published
2018
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20. Multiregion whole-exome sequencing of intraductal papillary mucinous neoplasms reveals frequent somatic KLF4mutations predominantly in low-grade regions

Author

Fujikura, Kohei, Hosoda, Waki, Felsenstein, Mattha¨us, Song, Qianqian, Reiter, Johannes G, Zheng, Lily, Beleva Guthrie, Violeta, Rincon, Natalia, Dal Molin, Marco, Dudley, Jonathan, Cohen, Joshua D, Wang, Pei, Fischer, Catherine G, Braxton, Alicia M, Noe¨, Michae¨l, Jongepier, Martine, Fernández-del Castillo, Carlos, Mino-Kenudson, Mari, Schmidt, C Max, Yip-Schneider, Michele T, Lawlor, Rita T, Salvia, Roberto, Roberts, Nicholas J, Thompson, Elizabeth D, Karchin, Rachel, Lennon, Anne Marie, Jiao, Yuchen, and Wood, Laura D

Abstract

ObjectiveIntraductal papillary mucinous neoplasms (IPMNs) are non-invasive precursor lesions that can progress to invasive pancreatic cancer and are classified as low-grade or high-grade based on the morphology of the neoplastic epithelium. We aimed to compare genetic alterations in low-grade and high-grade regions of the same IPMN in order to identify molecular alterations underlying neoplastic progression.DesignWe performed multiregion whole exome sequencing on tissue samples from 17 IPMNs with both low-grade and high-grade dysplasia (76 IPMN regions, including 49 from low-grade dysplasia and 27 from high-grade dysplasia). We reconstructed the phylogeny for each case, and we assessed mutations in a novel driver gene in an independent cohort of 63 IPMN cyst fluid samples.ResultsOur multiregion whole exome sequencing identified KLF4, a previously unreported genetic driver of IPMN tumorigenesis, with hotspot mutations in one of two codons identified in >50% of the analyzed IPMNs. Mutations in KLF4were significantly more prevalent in low-grade regions in our sequenced cases. Phylogenetic analyses of whole exome sequencing data demonstrated diverse patterns of IPMN initiation and progression. Hotspot mutations in KLF4were also identified in an independent cohort of IPMN cyst fluid samples, again with a significantly higher prevalence in low-grade IPMNs.ConclusionHotspot mutations in KLF4occur at high prevalence in IPMNs. Unique among pancreatic driver genes, KLF4mutations are enriched in low-grade IPMNs. These data highlight distinct molecular features of low-grade and high-grade dysplasia and suggest diverse pathways to high-grade dysplasia via the IPMN pathway.

Published
2021
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21. Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions.

Author

Braxton AM, Kiemen AL, Grahn MP, Forjaz A, Babu JM, Zheng L, Jiang L, Cheng H, Song Q, Reichel R, Graham S, Damanakis AI, Fischer CG, Mou S, Metz C, Granger J, Liu XD, Bachmann N, Almagro-Pérez C, Jiang AC, Yoo J, Kim B, Du S, Foster E, Hsu JY, Rivera PA, Chu LC, Liu F, Niknafs N, Fishman EK, Yuille A, Roberts NJ, Thompson ED, Scharpf RB, Cornish TC, Jiao Y, Karchin R, Hruban RH, Wu PH, Wirtz D, and Wood LD

Abstract

Pancreatic intraepithelial neoplasia (PanIN) is a precursor to pancreatic cancer and represents a critical opportunity for cancer interception. However, the number, size, shape, and connectivity of PanINs in human pancreatic tissue samples are largely unknown. In this study, we quantitatively assessed human PanINs using CODA, a novel machine-learning pipeline for 3D image analysis that generates quantifiable models of large pieces of human pancreas with single-cell resolution. Using a cohort of 38 large slabs of grossly normal human pancreas from surgical resection specimens, we identified striking multifocality of PanINs, with a mean burden of 13 spatially separate PanINs per cm 3 of sampled tissue. Extrapolating this burden to the entire pancreas suggested a median of approximately 1000 PanINs in an entire pancreas. In order to better understand the clonal relationships within and between PanINs, we developed a pipeline for CODA-guided multi-region genomic analysis of PanINs, including targeted and whole exome sequencing. Multi-region assessment of 37 PanINs from eight additional human pancreatic tissue slabs revealed that almost all PanINs contained hotspot mutations in the oncogene KRAS , but no gene other than KRAS was altered in more than 20% of the analyzed PanINs. PanINs contained a mean of 13 somatic mutations per region when analyzed by whole exome sequencing. The majority of analyzed PanINs originated from independent clonal events, with distinct somatic mutation profiles between PanINs in the same tissue slab. A subset of the analyzed PanINs contained multiple KRAS mutations, suggesting a polyclonal origin even in PanINs that are contiguous by rigorous 3D assessment. This study leverages a novel 3D genomic mapping approach to describe, for the first time, the spatial and genetic multifocality of human PanINs, providing important insights into the initiation and progression of pancreatic neoplasia., Competing Interests: Competing Interests Statement: A pending patent application “COMPUTATIONAL TECHNIQUES FOR THREE-DIMENSIONAL RECONSTRUCTION AND MULTI-LABELING OF SERIALLY SECTIONED TISSUE” was filed on 6/24/2022 by authors AK, RHH, PHW, DW, and LDW. The other authors report no competing interests.

Published
2023
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