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Article ; Online: Timing somatic events in the evolution of cancer

Clemency Jolly / Peter Van Loo

Genome Biology, Vol 19, Iss 1, Pp 1-

2018 Volume 9

Abstract: Abstract Cancer arises through the accumulation of somatic mutations over time. An understanding of the sequence of events during this process should allow both earlier diagnosis and better prediction of cancer progression. However, the pathways of tumor ...

Abstract	Abstract Cancer arises through the accumulation of somatic mutations over time. An understanding of the sequence of events during this process should allow both earlier diagnosis and better prediction of cancer progression. However, the pathways of tumor evolution have not yet been comprehensively characterized. With the advent of whole genome sequencing, it is now possible to infer the evolutionary history of single tumors from the snapshot of their genome taken at diagnosis, giving new insights into the biology of tumorigenesis.
Keywords	Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Timing somatic events in the evolution of cancer.

Jolly, Clemency / Van Loo, Peter

Genome biology

2018 Volume 19, Issue 1, Page(s) 95

Abstract: Cancer arises through the accumulation of somatic mutations over time. An understanding of the sequence of events during this process should allow both earlier diagnosis and better prediction of cancer progression. However, the pathways of tumor ... ...

Abstract	Cancer arises through the accumulation of somatic mutations over time. An understanding of the sequence of events during this process should allow both earlier diagnosis and better prediction of cancer progression. However, the pathways of tumor evolution have not yet been comprehensively characterized. With the advent of whole genome sequencing, it is now possible to infer the evolutionary history of single tumors from the snapshot of their genome taken at diagnosis, giving new insights into the biology of tumorigenesis.
MeSH term(s)	BRCA1 Protein/genetics ; BRCA1 Protein/metabolism ; Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Breast Neoplasms/pathology ; Carcinogenesis/genetics ; Carcinogenesis/metabolism ; Carcinogenesis/pathology ; Clonal Evolution ; Female ; Gene Expression Regulation, Neoplastic ; Genome, Human ; Humans ; Janus Kinase 2/genetics ; Janus Kinase 2/metabolism ; Leukemia, Lymphocytic, Chronic, B-Cell/genetics ; Leukemia, Lymphocytic, Chronic, B-Cell/metabolism ; Leukemia, Lymphocytic, Chronic, B-Cell/pathology ; Male ; Mutation ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; STAT3 Transcription Factor/genetics ; STAT3 Transcription Factor/metabolism ; Time Factors ; Whole Genome Sequencing
Chemical Substances	BRCA1 Protein ; BRCA1 protein, human ; Neoplasm Proteins ; STAT3 Transcription Factor ; STAT3 protein, human ; JAK2 protein, human (EC 2.7.10.2) ; Janus Kinase 2 (EC 2.7.10.2)
Language	English
Publishing date	2018-07-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-018-1476-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Timing somatic events in the evolution of cancer

Jolly, Clemency / Van Loo, Peter

Genome biology. 2018 Dec., v. 19, no. 1

2018

Abstract	Cancer arises through the accumulation of somatic mutations over time. An understanding of the sequence of events during this process should allow both earlier diagnosis and better prediction of cancer progression. However, the pathways of tumor evolution have not yet been comprehensively characterized. With the advent of whole genome sequencing, it is now possible to infer the evolutionary history of single tumors from the snapshot of their genome taken at diagnosis, giving new insights into the biology of tumorigenesis.
Keywords	carcinogenesis ; disease course ; genome ; neoplasms ; prediction ; sequence analysis ; somatic mutation
Language	English
Dates of publication	2018-12
Size	p. 95.
Publishing place	BioMed Central
Document type	Article
Note	Review
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-018-1476-3
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Author Correction: The evolutionary history of 2,658 cancers.

Gerstung, Moritz / Jolly, Clemency / Leshchiner, Ignaty / Dentro, Stefan C / Gonzalez, Santiago / Rosebrock, Daniel / Mitchell, Thomas J / Rubanova, Yulia / Anur, Pavana / Yu, Kaixian / Tarabichi, Maxime / Deshwar, Amit / Wintersinger, Jeff / Kleinheinz, Kortine / Vázquez-García, Ignacio / Haase, Kerstin / Jerman, Lara / Sengupta, Subhajit / Macintyre, Geoff /

Malikic, Salem / Donmez, Nilgun / Livitz, Dimitri G / Cmero, Marek / Demeulemeester, Jonas / Schumacher, Steven / Fan, Yu / Yao, Xiaotong / Lee, Juhee / Schlesner, Matthias / Boutros, Paul C / Bowtell, David D / Zhu, Hongtu / Getz, Gad / Imielinski, Marcin / Beroukhim, Rameen / Sahinalp, S Cenk / Ji, Yuan / Peifer, Martin / Markowetz, Florian / Mustonen, Ville / Yuan, Ke / Wang, Wenyi / Morris, Quaid D / Spellman, Paul T / Wedge, David C / Van Loo, Peter

Nature

2023 Volume 614, Issue 7948, Page(s) E42

Language	English
Publishing date	2023-01-23
Publishing country	England
Document type	Published Erratum
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-022-05601-4
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Article ; Online: Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

Daniel C. Jeffares / Clemency Jolly / Mimoza Hoti / Doug Speed / Liam Shaw / Charalampos Rallis / Francois Balloux / Christophe Dessimoz / Jürg Bähler / Fritz J. Sedlazeck

Nature Communications, Vol 8, Iss 1, Pp 1-

2017 Volume 11

Abstract: Fission yeastSchizosaccharomyces pombe has diverse traits. Jeffares et al. characterize large copy number variations (CNVs) and rearrangements in S. pombe, and show that CNVs are transient with effects on quantitative traits and gene expression, whereas ... ...

Abstract	Fission yeastSchizosaccharomyces pombe has diverse traits. Jeffares et al. characterize large copy number variations (CNVs) and rearrangements in S. pombe, and show that CNVs are transient with effects on quantitative traits and gene expression, whereas rearrangements influence intrinsic reproductive isolation.
Keywords	Science ; Q
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.

Jeffares, Daniel C / Jolly, Clemency / Hoti, Mimoza / Speed, Doug / Shaw, Liam / Rallis, Charalampos / Balloux, Francois / Dessimoz, Christophe / Bähler, Jürg / Sedlazeck, Fritz J

Nature communications

2017 Volume 8, Page(s) 14061

Abstract: Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. We analyse the effects of SVs on gene expression, quantitative traits ... ...

Abstract	Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. We analyse the effects of SVs on gene expression, quantitative traits and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalogue of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) show a variety of genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits, most notably intracellular amino acid concentrations, growth under stress and sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases.
MeSH term(s)	Chromosome Inversion/genetics ; Chromosomes, Fungal/genetics ; DNA Copy Number Variations/genetics ; Evolution, Molecular ; Gene Expression Regulation, Fungal ; Genome, Fungal/genetics ; Quantitative Trait, Heritable ; Reproductive Isolation ; Schizosaccharomyces/genetics ; Translocation, Genetic/genetics
Language	English
Publishing date	2017-01-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/ncomms14061
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture.

Álvarez, Eva G / Demeulemeester, Jonas / Otero, Paula / Jolly, Clemency / García-Souto, Daniel / Pequeño-Valtierra, Ana / Zamora, Jorge / Tojo, Marta / Temes, Javier / Baez-Ortega, Adrian / Rodriguez-Martin, Bernardo / Oitaben, Ana / Bruzos, Alicia L / Martínez-Fernández, Mónica / Haase, Kerstin / Zumalave, Sonia / Abal, Rosanna / Rodríguez-Castro, Jorge / Rodriguez-Casanova, Aitor /

Nature communications

2021 Volume 12, Issue 1, Page(s) 6910

Abstract: Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. Here, using multiplatform sequencing technologies, we identify and characterize a remarkable mutational ... ...

Abstract	Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. Here, using multiplatform sequencing technologies, we identify and characterize a remarkable mutational mechanism in human hepatocellular carcinoma caused by Hepatitis B virus, by which DNA molecules from the virus are inserted into the tumour genome causing dramatic changes in its configuration, including non-homologous chromosomal fusions, dicentric chromosomes and megabase-size telomeric deletions. This aberrant mutational mechanism, present in at least 8% of all HCC tumours, can provide the driver rearrangements that a cancer clone requires to survive and grow, including loss of relevant tumour suppressor genes. Most of these events are clonal and occur early during liver cancer evolution. Real-time timing estimation reveals some HBV-mediated rearrangements occur as early as two decades before cancer diagnosis. Overall, these data underscore the importance of characterising liver cancer genomes for patterns of HBV integration.
MeSH term(s)	Carcinoma, Hepatocellular/genetics ; Carcinoma, Hepatocellular/virology ; DNA, Viral ; Gene Expression Regulation, Neoplastic ; Genome, Human ; Hepatitis B virus/genetics ; Humans ; Liver Neoplasms/genetics ; Virus Integration ; Whole Genome Sequencing
Chemical Substances	DNA, Viral
Language	English
Publishing date	2021-11-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-26805-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.

Dentro, Stefan C / Leshchiner, Ignaty / Haase, Kerstin / Tarabichi, Maxime / Wintersinger, Jeff / Deshwar, Amit G / Yu, Kaixian / Rubanova, Yulia / Macintyre, Geoff / Demeulemeester, Jonas / Vázquez-García, Ignacio / Kleinheinz, Kortine / Livitz, Dimitri G / Malikic, Salem / Donmez, Nilgun / Sengupta, Subhajit / Anur, Pavana / Jolly, Clemency / Cmero, Marek /

Rosebrock, Daniel / Schumacher, Steven E / Fan, Yu / Fittall, Matthew / Drews, Ruben M / Yao, Xiaotong / Watkins, Thomas B K / Lee, Juhee / Schlesner, Matthias / Zhu, Hongtu / Adams, David J / McGranahan, Nicholas / Swanton, Charles / Getz, Gad / Boutros, Paul C / Imielinski, Marcin / Beroukhim, Rameen / Sahinalp, S Cenk / Ji, Yuan / Peifer, Martin / Martincorena, Inigo / Markowetz, Florian / Mustonen, Ville / Yuan, Ke / Gerstung, Moritz / Spellman, Paul T / Wang, Wenyi / Morris, Quaid D / Wedge, David C / Van Loo, Peter

Cell

2021 Volume 184, Issue 8, Page(s) 2239–2254.e39

Abstract: Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively ... ...

Abstract	Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.
MeSH term(s)	DNA Copy Number Variations ; DNA, Neoplasm/chemistry ; DNA, Neoplasm/metabolism ; Databases, Genetic ; Drug Resistance, Neoplasm/genetics ; Genetic Heterogeneity ; Humans ; Neoplasms/genetics ; Neoplasms/pathology ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing
Chemical Substances	DNA, Neoplasm
Language	English
Publishing date	2021-04-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.03.009
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The evolutionary history of 2,658 cancers.

Nature

2020 Volume 578, Issue 7793, Page(s) 122–128

Abstract: Cancer develops through a process of somatic ... ...

Abstract	Cancer develops through a process of somatic evolution
MeSH term(s)	DNA Repair/genetics ; Evolution, Molecular ; Gene Dosage ; Genes, Tumor Suppressor ; Genetic Variation ; Genome, Human/genetics ; Humans ; Mutagenesis, Insertional/genetics ; Neoplasms/genetics
Language	English
Publishing date	2020-02-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-019-1907-7
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Article ; Online: Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

Eva G. Álvarez / Jonas Demeulemeester / Paula Otero / Clemency Jolly / Daniel García-Souto / Ana Pequeño-Valtierra / Jorge Zamora / Marta Tojo / Javier Temes / Adrian Baez-Ortega / Bernardo Rodriguez-Martin / Ana Oitaben / Alicia L. Bruzos / Mónica Martínez-Fernández / Kerstin Haase / Sonia Zumalave / Rosanna Abal / Jorge Rodríguez-Castro / Aitor Rodriguez-Casanova /

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 12

Abstract: Hepatitis B virus (HBV) infection and DNA integration is a frequent cause of hepatocellular carcinoma (HCC), but the consequences of this process are not fully understood. Here the authors use whole-genome and long-read sequencing data from HCC patient ... ...

Abstract	Hepatitis B virus (HBV) infection and DNA integration is a frequent cause of hepatocellular carcinoma (HCC), but the consequences of this process are not fully understood. Here the authors use whole-genome and long-read sequencing data from HCC patient samples to study the timing and alterations induced by HBV insertions.
Keywords	Science ; Q
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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