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8. Optimizing the NGS-based discrimination of multiple lung cancers from the perspective of evolution

Author

Wang, Ziyang, primary, Yuan, Xiaoqiu, additional, Liu, Ke, additional, Sun, Kunkun, additional, Chervova, Olga, additional, Nie, Yuntao, additional, Yang, Airong, additional, Jin, Yichen, additional, Li, Jing, additional, Li, Yun, additional, Yang, Fan, additional, Wang, Jun, additional, Beck, Stephan, additional, Carbone, David, additional, and Chen, Kezhong, additional

Published
2024
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9. Time reversal method with stabilizing boundary conditions for Photoacoustic tomography

Author

Chervova, Olga and Oksanen, Lauri

Subjects
Mathematics - Analysis of PDEs
Abstract

We study an inverse initial source problem that models Photoacoustic tomography measurements with array detectors, and introduce a method that can be viewed as a modification of the so called back and forth nudging method. We show that the method converges at an exponential rate under a natural visibility condition, with data given only on a part of the boundary of the domain of wave propagation. In this paper we consider the case of noiseless measurements., Comment: Revised Version, accepted to the IOP Journal of Inverse Problems

Published
2016
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11. Spectral theoretic characterization of the massless Dirac operator

Author

Chervova, Olga, Downes, Robert J., and Vassiliev, Dmitri

Subjects
Mathematics - Spectral Theory, Mathematics - Differential Geometry, 35P20 (primary), 35J46, 35R01, 35Q41 (secondary)
Abstract

We consider an elliptic self-adjoint first order differential operator acting on pairs (2-columns) of complex-valued half-densities over a connected compact 3-dimensional manifold without boundary. The principal symbol of our operator is assumed to be trace-free. We study the spectral function which is the sum of squares of Euclidean norms of eigenfunctions evaluated at a given point of the manifold, with summation carried out over all eigenvalues between zero and a positive lambda. We derive an explicit two-term asymptotic formula for the spectral function as lambda tends to plus infinity, expressing the second asymptotic coefficient via the trace of the subprincipal symbol and the geometric objects encoded within the principal symbol - metric, torsion of the teleparallel connection and topological charge. We then address the question: is our operator a massless Dirac operator on half-densities? We prove that it is a massless Dirac operator on half-densities if and only if the following two conditions are satisfied at every point of the manifold: a) the subprincipal symbol is proportional to the identity matrix and b) the second asymptotic coefficient of the spectral function is zero., Comment: To appear in Journal of the LMS. Three typos corrected, two sentences edited and one bibliographic reference updated compared to the original version. arXiv admin note: substantial text overlap with arXiv:1204.6567

Published
2012
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12. The spectral function of a first order elliptic system

Author

Chervova, Olga, Downes, Robert J., and Vassiliev, Dmitri

Subjects
Mathematics - Spectral Theory, 35P20 (Primary), 35J46, 35R01 (Secondary)
Abstract

We consider an elliptic self-adjoint first order pseudodifferential operator acting on columns of complex-valued half-densities over a connected compact manifold without boundary. The eigenvalues of the principal symbol are assumed to be simple but no assumptions are made on their sign, so the operator is not necessarily semi-bounded. We study the following objects: the propagator (time-dependent operator which solves the Cauchy problem for the dynamic equation), the spectral function (sum of squares of Euclidean norms of eigenfunctions evaluated at a given point of the manifold, with summation carried out over all eigenvalues between zero and a positive lambda) and the counting function (number of eigenvalues between zero and a positive lambda). We derive explicit two-term asymptotic formulae for all three. For the propagator "asymptotic" is understood as asymptotic in terms of smoothness, whereas for the spectral and counting functions "asymptotic" is understood as asymptotic with respect to lambda tending to plus infinity., Comment: This preprint is "part a" (proper subset) of preprint arXiv:1204.6567. Preprint arXiv:1204.6567 is being split into two parts on the recommendation of the referee of Journal of Spectral Theory. "Part b" will appear as a separate preprint under the title "Spectral theoretic characterization of the massless Dirac operator"

Published
2012
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13. The spectral function of a first order system

Author

Chervova, Olga, Downes, Robert J., and Vassiliev, Dmitri

Subjects
Mathematics - Analysis of PDEs, Mathematics - Differential Geometry, 35P20 (Primary) 35J46, 35R01, 35Q41 (Secondary)
Abstract

We consider an elliptic self-adjoint first order pseudodifferential operator acting on columns of m complex-valued half-densities over a connected compact n-dimensional manifold without boundary. The eigenvalues of the principal symbol are assumed to be simple but no assumptions are made on their sign, so the operator is not necessarily semi-bounded. We study the spectral function, i.e. the sum of squares of Euclidean norms of eigenfunctions evaluated at a given point of the manifold, with summation carried out over all eigenvalues between zero and a positive lambda. We derive a two-term asymptotic formula for the spectral function as lambda tends to plus infinity. We then restrict our study to the case when m=2, n=3, the operator is differential and has trace-free principal symbol, and address the question: is our operator a massless Dirac operator? We prove that it is a massless Dirac operator if and only if the following two conditions are satisfied at every point of the manifold: a) the subprincipal symbol is proportional to the identity matrix and b) the second asymptotic coefficient of the spectral function is zero.

Published
2012

14. Modelling the neutrino in terms of Cosserat elasticity

Author

Chervova, Olga and Vassiliev, Dmitri

Subjects
Mathematical Physics, General Relativity and Quantum Cosmology, Mathematics - Differential Geometry
Abstract

The paper deals with the Weyl equation which is the massless Dirac equation. We study the Weyl equation in the stationary setting, i.e. when the the spinor field oscillates harmonically in time. We suggest a new geometric interpretation of the stationary Weyl equation, one which does not require the use of spinors, Pauli matrices or covariant differentiation. We think of our 3-dimensional space as an elastic continuum and assume that material points of this continuum can experience no displacements, only rotations. This framework is a special case of the Cosserat theory of elasticity. Rotations of material points of the space continuum are described mathematically by attaching to each geometric point an orthonormal basis which gives a field of orthonormal bases called the coframe. As the dynamical variables (unknowns) of our theory we choose the coframe and a density. We choose a particular potential energy which is conformally invariant and then incorporate time into our action in the standard Newtonian way, by subtracting kinetic energy. The main result of our paper is the theorem stating that in the stationary setting our model is equivalent to a pair of Weyl equations. The crucial element of the proof is the observation that our Lagrangian admits a factorisation., Comment: Submitted to the Proceedings of the Twelfth Marcel Grossmann Meeting

Published
2010

15. The stationary Weyl equation and Cosserat elasticity

Author

Chervova, Olga and Vassiliev, Dmitri

Subjects
General Relativity and Quantum Cosmology, Mathematical Physics, Mathematics - Differential Geometry
Abstract

The paper deals with the Weyl equation which is the massless Dirac equation. We study the Weyl equation in the stationary setting, i.e. when the spinor field oscillates harmonically in time. We suggest a new geometric interpretation of the stationary Weyl equation, one which does not require the use of spinors, Pauli matrices or covariant differentiation. We think of our 3-dimensional space as an elastic continuum and assume that material points of this continuum can experience no displacements, only rotations. This framework is a special case of the Cosserat theory of elasticity. Rotations of material points of the space continuum are described mathematically by attaching to each geometric point an orthonormal basis which gives a field of orthonormal bases called the coframe. As the dynamical variables (unknowns) of our theory we choose the coframe and a density. We choose a particular potential energy which is conformally invariant and then incorporate time into our action in the standard Newtonian way, by subtracting kinetic energy. The main result of our paper is the theorem stating that in the stationary setting our model is equivalent to a pair of Weyl equations. The crucial element of the proof is the observation that our Lagrangian admits a factorization.

Published
2010
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16. Massless Dirac equation as a special case of Cosserat elasticity

Author

Chervova, Olga and Vassiliev, Dmitri

Subjects
General Relativity and Quantum Cosmology, Mathematics - Differential Geometry
Abstract

We suggest an alternative mathematical model for the massless neutrino. Consider an elastic continuum in 3-dimensional Euclidean space and assume that points of this continuum can experience no displacements, only rotations. This framework is a special case of the so-called Cosserat theory of elasticity. Rotations of points of the continuum are described by attaching to each point an orthonormal basis which gives a field of orthonormal bases called the coframe. As the dynamical variables (unknowns) of our theory we choose a coframe and a density. We write down a potential energy which is conformally invariant and then incorporate time in the standard Newtonian way, by subtracting kinetic energy. Finally, we rewrite the resulting nonlinear variational problem in terms of an unknown spinor field. We look for quasi-stationary solutions, i.e. solutions that harmonically oscillate in time. We prove that in the quasi-stationary setting our model is equivalent to a pair of massless Dirac equations. The crucial element of the proof is the observation that our Lagrangian admits a factorisation., Comment: Submitted to the proceedings of the International Conference on Recent Trends in Mathematical Sciences, Bahrain, 10-12 November 2008

Published
2009

18. Dirac equation as a special case of Cosserat elasticity

Author

Burnett, James, Chervova, Olga, and Vassiliev, Dmitri

Subjects
General Relativity and Quantum Cosmology, Mathematics - Differential Geometry
Abstract

We suggest an alternative mathematical model for the electron in which the dynamical variables are a coframe (field of orthonormal bases) and a density. The electron mass and external electromagnetic field are incorporated into our model by means of a Kaluza-Klein extension. Our Lagrangian density is proportional to axial torsion squared. The advantage of our approach is that it does not require the use of spinors, Pauli matrices or covariant differentiation. The only geometric concepts we use are those of a metric, differential form, wedge product and exterior derivative. We prove that in the special case with no dependence on the third spatial coordinate our model is equivalent to the Dirac equation. The crucial element of the proof is the observation that our Lagrangian admits a factorisation., Comment: Submitted to Analysis, Partial Differential Equations and Applications - The Vladimir Maz'ya Anniversary Volume (Operator Theory: Advances and Applications) Birkauser Verlag

Published
2008

20. Subclassification of epithelioid sarcoma with potential therapeutic impact

Author

Haefliger, Simon, primary, Chervova, Olga, additional, Davies, Christopher, additional, Nottley, Steven, additional, Hargreaves, Steven, additional, Sumathi, Vaiyapuri P, additional, Amary, Fernanda, additional, Tirabosco, Roberto, additional, Pillay, Nischalan, additional, Beck, Stephan, additional, Flanagan, Adrienne M, additional, and Lyskjær, Iben, additional

Published
2023
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22. Body composition and lung cancer-associated cachexia in TRACERx

Author

Al-Sawaf, Othman, Weiss, Jakob, Skrzypski, Marcin, Lam, Jie Min, Karasaki, Takahiro, Zambrana, Francisco, Kidd, Andrew C, Frankell, Alexander M, Watkins, Thomas BK, Martinez-Ruiz, Carlos, Puttick, Clare, Black, James RM, Huebner, Ariana, Al Bakir, Maise, Sokac, Mateo, Collins, Susie, Veeriah, Selvaraju, Magno, Neil, Naceur-Lombardelli, Cristina, Prymas, Paulina, Toncheva, Antonia, Ward, Sophia, Jayanth, Nick, Salgado, Roberto, Bridge, Christopher P, Christiani, David C, Mak, Raymond H, Bay, Camden, Rosenthal, Michael, Sattar, Naveed, Welsh, Paul, Liu, Ying, Perrimon, Norbert, Popuri, Karteek, Beg, Mirza Faisal, McGranahan, Nicholas, Hackshaw, Allan, Breen, Danna M, O'Rahilly, Stephen, Birkbak, Nicolai J, Aerts, Hugo JWL, Jamal-Hanjani, Mariam, Swanton, Charles, Lester, Jason F, Bajaj, Amrita, Nakas, Apostolos, Sodha-Ramdeen, Azmina, Ang, Keng, Tufail, Mohamad, Chowdhry, Mohammed Fiyaz, Scotland, Molly, Boyles, Rebecca, Rathinam, Sridhar, Wilson, Claire, Marrone, Domenic, Dulloo, Sean, Fennell, Dean A, Matharu, Gurdeep, Shaw, Jacqui A, Riley, Joan, Primrose, Lindsay, Boleti, Ekaterini, Cheyne, Heather, Khalil, Mohammed, Richardson, Shirley, Cruickshank, Tracey, Price, Gillian, Kerr, Keith M, Benafif, Sarah, Gilbert, Kayleigh, Naidu, Babu, Patel, Akshay J, Osman, Aya, Lacson, Christer, Langman, Gerald, Shackleford, Helen, Djearaman, Madava, Kadiri, Salma, Middleton, Gary, Leek, Angela, Hodgkinson, Jack Davies, Totten, Nicola, Montero, Angeles, Smith, Elaine, Fontaine, Eustace, Granato, Felice, Doran, Helen, Novasio, Juliette, Rammohan, Kendadai, Joseph, Leena, Bishop, Paul, Shah, Rajesh, Moss, Stuart, Joshi, Vijay, Crosbie, Philip, Gomes, Fabio, Brown, Kate, Carter, Mathew, Chaturvedi, Anshuman, Priest, Lynsey, Oliveira, Pedro, Lindsay, Colin R, Blackhall, Fiona H, Krebs, Matthew G, Summers, Yvonne, Clipson, Alexandra, Tugwood, Jonathan, Kerr, Alastair, Rothwell, Dominic G, Kilgour, Elaine, Dive, Caroline, Schwarz, Roland F, Kaufmann, Tom L, Wilson, Gareth A, Rosenthal, Rachel, Van Loo, Peter, Szallasi, Zoltan, Kisistok, Judit, Diossy, Miklos, Demeulemeester, Jonas, Bunkum, Abigail, Stewart, Aengus, Magness, Alastair, Rowan, Andrew, Karamani, Angeliki, Chain, Benny, Campbell, Brittany B, Castignani, Carla, Bailey, Chris, Abbosh, Christopher, Weeden, Clare E, Lee, Claudia, Richard, Corentin, Hiley, Crispin T, Moore, David A, Pearce, David R, Karagianni, Despoina, Biswas, Dhruva, Levi, Dina, Hoxha, Elena, Cadieux, Elizabeth Larose, Lim, Emilia L, Colliver, Emma, Nye, Emma, Gronroos, Eva, Galvez-Cancino, Felip, Athanasopoulou, Foteini, Gimeno-Valiente, Francisco, Kassiotis, George, Stavrou, Georgia, Mastrokalos, Gerasimos, Zhai, Haoran, Lowe, Helen L, Matos, Ignacio Garcia, Goldman, Jacki, Reading, James L, Herrero, Javier, Rane, Jayant K, Nicod, Jerome, Hartley, John A, Peggs, Karl S, Enfield, Katey SS, Selvaraju, Kayalvizhi, Thol, Kerstin, Litchfield, Kevin, Ng, Kevin W, Chen, Kezhong, Dijkstra, Krijn, Grigoriadis, Kristiana, Thakkar, Krupa, Ensell, Leah, Shah, Mansi, Duran, Marcos Vasquez, Litovchenko, Maria, Sunderland, Mariana Werner, Hill, Mark S, Dietzen, Michelle, Leung, Michelle, Escudero, Mickael, Angelova, Mihaela, Tanic, Miljana, Sivakumar, Monica, Kanu, Nnennaya, Chervova, Olga, Lucas, Olivia, Pich, Oriol, Hobson, Philip, Pawlik, Piotr, Stone, Richard Kevin, Bentham, Robert, Hynds, Robert E, Vendramin, Roberto, Saghafinia, Sadegh, Lopez, Saioa, Gamble, Samuel, Ung, Seng Kuong Anakin, Quezada, Sergio A, Vanloo, Sharon, Zaccaria, Simone, Hessey, Sonya, Boeing, Stefan, Beck, Stephan, Bola, Supreet Kaur, Denner, Tamara, Marafioti, Teresa, Mourikis, Thanos P, Spanswick, Victoria, Barbe, Vittorio, Lu, Wei-Ting, Hill, William, Liu, Wing Kin, Wu, Yin, Naito, Yutaka, Ramsden, Zoe, Veiga, Catarina, Royle, Gary, Collins-Fekete, Charles-Antoine, Fraioli, Francesco, Ashford, Paul, Clark, Tristan, Forster, Martin D, Lee, Siow Ming, Borg, Elaine, Falzon, Mary, Papadatos-Pastos, Dionysis, Wilson, James, Ahmad, Tanya, Procter, Alexander James, Ahmed, Asia, Taylor, Magali N, Nair, Arjun, Lawrence, David, Patrini, Davide, Navani, Neal, Thakrar, Ricky M, Janes, Sam M, Hoogenboom, Emilie Martinoni, Monk, Fleur, Holding, James W, Choudhary, Junaid, Bhakhri, Kunal, Scarci, Marco, Hayward, Martin, Panagiotopoulos, Nikolaos, Gorman, Pat, Khiroya, Reena, Stephens, Robert CM, Wong, Yien Ning Sophia, Bandula, Steve, Sharp, Abigail, Smith, Sean, Gower, Nicole, Dhanda, Harjot Kaur, Chan, Kitty, Pilotti, Camilla, Leslie, Rachel, Grapa, Anca, Zhang, Hanyun, AbdulJabbar, Khalid, Pan, Xiaoxi, Yuan, Yinyin, Chuter, David, MacKenzie, Mairead, Chee, Serena, Alzetani, Aiman, Cave, Judith, Scarlett, Lydia, Richards, Jennifer, Ingram, Papawadee, Austin, Silvia, Lim, Eric, De Sousa, Paulo, Jordan, Simon, Rice, Alexandra, Raubenheimer, Hilgardt, Bhayani, Harshil, Ambrose, Lyn, Devaraj, Anand, Chavan, Hema, Begum, Sofina, Buderi, Silviu, Kaniu, Daniel, Malima, Mpho, Booth, Sarah, Nicholson, Andrew G, Fernandes, Nadia, Shah, Pratibha, Proli, Chiara, Hewish, Madeleine, Danson, Sarah, Shackcloth, Michael J, Robinson, Lily, Russell, Peter, Blyth, Kevin G, Dick, Craig, Le Quesne, John, Kirk, Alan, Asif, Mo, Bilancia, Rocco, Kostoulas, Nikos, and Thomas, Mathew

Subjects
Male, Proteomics, Cachexia, Lung Neoplasms, Antigens, Neoplasm, Carcinoma, Non-Small-Cell Lung, Body Weight, Body Composition, Humans, Neoplasm Recurrence, Local, Muscle, Skeletal, Neoplasm Proteins
Abstract

Cancer-associated cachexia (CAC) is a major contributor to morbidity and mortality in individuals with non-small cell lung cancer. Key features of CAC include alterations in body composition and body weight. Here, we explore the association between body composition and body weight with survival and delineate potential biological processes and mediators that contribute to the development of CAC. Computed tomography-based body composition analysis of 651 individuals in the TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy (Rx)) study suggested that individuals in the bottom 20th percentile of the distribution of skeletal muscle or adipose tissue area at the time of lung cancer diagnosis, had significantly shorter lung cancer-specific survival and overall survival. This finding was validated in 420 individuals in the independent Boston Lung Cancer Study. Individuals classified as having developed CAC according to one or more features at relapse encompassing loss of adipose or muscle tissue, or body mass index-adjusted weight loss were found to have distinct tumor genomic and transcriptomic profiles compared with individuals who did not develop such features. Primary non-small cell lung cancers from individuals who developed CAC were characterized by enrichment of inflammatory signaling and epithelial-mesenchymal transitional pathways, and differentially expressed genes upregulated in these tumors included cancer-testis antigen MAGEA6 and matrix metalloproteinases, such as ADAMTS3. In an exploratory proteomic analysis of circulating putative mediators of cachexia performed in a subset of 110 individuals from TRACERx, a significant association between circulating GDF15 and loss of body weight, skeletal muscle and adipose tissue was identified at relapse, supporting the potential therapeutic relevance of targeting GDF15 in the management of CAC. ispartof: NATURE MEDICINE vol:29 issue:4 ispartof: location:United States status: Published online

Published
2023

23. The evolution of non-small cell lung cancer metastases in TRACERx

Author

Al Bakir, Maise, Huebner, Ariana, Martinez-Ruiz, Carlos, Grigoriadis, Kristiana, Watkins, Thomas BK, Pich, Oriol, Moore, David A, Veeriah, Selvaraju, Ward, Sophia, Laycock, Joanne, Johnson, Diana, Rowan, Andrew, Razaq, Maryam, Akther, Mita, Naceur-Lombardelli, Cristina, Prymas, Paulina, Toncheva, Antonia, Hessey, Sonya, Dietzen, Michelle, Colliver, Emma, Frankell, Alexander, Bunkum, Abigail, Lim, Emilia L, Karasaki, Takahiro, Abbosh, Christopher, Hiley, Crispin T, Hill, Mark S, Cook, Daniel E, Wilson, Gareth A, Salgado, Roberto, Nye, Emma, Stone, Richard Kevin, Fennell, Dean A, Price, Gillian, Kerr, Keith M, Naidu, Babu, Middleton, Gary, Summers, Yvonne, Lindsay, Colin R, Blackhall, Fiona H, Cave, Judith, Blyth, Kevin G, Nair, Arjun, Ahmed, Asia, Taylor, Magali N, Procter, Alexander James, Falzon, Mary, Lawrence, David, Navani, Neal, Thakrar, Ricky M, Janes, Sam M, Papadatos-Pastos, Dionysis, Forster, Martin D, Lee, Siow Ming, Ahmad, Tanya, Quezada, Sergio, Peggs, Karl S, Van Loo, Peter, Dive, Caroline, Hackshaw, Allan, Birkbak, Nicolai J, Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, Swanton, Charles, Lester, Jason F, Bajaj, Amrita, Nakas, Apostolos, Sodha-Ramdeen, Azmina, Ang, Keng, Tufail, Mohamad, Chowdhry, Mohammed Fiyaz, Scotland, Molly, Boyles, Rebecca, Rathinam, Sridhar, Wilson, Claire, Marrone, Domenic, Dulloo, Sean, Matharu, Gurdeep, Shaw, Jacqui A, Riley, Joan, Primrose, Lindsay, Boleti, Ekaterini, Cheyne, Heather, Khalil, Mohammed, Richardson, Shirley, Cruickshank, Tracey, Benafif, Sarah, Gilbert, Kayleigh, Patel, Akshay J, Osman, Aya, Lacson, Christer, Langman, Gerald, Shackleford, Helen, Djearaman, Madava, Kadiri, Salma, Leek, Angela, Hodgkinson, Jack Davies, Totten, Nicola, Montero, Angeles, Smith, Elaine, Fontaine, Eustace, Granato, Felice, Doran, Helen, Novasio, Juliette, Rammohan, Kendadai, Joseph, Leena, Bishop, Paul, Shah, Rajesh, Moss, Stuart, Joshi, Vijay, Crosbie, Philip, Gomes, Fabio, Brown, Kate, Carter, Mathew, Chaturvedi, Anshuman, Priest, Lynsey, Oliveira, Pedro, Krebs, Matthew G, Clipson, Alexandra, Tugwood, Jonathan, Kerr, Alastair, Rothwell, Dominic G, Kilgour, Elaine, Aerts, Hugo JWL, Schwarz, Roland F, Kaufmann, Tom L, Rosenthal, Rachel, Szallasi, Zoltan, Kisistok, Judit, Sokac, Mateo, Diossy, Miklos, Demeulemeester, Jonas, Stewart, Aengus, Magness, Alastair, Karamani, Angeliki, Chain, Benny, Campbell, Brittany B, Castignani, Carla, Bailey, Chris, Puttick, Clare, Weeden, Clare E, Lee, Claudia, Richard, Corentin, Pearce, David R, Karagianni, Despoina, Biswas, Dhruva, Levi, Dina, Hoxha, Elena, Larose Cadieux, Elizabeth, Gronroos, Eva, Galvez-Cancino, Felip, Athanasopoulou, Foteini, Gimeno-Valiente, Francisco, Kassiotis, George, Stavrou, Georgia, Mastrokalos, Gerasimos, Zhai, Haoran, Lowe, Helen L, Matos, Ignacio, Goldman, Jacki, Reading, James L, Black, James RM, Herrero, Javier, Rane, Jayant K, Nicod, Jerome, Lam, Jie Min, Hartley, John A, Enfield, Katey SS, Selvaraju, Kayalvizhi, Thol, Kerstin, Litchfield, Kevin, Ng, Kevin W, Chen, Kezhong, Dijkstra, Krijn, Thakkar, Krupa, Ensell, Leah, Shah, Mansi, Vasquez, Marcos, Litovchenko, Maria, Werner Sunderland, Mariana, Leung, Michelle, Escudero, Mickael, Angelova, Mihaela, Tanic, Miljana, Sivakumar, Monica, Kanu, Nnennaya, Chervova, Olga, Lucas, Olivia, Al-Sawaf, Othman, Hobson, Philip, Pawlik, Piotr, Bentham, Robert, Hynds, Robert E, Vendramin, Roberto, Saghafinia, Sadegh, Lopez, Saioa, Gamble, Samuel, Ung, Seng Kuong Anakin, Vanloo, Sharon, Boeing, Stefan, Beck, Stephan, Bola, Supreet Kaur, Denner, Tamara, Marafioti, Teresa, Mourikis, Thanos P, Spanswick, Victoria, Barbe, Vittorio, Lu, Wei-Ting, Hill, William, Liu, Wing Kin, Wu, Yin, Naito, Yutaka, Ramsden, Zoe, Veiga, Catarina, Royle, Gary, Collins-Fekete, Charles-Antoine, Fraioli, Francesco, Ashford, Paul, Clark, Tristan, Borg, Elaine, Wilson, James, Patrini, Davide, Martinoni Hoogenboom, Emilie, Monk, Fleur, Holding, James W, Choudhary, Junaid, Bhakhri, Kunal, Scarci, Marco, Hayward, Martin, Panagiotopoulos, Nikolaos, Gorman, Pat, Khiroya, Reena, Stephens, Robert CM, Wong, Yien Ning Sophia, Bandula, Steve, Sharp, Abigail, Smith, Sean, Gower, Nicole, Dhanda, Harjot Kaur, Chan, Kitty, Pilotti, Camilla, Leslie, Rachel, Grapa, Anca, Zhang, Hanyun, AbdulJabbar, Khalid, Pan, Xiaoxi, Yuan, Yinyin, Chuter, David, MacKenzie, Mairead, Chee, Serena, Alzetani, Aiman, Scarlett, Lydia, Richards, Jennifer, Ingram, Papawadee, Austin, Silvia, Lim, Eric, De Sousa, Paulo, Jordan, Simon, Rice, Alexandra, Raubenheimer, Hilgardt, Bhayani, Harshil, Ambrose, Lyn, Devaraj, Anand, Chavan, Hema, Begum, Sofina, Buderi, Silviu, Kaniu, Daniel, Malima, Mpho, Booth, Sarah, Nicholson, Andrew G, Fernandes, Nadia, Shah, Pratibha, Proli, Chiara, Hewish, Madeleine, Danson, Sarah, Shackcloth, Michael J, Robinson, Lily, Russell, Peter, Dick, Craig, Le Quesne, John, Kirk, Alan, Asif, Mo, Bilancia, Rocco, Kostoulas, Nikos, and Thomas, Mathew

Subjects
Clonal Evolution, Cohort Studies, Evolution, Molecular, Lung Neoplasms, Carcinoma, Non-Small-Cell Lung, Disease Progression, Humans, Neoplasm Metastasis, Neoplasm Recurrence, Local, Clone Cells
Abstract

Metastatic disease is responsible for the majority of cancer-related deaths1. We report the longitudinal evolutionary analysis of 126 non-small cell lung cancer (NSCLC) tumours from 421 prospectively recruited patients in TRACERx who developed metastatic disease, compared with a control cohort of 144 non-metastatic tumours. In 25% of cases, metastases diverged early, before the last clonal sweep in the primary tumour, and early divergence was enriched for patients who were smokers at the time of initial diagnosis. Simulations suggested that early metastatic divergence more frequently occurred at smaller tumour diameters (less than 8 mm). Single-region primary tumour sampling resulted in 83% of late divergence cases being misclassified as early, highlighting the importance of extensive primary tumour sampling. Polyclonal dissemination, which was associated with extrathoracic disease recurrence, was found in 32% of cases. Primary lymph node disease contributed to metastatic relapse in less than 20% of cases, representing a hallmark of metastatic potential rather than a route to subsequent recurrences/disease progression. Metastasis-seeding subclones exhibited subclonal expansions within primary tumours, probably reflecting positive selection. Our findings highlight the importance of selection in metastatic clone evolution within untreated primary tumours, the distinction between monoclonal versus polyclonal seeding in dictating site of recurrence, the limitations of current radiological screening approaches for early diverging tumours and the need to develop strategies to target metastasis-seeding subclones before relapse. ispartof: NATURE vol:616 issue:7957 ispartof: location:England status: Published online

Published
2023

24. The evolution of lung cancer and impact of subclonal selection in TRACERx

Author

Frankell, Alexander M, Dietzen, Michelle, Al Bakir, Maise, Lim, Emilia L, Karasaki, Takahiro, Ward, Sophia, Veeriah, Selvaraju, Colliver, Emma, Huebner, Ariana, Bunkum, Abigail, Hill, Mark S, Grigoriadis, Kristiana, Moore, David A, Black, James RM, Liu, Wing Kin, Thol, Kerstin, Pich, Oriol, Watkins, Thomas BK, Naceur-Lombardelli, Cristina, Cook, Daniel E, Salgado, Roberto, Wilson, Gareth A, Bailey, Chris, Angelova, Mihaela, Bentham, Robert, Martinez-Ruiz, Carlos, Abbosh, Christopher, Nicholson, Andrew G, Le Quesne, John, Biswas, Dhruva, Rosenthal, Rachel, Puttick, Clare, Hessey, Sonya, Lee, Claudia, Prymas, Paulina, Toncheva, Antonia, Smith, Jon, Xing, Wei, Nicod, Jerome, Price, Gillian, Kerr, Keith M, Naidu, Babu, Middleton, Gary, Blyth, Kevin G, Fennell, Dean A, Forster, Martin D, Lee, Siow Ming, Falzon, Mary, Hewish, Madeleine, Shackcloth, Michael J, Lim, Eric, Benafif, Sarah, Russell, Peter, Boleti, Ekaterini, Krebs, Matthew G, Lester, Jason F, Papadatos-Pastos, Dionysis, Ahmad, Tanya, Thakrar, Ricky M, Lawrence, David, Navani, Neal, Janes, Sam M, Dive, Caroline, Blackhall, Fiona H, Summers, Yvonne, Cave, Judith, Marafioti, Teresa, Herrero, Javier, Quezada, Sergio A, Peggs, Karl S, Schwarz, Roland F, Van Loo, Peter, Miedema, Daniel M, Birkbak, Nicolai J, Hiley, Crispin T, Hackshaw, Allan, Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, Swanton, Charles, Bajaj, Amrita, Nakas, Apostolos, Sodha-Ramdeen, Azmina, Ang, Keng, Tufail, Mohamad, Chowdhry, Mohammed Fiyaz, Scotland, Molly, Boyles, Rebecca, Rathinam, Sridhar, Wilson, Claire, Marrone, Domenic, Dulloo, Sean, Matharu, Gurdeep, Shaw, Jacqui A, Riley, Joa, Primrose, Lindsay, Cheyne, Heather, Khalil, Mohammed, Richardson, Shirley, Cruickshank, Tracey, Gilbert, Kayleigh, Patel, Akshay J, Osman, Aya, Lacson, Christer, Langman, Gerald, Shackleford, Helen, Djearaman, Madava, Kadiri, Salma, Leek, Angela, Hodgkinson, Jack Davies, Totten, Nicola, Montero, Angeles, Smith, Elaine, Fontaine, Eustace, Granato, Felice, Doran, Helen, Novasio, Juliette, Rammohan, Kendadai, Joseph, Leena, Bishop, Paul, Shah, Rajesh, Moss, Stuart, Joshi, Vijay, Crosbie, Philip, Gomes, Fabio, Brown, Kate, Carter, Mathew, Chaturvedi, Anshuman, Priest, Lynsey, Oliveira, Pedro, Lindsay, Colin R, Clipson, Alexandra, Tugwood, Jonathan, Kerr, Alastair, Rothwell, Dominic G, Kilgour, Elaine, Aerts, Hugo JWL, Kaufmann, Tom L, Szallasi, Zoltan, Kisistok, Judit, Sokac, Mateo, Diossy, Miklos, Demeulemeester, Jonas, Stewart, Aengus, Magness, Alastair, Rowan, Andrew, Karamani, Angeliki, Chain, Benny, Campbell, Brittany B, Castignani, Carla, Weeden, Clare E, Richard, Corentin, Pearce, David R, Karagianni, Despoina, Levi, Dina, Hoxha, Elena, Larose Cadieux, Elizabeth, Nye, Emma, Gronroos, Eva, Galvez-Cancino, Felip, Athanasopoulou, Foteini, Gimeno-Valiente, Francisco, Kassiotis, George, Stavrou, Georgia, Mastrokalos, Gerasimos, Zhai, Haoran L, Lowe, Helen L, Matos, Ignacio, Goldman, Jacki, Reading, James L, Rane, Jayant K, Lam, Jie Min, Hartley, John A, Enfield, Katey SS, Selvaraju, Kayalvizhi, Litchfield, Kevin, Ng, Kevin W, Chen, Kezhong, Dijkstra, Krijn, Thakkar, Krupa, Ensell, Leah, Shah, Mansi, Vasquez, Marcos, Litovchenko, Maria, Werner Sunderland, Mariana, Leung, Michelle, Escudero, Mickael, Tanic, Miljana, Sivakumar, Monica, Kanu, Nnennaya, Chervova, Olga, Lucas, Olivia, Al-Sawaf, Othman, Hobson, Philip, Pawlik, Piotr, Stone, Richard Kevin, Hynds, Robert E, Vendramin, Roberto, Saghafinia, Sadegh, Lopez, Saioa, Gamble, Samuel, Ung, Seng Kuong Anakin, Vanloo, Sharon, Boeing, Stefan, Beck, Stephan, Bola, Supreet Kaur, Denner, Tamara, Mourikis, Thanos P, Spanswick, Victoria, Barbe, Vittorio, Lu, Wei-Ting, Hill, William, Wu, Yin, Naito, Yutaka, Ramsden, Zoe, Veiga, Catarina, Royle, Gary, Collins-Fekete, Charles-Antoine, Fraioli, Francesco, Ashford, Paul, Clark, Tristan, Borg, Elaine, Wilson, James, Procter, Alexander James, Ahmed, Asia, Taylor, Magali N, Nair, Arjun, Patrini, Davide, Martinoni Hoogenboom, Emilie, Monk, Fleur, Holding, James W, Choudhary, Junaid, Bhakhri, Kunal, Scarci, Marco, Hayward, Martin, Panagiotopoulos, Nikolaos, Gorman, Pat, Khiroya, Reena, Stephens, Robert CM, Wong, Yien Ning Sophia, Bandula, Steve, Sharp, Abigail, Smith, Sean, Gower, Nicole, Dhanda, Harjot Kaur, Chan, Kitty, Pilotti, Camilla, Leslie, Rachel, Grapa, Anca, Zhang, Hanyun, AbdulJabbar, Khalid, Pan, Xiaoxi, Yuan, Yinyin, Chuter, David, MacKenzie, Mairead, Chee, Serena, Alzetani, Aiman, Scarlett, Lydia, Richards, Jennifer, Ingram, Papawadee, Austin, Silvia, De Sousa, Paulo, Jordan, Simon, Rice, Alexandra, Raubenheimer, Hilgardt, Bhayani, Harshil, Ambrose, Lyn, Devaraj, Anand, Chavan, Hema, Begum, Sofina, Buderi, Silviu, Kaniu, Daniel, Malima, Mpho, Booth, Sarah, Fernandes, Nadia, Shah, Pratibha, Proli, Chiara, Danson, Sarah, Robinson, Lily, Dick, Craig, Kirk, Alan, Asif, Mo, Bilancia, Rocco, Kostoulas, Nikos, and Thomas, Mathew

Subjects
Lung Neoplasms, Treatment Outcome, DNA Copy Number Variations, Mutagenesis, Carcinoma, Non-Small-Cell Lung, Mutation, Smoking, Humans, Adenocarcinoma of Lung, Neoplasm Recurrence, Local, Phylogeny
Abstract

Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource. ispartof: NATURE vol:616 issue:7957 ispartof: location:England status: Published online

Published
2023

25. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx

Author

Karasaki, Takahiro, Moore, David A, Veeriah, Selvaraju, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Magno, Neil, Ward, Sophia, Al Bakir, Maise, Watkins, Thomas BK, Grigoriadis, Kristiana, Huebner, Ariana, Hill, Mark S, Frankell, Alexander M, Abbosh, Christopher, Puttick, Clare, Zhai, Haoran, Gimeno-Valiente, Francisco, Saghafinia, Sadegh, Kanu, Nnennaya, Dietzen, Michelle, Pich, Oriol, Lim, Emilia L, Martinez-Ruiz, Carlos, Black, James RM, Biswas, Dhruva, Campbell, Brittany B, Lee, Claudia, Colliver, Emma, Enfield, Katey SS, Hessey, Sonya, Hiley, Crispin T, Zaccaria, Simone, Litchfield, Kevin, Birkbak, Nicolai J, Cadieux, Elizabeth Larose, Demeulemeester, Jonas, Van Loo, Peter, Adusumilli, Prasad R, Tan, Kay See, Cheema, Waseem, Sanchez-Vega, Francisco, Jones, David R, Rekhtman, Natasha, Travis, William D, Hackshaw, Allan, Marafioti, Teresa, Salgado, Roberto, Le Quesne, John, Nicholson, Andrew G, McGranahan, Nicholas, Swanton, Charles, Jamal-Hanjani, Mariam, Lester, Jason F, Bajaj, Amrita, Nakas, Apostolos, Sodha-Ramdeen, Azmina, Ang, Keng, Tufail, Mohamad, Chowdhry, Mohammed Fiyaz, Scotland, Molly, Boyles, Rebecca, Rathinam, Sridhar, Wilson, Claire, Marrone, Domenic, Dulloo, Sean, Fennell, Dean A, Matharu, Gurdeep, Shaw, Jacqui A, Riley, Joan, Primrose, Lindsay, Boleti, Ekaterini, Cheyne, Heather, Khalil, Mohammed, Richardson, Shirley, Cruickshank, Tracey, Price, Gillian, Kerr, Keith M, Benafif, Sarah, Gilbert, Kayleigh, Naidu, Babu, Patel, Akshay J, Osman, Aya, Lacson, Christer, Langman, Gerald, Shackleford, Helen, Djearaman, Madava, Kadiri, Salma, Middleton, Gary, Leek, Angela, Hodgkinson, Jack Davies, Totten, Nicola, Montero, Angeles, Smith, Elaine, Fontaine, Eustace, Granato, Felice, Doran, Helen, Novasio, Juliette, Rammohan, Kendadai, Joseph, Leena, Bishop, Paul, Shah, Rajesh, Moss, Stuart, Joshi, Vijay, Crosbie, Philip, Gomes, Fabio, Brown, Kate, Carter, Mathew, Chaturvedi, Anshuman, Priest, Lynsey, Oliveira, Pedro, Lindsay, Colin R, Blackhall, Fiona H, Krebs, Matthew G, Summers, Yvonne, Clipson, Alexandra, Tugwood, Jonathan, Kerr, Alastair, Rothwell, Dominic G, Kilgour, Elaine, Dive, Caroline, Aerts, Hugo JWL, Schwarz, Roland F, Kaufmann, Tom L, Wilson, Gareth A, Rosenthal, Rachel, Szallasi, Zoltan, Kisistok, Judit, Sokac, Mateo, Diossy, Miklos, Bunkum, Abigail, Stewart, Aengus, Magness, Alastair, Rowan, Andrew, Karamani, Angeliki, Chain, Benny, Castignani, Carla, Bailey, Chris, Weeden, Clare E, Richard, Corentin, Pearce, David R, Karagianni, Despoina, Levi, Dina, Hoxha, Elena, Nye, Emma, Gronroos, Eva, Galvez-Cancino, Felip, Athanasopoulou, Foteini, Kassiotis, George, Stavrou, Georgia, Mastrokalos, Gerasimos, Lowe, Helen L, Matos, Ignacio Garcia, Goldman, Jacki, Reading, James L, Herrero, Javier, Rane, Jayant K, Nicod, Jerome, Lam, Jie Min, Hartley, John A, Peggs, Karl S, Selvaraju, Kayalvizhi, Thol, Kerstin, Ng, Kevin W, Chen, Kezhong, Dijkstra, Krijn, Thakkar, Krupa, Ensell, Leah, Shah, Mansi, Duran, Marcos Vasquez, Litovchenko, Maria, Sunderland, Mariana Werner, Leung, Michelle, Escudero, Mickael, Angelova, Mihaela, Tanic, Miljana, Sivakumar, Monica, Chervova, Olga, Lucas, Olivia, Al-Sawaf, Othman, Prymas, Paulina, Hobson, Philip, Pawlik, Piotr, Stone, Richard Kevin, Bentham, Robert, Hynds, Robert E, Vendramin, Roberto, Lopez, Saioa, Gamble, Samuel, Ung, Seng Kuong Anakin, Quezada, Sergio A, Vanloo, Sharon, Boeing, Stefan, Beck, Stephan, Bola, Supreet Kaur, Denner, Tamara, Mourikis, Thanos P, Spanswick, Victoria, Barbe, Vittorio, Lu, Wei-Ting, Hill, William, Liu, Wing Kin, Wu, Yin, Naito, Yutaka, Ramsden, Zoe, Veiga, Catarina, Royle, Gary, Collins-Fekete, Charles-Antoine, Fraioli, Francesco, Ashford, Paul, Clark, Tristan, Forster, Martin D, Lee, Siow Ming, Borg, Elaine, Falzon, Mary, Papadatos-Pastos, Dionysis, Wilson, James, Ahmad, Tanya, Procter, Alexander James, Ahmed, Asia, Taylor, Magali N, Nair, Arjun, Lawrence, David, Patrini, Davide, Navani, Neal, Thakrar, Ricky M, Janes, Sam M, Hoogenboom, Emilie Martinoni, Monk, Fleur, Holding, James W, Choudhary, Junaid, Bhakhri, Kunal, Scarci, Marco, Hayward, Martin, Panagiotopoulos, Nikolaos, Gorman, Pat, Khiroya, Reena, Stephens, Robert CM, Wong, Yien Ning Sophia, Bandula, Steve, Sharp, Abigail, Smith, Sean, Gower, Nicole, Dhanda, Harjot Kaur, Chan, Kitty, Pilotti, Camilla, Leslie, Rachel, Grapa, Anca, Zhang, Hanyun, AbdulJabbar, Khalid, Pan, Xiaoxi, Yuan, Yinyin, Chuter, David, MacKenzie, Mairead, Chee, Serena, Alzetani, Aiman, Cave, Judith, Scarlett, Lydia, Richards, Jennifer, Ingram, Papawadee, Austin, Silvia, Lim, Eric, De Sousa, Paulo, Jordan, Simon, Rice, Alexandra, Raubenheimer, Hilgardt, Bhayani, Harshil, Ambrose, Lyn, Devaraj, Anand, Chavan, Hema, Begum, Sofina, Buderi, Silviu, Kaniu, Daniel, Malima, Mpho, Booth, Sarah, Fernandes, Nadia, Shah, Pratibha, Proli, Chiara, Hewish, Madeleine, Danson, Sarah, Shackcloth, Michael J, Robinson, Lily, Russell, Peter, Blyth, Kevin G, Dick, Craig, Kirk, Alan, Asif, Mo, Bilancia, Rocco, Kostoulas, Nikos, and Thomas, Mathew

Subjects
TRACERx Consortium
Abstract

Lung adenocarcinomas (LUADs) display a broad histological spectrum from low-grade lepidic tumors through to mid-grade acinar and papillary and high-grade solid, cribriform and micropapillary tumors. How morphology reflects tumor evolution and disease progression is poorly understood. Whole-exome sequencing data generated from 805 primary tumor regions and 121 paired metastatic samples across 248 LUADs from the TRACERx 421 cohort, together with RNA-sequencing data from 463 primary tumor regions, were integrated with detailed whole-tumor and regional histopathological analysis. Tumors with predominantly high-grade patterns showed increased chromosomal complexity, with higher burden of loss of heterozygosity and subclonal somatic copy number alterations. Individual regions in predominantly high-grade pattern tumors exhibited higher proliferation and lower clonal diversity, potentially reflecting large recent subclonal expansions. Co-occurrence of truncal loss of chromosomes 3p and 3q was enriched in predominantly low-/mid-grade tumors, while purely undifferentiated solid-pattern tumors had a higher frequency of truncal arm or focal 3q gains and SMARCA4 gene alterations compared with mixed-pattern tumors with a solid component, suggesting distinct evolutionary trajectories. Clonal evolution analysis revealed that tumors tend to evolve toward higher-grade patterns. The presence of micropapillary pattern and 'tumor spread through air spaces' were associated with intrathoracic recurrence, in contrast to the presence of solid/cribriform patterns, necrosis and preoperative circulating tumor DNA detection, which were associated with extra-thoracic recurrence. These data provide insights into the relationship between LUAD morphology, the underlying evolutionary genomic landscape, and clinical and anatomical relapse risk. ispartof: NATURE MEDICINE vol:29 issue:4 ispartof: location:United States status: Published online

Published
2023

28. Evaluation of Epigenetic Age Acceleration Scores and Their Associations with CVD-Related Phenotypes in a Population Cohort

Author

Chervova, Olga, primary, Chernysheva , Elizabeth, additional, Panteleeva , Kseniia, additional, Widayati , Tyas Arum, additional, Hrbkova, Natalie, additional, Schneider , Jadesada, additional, Maximov , Vladimir, additional, Ryabikov , Andrew, additional, Tillmann , Taavi, additional, Pikhart, Hynek, additional, Bobak , Martin, additional, Voloshin , Vitaly, additional, Malyutina , Sofia, additional, and Beck , Stephan, additional

Published
2022
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29. Additional file 3 of Individualized dynamic methylation-based analysis of cell-free DNA in postoperative monitoring of lung cancer

Author

Chen, Kezhong, Kang, Guannan, Zhang, Zhihong, Lizaso, Analyn, Beck, Stephan, Lyskjær, Iben, Chervova, Olga, Li, Bingsi, Shen, Haifeng, Wang, Chenyang, Li, Bing, Zhao, Heng, Li, Xi, Yang, Fan, Kanu, Nnennaya, and Wang, Jun

Abstract

Additional file 3: Table S1. Baseline clinicopathologic characteristics of the 36 patients in the DYNAMIC cohort. Table S2. Summary of data in related studies on ctDNA-based MRD detection in early-stage lung cancer. Table S3. Analytical performance of timMRD model at various cutoff levels (percentile of chi-square distribution for timMRD scores) and tumor-informed ctDNA mutation status for the 155 patients with tumor-informed ctDNA mutation data at the last follow-up. Of the 155 patients, 11 patients had follow-up data at 120 days before relapse and 52 patients had follow-up data at the same time-point.

Published
2023
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31. Additional file 2 of Individualized dynamic methylation-based analysis of cell-free DNA in postoperative monitoring of lung cancer

Author

Chen, Kezhong, Kang, Guannan, Zhang, Zhihong, Lizaso, Analyn, Beck, Stephan, Lyskjær, Iben, Chervova, Olga, Li, Bingsi, Shen, Haifeng, Wang, Chenyang, Li, Bing, Zhao, Heng, Li, Xi, Yang, Fan, Kanu, Nnennaya, and Wang, Jun

Abstract

Additional file 2: Figure S1. Detailed workflow of the methylation-based analysis and timMRD model. Figure S2. Quality control of bisulfite sequencing for all patient tissue and blood samples. Figure S3. Distinct methylation profile of tumor tissues. Figure S4. Somatic mutation profile of baseline blood samples for 155 patients with paired tissue-based mutation data. Figure S5. Spike-in dilution experiments and numerical simulation trials demonstrate accuracy and robustness of the timMRD model. Figure S6. Relationship between tumor-informed ctDNA mutation, methylation status, and clinical features. Figure S7. Perioperative dynamics of timMRD scores, MethylMean, and tumor-informed ctDNA somatic mutation status. Figure S8. Perioperative management does not affect timMRD scores. Figure S9. TimMRD scores are positively correlated with somatic mutations (maxAF) in all ctDNA-positive samples. Figure S10. Plasma B and Plasma C reflect disease relapse using timMRD scores and tumor-informed ctDNA somatic mutations at postoperative time-points, but not MethylMean. Figure S11. Prognostication using ctDNA mutation status or timMRD score evaluated at postoperative follow-up time-points for either Plasma B or Plasma C in MEDAL cohort. Figure S12. Two-year prognostication using timMRD score evaluated at postoperative follow-up time-points using Plasma B or Plasma C in MEDAL cohort. Figure S13. Dynamics of ctDNA mutation and timMRD score in two relapsed patients of the MEDAL cohort.

Published
2023
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32. Dirac Equation as a Special Case of Cosserat Elasticity

Author

Burnett, James, Chervova, Olga, Vassiliev, Dmitri, Gohberg, I., editor, Alpay, D., editor, Arazy, J., editor, Atzmon, A., editor, Ball, J. A., editor, Bart, H., editor, Ben-Artzi, A., editor, Bercovici, H., editor, Böttcher, A., editor, Clancey, K., editor, Curto, R., editor, Davidson, K. R., editor, Demuth, M., editor, Dijksma, A., editor, Douglas, R. G., editor, Duduchava, R., editor, Ferreira dos Santos, A., editor, Frazho, A. E., editor, Fuhrmann, P. A., editor, Gramsch, B., editor, Kaper, H. G., editor, Kuroda, S. T., editor, Lerer, L. E., editor, Mityagin, B., editor, Olshevski, V., editor, Putinar, M., editor, Ran, A. C. M., editor, Rodman, L., editor, Rovnyak, J., editor, Schulze, B.-W., editor, Speck, F., editor, Spitkovsky, I. M., editor, Treil, S., editor, Tretter, C., editor, Upmeier, H., editor, Vasilevski, N., editor, Lunel, S. Verduyn, editor, Voiculescu, D., editor, Xia, D., editor, Yafaev, D., editor, Cialdea, Alberto, editor, Ricci, Paolo Emilio, editor, and Lanzara, Flavia, editor

Published
2009
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33. Abstract 5710: Identification of convergent gene repression mechanisms through integrative genomic and DNA methylation analysis in TRACERx

Author

Gimeno-Valiente, Francisco, primary, Castignani, Carla, additional, Larose-Cadieux, Elizabeth, additional, Chen, Kezhong, additional, Mensah, Nana, additional, Chervova, Olga, additional, Watkins, Thomas, additional, Dhami, Pawan, additional, Vaikkinen, Heli, additional, Feber, Andrew, additional, Consortium, TRACERx, additional, Demeulemeester, Jonas, additional, Tanic, Miljana, additional, Beck, Stephan, additional, Van Loo, Peter, additional, Swanton, Charles, additional, and Kanu, Nnennaya, additional

Published
2022
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35. A WGS-Based Hyper-Accurate Method for Lung Cancer Screening and Postoperative MRD Detection

Author

Li, Yun, primary, Jiang, Guanchao, additional, Wu, Wendy, additional, Wu, Manqi, additional, Jin, Yichen, additional, Yang, Hao, additional, Liu, Wenjie, additional, Yang, Airong, additional, Chervova, Olga, additional, Zhang, Sujie, additional, Zheng, Lu, additional, Zhang, Xueying, additional, Du, Fengxia, additional, Kanu, Nnennaya, additional, Wu, Lin, additional, Yang, Fan, additional, Wang, Jun, additional, and Chen, Kezhong, additional

Published
2022
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36. Evaluation of Epigenetic Age Acceleration Scores and Their Associations with CVD-Related Phenotypes in a Population Cohort.

Author

Chervova, Olga, Chernysheva, Elizabeth, Panteleeva, Kseniia, Widayati, Tyas Arum, Hrbkova, Natalie, Schneider, Jadesada, Maximov, Vladimir, Ryabikov, Andrew, Tillmann, Taavi, Pikhart, Hynek, Bobak, Martin, Voloshin, Vitaly, Malyutina, Sofia, and Beck, Stephan

Subjects
*PHENOTYPES, *AGE, *EPIGENETICS, *CORONARY disease, *ATHEROSCLEROTIC plaque
Abstract

Simple Summary: We consider a subset (n = 306) of an Eastern European ageing population cohort which was followed up for 15 years. Using blood DNA methylation data, we calculated nine epigenetic age acceleration scores, which are defined as deviations of epigenetic age from chronological age. We then evaluated how those scores are associated with available phenotypic data. This was implemented by splitting the phenotypic data into groups with positive and negative epigenetic age acceleration, and evaluating the difference between those groups. We observed strong association between all the considered epigenetic age acceleration and sex, suggesting that any analysis of these scores should be adjusted for sex. Moreover, even after adjusting for sex, the associations between the scores and considered phenotypes remain sex-specific. The only two associations that persisted through the entire dataset and both male and female subsets are incident coronary heart disease and smoking status. The observed associations of the various epigenetic age acceleration scores with both individual and groups of phenotypes suggest that these scores are sensitive to various cardiometabolic parameters, which might indicate their prognostic potential for related disorders. We evaluated associations between nine epigenetic age acceleration (EAA) scores and 18 cardiometabolic phenotypes using an Eastern European ageing population cohort richly annotated for a diverse set of phenotypes (subsample, n = 306; aged 45–69 years). This was implemented by splitting the data into groups with positive and negative EAAs. We observed strong association between all EAA scores and sex, suggesting that any analysis of EAAs should be adjusted by sex. We found that some sex-adjusted EAA scores were significantly associated with several phenotypes such as blood levels of gamma-glutamyl transferase and low-density lipoprotein, smoking status, annual alcohol consumption, multiple carotid plaques, and incident coronary heart disease status (not necessarily the same phenotypes for different EAAs). We demonstrated that even after adjusting EAAs for sex, EAA–phenotype associations remain sex-specific, which should be taken into account in any downstream analysis involving EAAs. The obtained results suggest that in some EAA–phenotype associations, negative EAA scores (i.e., epigenetic age below chronological age) indicated more harmful phenotype values, which is counterintuitive. Among all considered epigenetic clocks, GrimAge was significantly associated with more phenotypes than any other EA scores in this Russian sample. [ABSTRACT FROM AUTHOR]

Published
2023
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38. The Personal Genome Project-UK: an open access resource of human multi-omics data

Author

Chervova, Olga, primary, Conde, Lucia, additional, Guerra-Assunção, José Afonso, additional, Moghul, Ismail, additional, Webster, Amy P., additional, Berner, Alison, additional, Cadieux, Elizabeth Larose, additional, Tian, Yuan, additional, Voloshin, Vitaly, additional, Hamoudi, Rifat, additional, Herrero, Javier, additional, and Beck, Stephan, additional

Published
2019
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43. Spectral theoretic characterization of the massless Dirac operator.

Author

Chervova, Olga, Downes, Robert J., and Vassiliev, Dmitri

Subjects
*SPECTRAL theory, *DIRAC operators, *ELLIPTIC operators, *MATHEMATICAL complex analysis, *MANIFOLDS (Mathematics), *DIMENSIONAL analysis, *COMPACT operators
Abstract

We consider an elliptic self-adjoint first-order differential operator acting on pairs (2-columns) of complex-valued half-densities over a connected compact three-dimensional manifold without boundary. The principal symbol of our operator is assumed to be trace-free. We study the spectral function which is the sum of squares of Euclidean norms of eigenfunctions evaluated at a given point of the manifold, with summation carried out over all eigenvalues between zero and a positive $\lambda$. We derive an explicit two-term asymptotic formula for the spectral function as $\lambda \to + \infty$, expressing the second asymptotic coefficient via the trace of the subprincipal symbol and the geometric objects encoded within the principal symbol-metric, torsion of the teleparallel connection and topological charge. We then address the question: is our operator a massless Dirac operator on half-densities? We prove that it is a massless Dirac operator on half-densities if and only if the following two conditions are satisfied at every point of the manifold: (a) the subprincipal symbol is proportional to the identity matrix; and (b) the second asymptotic coefficient of the spectral function is zero. [ABSTRACT FROM AUTHOR]

Published
2014
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44. Spatial immunogenomic patterns associated with lymph node metastasis in lung adenocarcinoma.

Author

Meng F, Li H, Jin R, Yang A, Luo H, Li X, Wang P, Zhao Y, Chervova O, Tang K, Cheng S, Hu B, Li Y, Sheng J, Yang F, Carbone D, Chen K, and Wang J

Abstract

Background: Lung adenocarcinoma (LUAD) with lymph node (LN) metastasis is linked to poor prognosis, yet the underlying mechanisms remain largely undefined. This study aimed to elucidate the immunogenomic landscape associated with LN metastasis in LUAD., Methods: We employed broad-panel next-generation sequencing (NGS) on a cohort of 257 surgically treated LUAD patients to delineate the molecular landscape of primary tumors and identify actionable driver-gene alterations. Additionally, we used multiplex immunohistochemistry (mIHC) on a propensity score-matched cohort, which enabled us to profile the immune microenvironment of primary tumors in detail while preserving cellular metaclusters, interactions, and neighborhood functional units. By integrating data from NGS and mIHC, we successfully identified spatial immunogenomic patterns and developed a predictive model for LN metastasis, which was subsequently validated independently., Results: Our analysis revealed distinct immunogenomic alteration patterns associated with LN metastasis stages. Specifically, we observed increased mutation frequencies in genes such as PIK3CG and ATM in LN metastatic primary tumors. Moreover, LN positive primary tumors exhibited a higher presence of macrophage and regulatory T cell metaclusters, along with their enriched neighborhood units (p < 0.05), compared to LN negative tumors. Furthermore, we developed a novel predictive model for LN metastasis likelihood, designed to inform non-surgical treatment strategies, optimize personalized therapy plans, and potentially improve outcomes for patients who are ineligible for surgery., Conclusions: This study offers a comprehensive analysis of the genetic and immune profiles in LUAD primary tumors with LN metastasis, identifying key immunogenomic patterns linked to metastatic progression. The predictive model derived from these insights marks a substantial advancement in personalized treatment, underscoring its potential to improve patient management., (© 2024. The Author(s).)

Published
2024
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