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4. A Pan-Cancer Study of Somatic TERT Promoter Mutations and Amplification in 30,773 Tumors Profiled by Clinical Genomic Sequencing

Author

Gupta, Sounak, Vanderbilt, Chad M., Lin, Yun-Te, Benhamida, Jamal K., Jungbluth, Achim A., Rana, Satshil, Momeni-Boroujeni, Amir, Chang, Jason C., Mcfarlane, Tiffany, Salazar, Paulo, Mullaney, Kerry, Middha, Sumit, Zehir, Ahmet, Gopalan, Anuradha, Bale, Tejus A., Ganly, Ian, Arcila, Maria E., Benayed, Ryma, Berger, Michael F., Ladanyi, Marc, and Dogan, Snjezana

Published
2021
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5. Detection of GRM1 gene rearrangements in chondromyxoid fibroma: a comparison of fluorescence in‐situ hybridisation, RNA sequencing and immunohistochemical analysis.

Author

Torrence, Dianne, Dermawan, Josephine K, Zhang, Yanming, Vanderbilt, Chad, Hwang, Sinchun, Mullaney, Kerry, Jungbluth, Achim, Rao, Mamta, Gao, Kate, Sukhadia, Purvil, Linos, Konstantinos, Agaram, Narasimhan, and Hameed, Meera

Subjects
GENE rearrangement, RNA sequencing, GENE expression, PROTEIN overexpression, GENE fusion, ANAPLASTIC lymphoma kinase
Abstract

Aims: Chondromyxoid fibroma (CMF) is a rare, benign bone tumour which arises primarily in young adults and is occasionally diagnostically challenging. Glutamate metabotropic receptor 1 (GRM1) gene encodes a metabotropic glutamate receptor and was recently shown to be up‐regulated in chondromyxoid fibroma through gene fusion and promoter swapping. The aim of this study was to interrogate cases of CMF for the presence of GRM1 gene rearrangements, gene fusions and GRM1 protein overexpression. Methods and results: Selected cases were subjected to testing by fluorescent in‐situ hybridisation (FISH) with a GRM1 break‐apart probe, a targeted RNA sequencing method and immunohistochemical study with an antibody to GRM1 protein. Two cases were subjected to whole transcriptomic sequencing. In 13 of 13 cases, GRM1 protein overexpression was detected by immunohistochemistry using the GRM1 antibody. Of the 12 cases successfully tested by FISH, nine of 12 showed GRM1 rearrangements by break‐apart probe assay. Targeted RNA sequencing analysis did not detect gene fusions in any of the eight cases tested, but there was an increase in GRM1 mRNA expression in all eight cases. Two cases subjected to whole transcriptomic sequencing (WTS) showed elevated GRM1 expression and no gene fusions. Conclusion: GRM1 gene rearrangements can be detected using FISH break‐apart probes in approximately 75% of cases, and immunohistochemical detection of GRM1 protein over‐expression is a sensitive diagnostic method. The gene fusion was not detected by targeted RNA sequencing, due most probably to the complexity of fusion mechanism, and is not yet a reliable method for confirming a diagnosis of CMF in the clinical setting. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Data from Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors

Author

Galbraith, Kristyn, primary, Serrano, Jonathan, primary, Shen, Guomiao, primary, Tran, Ivy, primary, Slocum, Cheyanne C., primary, Ketchum, Courtney, primary, Abdullaev, Zied, primary, Turakulov, Rust, primary, Bale, Tejus, primary, Ladanyi, Marc, primary, Sukhadia, Purvil, primary, Zaidinski, Michael, primary, Mullaney, Kerry, primary, DiNapoli, Sara, primary, Liechty, Benjamin L., primary, Barbaro, Marissa, primary, Allen, Jeffrey C., primary, Gardner, Sharon L., primary, Wisoff, Jeffrey, primary, Harter, David, primary, Hidalgo, Eveline Teresa, primary, Golfinos, John G., primary, Orringer, Daniel A., primary, Aldape, Kenneth, primary, Benhamida, Jamal, primary, Wrzeszczynski, Kazimierz O., primary, Jour, George, primary, and Snuderl, Matija, primary

Published
2024
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10. Supplementary Table 2 from Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors

Author

Galbraith, Kristyn, primary, Serrano, Jonathan, primary, Shen, Guomiao, primary, Tran, Ivy, primary, Slocum, Cheyanne C., primary, Ketchum, Courtney, primary, Abdullaev, Zied, primary, Turakulov, Rust, primary, Bale, Tejus, primary, Ladanyi, Marc, primary, Sukhadia, Purvil, primary, Zaidinski, Michael, primary, Mullaney, Kerry, primary, DiNapoli, Sara, primary, Liechty, Benjamin L., primary, Barbaro, Marissa, primary, Allen, Jeffrey C., primary, Gardner, Sharon L., primary, Wisoff, Jeffrey, primary, Harter, David, primary, Hidalgo, Eveline Teresa, primary, Golfinos, John G., primary, Orringer, Daniel A., primary, Aldape, Kenneth, primary, Benhamida, Jamal, primary, Wrzeszczynski, Kazimierz O., primary, Jour, George, primary, and Snuderl, Matija, primary

Published
2024
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11. Supplementary Table 1 from Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors

Author

Galbraith, Kristyn, primary, Serrano, Jonathan, primary, Shen, Guomiao, primary, Tran, Ivy, primary, Slocum, Cheyanne C., primary, Ketchum, Courtney, primary, Abdullaev, Zied, primary, Turakulov, Rust, primary, Bale, Tejus, primary, Ladanyi, Marc, primary, Sukhadia, Purvil, primary, Zaidinski, Michael, primary, Mullaney, Kerry, primary, DiNapoli, Sara, primary, Liechty, Benjamin L., primary, Barbaro, Marissa, primary, Allen, Jeffrey C., primary, Gardner, Sharon L., primary, Wisoff, Jeffrey, primary, Harter, David, primary, Hidalgo, Eveline Teresa, primary, Golfinos, John G., primary, Orringer, Daniel A., primary, Aldape, Kenneth, primary, Benhamida, Jamal, primary, Wrzeszczynski, Kazimierz O., primary, Jour, George, primary, and Snuderl, Matija, primary

Published
2024
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13. Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors

Author

Galbraith, Kristyn, primary, Serrano, Jonathan, additional, Shen, Guomiao, additional, Tran, Ivy, additional, Slocum, Cheyanne C., additional, Ketchum, Courtney, additional, Abdullaev, Zied, additional, Turakulov, Rust, additional, Bale, Tejus, additional, Ladanyi, Marc, additional, Sukhadia, Purvil, additional, Zaidinski, Michael, additional, Mullaney, Kerry, additional, DiNapoli, Sara, additional, Liechty, Benjamin L., additional, Barbaro, Marissa, additional, Allen, Jeffrey C., additional, Gardner, Sharon L., additional, Wisoff, Jeffrey, additional, Harter, David, additional, Hidalgo, Eveline Teresa, additional, Golfinos, John G., additional, Orringer, Daniel A., additional, Aldape, Kenneth, additional, Benhamida, Jamal, additional, Wrzeszczynski, Kazimierz O., additional, Jour, George, additional, and Snuderl, Matija, additional

Published
2023
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15. Oncogenic TRK fusions are amenable to inhibition in hematologic malignancies

Author

Taylor, Justin, Pavlick, Dean, Yoshimi, Akihide, Marcelus, Christina, Chung, Stephen S., Hechtman, Jaclyn F., Benayed, Ryma, Cocco, Emiliano, Durham, Benjamin H., Bitner, Lillian, Inoue, Daichi, Chung, Young Rock, Mullaney, Kerry, Watts, Justin M., Diamond, Eli L., Albacker, Lee A., Mughal, Tariq I., Ebata, Kevin, Tuch, Brian B., Ku, Nora, Scaltriti, Maurizio, Roshal, Mikhail, Arcila, Maria, Ali, Siraj, Hyman, David M., Park, Jae H., and Abdel-Wahab, Omar

Subjects
Physiological aspects, Development and progression, Genetic aspects, Research, Health aspects, Protein-tyrosine kinase -- Physiological aspects -- Health aspects, Cancer genetics -- Research, Kinase inhibitors -- Research, Medical research, Hematologic diseases -- Genetic aspects -- Development and progression
Abstract

Introduction Fusions involving neurotrophic receptor tyrosine kinases (NTRKs) were among the first gene translocations described in cancer (1, 2). NTRK1, NTRK2, and NTRK3 (encoding TrkA, TrkB, and TrkC, respectively; hereafter [...], Rearrangements involving the neurotrophic receptor kinase genes (NTRK1, NTRK2, and NTRK3; hereafter referred to as TRK) produce oncogenic fusions in a wide variety of cancers in adults and children. Although TRK fusions occur in fewer than 1% of all solid tumors, inhibition of TRK results in profound therapeutic responses, resulting in Breakthrough Therapy FDA approval of the TRK inhibitor larotrectinib for adult and pediatric patients with solid tumors, regardless of histology. In contrast to solid tumors, the frequency of TRK fusions and the clinical effects of targeting TRK in hematologic malignancies are unknown. Here, through an evaluation for TRK fusions across more than 7,000 patients with hematologic malignancies, we identified TRK fusions in acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), histiocytosis, multiple myeloma, and dendritic cell neoplasms. Although TRK fusions occurred in only 0.1% of patients (8 of 7,311 patients), they conferred responsiveness to TRK inhibition in vitro and in vivo in a patient-derived xenograft and a corresponding AML patient with ETV6-NTRK2 fusion. These data identify that despite their individual rarity, collectively, TRK fusions are present in a wide variety of hematologic malignancies and predict clinically significant therapeutic responses to TRK inhibition.

Published
2018
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16. Recurrent TRAK1::RAF1 Fusions in pediatric low‐grade gliomas

Author

Benhamida, Jamal K., primary, Harmsen, Hannah J., additional, Ma, Deqin, additional, William, Christopher M., additional, Li, Bryan K., additional, Villafania, Liliana, additional, Sukhadia, Purvil, additional, Mullaney, Kerry A., additional, Dewan, Michael C., additional, Vakiani, Efsevia, additional, Karajannis, Matthias A., additional, Snuderl, Matija, additional, Zagzag, David, additional, Ladanyi, Marc, additional, Rosenblum, Marc K., additional, and Bale, Tejus A., additional

Published
2023
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18. FGFR1/2/3‐rearranged carcinoma of the head and neck: expanded histological spectrum crossing path with high‐risk HPV in the sinonasal tract.

Author

Chu, Ying‐Hsia, Mullaney, Kerry, DiNapoli, Sara E, Cohen, Marc A, Xu, Bin, Ghossein, Ronald, Katabi, Nora, and Dogan, Snjezana

Subjects
*PAPILLOMAVIRUSES, *HUMAN papillomavirus, *PARANASAL sinuses, *SQUAMOUS cell carcinoma, *ELECTRONIC health records, *NECK, *BREAST
Abstract

Aims: Oncogenic FGFR1/2/3 rearrangements are found in various cancers. Reported cases in head and neck (HN) are mainly squamous cell carcinomas (SCCs) with FGFR3::TACC3 fusions, a subset of which also harbour high‐risk human papillomavirus (HPV). However, the knowledge of the clinicopathological spectrum of FGFR‐rearranged head and neck carcinomas (FHNC) is limited. Methods and results: A retrospective MSK‐fusion clinical sequencing cohort 2016–23 was searched to identify malignant tumours in the HN region harbouring FGFR1/2/3 fusion. FHNC were characterised by histological examination, immunohistochemistry and molecular analysis. Electronic medical records were reviewed. Three FHNC were identified. Two cases (cases 1 and 2) involved sinonasal tract and were high‐grade carcinomas with squamous, basaloid, glandular and/or ductal–myoepithelial features. Case 1 arose in a 79‐year‐old man and harboured FGFR2::KIF1A fusion. Case 2 arose in a 58‐year‐old man, appeared as HPV‐related multiphenotypic sinonasal carcinoma (HMSC), and was positive for FGFR2::TACC2 fusion and concurrent high‐risk HPV, non‐type 16/18. Case 3 was FGFR3::TACC3 fusion‐positive keratinising SCCs arising in the parotid of a 60‐year‐old man. All three cases presented at stage T4. Clinical follow‐up was available in two cases; case 1 remained disease‐free for 41 months post‐treatment and case 3 died of disease 2 months after the diagnosis. Conclusions: FHNC include a morphological spectrum of carcinomas with squamous features and may occur in different HN locations, such as parotid gland and the sinonasal tract. Sinonasal cases can harbour FGFR2 rearrangement with or without associated high‐risk HPV. Timely recognition of FHNC could help select patients potentially amenable to targeted therapy with FGFR inhibitors. Further studies are needed (1) to determine if FGFR2 rearranged/HPV‐positive sinonasal carcinomas are biologically distinct from HMSC, and (2) to elucidate the biological and clinical significance of FGFR2 rearrangement in the context of high‐risk HPV. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Abstract 3931: BRD4, BRD3, NSD3, and ZNF532 fusions in histologies beyond NUT carcinomas: Investigation of a large pan-cancer cohort

Author

Nykaza, Ian R., primary, Febres-Aldana, Christopher A., additional, Lin, Sabrina T., additional, Benayed, Ryma, additional, Mullaney, Kerry, additional, Cocco, Emiliano, additional, Iasonos, Alexia, additional, Ladanyi, Marc, additional, Drilon, Alexander E., additional, and Murciano-Goroff, Yonina R., additional

Published
2023
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20. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

Author

Zehir, Ahmet, Benayed, Ryma, Shah, Ronak H, Syed, Aijazuddin, Middha, Sumit, Kim, Hyunjae R, Srinivasan, Preethi, Gao, Jianjiong, Chakravarty, Debyani, Devlin, Sean M, Hellmann, Matthew D, Barron, David A, Schram, Alison M, Hameed, Meera, Dogan, Snjezana, Ross, Dara S, Hechtman, Jaclyn F, DeLair, Deborah F, Yao, JinJuan, Mandelker, Diana L, Cheng, Donavan T, Chandramohan, Raghu, Mohanty, Abhinita S, Ptashkin, Ryan N, Jayakumaran, Gowtham, Prasad, Meera, Syed, Mustafa H, Rema, Anoop Balakrishnan, Liu, Zhen Y, Nafa, Khedoudja, Borsu, Laetitia, Sadowska, Justyna, Casanova, Jacklyn, Bacares, Ruben, Kiecka, Iwona J, Razumova, Anna, Son, Julie B, Stewart, Lisa, Baldi, Tessara, Mullaney, Kerry A, Al-Ahmadie, Hikmat, Vakiani, Efsevia, Abeshouse, Adam A, Penson, Alexander V, Jonsson, Philip, Camacho, Niedzica, Chang, Matthew T, Won, Helen H, Gross, Benjamin E, Kundra, Ritika, Heins, Zachary J, Chen, Hsiao-Wei, Phillips, Sarah, Zhang, Hongxin, Wang, Jiaojiao, Ochoa, Angelica, Wills, Jonathan, Eubank, Michael, Thomas, Stacy B, Gardos, Stuart M, Reales, Dalicia N, Galle, Jesse, Durany, Robert, Cambria, Roy, Abida, Wassim, Cercek, Andrea, Feldman, Darren R, Gounder, Mrinal M, Hakimi, A Ari, Harding, James J, Iyer, Gopa, Janjigian, Yelena Y, Jordan, Emmet J, Kelly, Ciara M, Lowery, Maeve A, Morris, Luc G T, Omuro, Antonio M, Raj, Nitya, Razavi, Pedram, Shoushtari, Alexander N, Shukla, Neerav, Soumerai, Tara E, Varghese, Anna M, Yaeger, Rona, Coleman, Jonathan, Bochner, Bernard, Riely, Gregory J, Saltz, Leonard B, Scher, Howard I, Sabbatini, Paul J, Robson, Mark E, Klimstra, David S, Taylor, Barry S, Baselga, Jose, Schultz, Nikolaus, Hyman, David M, Arcila, Maria E, Solit, David B, Ladanyi, Marc, and Berger, Michael F

Subjects
Development and progression, Genetic aspects, Research, Cancer -- Genetic aspects -- Research, Gene mutation -- Research, Cancer metastasis -- Genetic aspects -- Development and progression
Abstract

Author(s): Ahmet Zehir [1]; Ryma Benayed [1]; Ronak H Shah [1]; Aijazuddin Syed [1]; Sumit Middha [1]; Hyunjae R Kim [1]; Preethi Srinivasan [1]; Jianjiong Gao [2]; Debyani Chakravarty [2]; [...], Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.

Published
2017
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21. Supplementary Table 1 from A Performance Comparison of Commonly Used Assays to Detect RET Fusions

Author

Yang, Soo-Ryum, primary, Aypar, Umut, primary, Rosen, Ezra Y., primary, Mata, Douglas A., primary, Benayed, Ryma, primary, Mullaney, Kerry, primary, Jayakumaran, Gowtham, primary, Zhang, Yanming, primary, Frosina, Denise, primary, Drilon, Alexander, primary, Ladanyi, Marc, primary, Jungbluth, Achim A., primary, Rekhtman, Natasha, primary, and Hechtman, Jaclyn F., primary

Published
2023
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22. Supplementary Table 3 from A Performance Comparison of Commonly Used Assays to Detect RET Fusions

Author

Yang, Soo-Ryum, primary, Aypar, Umut, primary, Rosen, Ezra Y., primary, Mata, Douglas A., primary, Benayed, Ryma, primary, Mullaney, Kerry, primary, Jayakumaran, Gowtham, primary, Zhang, Yanming, primary, Frosina, Denise, primary, Drilon, Alexander, primary, Ladanyi, Marc, primary, Jungbluth, Achim A., primary, Rekhtman, Natasha, primary, and Hechtman, Jaclyn F., primary

Published
2023
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23. Supplementary Table 4 from A Performance Comparison of Commonly Used Assays to Detect RET Fusions

Author

Yang, Soo-Ryum, primary, Aypar, Umut, primary, Rosen, Ezra Y., primary, Mata, Douglas A., primary, Benayed, Ryma, primary, Mullaney, Kerry, primary, Jayakumaran, Gowtham, primary, Zhang, Yanming, primary, Frosina, Denise, primary, Drilon, Alexander, primary, Ladanyi, Marc, primary, Jungbluth, Achim A., primary, Rekhtman, Natasha, primary, and Hechtman, Jaclyn F., primary

Published
2023
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24. Legends for Supplementary Figure S1 from A Performance Comparison of Commonly Used Assays to Detect RET Fusions

Author

Yang, Soo-Ryum, primary, Aypar, Umut, primary, Rosen, Ezra Y., primary, Mata, Douglas A., primary, Benayed, Ryma, primary, Mullaney, Kerry, primary, Jayakumaran, Gowtham, primary, Zhang, Yanming, primary, Frosina, Denise, primary, Drilon, Alexander, primary, Ladanyi, Marc, primary, Jungbluth, Achim A., primary, Rekhtman, Natasha, primary, and Hechtman, Jaclyn F., primary

Published
2023
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25. Supplementary Table 2 from A Performance Comparison of Commonly Used Assays to Detect RET Fusions

Author

Yang, Soo-Ryum, primary, Aypar, Umut, primary, Rosen, Ezra Y., primary, Mata, Douglas A., primary, Benayed, Ryma, primary, Mullaney, Kerry, primary, Jayakumaran, Gowtham, primary, Zhang, Yanming, primary, Frosina, Denise, primary, Drilon, Alexander, primary, Ladanyi, Marc, primary, Jungbluth, Achim A., primary, Rekhtman, Natasha, primary, and Hechtman, Jaclyn F., primary

Published
2023
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26. Supplementary Methods from A Performance Comparison of Commonly Used Assays to Detect RET Fusions

Author

Yang, Soo-Ryum, primary, Aypar, Umut, primary, Rosen, Ezra Y., primary, Mata, Douglas A., primary, Benayed, Ryma, primary, Mullaney, Kerry, primary, Jayakumaran, Gowtham, primary, Zhang, Yanming, primary, Frosina, Denise, primary, Drilon, Alexander, primary, Ladanyi, Marc, primary, Jungbluth, Achim A., primary, Rekhtman, Natasha, primary, and Hechtman, Jaclyn F., primary

Published
2023
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27. Supplementary Figures from High Yield of RNA Sequencing for Targetable Kinase Fusions in Lung Adenocarcinomas with No Mitogenic Driver Alteration Detected by DNA Sequencing and Low Tumor Mutation Burden

Author

Benayed, Ryma, primary, Offin, Michael, primary, Mullaney, Kerry, primary, Sukhadia, Purvil, primary, Rios, Kelly, primary, Desmeules, Patrice, primary, Ptashkin, Ryan, primary, Won, Helen, primary, Chang, Jason, primary, Halpenny, Darragh, primary, Schram, Alison M., primary, Rudin, Charles M., primary, Hyman, David M., primary, Arcila, Maria E., primary, Berger, Michael F., primary, Zehir, Ahmet, primary, Kris, Mark G., primary, Drilon, Alexander, primary, and Ladanyi, Marc, primary

Published
2023
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28. Supplementary Figure S1 from A Performance Comparison of Commonly Used Assays to Detect RET Fusions

Author

Yang, Soo-Ryum, primary, Aypar, Umut, primary, Rosen, Ezra Y., primary, Mata, Douglas A., primary, Benayed, Ryma, primary, Mullaney, Kerry, primary, Jayakumaran, Gowtham, primary, Zhang, Yanming, primary, Frosina, Denise, primary, Drilon, Alexander, primary, Ladanyi, Marc, primary, Jungbluth, Achim A., primary, Rekhtman, Natasha, primary, and Hechtman, Jaclyn F., primary

Published
2023
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29. Supplementary Tables from High Yield of RNA Sequencing for Targetable Kinase Fusions in Lung Adenocarcinomas with No Mitogenic Driver Alteration Detected by DNA Sequencing and Low Tumor Mutation Burden

Author

Benayed, Ryma, primary, Offin, Michael, primary, Mullaney, Kerry, primary, Sukhadia, Purvil, primary, Rios, Kelly, primary, Desmeules, Patrice, primary, Ptashkin, Ryan, primary, Won, Helen, primary, Chang, Jason, primary, Halpenny, Darragh, primary, Schram, Alison M., primary, Rudin, Charles M., primary, Hyman, David M., primary, Arcila, Maria E., primary, Berger, Michael F., primary, Zehir, Ahmet, primary, Kris, Mark G., primary, Drilon, Alexander, primary, and Ladanyi, Marc, primary

Published
2023
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30. Malignant undifferentiated epithelioid neoplasms with MAML2 rearrangements: A clinicopathologic study of seven cases demonstrating a heterogenous entity

Author

Dermawan, Josephine K., primary, DiNapoli, Sara E., additional, Sukhadia, Purvil, additional, Mullaney, Kerry A., additional, Gladdy, Rebecca, additional, Healey, John H., additional, Agaimy, Abbas, additional, Cleven, Arjen H., additional, Suurmeijer, Albert J. H., additional, Dickson, Brendan C., additional, and Antonescu, Cristina R., additional

Published
2023
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34. EWSR1::YY1 fusion positive peritoneal epithelioid mesothelioma harbors mesothelioma epigenetic signature: Report of 3 cases in support of an emerging entity

Author

Dermawan, Josephine K., primary, Torrence, Dianne, additional, Lee, Cheng‐Han, additional, Villafania, Liliana, additional, Mullaney, Kerry A., additional, DiNapoli, Sara, additional, Sukhadia, Purvil, additional, Benayed, Ryma, additional, Borsu, Laetitia, additional, Agaram, Narasimhan P., additional, Nash, Garrett M., additional, Dickson, Brendan C., additional, Benhamida, Jamal, additional, and Antonescu, Cristina R., additional

Published
2022
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37. A Performance Comparison of Commonly Used Assays to Detect RET Fusions

Author

Yang, Soo-Ryum, primary, Aypar, Umut, additional, Rosen, Ezra Y., additional, Mata, Douglas A., additional, Benayed, Ryma, additional, Mullaney, Kerry, additional, Jayakumaran, Gowtham, additional, Zhang, Yanming, additional, Frosina, Denise, additional, Drilon, Alexander, additional, Ladanyi, Marc, additional, Jungbluth, Achim A., additional, Rekhtman, Natasha, additional, and Hechtman, Jaclyn F., additional

Published
2021
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38. P2RY8-CRLF2 Fusion–Positive Acute Myeloid Leukemia With Myelodysplasia-Related Changes: Response to Novel Therapy

Author

Aypar, Umut, primary, Taylor, Justin, additional, Garcia, Jacqueline S., additional, Momeni-Boroujeni, Amir, additional, Gao, Qi, additional, Baik, Jeeyeon, additional, Londono, Dory, additional, Benayed, Ryma, additional, Sigler, Allison, additional, Haddadin, Michael, additional, Penson, Alexander V., additional, Arcila, Maria E., additional, Mullaney, Kerry, additional, Sukhadia, Purvil, additional, Quesada, Andres E., additional, Roshal, Mikhail, additional, Cullen, Nicole, additional, Lako, Ana, additional, Rodig, Scott J., additional, Goldberg, Aaron D., additional, Zhang, Yanming, additional, Xiao, Wenbin, additional, and Ho, Caleb, additional

Published
2020
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39. High Yield of RNA Sequencing for Targetable Kinase Fusions in Lung Adenocarcinomas with No Mitogenic Driver Alteration Detected by DNA Sequencing and Low Tumor Mutation Burden

Author

Benayed, Ryma, primary, Offin, Michael, additional, Mullaney, Kerry, additional, Sukhadia, Purvil, additional, Rios, Kelly, additional, Desmeules, Patrice, additional, Ptashkin, Ryan, additional, Won, Helen, additional, Chang, Jason, additional, Halpenny, Darragh, additional, Schram, Alison M., additional, Rudin, Charles M., additional, Hyman, David M., additional, Arcila, Maria E., additional, Berger, Michael F., additional, Zehir, Ahmet, additional, Kris, Mark G., additional, Drilon, Alexander, additional, and Ladanyi, Marc, additional

Published
2019
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40. Colorectal Carcinomas Containing Hypermethylated MLH1 Promoter and Wild-Type BRAF/KRAS Are Enriched for Targetable Kinase Fusions

Author

Cocco, Emiliano, primary, Benhamida, Jamal, additional, Middha, Sumit, additional, Zehir, Ahmet, additional, Mullaney, Kerry, additional, Shia, Jinru, additional, Yaeger, Rona, additional, Zhang, Liying, additional, Wong, Donna, additional, Villafania, Liliana, additional, Nafa, Khedoudja, additional, Scaltriti, Maurizio, additional, Drilon, Alexander, additional, Saltz, Leonard, additional, Schram, Alison M., additional, Stadler, Zsofia K., additional, Hyman, David M., additional, Benayed, Ryma, additional, Ladanyi, Marc, additional, and Hechtman, Jaclyn F., additional

Published
2019
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41. Comprehensive detection of targetable fusions in lung adenocarcinomas by complementary targeted DNAseq and RNAseq assays.

Author

Benayed, Ryma, primary, Offin, Michael David, additional, Mullaney, Kerry A., additional, Sukhadia, Purvil, additional, Rios, Kelly M., additional, Desmeules, Patrice, additional, Chang, Jason C., additional, Hyman, David Michael, additional, Berger, Michael F., additional, Zehir, Ahmet, additional, Arcila, Maria E., additional, Kris, Mark G., additional, Drilon, Alexander E., additional, and Ladanyi, Marc, additional

Published
2018
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42. Characterization of Ntrk fusions and Therapeutic Response to Ntrk Inhibition in Hematologic Malignancies

Author

Taylor, Justin, primary, Marcelus, Christina, additional, Pavlick, Dean, additional, Benayed, Ryma, additional, Yoshimi, Akihide, additional, Cocco, Emiliano, additional, Durham, Benjamin H, additional, Hechtman, Jaclyn F, additional, Chung, Young Rock, additional, Mullaney, Kerry, additional, Watts, Justin M, additional, Diamond, Eli L, additional, Albacker, Lee A, additional, Mughal, Tariq I, additional, Ebata, Kevin, additional, Tuch, Brian B., additional, Ku, Nora, additional, Scaltriti, Maurizio, additional, Arcila, Maria E., additional, Ali, Siraj M, additional, Hyman, David M., additional, Abdel-Wahab, Omar, additional, and Park, Jae H., additional

Published
2017
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43. Erratum: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

Author

Zehir, Ahmet, primary, Benayed, Ryma, additional, Shah, Ronak H, additional, Syed, Aijazuddin, additional, Middha, Sumit, additional, Kim, Hyunjae R, additional, Srinivasan, Preethi, additional, Gao, Jianjiong, additional, Chakravarty, Debyani, additional, Devlin, Sean M, additional, Hellmann, Matthew D, additional, Barron, David A, additional, Schram, Alison M, additional, Hameed, Meera, additional, Dogan, Snjezana, additional, Ross, Dara S, additional, Hechtman, Jaclyn F, additional, DeLair, Deborah F, additional, Yao, JinJuan, additional, Mandelker, Diana L, additional, Cheng, Donavan T, additional, Chandramohan, Raghu, additional, Mohanty, Abhinita S, additional, Ptashkin, Ryan N, additional, Jayakumaran, Gowtham, additional, Prasad, Meera, additional, Syed, Mustafa H, additional, Rema, Anoop Balakrishnan, additional, Liu, Zhen Y, additional, Nafa, Khedoudja, additional, Borsu, Laetitia, additional, Sadowska, Justyna, additional, Casanova, Jacklyn, additional, Bacares, Ruben, additional, Kiecka, Iwona J, additional, Razumova, Anna, additional, Son, Julie B, additional, Stewart, Lisa, additional, Baldi, Tessara, additional, Mullaney, Kerry A, additional, Al-Ahmadie, Hikmat, additional, Vakiani, Efsevia, additional, Abeshouse, Adam A, additional, Penson, Alexander V, additional, Jonsson, Philip, additional, Camacho, Niedzica, additional, Chang, Matthew T, additional, Won, Helen H, additional, Gross, Benjamin E, additional, Kundra, Ritika, additional, Heins, Zachary J, additional, Chen, Hsiao-Wei, additional, Phillips, Sarah, additional, Zhang, Hongxin, additional, Wang, Jiaojiao, additional, Ochoa, Angelica, additional, Wills, Jonathan, additional, Eubank, Michael, additional, Thomas, Stacy B, additional, Gardos, Stuart M, additional, Reales, Dalicia N, additional, Galle, Jesse, additional, Durany, Robert, additional, Cambria, Roy, additional, Abida, Wassim, additional, Cercek, Andrea, additional, Feldman, Darren R, additional, Gounder, Mrinal M, additional, Hakimi, A Ari, additional, Harding, James J, additional, Iyer, Gopa, additional, Janjigian, Yelena Y, additional, Jordan, Emmet J, additional, Kelly, Ciara M, additional, Lowery, Maeve A, additional, Morris, Luc G T, additional, Omuro, Antonio M, additional, Raj, Nitya, additional, Razavi, Pedram, additional, Shoushtari, Alexander N, additional, Shukla, Neerav, additional, Soumerai, Tara E, additional, Varghese, Anna M, additional, Yaeger, Rona, additional, Coleman, Jonathan, additional, Bochner, Bernard, additional, Riely, Gregory J, additional, Saltz, Leonard B, additional, Scher, Howard I, additional, Sabbatini, Paul J, additional, Robson, Mark E, additional, Klimstra, David S, additional, Taylor, Barry S, additional, Baselga, Jose, additional, Schultz, Nikolaus, additional, Hyman, David M, additional, Arcila, Maria E, additional, Solit, David B, additional, Ladanyi, Marc, additional, and Berger, Michael F, additional

Published
2017
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44. A Pan-Cancer Study of Somatic TERTPromoter Mutations and Amplification in 30,773 Tumors Profiled by Clinical Genomic Sequencing

Author

Gupta, Sounak, Vanderbilt, Chad M., Lin, Yun-Te, Benhamida, Jamal K., Jungbluth, Achim A., Rana, Satshil, Momeni-Boroujeni, Amir, Chang, Jason C., Mcfarlane, Tiffany, Salazar, Paulo, Mullaney, Kerry, Middha, Sumit, Zehir, Ahmet, Gopalan, Anuradha, Bale, Tejus A., Ganly, Ian, Arcila, Maria E., Benayed, Ryma, Berger, Michael F., Ladanyi, Marc, and Dogan, Snjezana

Abstract

TERTgene promoter mutations are known in multiple cancer types. Other TERTalterations remain poorly characterized. Sequencing data from 30,773 tumors analyzed by a hybridization capture next-generation sequencing assay (Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets) were analyzed for the presence of TERTalterations. Promoter rearrangements (500 bases upstream of the transcriptional start site), hypermethylation (n= 57), and gene expression (n= 155) were evaluated for a subset of cases. Mutually exclusive and recurrent promoter mutations were identified at three hot spots upstream of the transcriptional start site in 11.3% of cases (−124: 74%; −146: 24%; and −138: <2%). Mutually exclusive amplification events were identified in another 2.3% of cases, whereas mutually exclusive rearrangements proximal to the TERTgene were seen in 24 cases. The highest incidence of TERTpromoter mutations was seen in cutaneous melanoma (82%), whereas amplification events significantly outnumbered promoter mutations in well-differentiated/dedifferentiated liposarcoma (14.1% versus 2.4%) and adrenocortical carcinoma (13.6% versus 4.5%). Gene expression analysis suggests that the highest levels of gene expression are seen in cases with amplifications and rearrangements. Hypermethylation events upstream of the TERTcoding sequence were not mutually exclusive with known pathogenic alterations. Studies aimed at defining the prevalence and prognostic impact of TERTalterations should incorporate other pathogenic TERTalterations as these may impact telomerase function.

Published
2021
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45. Androgen receptor splice variant-7 in breast cancer: clinical and pathologic correlations

Author

Ferguson, Donna C., Mata, Douglas A., Tay, Timothy KY., Traina, Tiffany A., Gucalp, Ayca, Chandarlapaty, Sarat, D’Alfonso, Timothy M., Brogi, Edi, Mullaney, Kerry, Ladanyi, Marc, Arcila, Maria E., Benayed, Ryma, and Ross, Dara S.

Abstract

Androgen receptor (AR) inhibitor therapy is a developing treatment for AR-positive breast cancer (BC) with ongoing clinical trials. AR splice variant-7 (AR-V7) is a truncated variant of AR that leads to AR inhibitor therapy resistance in prostate cancer; recent studies have identified AR-V7 in BC and theorized that AR-V7 can have a similar impact. This study assessed the prevalence and clinicopathologic features associated with AR-V7 in a large BC cohort. BC samples were evaluated by MSK-Fusion targeted RNAseq for AR-V7 detection and MSK-IMPACT targeted DNAseq, including triple-negative tumors with no driver alteration and estrogen receptor-positive/ESR1wildtype tumors progressing on therapy. Among 196 primary and metastatic/recurrent cases (196 RNAseq, 194DNAseq), 9.7% (19/196) were AR-V7 positive and 90.3% (177/196) AR-V7 negative. All AR-V7 positive BC were AR-positive by immunohistochemistry (19/19). The prevalence of AR-V7 by receptor subtype (N= 189) was: 18% (12/67) in ER-/PgR-/HER2-negative BC, 3.7% (4/109) in ER-positive/HER2-negative BC, and 15.4% (2/13) in HER2-positive BC; AR-V7 was detected in one ER-positive/HER2-unknown BC. Apocrine morphology was observed in 42.1% (8/19) of AR-V7 positive BC and 3.4% (6/177) AR-V7 negative BC (P< 0.00001). Notably, AR-V7 was detected in 2 primary BC and 7 metastatic/recurrent BC patients with no prior endocrine therapy. We conclude that positive AR IHC and apocrine morphology are pathologic features that may indicate testing for AR-V7 is warranted in both primary and metastatic BC in the appropriate clinical context. The study findings further encourage the assessment of AR-V7 as a predictive biomarker for AR antagonist benefit in ongoing clinical BC trials.

Published
2021
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46. Myositis ossificans-like soft tissue aneurysmal bone cyst: a clinical, radiological, and pathological study of seven cases with COL1A1-USP6fusion and a novel ANGPTL2-USP6fusion

Author

Zhang, Lingxin, Hwang, Sinchun, Benayed, Ryma, Zhu, Guo Gord, Mullaney, Kerry A., Rios, Kelly M., Sukhadia, Purvil Y., Agaram, Narasimhan, Zhang, Yanming, Bridge, Julia A., Healey, John H., Athanasian, Edward A., and Hameed, Meera

Abstract

Herein we described the clinical, radiological, histological, and molecular characteristics of seven soft tissue aneurysmal bone cysts (STABCs) diagnosed and managed at a tertiary cancer center and to elucidate their relationship with myositis ossificans (MO). All cases had established imaging and histopathological diagnosis of STABC and were subject to fluorescence in situ hybridization (FISH) for USP6rearrangement and Archer® FusionPlex® targeted RNA sequencing (RNASeq) analysis to identify the fusion partner. A thorough literature review of STABC and MO was conducted. The patients presented with painful masses unpreceded by trauma, occurring most commonly in the deep soft tissue of the thigh/gluteus (4/7), and also in the supraclavicular region, the axilla, and the hand. On imaging, the lesions were frequently associated with peripheral calcification on conventional radiographs and CT (6/7), cystic components on ultrasound, as well as perilesional edema (7/7) and fluid levels (3/7) on MRI. Bone scan (1/1) showed intense radiotracer uptake. Histologically, 6/7 cases demonstrated zonal arrangements reminiscent of MO. USP6rearrangement was found in all seven cases by FISH and/or RNASeq. RNASeq further detected COL1A1-USP6fusion in six cases and a novel ANGPTL2-USP6fusion in one case. Four patients underwent resection of the tumors and were disease free at their last follow-up. Three patients who underwent incisional or needle biopsies had no evidence of disease progression on imaging studies. In conclusion, the clinical, radiological, and pathological overlap between STABC and MO suggests that they are closely related entities. A novel fusion ANGPTL2-USP6is associated with distinct clinical and pathological presentation.

Published
2020
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47. Expanding the Spectrum of NR4A3Fusion–Positive Gynecologic Leiomyosarcomas

Author

Momeni-Boroujeni, Amir, Mullaney, Kerry, DiNapoli, Sara E., Leitao, Mario M., Hensley, Martee L., Katabi, Nora, Allison, Douglas H.R., Park, Kay J., Antonescu, Cristina R., and Chiang, Sarah

Abstract

Recurrent gene fusions have been observed in epithelioid and myxoid variants of uterine leiomyosarcoma. PGR::NR4A3fusions were recently described in a subset of epithelioid leiomyosarcomas exhibiting rhabdoid morphology. In this study, we sought to expand the clinical, morphologic, immunohistochemical, and genetic features of gynecologic leiomyosarcomas harboring NR4A3rearrangements with PGRand novel fusion partners. We identified 9 gynecologic leiomyosarcomas harboring PGR::NR4A3, CARMN::NR4A3, ACTB::NR4A3, and possible SLCO5A1::NR4A3fusions by targeted RNA sequencing. Tumors frequently affected premenopausal women, involving the uterine corpus, uterine cervix, or pelvis. All were similarly characterized by lobules of monomorphic epithelioid and/or spindled cells arranged in sheets, cords, trabeculae, and micro- and macrocysts associated with abundant myxoid matrix and hemorrhage, creating labyrinth-like or pulmonary edema–like architecture. Myogenic differentiation with frequent estrogen receptor and progesterone receptor staining and no CD10 expression characterized all tumors. All cases showed high NR4A3RNA expression levels and NOR1 (NR4A3) nuclear staining similar to salivary gland acinic cell carcinomas and a subset of extraskeletal myxoid chondrosarcomas harboring NR4A3rearrangements. NOR1 (NR4A3) immunohistochemistry may serve as a useful diagnostic marker of NR4A3fusion–positive gynecologic leiomyosarcomas.

Published
2024
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49. NTRKfusion detection across multiple assays and 33,997 cases: diagnostic implications and pitfalls

Author

Solomon, James P., Linkov, Irina, Rosado, Andrea, Mullaney, Kerry, Rosen, Ezra Y., Frosina, Denise, Jungbluth, Achim A., Zehir, Ahmet, Benayed, Ryma, Drilon, Alexander, Hyman, David M., Ladanyi, Marc, Sireci, Anthony N., and Hechtman, Jaclyn F.

Abstract

With the FDA approval of larotrectinib, NTRKfusion assessment has recently become a standard part of management for patients with locally advanced or metastatic cancers. Unlike somatic mutation assessment, the detection of NTRKfusions is not straightforward, and various assays exist at the DNA, RNA, and protein level. Here, we investigate the performance of immunohistochemistry and DNA-based next-generation sequencing to indirectly or directly detect NTRKfusions relative to an RNA-based next-generation sequencing approach in the largest cohort of NTRKfusion positive solid tumors to date. A retrospective analysis of 38,095 samples from 33,997 patients sequenced by a targeted DNA-based next-generation sequencing panel (MSK-IMPACT), 2189 of which were also examined by an RNA-based sequencing assay (MSK-Fusion), identified 87 patients with oncogenic NTRK1-3fusions. All available institutional NTRKfusion positive cases were assessed by pan-Trk immunohistochemistry along with a cohort of control cases negative for NTRKfusions by next-generation sequencing. DNA-based sequencing showed an overall sensitivity and specificity of 81.1% and 99.9%, respectively, for the detection of NTRKfusions when compared to RNA-based sequencing. False negatives occurred when fusions involved breakpoints not covered by the assay. Immunohistochemistry showed overall sensitivity of 87.9% and specificity of 81.1%, with high sensitivity for NTRK1(96%) and NTRK2(100%) fusions and lower sensitivity for NTRK3fusions (79%). Specificity was 100% for carcinomas of the colon, lung, thyroid, pancreas, and biliary tract. Decreased specificity was seen in breast and salivary gland carcinomas (82% and 52%, respectively), and positive staining was often seen in tumors with neural differentiation. Both sensitivity and specificity were poor in sarcomas. Selection of the appropriate assay for NTRKfusion detection therefore depends on tumor type and genes involved, as well as consideration of other factors such as available material, accessibility of various clinical assays, and whether comprehensive genomic testing is needed concurrently.

Published
2020
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50. Diagnosis of known sarcoma fusions and novel fusion partners by targeted RNA sequencing with identification of a recurrent ACTB-FOSBfusion in pseudomyogenic hemangioendothelioma

Author

Zhu, Guo, Benayed, Ryma, Ho, Caleb, Mullaney, Kerry, Sukhadia, Purvil, Rios, Kelly, Berry, Ryan, Rubin, Brian P., Nafa, Khedoudja, Wang, Lu, Klimstra, David S., Ladanyi, Marc, and Hameed, Meera R.

Abstract

Integration of morphological, immunohistochemical, and molecular methods is often necessary for the precise diagnosis and optimal clinical management of sarcomas. We have validated and implemented a clinical molecular diagnostic assay, MSK- Fusion Solid, for detection of gene fusions in solid tumors, including sarcomas. Starting with RNA extracted from formalin-fixed paraffin-embedded tumor material, this targeted RNA sequencing assay utilizes anchored multiplex PCR to detect oncogenic fusion transcripts involving 62 genes known to be recurrently rearranged in solid tumors including sarcomas without prior knowledge of fusion partners. From 1/2016 to 1/2018, 192 bone and soft tissue tumors were submitted for MSK- Fusion Solid analysis and 96% (184/192) successfully passed all the pre-sequencing quality control parameters and sequencing steps. These sarcomas encompass 24 major tumor types, including 175 soft tissue tumors and 9 osteosarcomas. Ewing and Ewing-like sarcomas, rhabdomyosarcoma, and sarcoma-not otherwise specified were the three most common tumor types. Diagnostic in-frame fusion transcripts were detected in 43% of cases, including 3% (6/184) with novel fusion partners, specifically TRPS1-PLAG1, VCP-TFE3, MYLK-BRAF, FUS-TFCP2, and ACTB-FOSB, the latter in two cases of pseudomyogenic hemangioendothelioma, representing a novel observation in this sarcoma. Our experience shows that this targeted RNA sequencing assay performs in a robust and sensitive fashion on RNA extracted from most routine clinical specimens of sarcomas thereby facilitating precise diagnosis and providing opportunities for novel fusion partner discovery.

Published
2019
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