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474 results on '"Tyekucheva, Svitlana"'

1. Phase II Study of Acalabrutinib, Venetoclax, and Obinutuzumab in a Treatment-Naïve Chronic Lymphocytic Leukemia Population Enriched for High-Risk Disease

Author

Davids, Matthew S., Ryan, Christine E., Lampson, Benjamin L., Ren, Yue, Tyekucheva, Svitlana, Fernandes, Stacey M., Crombie, Jennifer L., Kim, Austin I., Weinstock, Matthew, Montegaard, Josie, Walker, Heather A., Greenman, Claire, Patterson, Victoria, Jacobson, Caron A., LaCasce, Ann S., Armand, Philippe, Fisher, David C., Lo, Steve, Olszewski, Adam J., Arnason, Jon E., Ahn, Inhye E., and Brown, Jennifer R.

Published
2024
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3. Cross-Study Replicability in Cluster Analysis

Author

Masoero, Lorenzo, Thomas, Emma, Parmigiani, Giovanni, Tyekucheva, Svitlana, and Trippa, Lorenzo

Subjects
Statistics - Methodology, Statistics - Applications
Abstract

In cancer research, clustering techniques are widely used for exploratory analyses and dimensionality reduction, playing a critical role in the identification of novel cancer subtypes, often with direct implications for patient management. As data collected by multiple research groups grows, it is increasingly feasible to investigate the replicability of clustering procedures, that is, their ability to consistently recover biologically meaningful clusters across several datasets. In this paper, we review existing methods to assess replicability of clustering analyses, and discuss a framework for evaluating cross-study clustering replicability, useful when two or more studies are available. These approaches can be applied to any clustering algorithm and can employ different measures of similarity between partitions to quantify replicability, globally (i.e. for the whole sample) as well as locally (i.e. for individual clusters). Using experiments on synthetic and real gene expression data, we illustrate the utility of replicability metrics to evaluate if the same clusters are identified consistently across a collection of datasets., Comment: Accepted for publication in Statistical Science

Published
2022
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6. Five-year follow-up of a phase 2 study of ibrutinib plus fludarabine, cyclophosphamide, and rituximab as initial therapy in CLL

Author

Ahn, Inhye E., Brander, Danielle M., Ren, Yue, Zhou, Yinglu, Tyekucheva, Svitlana, Walker, Heather A., Black, Robert, Montegaard, Josie, Alencar, Alvaro, Shune, Leyla, Omaira, Mohammad, Jacobson, Caron A., Armand, Philippe, Ng, Samuel Y., Crombie, Jennifer, Fisher, David C., LaCasce, Ann S., Arnason, Jon, Hochberg, Ephraim P., Takvorian, Ronald W., Abramson, Jeremy S., Brown, Jennifer R., and Davids, Matthew S.

Published
2024
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7. A phase 1b study of ibrutinib in combination with obinutuzumab in patients with relapsed or refractory chronic lymphocytic leukemia

Author

Ryan, Christine E., Brander, Danielle M., Barr, Paul M., Tyekucheva, Svitlana, Hackett, Liam R., Collins, Mary C., Fernandes, Stacey M., Ren, Yue, Zhou, Yinglu, McDonough, Mikaela M., Walker, Heather A., McEwan, Monica R., Abramson, Jeremy S., Jacobsen, Eric D., LaCasce, Ann S., Fisher, David C., Brown, Jennifer R., and Davids, Matthew S.

Published
2023
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8. Systematic Assessment of Tumor Purity and Its Clinical Implications

Author

Haider, Syed, Tyekucheva, Svitlana, Prandi, Davide, Fox, Natalie S, Ahn, Jaeil, Xu, Andrew Wei, Pantazi, Angeliki, Park, Peter J, Laird, Peter W, Sander, Chris, Wang, Wenyi, Demichelis, Francesca, Loda, Massimo, and Boutros, Paul C

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Human Genome, Cancer, Genetics, Biotechnology, Cancer Genomics, Prostate Cancer, Urologic Diseases, Cancer Genome Atlas Research Network, Oncology and carcinogenesis
Abstract

PurposeThe tumor microenvironment is complex, comprising heterogeneous cellular populations. As molecular profiles are frequently generated using bulk tissue sections, they represent an admixture of multiple cell types (including immune, stromal, and cancer cells) interacting with each other. Therefore, these molecular profiles are confounded by signals emanating from many cell types. Accurate assessment of residual cancer cell fraction is crucial for parameterization and interpretation of genomic analyses, as well as for accurately interpreting the clinical properties of the tumor.Materials and methodsTo benchmark cancer cell fraction estimation methods, 10 estimators were applied to a clinical cohort of 333 patients with prostate cancer. These methods include gold-standard multiobserver pathology estimates, as well as estimates inferred from genome, epigenome, and transcriptome data. In addition, two methods based on genomic and transcriptomic profiles were used to quantify tumor purity in 4,497 tumors across 12 cancer types. Bulk mRNA and microRNA profiles were subject to in silico deconvolution to estimate cancer cell-specific mRNA and microRNA profiles.ResultsWe present a systematic comparison of 10 tumor purity estimation methods on a cohort of 333 prostate tumors. We quantify variation among purity estimation methods and demonstrate how this influences interpretation of clinico-genomic analyses. Our data show poor concordance between pathologic and molecular purity estimates, necessitating caution when interpreting molecular results. Limited concordance between DNA- and mRNA-derived purity estimates remained a general pan-cancer phenomenon when tested in an additional 4,497 tumors spanning 12 cancer types.ConclusionThe choice of tumor purity estimation method may have a profound impact on the interpretation of genomic assays. Taken together, these data highlight the need for improved assessment of tumor purity and quantitation of its influences on the molecular hallmarks of cancers.

Published
2020

9. Genetic events associated with venetoclax resistance in CLL identified by whole-exome sequencing of patient samples

Author

Khalsa, Jasneet Kaur, Cha, Justin, Utro, Filippo, Naeem, Aishath, Murali, Ishwarya, Kuang, Yanan, Vasquez, Kevin, Li, Liang, Tyekucheva, Svitlana, Fernandes, Stacey M., Veronese, Lauren, Guieze, Romain, Sasi, Binu Kandathilparambil, Wang, Zixu, Machado, John-Hanson, Bai, Harrison, Alasfour, Maryam, Rhrissorrakrai, Kahn, Levovitz, Chaya, Danysh, Brian P., Slowik, Kara, Jacobs, Raquel A., Davids, Matthew S., Paweletz, Cloud P., Leshchiner, Ignaty, Parida, Laxmi, Getz, Gad, and Brown, Jennifer R.

Published
2023
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10. Pirtobrutinib targets BTK C481S in ibrutinib-resistant CLL but second-site BTK mutations lead to resistance

Author

Naeem, Aishath, Utro, Filippo, Wang, Qing, Cha, Justin, Vihinen, Mauno, Martindale, Stephen, Zhou, Yinglu, Ren, Yue, Tyekucheva, Svitlana, Kim, Annette S., Fernandes, Stacey M., Saksena, Gordon, Rhrissorrakrai, Kahn, Levovitz, Chaya, Danysh, Brian P., Slowik, Kara, Jacobs, Raquel A., Davids, Matthew S., Lederer, James A., Zain, Rula, Smith, C. I. Edvard, Leshchiner, Ignaty, Parida, Laxmi, Getz, Gad, and Brown, Jennifer R.

Published
2023
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11. A T cell inflammatory phenotype is associated with autoimmune toxicity of the PI3K inhibitor duvelisib in chronic lymphocytic leukemia

Author

Gadi, Deepti, Griffith, Alec, Tyekucheva, Svitlana, Wang, Zixu, Rai, Vanessa, Vartanov, Alexander, Thrash, Emily, Fernandes, Stacey M., Lehmberg, Timothy Z., Lee, Brandon, Martindale, Stephen P., Machado, John-Hanson, Odejide, Oreofe, Armand, Philippe, Fisher, David C., Arnason, Jon, Davids, Matthew S., Lederer, James A., and Brown, Jennifer R.

Published
2022
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12. Logistic push: a regression framework for partial AUC optimization

Author

Gerke, Travis, Tyekucheva, Svitlana, Mucci, Lorelei, and Parmigiani, Giovanni

Subjects
Statistics - Applications
Abstract

The area under the receiver operating characteristic curve (AUC) is often used to evaluate the performance of clinical prediction models. Recently, a more refined strategy has been proposed to examine a partial area under the curve (pAUC), which can account for differing costs associated with false negative versus false positive results. Such consideration can substantially increase the clinical utility of prediction models depending on the clinical question. Properties of the pAUC estimator create significant challenges for pAUC-optimal marker selection and model building. As such, current approaches towards these aims can be complex and computationally intensive. We present a simpler method based on weighted logistic regressions. We refer to our strategy as logistic push, due to shared heuristics with the ranking algorithm P-norm push. Logistic push is particularly useful in the high-dimensional setting, where fast and broadly available algorithms for fitting penalized regressions can be used for both marker selection and model fitting.

Published
2016

13. Acalabrutinib, venetoclax, and obinutuzumab as frontline treatment for chronic lymphocytic leukaemia: a single-arm, open-label, phase 2 study

Author

Davids, Matthew S, Lampson, Benjamin L, Tyekucheva, Svitlana, Wang, Zixu, Lowney, Jessica C, Pazienza, Samantha, Montegaard, Josie, Patterson, Victoria, Weinstock, Matthew, Crombie, Jennifer L, Ng, Samuel Y, Kim, Austin I, Jacobson, Caron A, LaCasce, Ann S, Armand, Philippe, Arnason, Jon E, Fisher, David C, and Brown, Jennifer R

Published
2021
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15. Abstract P01: Impact of Germline and Somatic ATM Variants in Chronic Lymphocytic Leukemia (CLL): Clinical Implications and Response to PARP Inhibition

Author

Mashima, Kiyomi, primary, Moore, Nicholas, additional, Mikhaleva, Mariia, additional, Petráčková, Anna, additional, Shupe, Samantha, additional, Fernandes, Stacey M, additional, Taylor-Weiner, Amaro, additional, Gillani, Riaz, additional, Chu, Hoyin, additional, Han, Seunghun, additional, Camp, Sabrina, additional, Kofman, Eric, additional, Getz, Gad, additional, Wu, Catherine J., additional, Tyekucheva, Svitlana, additional, Davids, Matthew S, additional, Van Allen, Eliezer Mendel, additional, AlDubayan, Saud, additional, and Brown, Jennifer R, additional

Published
2024
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19. Ibrutinib plus fludarabine, cyclophosphamide, and rituximab as initial treatment for younger patients with chronic lymphocytic leukaemia: a single-arm, multicentre, phase 2 trial

Author

Davids, Matthew S, Brander, Danielle M, Kim, Haesook T, Tyekucheva, Svitlana, Bsat, Jad, Savell, Alexandra, Hellman, Jeffrey M, Bazemore, Josie, Francoeur, Karen, Alencar, Alvaro, Shune, Leyla, Omaira, Mohammad, Jacobson, Caron A, Armand, Philippe, Ng, Samuel, Crombie, Jennifer, LaCasce, Ann S, Arnason, Jon, Hochberg, Ephraim P, Takvorian, Ronald W, Abramson, Jeremy S, Fisher, David C, and Brown, Jennifer R

Published
2019
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20. Inhibition of de novo lipogenesis targets androgen receptor signaling in castration-resistant prostate cancer

Author

Zadra, Giorgia, Ribeiro, Caroline F., Chetta, Paolo, Ho, Yeung, Cacciatore, Stefano, Gao, Xueliang, Syamala, Sudeepa, Bango, Clyde, Photopoulos, Cornelia, Huang, Ying, Tyekucheva, Svitlana, Bastos, Debora C., Tchaicha, Jeremy, Lawney, Brian, Uo, Takuma, D’Anello, Laura, Csibi, Alfredo, Kalekar, Radha, Larimer, Benjamin, Ellis, Leigh, Butler, Lisa M., Morrissey, Colm, McGovern, Karen, Palombella, Vito J., Kutok, Jeffery L., Mahmood, Umar, Bosari, Silvano, Adams, Julian, Peluso, Stephane, Dehm, Scott M., Plymate, Stephen R., and Loda, Massimo

Published
2019

27. Supplementary Figure 1 from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum

Author

Penney, Kathryn L., primary, Tyekucheva, Svitlana, primary, Rosenthal, Jacob, primary, El Fandy, Habiba, primary, Carelli, Ryan, primary, Borgstein, Stephanie, primary, Zadra, Giorgia, primary, Fanelli, Giuseppe Nicolò, primary, Stefanizzi, Lavinia, primary, Giunchi, Francesca, primary, Pomerantz, Mark, primary, Peisch, Samuel, primary, Coulson, Hannah, primary, Lis, Rosina, primary, Kibel, Adam S., primary, Fiorentino, Michelangelo, primary, Umeton, Renato, primary, and Loda, Massimo, primary

Published
2023
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28. Supplementary Figure 4 from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum

Author

Penney, Kathryn L., primary, Tyekucheva, Svitlana, primary, Rosenthal, Jacob, primary, El Fandy, Habiba, primary, Carelli, Ryan, primary, Borgstein, Stephanie, primary, Zadra, Giorgia, primary, Fanelli, Giuseppe Nicolò, primary, Stefanizzi, Lavinia, primary, Giunchi, Francesca, primary, Pomerantz, Mark, primary, Peisch, Samuel, primary, Coulson, Hannah, primary, Lis, Rosina, primary, Kibel, Adam S., primary, Fiorentino, Michelangelo, primary, Umeton, Renato, primary, and Loda, Massimo, primary

Published
2023
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29. Figure S6 from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate

Author

Elfandy, Habiba, primary, Armenia, Joshua, primary, Pederzoli, Filippo, primary, Pullman, Eli, primary, Pertega-Gomes, Nelma, primary, Schultz, Nikolaus, primary, Viswanathan, Kartik, primary, Vosoughi, Aram, primary, Blattner, Mirjam, primary, Stopsack, Konrad H., primary, Zadra, Giorgia, primary, Penney, Kathryn L., primary, Mosquera, Juan Miguel, primary, Tyekucheva, Svitlana, primary, Mucci, Lorelei A., primary, Barbieri, Christopher, primary, and Loda, Massimo, primary

Published
2023
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31. Supplementary Figure 2 from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum

Author

Penney, Kathryn L., primary, Tyekucheva, Svitlana, primary, Rosenthal, Jacob, primary, El Fandy, Habiba, primary, Carelli, Ryan, primary, Borgstein, Stephanie, primary, Zadra, Giorgia, primary, Fanelli, Giuseppe Nicolò, primary, Stefanizzi, Lavinia, primary, Giunchi, Francesca, primary, Pomerantz, Mark, primary, Peisch, Samuel, primary, Coulson, Hannah, primary, Lis, Rosina, primary, Kibel, Adam S., primary, Fiorentino, Michelangelo, primary, Umeton, Renato, primary, and Loda, Massimo, primary

Published
2023
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32. Table S1, S2, S3 from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate

Author

Elfandy, Habiba, primary, Armenia, Joshua, primary, Pederzoli, Filippo, primary, Pullman, Eli, primary, Pertega-Gomes, Nelma, primary, Schultz, Nikolaus, primary, Viswanathan, Kartik, primary, Vosoughi, Aram, primary, Blattner, Mirjam, primary, Stopsack, Konrad H., primary, Zadra, Giorgia, primary, Penney, Kathryn L., primary, Mosquera, Juan Miguel, primary, Tyekucheva, Svitlana, primary, Mucci, Lorelei A., primary, Barbieri, Christopher, primary, and Loda, Massimo, primary

Published
2023
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34. Supplementary Figure 3 from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum

Author

Penney, Kathryn L., primary, Tyekucheva, Svitlana, primary, Rosenthal, Jacob, primary, El Fandy, Habiba, primary, Carelli, Ryan, primary, Borgstein, Stephanie, primary, Zadra, Giorgia, primary, Fanelli, Giuseppe Nicolò, primary, Stefanizzi, Lavinia, primary, Giunchi, Francesca, primary, Pomerantz, Mark, primary, Peisch, Samuel, primary, Coulson, Hannah, primary, Lis, Rosina, primary, Kibel, Adam S., primary, Fiorentino, Michelangelo, primary, Umeton, Renato, primary, and Loda, Massimo, primary

Published
2023
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36. Data from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate

Author

Elfandy, Habiba, primary, Armenia, Joshua, primary, Pederzoli, Filippo, primary, Pullman, Eli, primary, Pertega-Gomes, Nelma, primary, Schultz, Nikolaus, primary, Viswanathan, Kartik, primary, Vosoughi, Aram, primary, Blattner, Mirjam, primary, Stopsack, Konrad H., primary, Zadra, Giorgia, primary, Penney, Kathryn L., primary, Mosquera, Juan Miguel, primary, Tyekucheva, Svitlana, primary, Mucci, Lorelei A., primary, Barbieri, Christopher, primary, and Loda, Massimo, primary

Published
2023
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37. Supplementary Data from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum

Author

Penney, Kathryn L., primary, Tyekucheva, Svitlana, primary, Rosenthal, Jacob, primary, El Fandy, Habiba, primary, Carelli, Ryan, primary, Borgstein, Stephanie, primary, Zadra, Giorgia, primary, Fanelli, Giuseppe Nicolò, primary, Stefanizzi, Lavinia, primary, Giunchi, Francesca, primary, Pomerantz, Mark, primary, Peisch, Samuel, primary, Coulson, Hannah, primary, Lis, Rosina, primary, Kibel, Adam S., primary, Fiorentino, Michelangelo, primary, Umeton, Renato, primary, and Loda, Massimo, primary

Published
2023
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38. Table S9, S10 from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate

Author

Elfandy, Habiba, primary, Armenia, Joshua, primary, Pederzoli, Filippo, primary, Pullman, Eli, primary, Pertega-Gomes, Nelma, primary, Schultz, Nikolaus, primary, Viswanathan, Kartik, primary, Vosoughi, Aram, primary, Blattner, Mirjam, primary, Stopsack, Konrad H., primary, Zadra, Giorgia, primary, Penney, Kathryn L., primary, Mosquera, Juan Miguel, primary, Tyekucheva, Svitlana, primary, Mucci, Lorelei A., primary, Barbieri, Christopher, primary, and Loda, Massimo, primary

Published
2023
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39. Data from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum

Author

Penney, Kathryn L., primary, Tyekucheva, Svitlana, primary, Rosenthal, Jacob, primary, El Fandy, Habiba, primary, Carelli, Ryan, primary, Borgstein, Stephanie, primary, Zadra, Giorgia, primary, Fanelli, Giuseppe Nicolò, primary, Stefanizzi, Lavinia, primary, Giunchi, Francesca, primary, Pomerantz, Mark, primary, Peisch, Samuel, primary, Coulson, Hannah, primary, Lis, Rosina, primary, Kibel, Adam S., primary, Fiorentino, Michelangelo, primary, Umeton, Renato, primary, and Loda, Massimo, primary

Published
2023
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40. Table S11 from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate

Author

Elfandy, Habiba, primary, Armenia, Joshua, primary, Pederzoli, Filippo, primary, Pullman, Eli, primary, Pertega-Gomes, Nelma, primary, Schultz, Nikolaus, primary, Viswanathan, Kartik, primary, Vosoughi, Aram, primary, Blattner, Mirjam, primary, Stopsack, Konrad H., primary, Zadra, Giorgia, primary, Penney, Kathryn L., primary, Mosquera, Juan Miguel, primary, Tyekucheva, Svitlana, primary, Mucci, Lorelei A., primary, Barbieri, Christopher, primary, and Loda, Massimo, primary

Published
2023
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42. Supplementary Figures S1-S6 from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate

Author

Elfandy, Habiba, primary, Armenia, Joshua, primary, Pederzoli, Filippo, primary, Pullman, Eli, primary, Pertega-Gomes, Nelma, primary, Schultz, Nikolaus, primary, Viswanathan, Kartik, primary, Vosoughi, Aram, primary, Blattner, Mirjam, primary, Stopsack, Konrad H., primary, Zadra, Giorgia, primary, Penney, Kathryn L., primary, Mosquera, Juan Miguel, primary, Tyekucheva, Svitlana, primary, Mucci, Lorelei A., primary, Barbieri, Christopher, primary, and Loda, Massimo, primary

Published
2023
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43. Supplementary Table 1 from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum

Author

Penney, Kathryn L., primary, Tyekucheva, Svitlana, primary, Rosenthal, Jacob, primary, El Fandy, Habiba, primary, Carelli, Ryan, primary, Borgstein, Stephanie, primary, Zadra, Giorgia, primary, Fanelli, Giuseppe Nicolò, primary, Stefanizzi, Lavinia, primary, Giunchi, Francesca, primary, Pomerantz, Mark, primary, Peisch, Samuel, primary, Coulson, Hannah, primary, Lis, Rosina, primary, Kibel, Adam S., primary, Fiorentino, Michelangelo, primary, Umeton, Renato, primary, and Loda, Massimo, primary

Published
2023
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48. Data from Stress-Related Signaling Pathways in Lethal and Nonlethal Prostate Cancer

Author

Lu, Donghao, primary, Sinnott, Jennifer A., primary, Valdimarsdóttir, Unnur, primary, Fang, Fang, primary, Gerke, Travis, primary, Tyekucheva, Svitlana, primary, Fiorentino, Michelangelo, primary, Lambe, Mats, primary, Sesso, Howard D., primary, Sweeney, Christopher J., primary, Wilson, Kathryn M., primary, Giovannucci, Edward L., primary, Loda, Massimo, primary, Mucci, Lorelei A., primary, and Fall, Katja, primary

Published
2023
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50. Supplementary Data from Multiplex Immunofluorescence in Formalin-Fixed Paraffin-Embedded Tumor Tissue to Identify Single-Cell–Level PI3K Pathway Activation

Author

Stopsack, Konrad H., primary, Huang, Ying, primary, Tyekucheva, Svitlana, primary, Gerke, Travis A., primary, Bango, Clyde, primary, Elfandy, Habiba, primary, Bowden, Michaela, primary, Penney, Kathryn L., primary, Roberts, Thomas M., primary, Parmigiani, Giovanni, primary, Kantoff, Philip W., primary, Mucci, Lorelei A., primary, and Loda, Massimo, primary

Published
2023
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