---
_id: '8707'
abstract:
- lang: eng
text: Dynamic changes in the three-dimensional (3D) organization of chromatin are
associated with central biological processes, such as transcription, replication
and development. Therefore, the comprehensive identification and quantification
of these changes is fundamental to understanding of evolutionary and regulatory
mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity
(CHESS), an algorithm for the comparison of chromatin contact maps and automatic
differential feature extraction. We demonstrate the robustness of CHESS to experimental
variability and showcase its biological applications on (1) interspecies comparisons
of syntenic regions in human and mouse models; (2) intraspecies identification
of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific
aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and
(4) the systematic identification of chromatin contact differences in high-resolution
Capture-C data. In summary, CHESS is a computationally efficient method for the
comparison and classification of changes in chromatin contact data.
acknowledgement: 'Work in the Vaquerizas laboratory is funded by the Max Planck Society,
the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome
Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the
DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project
no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN
to J.M.V.) and the Medical Research Council in the UK. This research was partially
funded by the European Union’s H2020 Framework Programme through the European Research
Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio
de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R.
The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia,
Innovación y Universidades to the European Molecular Biology Laboratory partnership,
the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208,
the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación
y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya
through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing
by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from
the European Regional Development Fund corresponding to the 2014–2020 Smart Growth
Operating Program. S.G. thanks the support from the Company of Biologists (grant
no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship
programme.'
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
full_name: ' Galan, Silvia'
last_name: ' Galan'
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
orcid: 0000-0001-6617-9742
- first_name: Kai
full_name: Kruse, Kai
last_name: Kruse
- first_name: Noelia
full_name: Díaz, Noelia
last_name: Díaz
- first_name: Marc A
full_name: Marti-Renom, Marc A
last_name: Marti-Renom
- first_name: Juan M
full_name: Vaquerizas, Juan M
last_name: Vaquerizas
citation:
ama: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS
enables quantitative comparison of chromatin contact data and automatic feature
extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y
apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas,
J. M. (2020). CHESS enables quantitative comparison of chromatin contact data
and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y
chicago: Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom,
and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature,
2020. https://doi.org/10.1038/s41588-020-00712-y.
ieee: S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M.
Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and
automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature,
pp. 1247–1255, 2020.
ista: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020.
CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction. Nature Genetics. 52, 1247–1255.
mla: Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer
Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.
short: S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas,
Nature Genetics 52 (2020) 1247–1255.
date_created: 2020-10-25T23:01:20Z
date_published: 2020-10-19T00:00:00Z
date_updated: 2023-08-22T10:37:10Z
day: '19'
department:
- _id: FyKo
doi: 10.1038/s41588-020-00712-y
external_id:
isi:
- '000579693500004'
pmid:
- '33077914'
intvolume: ' 52'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 1247-1255
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- '15461718'
issn:
- '10614036'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2020'
...
---
_id: '653'
abstract:
- lang: eng
text: The extent of heterogeneity among driver gene mutations present in naturally
occurring metastases - that is, treatment-naive metastatic disease - is largely
unknown. To address this issue, we carried out 60× whole-genome sequencing of
26 metastases from four patients with pancreatic cancer. We found that identical
mutations in known driver genes were present in every metastatic lesion for each
patient studied. Passenger gene mutations, which do not have known or predicted
functional consequences, accounted for all intratumoral heterogeneity. Even with
respect to these passenger mutations, our analysis suggests that the genetic similarity
among the founding cells of metastases was higher than that expected for any two
cells randomly taken from a normal tissue. The uniformity of known driver gene
mutations among metastases in the same patient has critical and encouraging implications
for the success of future targeted therapies in advanced-stage disease.
acknowledgement: 'We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology
core facility for immunohistochemistry staining. This work was supported by Office
of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation
(OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes
of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460
(B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund
for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the
Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center,
ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund
(FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE
(J.G.R., D.K., and C.K.).'
article_processing_charge: No
article_type: original
author:
- first_name: Alvin
full_name: Makohon Moore, Alvin
last_name: Makohon Moore
- first_name: Ming
full_name: Zhang, Ming
last_name: Zhang
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Ivana
full_name: Božić, Ivana
last_name: Božić
- first_name: Benjamin
full_name: Allen, Benjamin
last_name: Allen
- first_name: Deepanjan
full_name: Kundu, Deepanjan
id: 1d4c0f4f-e8a3-11ec-a351-e36772758c45
last_name: Kundu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Fay
full_name: Wong, Fay
last_name: Wong
- first_name: Yuchen
full_name: Jiao, Yuchen
last_name: Jiao
- first_name: Zachary
full_name: Kohutek, Zachary
last_name: Kohutek
- first_name: Jungeui
full_name: Hong, Jungeui
last_name: Hong
- first_name: Marc
full_name: Attiyeh, Marc
last_name: Attiyeh
- first_name: Breanna
full_name: Javier, Breanna
last_name: Javier
- first_name: Laura
full_name: Wood, Laura
last_name: Wood
- first_name: Ralph
full_name: Hruban, Ralph
last_name: Hruban
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
- first_name: Nickolas
full_name: Papadopoulos, Nickolas
last_name: Papadopoulos
- first_name: Kenneth
full_name: Kinzler, Kenneth
last_name: Kinzler
- first_name: Bert
full_name: Vogelstein, Bert
last_name: Vogelstein
- first_name: Christine
full_name: Iacobuzio Donahue, Christine
last_name: Iacobuzio Donahue
citation:
ama: Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver
gene mutations among the metastases of individual patients with pancreatic cancer.
Nature Genetics. 2017;49(3):358-366. doi:10.1038/ng.3764
apa: Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D.,
… Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations
among the metastases of individual patients with pancreatic cancer. Nature
Genetics. Nature Publishing Group. https://doi.org/10.1038/ng.3764
chicago: Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin
Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of
Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic
Cancer.” Nature Genetics. Nature Publishing Group, 2017. https://doi.org/10.1038/ng.3764.
ieee: A. Makohon Moore et al., “Limited heterogeneity of known driver gene
mutations among the metastases of individual patients with pancreatic cancer,”
Nature Genetics, vol. 49, no. 3. Nature Publishing Group, pp. 358–366,
2017.
ista: Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee
K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak
M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited
heterogeneity of known driver gene mutations among the metastases of individual
patients with pancreatic cancer. Nature Genetics. 49(3), 358–366.
mla: Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations
among the Metastases of Individual Patients with Pancreatic Cancer.” Nature
Genetics, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:10.1038/ng.3764.
short: A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee,
F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban,
M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature
Genetics 49 (2017) 358–366.
date_created: 2018-12-11T11:47:43Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2022-06-10T09:55:08Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/ng.3764
ec_funded: 1
external_id:
pmid:
- '28092682'
file:
- access_level: open_access
checksum: e442dc3b7420a36ec805e9bb45cc1a2e
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:13:50Z
date_updated: 2020-07-14T12:47:33Z
file_id: '7050'
file_name: 2017_NatureGenetics_Makohon.pdf
file_size: 908099
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file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 49'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 358 - 366
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Nature Genetics
publication_identifier:
issn:
- '10614036'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7092'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limited heterogeneity of known driver gene mutations among the metastases of
individual patients with pancreatic cancer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2017'
...