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glass_consortium_publications.bib
@ARTICLE{Bakas2020-ee,
title = "{iGLASS}: imaging integration into the Glioma Longitudinal
Analysis Consortium",
author = "Bakas, Spyridon and Ormond, David Ryan and Alfaro-Munoz, Kristin
D and Smits, Marion and Cooper, Lee Alex Donald and Verhaak, Roel
and Poisson, Laila M",
journal = "Neuro. Oncol.",
volume = 22,
number = 10,
pages = "1545-1546",
month = oct,
year = 2020,
url = "http://dx.doi.org/10.1093/neuonc/noaa160",
language = "en",
issn = "1522-8517, 1523-5866",
pmid = "32644158",
doi = "10.1093/neuonc/noaa160",
pmc = "PMC7566469"
}
@ARTICLE{Varn2022-bt,
title = "Glioma progression is shaped by genetic evolution and
microenvironment interactions",
author = "Varn, Frederick S and Johnson, Kevin C and Martinek, Jan and
Huse, Jason T and Nasrallah, Maclean P and Wesseling, Pieter and
Cooper, Lee A D and Malta, Tathiane M and Wade, Taylor E and
Sabedot, Thais S and Brat, Daniel and Gould, Peter V and
W{\"o}ehrer, Adelheid and Aldape, Kenneth and Ismail, Azzam and
Sivajothi, Santhosh K and Barthel, Floris P and Kim, Hoon and
Kocakavuk, Emre and Ahmed, Nazia and White, Kieron and Datta,
Indrani and Moon, Hyo-Eun and Pollock, Steven and Goldfarb,
Christine and Lee, Ga-Hyun and Garofano, Luciano and Anderson,
Kevin J and Nehar-Belaid, Djamel and Barnholtz-Sloan, Jill S and
Bakas, Spyridon and Byrne, Annette T and D'Angelo, Fulvio and
Gan, Hui K and Khasraw, Mustafa and Migliozzi, Simona and Ryan
Ormond, D and Paek, Sun Ha and Van Meir, Erwin G and Walenkamp,
Annemiek M E and Watts, Colin and Weiss, Tobias and Weller,
Michael and Palucka, Karolina and Stead, Lucy F and Poisson,
Laila M and Noushmehr, Houtan and Iavarone, Antonio and Verhaak,
Roel G W and Alfaro, Kristin D and Amin, Samirkumar B and
Ashley, David M and Bock, Christoph and Brodbelt, Andrew and
Bulsara, Ketan R and Castro, Ana Valeria and Connelly, Jennifer
M and Costello, Joseph F and de Groot, John F and Finocchiaro,
Gaetano and French, Pim J and Golebiewska, Anna and Hau, Ann C
and Hong, Chibo and Horbinski, Craig and Kannan, Kasthuri S and
Kouwenhoven, Mathilde C M and Lasorella, Anna and LaViolette,
Peter S and Ligon, Keith L and Lowman, Allison K and Mehta,
Shwetal and Miletic, Hrvoje and Molinaro, Annette M and Ng, Ho
Keung and Niclou, Simone P and Niers, Johanna M and Phillips,
Joanna J and Rabadan, Raul and Rao, Ganesh and Reifenberger,
Guido and Sanai, Nader and Short, Susan C and Smitt, Peter
Sillevis and Sloan, Andrew E and Smits, Marion and Snyder, James
M and Suzuki, Hiromichi and Tabatabai, Ghazaleh and Tanner,
Georgette and Tomaszewski, William H and Wells, Michael and
Westerman, Bart A and Wheeler, Helen and Xie, Jichun and Alfred
Yung, W K and Zadeh, Gelareh and Zhao, Junfei and Verhaak, Roel
G W",
abstract = "SummaryThe factors driving therapy resistance in diffuse glioma
remain poorly understood. To identify treatment-associated
cellular and genetic changes, we analyzed RNA and/or DNA
sequencing data from the temporally separated tumor pairs of 304
adult patients with isocitrate dehydrogenase (IDH)-wild-type and
IDH-mutant glioma. Tumors recurred in distinct manners that were
dependent on IDH mutation status and attributable to changes in
histological feature composition, somatic alterations, and
microenvironment interactions. Hypermutation and acquired CDKN2A
deletions were associated with an increase in proliferating
neoplastic cells at recurrence in both glioma subtypes,
reflecting active tumor growth. IDH-wild-type tumors were more
invasive at recurrence, and their neoplastic cells exhibited
increased expression of neuronal signaling programs that
reflected a possible role for neuronal interactions in promoting
glioma progression. Mesenchymal transition was associated with
the presence of a myeloid cell state defined by specific
ligand-receptor interactions with neoplastic cells.
Collectively, these recurrence-associated phenotypes represent
potential targets to alter disease progression.",
journal = "Cell",
publisher = "Elsevier",
volume = 0,
number = 0,
month = may,
year = 2022,
url = "http://www.cell.com/article/S0092867422005360/abstract",
language = "en",
issn = "0092-8674, 1097-4172",
doi = "10.1016/j.cell.2022.04.038"
}
@ARTICLE{Barthel2019-kv,
title = "Longitudinal molecular trajectories of diffuse glioma in adults",
author = "Barthel, Floris P and Johnson, Kevin C and Varn, Frederick S and
Moskalik, Anzhela D and Tanner, Georgette and Kocakavuk, Emre and
Anderson, Kevin J and Abiola, Olajide and Aldape, Kenneth and
Alfaro, Kristin D and Alpar, Donat and Amin, Samirkumar B and
Ashley, David M and Bandopadhayay, Pratiti and Barnholtz-Sloan,
Jill S and Beroukhim, Rameen and Bock, Christoph and Brastianos,
Priscilla K and Brat, Daniel J and Brodbelt, Andrew R and Bruns,
Alexander F and Bulsara, Ketan R and Chakrabarty, Aruna and
Chakravarti, Arnab and Chuang, Jeffrey H and Claus, Elizabeth B
and Cochran, Elizabeth J and Connelly, Jennifer and Costello,
Joseph F and Finocchiaro, Gaetano and Fletcher, Michael N and
French, Pim J and Gan, Hui K and Gilbert, Mark R and Gould, Peter
V and Grimmer, Matthew R and Iavarone, Antonio and Ismail, Azzam
and Jenkinson, Michael D and Khasraw, Mustafa and Kim, Hoon and
Kouwenhoven, Mathilde C M and LaViolette, Peter S and Li, Meihong
and Lichter, Peter and Ligon, Keith L and Lowman, Allison K and
Malta, Tathiane M and Mazor, Tali and McDonald, Kerrie L and
Molinaro, Annette M and Nam, Do-Hyun and Nayyar, Naema and Ng, Ho
Keung and Ngan, Chew Yee and Niclou, Simone P and Niers, Johanna
M and Noushmehr, Houtan and Noorbakhsh, Javad and Ormond, D Ryan
and Park, Chul-Kee and Poisson, Laila M and Rabadan, Raul and
Radlwimmer, Bernhard and Rao, Ganesh and Reifenberger, Guido and
Sa, Jason K and Schuster, Michael and Shaw, Brian L and Short,
Susan C and Smitt, Peter A Sillevis and Sloan, Andrew E and
Smits, Marion and Suzuki, Hiromichi and Tabatabai, Ghazaleh and
Van Meir, Erwin G and Watts, Colin and Weller, Michael and
Wesseling, Pieter and Westerman, Bart A and Widhalm, Georg and
Woehrer, Adelheid and Yung, W K Alfred and Zadeh, Gelareh and
Huse, Jason T and De Groot, John F and Stead, Lucy F and Verhaak,
Roel G W and Barthel, Floris P and Johnson, Kevin C and Varn,
Frederick S and Moskalik, Anzhela D and Tanner, Georgette and
Kocakavuk, Emre and Anderson, Kevin J and Aldape, Kenneth and
Alfaro, Kristin D and Amin, Samirkumar B and Ashley, David M and
Bandopadhayay, Pratiti and Barnholtz-Sloan, Jill S and Beroukhim,
Rameen and Bock, Christoph and Brastianos, Priscilla K and Brat,
Daniel J and Brodbelt, Andrew R and Bulsara, Ketan R and
Chakrabarty, Aruna and Chuang, Jeffrey H and Claus, Elizabeth B
and Cochran, Elizabeth J and Connelly, Jennifer and Costello,
Joseph F and Finocchiaro, Gaetano and Fletcher, Michael N and
French, Pim J and Gan, Hui K and Gilbert, Mark R and Gould, Peter
V and Iavarone, Antonio and Ismail, Azzam and Jenkinson, Michael
D and Khasraw, Mustafa and Kim, Hoon and Kouwenhoven, Mathilde C
M and LaViolette, Peter S and Lichter, Peter and Ligon, Keith L
and Lowman, Allison K and Malta, Tathiane M and McDonald, Kerrie
L and Molinaro, Annette M and Nam, Do-Hyun and Ng, Ho Keung and
Niclou, Simone P and Niers, Johanna M and Noushmehr, Houtan and
Ormond, D Ryan and Park, Chul-Kee and Poisson, Laila M and
Rabadan, Raul and Radlwimmer, Bernhard and Rao, Ganesh and
Reifenberger, Guido and Sa, Jason K and Short, Susan C and Smitt,
Peter A Sillevis and Sloan, Andrew E and Smits, Marion and
Suzuki, Hiromichi and Tabatabai, Ghazaleh and Van Meir, Erwin G
and Watts, Colin and Weller, Michael and Wesseling, Pieter and
Westerman, Bart A and Woehrer, Adelheid and Yung, W K Alfred and
Zadeh, Gelareh and Huse, Jason T and De Groot, John F and Stead,
Lucy F and Verhaak, Roel G W and {The GLASS Consortium}",
abstract = "The evolutionary processes that drive universal therapeutic
resistance in adult patients with diffuse glioma remain
unclear1,2. Here we analysed temporally separated DNA-sequencing
data and matched clinical annotation from 222 adult patients with
glioma. By analysing mutations and copy numbers across the three
major subtypes of diffuse glioma, we found that driver genes
detected at the initial stage of disease were retained at
recurrence, whereas there was little evidence of
recurrence-specific gene alterations. Treatment with alkylating
agents resulted in a hypermutator phenotype at different rates
across the glioma subtypes, and hypermutation was not associated
with differences in overall survival. Acquired aneuploidy was
frequently detected in recurrent gliomas and was characterized by
IDH mutation but without co-deletion of chromosome arms 1p/19q,
and further converged with acquired alterations in the cell cycle
and poor outcomes. The clonal architecture of each tumour
remained similar over time, but the presence of subclonal
selection was associated with decreased survival. Finally, there
were no differences in the levels of immunoediting between
initial and recurrent gliomas. Collectively, our results suggest
that the strongest selective pressures occur during early glioma
development and that current therapies shape this evolution in a
largely stochastic manner.",
journal = "Nature",
month = nov,
year = 2019,
url = "https://doi.org/10.1038/s41586-019-1775-1",
issn = "0028-0836, 1476-4687",
doi = "10.1038/s41586-019-1775-1"
}
@ARTICLE{Aldape2018-qf,
title = "Glioma Through the Looking {GLASS}: Molecular Evolution of
Diffuse Gliomas and the Glioma Longitudinal {AnalySiS} Consortium",
author = "Aldape, Kenneth and Amin, Samirkumar B and Ashley, David M and
Barnholtz-Sloan, Jill S and Bates, Amanda J and Beroukhim, Rameen
and Bock, Christoph and Brat, Daniel J and Claus, Elizabeth B and
Costello, Joseph F and de Groot, John F and Finocchiaro, Gaetano
and French, Pim J and Gan, Hui K and Griffith, Brent and
Herold-Mende, Christel C and Horbinski, Craig and Iavarone,
Antonio and Kalkanis, Steven N and Karabatsou, Konstantina and
Kim, Hoon and Kouwenhoven, Mathilde C M and McDonald, Kerrie L
and Miletic, Hrvoje and Nam, Do-Hyun and Ng, Ho Keung and Niclou,
Simone P and Noushmehr, Houtan and Ormond, Ryan and Poisson,
Laila M and Reifenberger, Guido and Roncaroli, Federico and Sa,
Jason K and Sillevis Smitt, Peter A E and Smits, Marion and
Souza, Camila F and Tabatabai, Ghazaleh and Van Meir, Erwin G and
Verhaak, Roel G W and Watts, Colin and Wesseling, Pieter and
Woehrer, Adelheid and Yung, W K Alfred and Jungk, Christine and
Hau, Ann-Christin and van Dyck, Eric and Westerman, Bart A and
Yin, Julia and Abiola, Olajide and Zeps, Nikolaj and Grimmond,
Sean and Buckland, Michael and Khasraw, Mustafa and Sulman, Erik
P and Muscat, Andrea M and Stead, Lucy and {GLASS Consortium}",
abstract = "Adult diffuse gliomas are a diverse group of brain neoplasms that
inflict a high emotional toll on patients and their families. The
Cancer Genome Atlas (TCGA) and similar projects have provided a
comprehensive understanding of the somatic alterations and
molecular subtypes of glioma at diagnosis. However, gliomas
undergo significant cellular and molecular evolution during
disease progression. We review the current knowledge on the
genomic and epigenetic abnormalities in primary tumors and after
disease recurrence, highlight the gaps in the literature, and
elaborate on the need for a new multi-institutional effort to
bridge these knowledge gaps and how the Glioma Longitudinal
AnalySiS Consortium (GLASS) aims to systemically catalog the
longitudinal changes in gliomas. The GLASS initiative will
provide essential insights into the evolution of glioma toward a
lethal phenotype, with the potential to reveal targetable
vulnerabilities, and ultimately, improved outcomes for a patient
population in need.",
journal = "Neuro. Oncol.",
month = feb,
year = 2018,
url = "https://academic.oup.com/neuro-oncology/advance-article-abstract/doi/10.1093/neuonc/noy020/4843984",
language = "en",
issn = "1522-8517, 1523-5866",
pmid = "29432615",
doi = "10.1093/neuonc/noy020"
}
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