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Global mapping of cancers: The Cancer Genome Atlas and beyond

Cancer genomes have been explored from the early 2000s through massive exome sequencing efforts, leading to the publication of The Cancer Genome Atlas in 2013. Sequencing techniques have been developed alongside this project and have allowed scientists to bypass the limitation of costs for whole‐gen...

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Autores principales: Ganini, Carlo, Amelio, Ivano, Bertolo, Riccardo, Bove, Pierluigi, Buonomo, Oreste Claudio, Candi, Eleonora, Cipriani, Chiara, Di Daniele, Nicola, Juhl, Hartmut, Mauriello, Alessandro, Marani, Carla, Marshall, John, Melino, Sonia, Marchetti, Paolo, Montanaro, Manuela, Natale, Maria Emanuela, Novelli, Flavia, Palmieri, Giampiero, Piacentini, Mauro, Rendina, Erino Angelo, Roselli, Mario, Sica, Giuseppe, Tesauro, Manfredi, Rovella, Valentina, Tisone, Giuseppe, Shi, Yufang, Wang, Ying, Melino, Gerry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8564642/
https://www.ncbi.nlm.nih.gov/pubmed/34245122
http://dx.doi.org/10.1002/1878-0261.13056
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author Ganini, Carlo
Amelio, Ivano
Bertolo, Riccardo
Bove, Pierluigi
Buonomo, Oreste Claudio
Candi, Eleonora
Cipriani, Chiara
Di Daniele, Nicola
Juhl, Hartmut
Mauriello, Alessandro
Marani, Carla
Marshall, John
Melino, Sonia
Marchetti, Paolo
Montanaro, Manuela
Natale, Maria Emanuela
Novelli, Flavia
Palmieri, Giampiero
Piacentini, Mauro
Rendina, Erino Angelo
Roselli, Mario
Sica, Giuseppe
Tesauro, Manfredi
Rovella, Valentina
Tisone, Giuseppe
Shi, Yufang
Wang, Ying
Melino, Gerry
author_facet Ganini, Carlo
Amelio, Ivano
Bertolo, Riccardo
Bove, Pierluigi
Buonomo, Oreste Claudio
Candi, Eleonora
Cipriani, Chiara
Di Daniele, Nicola
Juhl, Hartmut
Mauriello, Alessandro
Marani, Carla
Marshall, John
Melino, Sonia
Marchetti, Paolo
Montanaro, Manuela
Natale, Maria Emanuela
Novelli, Flavia
Palmieri, Giampiero
Piacentini, Mauro
Rendina, Erino Angelo
Roselli, Mario
Sica, Giuseppe
Tesauro, Manfredi
Rovella, Valentina
Tisone, Giuseppe
Shi, Yufang
Wang, Ying
Melino, Gerry
author_sort Ganini, Carlo
collection PubMed
description Cancer genomes have been explored from the early 2000s through massive exome sequencing efforts, leading to the publication of The Cancer Genome Atlas in 2013. Sequencing techniques have been developed alongside this project and have allowed scientists to bypass the limitation of costs for whole‐genome sequencing (WGS) of single specimens by developing more accurate and extensive cancer sequencing projects, such as deep sequencing of whole genomes and transcriptomic analysis. The Pan‐Cancer Analysis of Whole Genomes recently published WGS data from more than 2600 human cancers together with almost 1200 related transcriptomes. The application of WGS on a large database allowed, for the first time in history, a global analysis of features such as molecular signatures, large structural variations and noncoding regions of the genome, as well as the evaluation of RNA alterations in the absence of underlying DNA mutations. The vast amount of data generated still needs to be thoroughly deciphered, and the advent of machine‐learning approaches will be the next step towards the generation of personalized approaches for cancer medicine. The present manuscript wants to give a broad perspective on some of the biological evidence derived from the largest sequencing attempts on human cancers so far, discussing advantages and limitations of this approach and its power in the era of machine learning.
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spelling pubmed-85646422021-11-09 Global mapping of cancers: The Cancer Genome Atlas and beyond Ganini, Carlo Amelio, Ivano Bertolo, Riccardo Bove, Pierluigi Buonomo, Oreste Claudio Candi, Eleonora Cipriani, Chiara Di Daniele, Nicola Juhl, Hartmut Mauriello, Alessandro Marani, Carla Marshall, John Melino, Sonia Marchetti, Paolo Montanaro, Manuela Natale, Maria Emanuela Novelli, Flavia Palmieri, Giampiero Piacentini, Mauro Rendina, Erino Angelo Roselli, Mario Sica, Giuseppe Tesauro, Manfredi Rovella, Valentina Tisone, Giuseppe Shi, Yufang Wang, Ying Melino, Gerry Mol Oncol Review Cancer genomes have been explored from the early 2000s through massive exome sequencing efforts, leading to the publication of The Cancer Genome Atlas in 2013. Sequencing techniques have been developed alongside this project and have allowed scientists to bypass the limitation of costs for whole‐genome sequencing (WGS) of single specimens by developing more accurate and extensive cancer sequencing projects, such as deep sequencing of whole genomes and transcriptomic analysis. The Pan‐Cancer Analysis of Whole Genomes recently published WGS data from more than 2600 human cancers together with almost 1200 related transcriptomes. The application of WGS on a large database allowed, for the first time in history, a global analysis of features such as molecular signatures, large structural variations and noncoding regions of the genome, as well as the evaluation of RNA alterations in the absence of underlying DNA mutations. The vast amount of data generated still needs to be thoroughly deciphered, and the advent of machine‐learning approaches will be the next step towards the generation of personalized approaches for cancer medicine. The present manuscript wants to give a broad perspective on some of the biological evidence derived from the largest sequencing attempts on human cancers so far, discussing advantages and limitations of this approach and its power in the era of machine learning. John Wiley and Sons Inc. 2021-07-20 2021-11 /pmc/articles/PMC8564642/ /pubmed/34245122 http://dx.doi.org/10.1002/1878-0261.13056 Text en © 2021 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
Ganini, Carlo
Amelio, Ivano
Bertolo, Riccardo
Bove, Pierluigi
Buonomo, Oreste Claudio
Candi, Eleonora
Cipriani, Chiara
Di Daniele, Nicola
Juhl, Hartmut
Mauriello, Alessandro
Marani, Carla
Marshall, John
Melino, Sonia
Marchetti, Paolo
Montanaro, Manuela
Natale, Maria Emanuela
Novelli, Flavia
Palmieri, Giampiero
Piacentini, Mauro
Rendina, Erino Angelo
Roselli, Mario
Sica, Giuseppe
Tesauro, Manfredi
Rovella, Valentina
Tisone, Giuseppe
Shi, Yufang
Wang, Ying
Melino, Gerry
Global mapping of cancers: The Cancer Genome Atlas and beyond
title Global mapping of cancers: The Cancer Genome Atlas and beyond
title_full Global mapping of cancers: The Cancer Genome Atlas and beyond
title_fullStr Global mapping of cancers: The Cancer Genome Atlas and beyond
title_full_unstemmed Global mapping of cancers: The Cancer Genome Atlas and beyond
title_short Global mapping of cancers: The Cancer Genome Atlas and beyond
title_sort global mapping of cancers: the cancer genome atlas and beyond
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8564642/
https://www.ncbi.nlm.nih.gov/pubmed/34245122
http://dx.doi.org/10.1002/1878-0261.13056
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