Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution

Research output: Contribution to journalArticlepeer-review

Standard

Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution. / Baker, Ann-Marie; Huang, Weini; Wang, Xiao-Ming Mindy; Jansen, Marnix; Ma, Xiao-Jun; Kim, Jeffrey; Anderson, Courtney M; Wu, Xingyong; Pan, Liuliu; Su, Nan; Luo, Yuling; Domingo, Enric; Heide, Timon; Sottoriva, Andrea; Lewis, Annabelle; Beggs, Andrew D; Wright, Nicholas A; Rodriguez-Justo, Manuel; Park, Emily; Tomlinson, Ian; Graham, Trevor A.

In: Nature Communications, Vol. 8, No. 1, 1998, 08.12.2017.

Research output: Contribution to journalArticlepeer-review

Harvard

Baker, A-M, Huang, W, Wang, X-MM, Jansen, M, Ma, X-J, Kim, J, Anderson, CM, Wu, X, Pan, L, Su, N, Luo, Y, Domingo, E, Heide, T, Sottoriva, A, Lewis, A, Beggs, AD, Wright, NA, Rodriguez-Justo, M, Park, E, Tomlinson, I & Graham, TA 2017, 'Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution', Nature Communications, vol. 8, no. 1, 1998. https://doi.org/10.1038/s41467-017-02295-5

APA

Baker, A-M., Huang, W., Wang, X-M. M., Jansen, M., Ma, X-J., Kim, J., Anderson, C. M., Wu, X., Pan, L., Su, N., Luo, Y., Domingo, E., Heide, T., Sottoriva, A., Lewis, A., Beggs, A. D., Wright, N. A., Rodriguez-Justo, M., Park, E., ... Graham, T. A. (2017). Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution. Nature Communications, 8(1), [1998]. https://doi.org/10.1038/s41467-017-02295-5

Vancouver

Author

Baker, Ann-Marie ; Huang, Weini ; Wang, Xiao-Ming Mindy ; Jansen, Marnix ; Ma, Xiao-Jun ; Kim, Jeffrey ; Anderson, Courtney M ; Wu, Xingyong ; Pan, Liuliu ; Su, Nan ; Luo, Yuling ; Domingo, Enric ; Heide, Timon ; Sottoriva, Andrea ; Lewis, Annabelle ; Beggs, Andrew D ; Wright, Nicholas A ; Rodriguez-Justo, Manuel ; Park, Emily ; Tomlinson, Ian ; Graham, Trevor A. / Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution. In: Nature Communications. 2017 ; Vol. 8, No. 1.

Bibtex

@article{12e845c508d7462787706b8e72f9bf0c,
title = "Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution",
abstract = "Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not detect rare subclones. Here, we address these shortfalls by developing and validating BaseScope-a novel mutation-specific RNA in situ hybridization assay. We target common point mutations in the BRAF, KRAS and PIK3CA oncogenes in archival colorectal cancer samples to precisely map the spatial and morphological context of mutant subclones. Computational modeling suggests that subclones must arise sufficiently early, or carry a considerable fitness advantage, to form large or spatially disparate subclones. Examples of putative treatment-resistant cells isolated in small topographical areas are observed. The BaseScope assay represents a significant technical advance for in situ mutation detection that provides new insight into tumor evolution, and could have ramifications for selecting patients for treatment.",
author = "Ann-Marie Baker and Weini Huang and Wang, {Xiao-Ming Mindy} and Marnix Jansen and Xiao-Jun Ma and Jeffrey Kim and Anderson, {Courtney M} and Xingyong Wu and Liuliu Pan and Nan Su and Yuling Luo and Enric Domingo and Timon Heide and Andrea Sottoriva and Annabelle Lewis and Beggs, {Andrew D} and Wright, {Nicholas A} and Manuel Rodriguez-Justo and Emily Park and Ian Tomlinson and Graham, {Trevor A}",
year = "2017",
month = dec,
day = "8",
doi = "10.1038/s41467-017-02295-5",
language = "English",
volume = "8",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Springer",
number = "1",

}

RIS

TY - JOUR

T1 - Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution

AU - Baker, Ann-Marie

AU - Huang, Weini

AU - Wang, Xiao-Ming Mindy

AU - Jansen, Marnix

AU - Ma, Xiao-Jun

AU - Kim, Jeffrey

AU - Anderson, Courtney M

AU - Wu, Xingyong

AU - Pan, Liuliu

AU - Su, Nan

AU - Luo, Yuling

AU - Domingo, Enric

AU - Heide, Timon

AU - Sottoriva, Andrea

AU - Lewis, Annabelle

AU - Beggs, Andrew D

AU - Wright, Nicholas A

AU - Rodriguez-Justo, Manuel

AU - Park, Emily

AU - Tomlinson, Ian

AU - Graham, Trevor A

PY - 2017/12/8

Y1 - 2017/12/8

N2 - Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not detect rare subclones. Here, we address these shortfalls by developing and validating BaseScope-a novel mutation-specific RNA in situ hybridization assay. We target common point mutations in the BRAF, KRAS and PIK3CA oncogenes in archival colorectal cancer samples to precisely map the spatial and morphological context of mutant subclones. Computational modeling suggests that subclones must arise sufficiently early, or carry a considerable fitness advantage, to form large or spatially disparate subclones. Examples of putative treatment-resistant cells isolated in small topographical areas are observed. The BaseScope assay represents a significant technical advance for in situ mutation detection that provides new insight into tumor evolution, and could have ramifications for selecting patients for treatment.

AB - Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not detect rare subclones. Here, we address these shortfalls by developing and validating BaseScope-a novel mutation-specific RNA in situ hybridization assay. We target common point mutations in the BRAF, KRAS and PIK3CA oncogenes in archival colorectal cancer samples to precisely map the spatial and morphological context of mutant subclones. Computational modeling suggests that subclones must arise sufficiently early, or carry a considerable fitness advantage, to form large or spatially disparate subclones. Examples of putative treatment-resistant cells isolated in small topographical areas are observed. The BaseScope assay represents a significant technical advance for in situ mutation detection that provides new insight into tumor evolution, and could have ramifications for selecting patients for treatment.

U2 - 10.1038/s41467-017-02295-5

DO - 10.1038/s41467-017-02295-5

M3 - Article

C2 - 29222441

VL - 8

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 1998

ER -