Search

Your search keyword '"Nsengimana, Jérémie"' showing total 239 results
Start Over Author "Nsengimana, Jérémie"
239 results on '"Nsengimana, Jérémie"'

1. Utilising high-dimensional data in randomised clinical trials: a review of methods and practice

Author

Cherlin, Svetlana, Bigirumurame, Theophile, Grayling, Michael J, Nsengimana, Jérémie, Ouma, Luke, Santaolalla, Aida, Wan, Fang, Williamson, S Faye, and Wason, James M S

Subjects
Statistics - Applications
Abstract

Introduction: Even in effectively conducted randomised trials, the probability of a successful study remains relatively low. With recent advances in the next-generation sequencing technologies, there is a rapidly growing number of high-dimensional data, including genetic, molecular and phenotypic information, that have improved our understanding of driver genes, drug targets, and drug mechanisms of action. The leveraging of high-dimensional data holds promise for increased success of clinical trials. Methods: We provide an overview of methods for utilising high-dimensional data in clinical trials. We also investigate the use of these methods in practice through a review of recently published randomised clinical trials that utilise high-dimensional genetic data. The review includes articles that were published between 2019 and 2021, identified through the PubMed database. Results: Out of 174 screened articles, 100 (57.5%) were randomised clinical trials that collected high-dimensional data. The most common clinical area was oncology (30%), followed by chronic diseases (28%), nutrition and ageing (18%) and cardiovascular diseases (7%). The most common types of data analysed were gene expression data (70%), followed by DNA data (21%). The most common method of analysis (36.3%) was univariable analysis. Articles that described multivariable analyses used standard statistical methods. Most of the clinical trials had two arms. Discussion: New methodological approaches are required for more efficient analysis of the increasing amount of high-dimensional data collected in randomised clinical trials. We highlight the limitations and barriers to the current use of high-dimensional data in trials, and suggest potential avenues for improvement and future work., Comment: 17 pages, 3 figures, 2 tables

Published
2023

2. Multi-level Graph Representations of Melanoma Whole Slide Images for Identifying Immune Subgroups

Author

Godson, Lucy, Alemi, Navid, Nsengimana, Jérémie, Cook, Graham P., Clarke, Emily L., Treanor, Darren, Bishop, D. Timothy, Newton-Bishop, Julia, Magee, Derek, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Ahmadi, Seyed-Ahmad, editor, and Pereira, Sérgio, editor

Published
2024
Full Text
View/download PDF

3. Monitoring immunE DysregulAtion foLLowing Immune checkpOint-inhibitioN (MEDALLION): protocol for an observational cancer immunotherapy cohort study

Author

Gault, Abigail, Hogarth, Linda, Williams, Kristian C, Greystoke, Alastair, Rajan, Neil, Speight, Ally, Lamb, Christopher A, Bridgewood, Alison, Brown-Schofield, Lisa-Jayne, Rayner, Fiona, Isaacs, John D, Nsengimana, Jérémie, Stewart, Christopher J, Anderson, Amy E, Plummer, Ruth, and Pratt, Arthur G

Published
2024
Full Text
View/download PDF

4. Weakly-supervised learning for image-based classification of primary melanomas into genomic immune subgroups

Author

Godson, Lucy, Alemi, Navid, Nsengimana, Jeremie, Cook, Graham P., Clarke, Emily L., Treanor, Darren, Bishop, D. Timothy, Newton-Bishop, Julia, and Gooya, Ali

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Quantitative Biology - Quantitative Methods
Abstract

Determining early-stage prognostic markers and stratifying patients for effective treatment are two key challenges for improving outcomes for melanoma patients. Previous studies have used tumour transcriptome data to stratify patients into immune subgroups, which were associated with differential melanoma specific survival and potential treatment strategies. However, acquiring transcriptome data is a time-consuming and costly process. Moreover, it is not routinely used in the current clinical workflow. Here we attempt to overcome this by developing deep learning models to classify gigapixel H&E stained pathology slides, which are well established in clinical workflows, into these immune subgroups. Previous subtyping approaches have employed supervised learning which requires fully annotated data, or have only examined single genetic mutations in melanoma patients. We leverage a multiple-instance learning approach, which only requires slide-level labels and uses an attention mechanism to highlight regions of high importance to the classification. Moreover, we show that pathology-specific self-supervised models generate better representations compared to pathology-agnostic models for improving our model performance, achieving a mean AUC of 0.76 for classifying histopathology images as high or low immune subgroups. We anticipate that this method may allow us to find new biomarkers of high importance and could act as a tool for clinicians to infer the immune landscape of tumours and stratify patients, without needing to carry out additional expensive genetic tests., Comment: 8 pages (without appendices), 2 figures, submitted to MIDL 2022 conference proceedings

Published
2022

9. Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes

Author

Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie, Fonseca, Nuno A., Wongchenko, Matthew, Yan, Yibing, Lauss, Martin, Jönsson, Göran B., Newton-Bishop, Julia, Parkinson, Christine, Middleton, Mark R., Bishop, D. Timothy, McDonald, Sarah, Stefanos, Nikki, Tadross, John, Vergara, Ismael A., Lo, Serigne, Newell, Felicity, Wilmott, James S., Thompson, John F., Long, Georgina V., Scolyer, Richard A., Corrie, Pippa, Adams, David J., Brazma, Alvis, and Rabbie, Roy

Published
2022
Full Text
View/download PDF

11. Inherited duplications of PPP2R3B predispose to nevi and melanoma via a C21orf91-driven proliferative phenotype

Author

Polubothu, Satyamaanasa, Zecchin, Davide, Al-Olabi, Lara, Lionarons, Daniël A., Harland, Mark, Horswell, Stuart, Thomas, Anna C., Hunt, Lilian, Wlodarchak, Nathan, Aguilera, Paula, Brand, Sarah, Bryant, Dale, Carrera, Cristina, Chen, Hui, Elgar, Greg, Harwood, Catherine A., Howell, Michael, Larue, Lionel, Loughlin, Sam, MacDonald, Jeff, Malvehy, Josep, Barberan, Sara Martin, da Silva, Vanessa Martins, Molina, Miriam, Morrogh, Deborah, Moulding, Dale, Nsengimana, Jérémie, Pittman, Alan, Puig-Butillé, Joan-Anton, Parmar, Kiran, Sebire, Neil J., Scherer, Stephen, Stadnik, Paulina, Stanier, Philip, Tell, Gemma, Waelchli, Regula, Zarrei, Mehdi, Puig, Susana, Bataille, Véronique, Xing, Yongna, Healy, Eugene, Moore, Gudrun E., Di, Wei-Li, Newton-Bishop, Julia, Downward, Julian, and Kinsler, Veronica A.

Published
2021
Full Text
View/download PDF

12. Transcriptional signatures underlying dynamic phenotypic switching and novel disease biomarkers in a linear cellular model of melanoma progression

Author

Pessoa, Diogo de Oliveira, Rius, Flávia Eichemberger, Papaiz, Debora D'Angelo, Ayub, Ana Luísa Pedroso, Morais, Alice Santana, de Souza, Camila Ferreira, da Paixão, Vinicius Ferreira, Setubal, João Carlos, Newton-Bishop, Julia, Nsengimana, Jérémie, Azevedo, Hatylas, Reis, Eduardo Moraes, and Jasiulionis, Miriam Galvonas

Published
2021
Full Text
View/download PDF

15. Identification of 22 susceptibility loci associated with testicular germ cell tumors

Author

Pluta, John, Pyle, Louise C., Nead, Kevin T., Wilf, Rona, Li, Mingyao, Mitra, Nandita, Weathers, Benita, D’Andrea, Kurt, Almstrup, Kristian, Anson-Cartwright, Lynn, Benitez, Javier, Brown, Christopher D., Chanock, Stephen, Chen, Chu, Cortessis, Victoria K., Ferlin, Alberto, Foresta, Carlo, Gamulin, Marija, Gietema, Jourik A., Grasso, Chiara, Greene, Mark H., Grotmol, Tom, Hamilton, Robert J., Haugen, Trine B., Hauser, Russ, Hildebrandt, Michelle A. T., Johnson, Matthew E., Karlsson, Robert, Kiemeney, Lambertus A., Lessel, Davor, Lothe, Ragnhild A., Loud, Jennifer T., Loveday, Chey, Martin-Gimeno, Paloma, Meijer, Coby, Nsengimana, Jérémie, Quinn, David I., Rafnar, Thorunn, Ramdas, Shweta, Richiardi, Lorenzo, Skotheim, Rolf I., Stefansson, Kari, Turnbull, Clare, Vaughn, David J., Wiklund, Fredrik, Wu, Xifeng, Yang, Daphne, Zheng, Tongzhang, Wells, Andrew D., Grant, Struan F. A., Rajpert-De Meyts, Ewa, Schwartz, Stephen M., Bishop, D. Timothy, McGlynn, Katherine A., Kanetsky, Peter A., and Nathanson, Katherine L.

Published
2021
Full Text
View/download PDF

17. Tumour gene expression signature in primary melanoma predicts long-term outcomes

Author

Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie, Fonseca, Nuno A., Wongchenko, Matthew, Yan, Yibing, Lauss, Martin, Jönsson, Göran B., Newton-Bishop, Julia, Parkinson, Christine, Middleton, Mark R., Bishop, D. Timothy, McDonald, Sarah, Stefanos, Nikki, Tadross, John, Vergara, Ismael A., Lo, Serigne, Newell, Felicity, Wilmott, James S., Thompson, John F., Long, Georgina V., Scolyer, Richard A., Corrie, Pippa, Adams, David J., Brazma, Alvis, and Rabbie, Roy

Published
2021
Full Text
View/download PDF

19. Supp Table S2 from Identifying the Transcriptional Drivers of Metastasis Embedded within Localized Melanoma

Author

Suresh, Shruthy, primary, Rabbie, Roy, primary, Garg, Manik, primary, Lumaquin, Dianne, primary, Huang, Ting-Hsiang, primary, Montal, Emily, primary, Ma, Yilun, primary, Cruz, Nelly M, primary, Tang, Xinran, primary, Nsengimana, Jérémie, primary, Newton-Bishop, Julia, primary, Hunter, Miranda V., primary, Zhu, Yuxin, primary, Chen, Kevin, primary, de Stanchina, Elisa, primary, Adams, David J., primary, and White, Richard M., primary

Published
2023
Full Text
View/download PDF

20. Supplementary Figure S8 from Identifying the Transcriptional Drivers of Metastasis Embedded within Localized Melanoma

Author

Suresh, Shruthy, primary, Rabbie, Roy, primary, Garg, Manik, primary, Lumaquin, Dianne, primary, Huang, Ting-Hsiang, primary, Montal, Emily, primary, Ma, Yilun, primary, Cruz, Nelly M, primary, Tang, Xinran, primary, Nsengimana, Jérémie, primary, Newton-Bishop, Julia, primary, Hunter, Miranda V., primary, Zhu, Yuxin, primary, Chen, Kevin, primary, de Stanchina, Elisa, primary, Adams, David J., primary, and White, Richard M., primary

Published
2023
Full Text
View/download PDF

21. Data from Identifying the Transcriptional Drivers of Metastasis Embedded within Localized Melanoma

Author

Suresh, Shruthy, primary, Rabbie, Roy, primary, Garg, Manik, primary, Lumaquin, Dianne, primary, Huang, Ting-Hsiang, primary, Montal, Emily, primary, Ma, Yilun, primary, Cruz, Nelly M, primary, Tang, Xinran, primary, Nsengimana, Jérémie, primary, Newton-Bishop, Julia, primary, Hunter, Miranda V., primary, Zhu, Yuxin, primary, Chen, Kevin, primary, de Stanchina, Elisa, primary, Adams, David J., primary, and White, Richard M., primary

Published
2023
Full Text
View/download PDF

22. Data from Patterns of Expression of DNA Repair Genes and Relapse From Melanoma

Author

Jewell, Rosalyn, primary, Conway, Caroline, primary, Mitra, Angana, primary, Randerson-Moor, Juliette, primary, Lobo, Samira, primary, Nsengimana, Jérémie, primary, Harland, Mark, primary, Marples, Maria, primary, Edward, Sara, primary, Cook, Martin, primary, Powell, Barry, primary, Boon, Andy, primary, de Kort, Floor, primary, Parker, Katharine A., primary, Cree, Ian A., primary, Barrett, Jennifer H., primary, Knowles, Margaret A., primary, Bishop, D. Timothy, primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

23. Supplementary methods and results from Genetic and Environmental Determinants of Immune Response to Cutaneous Melanoma

Author

Poźniak, Joanna, primary, Nsengimana, Jérémie, primary, Laye, Jonathan P., primary, O’Shea, Sally J., primary, Diaz, Joey Mark S., primary, Droop, Alastair P., primary, Filia, Anastasia, primary, Harland, Mark, primary, Davies, John R., primary, Mell, Tracey, primary, Randerson-Moor, Juliette A., primary, Muralidhar, Sathya, primary, Hogan, Sabrina A., primary, Freiberger, Sandra Nicole, primary, Levesque, Mitchell P., primary, Cook, Graham P., primary, Bishop, D. Timothy, primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

24. Supplementary Data 2 from Genetic and Environmental Determinants of Immune Response to Cutaneous Melanoma

Author

Poźniak, Joanna, primary, Nsengimana, Jérémie, primary, Laye, Jonathan P., primary, O’Shea, Sally J., primary, Diaz, Joey Mark S., primary, Droop, Alastair P., primary, Filia, Anastasia, primary, Harland, Mark, primary, Davies, John R., primary, Mell, Tracey, primary, Randerson-Moor, Juliette A., primary, Muralidhar, Sathya, primary, Hogan, Sabrina A., primary, Freiberger, Sandra Nicole, primary, Levesque, Mitchell P., primary, Cook, Graham P., primary, Bishop, D. Timothy, primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

25. Data from Vitamin D–VDR Signaling Inhibits Wnt/β-Catenin–Mediated Melanoma Progression and Promotes Antitumor Immunity

Author

Muralidhar, Sathya, primary, Filia, Anastasia, primary, Nsengimana, Jérémie, primary, Poźniak, Joanna, primary, O'Shea, Sally J., primary, Diaz, Joey M., primary, Harland, Mark, primary, Randerson-Moor, Juliette A., primary, Reichrath, Jörg, primary, Laye, Jonathan P., primary, van der Weyden, Louise, primary, Adams, David J., primary, Bishop, D.T., primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

26. Supplementary Data from Transcriptomic Analysis Reveals Prognostic Molecular Signatures of Stage I Melanoma

Author

Thakur, Rohit, primary, Laye, Jonathan P., primary, Lauss, Martin, primary, Diaz, Joey Mark S., primary, O'Shea, Sally Jane, primary, Poźniak, Joanna, primary, Filia, Anastasia, primary, Harland, Mark, primary, Gascoyne, Joanne, primary, Randerson-Moor, Juliette A., primary, Chan, May, primary, Mell, Tracey, primary, Jönsson, Göran, primary, Bishop, D. Timothy, primary, Newton-Bishop, Julia, primary, Barrett, Jennifer H., primary, and Nsengimana, Jérémie, primary

Published
2023
Full Text
View/download PDF

27. Supplementary Data from Patterns of Expression of DNA Repair Genes and Relapse From Melanoma

Author

Jewell, Rosalyn, primary, Conway, Caroline, primary, Mitra, Angana, primary, Randerson-Moor, Juliette, primary, Lobo, Samira, primary, Nsengimana, Jérémie, primary, Harland, Mark, primary, Marples, Maria, primary, Edward, Sara, primary, Cook, Martin, primary, Powell, Barry, primary, Boon, Andy, primary, de Kort, Floor, primary, Parker, Katharine A., primary, Cree, Ian A., primary, Barrett, Jennifer H., primary, Knowles, Margaret A., primary, Bishop, D. Timothy, primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

28. Data from Genetic and Environmental Determinants of Immune Response to Cutaneous Melanoma

Author

Poźniak, Joanna, primary, Nsengimana, Jérémie, primary, Laye, Jonathan P., primary, O’Shea, Sally J., primary, Diaz, Joey Mark S., primary, Droop, Alastair P., primary, Filia, Anastasia, primary, Harland, Mark, primary, Davies, John R., primary, Mell, Tracey, primary, Randerson-Moor, Juliette A., primary, Muralidhar, Sathya, primary, Hogan, Sabrina A., primary, Freiberger, Sandra Nicole, primary, Levesque, Mitchell P., primary, Cook, Graham P., primary, Bishop, D. Timothy, primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

29. Supplementary Figure 4 from Vitamin D–VDR Signaling Inhibits Wnt/β-Catenin–Mediated Melanoma Progression and Promotes Antitumor Immunity

Author

Muralidhar, Sathya, primary, Filia, Anastasia, primary, Nsengimana, Jérémie, primary, Poźniak, Joanna, primary, O'Shea, Sally J., primary, Diaz, Joey M., primary, Harland, Mark, primary, Randerson-Moor, Juliette A., primary, Reichrath, Jörg, primary, Laye, Jonathan P., primary, van der Weyden, Louise, primary, Adams, David J., primary, Bishop, D.T., primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

30. Supplementary Figure 2 from Vitamin D–VDR Signaling Inhibits Wnt/β-Catenin–Mediated Melanoma Progression and Promotes Antitumor Immunity

Author

Muralidhar, Sathya, primary, Filia, Anastasia, primary, Nsengimana, Jérémie, primary, Poźniak, Joanna, primary, O'Shea, Sally J., primary, Diaz, Joey M., primary, Harland, Mark, primary, Randerson-Moor, Juliette A., primary, Reichrath, Jörg, primary, Laye, Jonathan P., primary, van der Weyden, Louise, primary, Adams, David J., primary, Bishop, D.T., primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

31. Legend for Supplementary tables from Vitamin D–VDR Signaling Inhibits Wnt/β-Catenin–Mediated Melanoma Progression and Promotes Antitumor Immunity

Author

Muralidhar, Sathya, primary, Filia, Anastasia, primary, Nsengimana, Jérémie, primary, Poźniak, Joanna, primary, O'Shea, Sally J., primary, Diaz, Joey M., primary, Harland, Mark, primary, Randerson-Moor, Juliette A., primary, Reichrath, Jörg, primary, Laye, Jonathan P., primary, van der Weyden, Louise, primary, Adams, David J., primary, Bishop, D.T., primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

32. Supplementary Figure 1 from Vitamin D–VDR Signaling Inhibits Wnt/β-Catenin–Mediated Melanoma Progression and Promotes Antitumor Immunity

Author

Muralidhar, Sathya, primary, Filia, Anastasia, primary, Nsengimana, Jérémie, primary, Poźniak, Joanna, primary, O'Shea, Sally J., primary, Diaz, Joey M., primary, Harland, Mark, primary, Randerson-Moor, Juliette A., primary, Reichrath, Jörg, primary, Laye, Jonathan P., primary, van der Weyden, Louise, primary, Adams, David J., primary, Bishop, D.T., primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

33. Supplementary Figure 3 from Vitamin D–VDR Signaling Inhibits Wnt/β-Catenin–Mediated Melanoma Progression and Promotes Antitumor Immunity

Author

Muralidhar, Sathya, primary, Filia, Anastasia, primary, Nsengimana, Jérémie, primary, Poźniak, Joanna, primary, O'Shea, Sally J., primary, Diaz, Joey M., primary, Harland, Mark, primary, Randerson-Moor, Juliette A., primary, Reichrath, Jörg, primary, Laye, Jonathan P., primary, van der Weyden, Louise, primary, Adams, David J., primary, Bishop, D.T., primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

34. Supplementary Tables from Vitamin D–VDR Signaling Inhibits Wnt/β-Catenin–Mediated Melanoma Progression and Promotes Antitumor Immunity

Author

Muralidhar, Sathya, primary, Filia, Anastasia, primary, Nsengimana, Jérémie, primary, Poźniak, Joanna, primary, O'Shea, Sally J., primary, Diaz, Joey M., primary, Harland, Mark, primary, Randerson-Moor, Juliette A., primary, Reichrath, Jörg, primary, Laye, Jonathan P., primary, van der Weyden, Louise, primary, Adams, David J., primary, Bishop, D.T., primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

35. Supplementary Methods from Vitamin D–VDR Signaling Inhibits Wnt/β-Catenin–Mediated Melanoma Progression and Promotes Antitumor Immunity

Author

Muralidhar, Sathya, primary, Filia, Anastasia, primary, Nsengimana, Jérémie, primary, Poźniak, Joanna, primary, O'Shea, Sally J., primary, Diaz, Joey M., primary, Harland, Mark, primary, Randerson-Moor, Juliette A., primary, Reichrath, Jörg, primary, Laye, Jonathan P., primary, van der Weyden, Louise, primary, Adams, David J., primary, Bishop, D.T., primary, and Newton-Bishop, Julia, primary

Published
2023
Full Text
View/download PDF

38. Identifying the Transcriptional Drivers of Metastasis Embedded within Localized Melanoma

Author

Suresh, Shruthy, primary, Rabbie, Roy, additional, Garg, Manik, additional, Lumaquin, Dianne, additional, Huang, Ting-Hsiang, additional, Montal, Emily, additional, Ma, Yilun, additional, Cruz, Nelly M, additional, Tang, Xinran, additional, Nsengimana, Jérémie, additional, Newton-Bishop, Julia, additional, Hunter, Miranda V., additional, Zhu, Yuxin, additional, Chen, Kevin, additional, de Stanchina, Elisa, additional, Adams, David J., additional, and White, Richard M., additional

Published
2022
Full Text
View/download PDF

41. Association Study between Polymorphisms in DNA Methylation–Related Genes and Testicular Germ Cell Tumor Risk

Author

Grasso, Chiara, primary, Popovic, Maja, additional, Isaevska, Elena, additional, Lazzarato, Fulvio, additional, Fiano, Valentina, additional, Zugna, Daniela, additional, Pluta, John, additional, Weathers, Benita, additional, D'Andrea, Kurt, additional, Almstrup, Kristian, additional, Anson-Cartwright, Lynn, additional, Bishop, D. Timothy, additional, Chanock, Stephen J., additional, Chen, Chu, additional, Cortessis, Victoria K., additional, Dalgaard, Marlene D., additional, Daneshmand, Siamak, additional, Ferlin, Alberto, additional, Foresta, Carlo, additional, Frone, Megan N., additional, Gamulin, Marija, additional, Gietema, Jourik A., additional, Greene, Mark H., additional, Grotmol, Tom, additional, Hamilton, Robert J., additional, Haugen, Trine B., additional, Hauser, Russ, additional, Karlsson, Robert, additional, Kiemeney, Lambertus A., additional, Lessel, Davor, additional, Lista, Patrizia, additional, Lothe, Ragnhild A., additional, Loveday, Chey, additional, Meijer, Coby, additional, Nead, Kevin T., additional, Nsengimana, Jérémie, additional, Skotheim, Rolf I., additional, Turnbull, Clare, additional, Vaughn, David J., additional, Wiklund, Fredrik, additional, Zheng, Tongzhang, additional, Zitella, Andrea, additional, Schwartz, Stephen M., additional, McGlynn, Katherine A., additional, Kanetsky, Peter A., additional, Nathanson, Katherine L., additional, and Richiardi, Lorenzo, additional

Published
2022
Full Text
View/download PDF

42. Genes regulated by DNA methylation are involved in distinct phenotypes during melanoma progression and are prognostic factors for patients

Author

Papaiz, Debora D’Angelo, primary, Rius, Flávia Eichemberger, additional, Ayub, Ana Luísa Pedroso, additional, Origassa, Clarice S., additional, Gujar, Hemant, additional, Pessoa, Diogo de Oliveira, additional, Reis, Eduardo Moraes, additional, Nsengimana, Jérémie, additional, Newton‐Bishop, Julia, additional, Mason, Christopher E., additional, Weisenberger, Daniel J., additional, Liang, Gangning, additional, and Jasiulionis, Miriam Galvonas, additional

Published
2022
Full Text
View/download PDF

43. Ulcerated melanoma: Systems biology evidence of inflammatory imbalance towards pro‐tumourigenicity

Author

Davies, John, primary, Muralidhar, Sathya, additional, Randerson‐Moor, Juliette, additional, Harland, Mark, additional, O’Shea, Sally, additional, Diaz, Joey, additional, Walker, Christy, additional, Nsengimana, Jérémie, additional, Laye, Jon, additional, Mell, Tracey, additional, Chan, May, additional, Appleton, Lizzie, additional, Birkeälv, Sofia, additional, Adams, David J., additional, Cook, Graham P., additional, Ball, Graham, additional, Bishop, David T., additional, and Newton‐Bishop, Julia A., additional

Published
2021
Full Text
View/download PDF

45. Cooperation between melanoma cell states promotes metastasis through heterotypic cluster formation

Author

Campbell, Nathaniel R., primary, Rao, Anjali, additional, Hunter, Miranda V., additional, Sznurkowska, Magdalena K., additional, Briker, Luzia, additional, Zhang, Maomao, additional, Baron, Maayan, additional, Heilmann, Silja, additional, Deforet, Maxime, additional, Kenny, Colin, additional, Ferretti, Lorenza P., additional, Huang, Ting-Hsiang, additional, Perlee, Sarah, additional, Garg, Manik, additional, Nsengimana, Jérémie, additional, Saini, Massimo, additional, Montal, Emily, additional, Tagore, Mohita, additional, Newton-Bishop, Julia, additional, Middleton, Mark R., additional, Corrie, Pippa, additional, Adams, David J., additional, Rabbie, Roy, additional, Aceto, Nicola, additional, Levesque, Mitchell P., additional, Cornell, Robert A., additional, Yanai, Itai, additional, Xavier, Joao B., additional, and White, Richard M., additional

Published
2021
Full Text
View/download PDF

46. Linkage disequilibrium and the genetic distance in livestock populations: the impact of inbreeding

Author

Baret Philippe V and Nsengimana Jérémie

Subjects
Linkage disequilibrium, livestock, inbreeding, genetic distance, exponential function, Animal culture, SF1-1100, Genetics, QH426-470
Abstract

Abstract Genome-wide linkage disequilibrium (LD) is subject to intensive investigation in human and livestock populations since it can potentially reveal aspects of a population history, permit to date them and help in fine-gene mapping. The most commonly used measure of LD between multiallelic loci is the coefficient D'. Data based on D' were recently published in humans, livestock and model animals. However, the properties of this coefficient are not well understood. Its sampling distribution and variance has received recent attention, but its expected behaviour with respect to genetic or physical distance remains unknown. Using stochastic simulations of populations having a finite size, we show that D' fits an exponential function having two parameters of simple biological interpretation: the residual value (rs) towards which D' tends as the genetic distance increases and the distance R at which this value is reached. Properties of this model are evaluated as a function of the inbreeding coefficient (F). It was found that R and rs increase when F increases. The proposed model offers opportunities to better understand the patterns and the origins of LD in different populations and along different chromosomes.

Published
2004
Full Text
View/download PDF

48. The clinicopathological and gene expression patterns associated with ulceration of primary melanoma

Author

Jewell, Rosalyn, Elliott, Faye, Laye, Jonathan, Nsengimana, Jérémie, Davies, John, Walker, Christy, Conway, Caroline, Mitra, Angana, Harland, Mark, Cook, Martin G., Boon, Andy, Storr, Sarah, Safuan, Sabreena, Martin, Stewart G., Jirström, Karin, Olsson, Håkan, Ingvar, Christian, Lauss, Martin, Bishop, Tim, Jönsson, Göran, and Newton-Bishop, Julia

Published
2015
Full Text
View/download PDF

50. Genes regulated by DNA methylation are involved in distinct phenotypes during melanoma progression and are prognostic factors for patients.

Author

D'Angelo Papaiz, Debora, Eichemberger Rius, Flávia, Pedroso Ayub, Ana Luísa, Origassa, Clarice S., Gujar, Hemant, de Oliveira Pessoa, Diogo, Moraes Reis, Eduardo, Nsengimana, Jérémie, Newton-Bishop, Julia, Mason, Christopher E., Weisenberger, Daniel J., Gangning Liang, and Galvonas Jasiulionis, Miriam

Abstract

In addition to mutations, epigenetic alterations are important contributors to malignant transformation and tumor progression. The aim of this work was to identify epigenetic events in which promoter or gene body DNA methylation induces gene expression changes that drive melanocyte malignant transformation and metastasis. We previously developed a linear mouse model of melanoma progression consisting of spontaneously immortalized melanocytes, premalignant melanocytes, a nonmetastatic tumorigenic, and a metastatic cell line. Here, through the integrative analysis of methylome and transcriptome data, we identified the relationship between promoter and/or gene body DNA methylation alterations and gene expression in early, intermediate, and late stages of melanoma progression. We identified adenylate cyclase type 3 (Adcy3) and inositol polyphosphate 4-phosphatase type II (Inpp4b), which affect tumor growth and metastatic potential, respectively. Importantly, the gene expression and DNA methylation profiles found in this murine model of melanoma progression were correlated with available clinical data from large population-based primary melanoma cohorts, revealing potential prognostic markers. [ABSTRACT FROM AUTHOR]

Published
2022
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results