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Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival

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Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival. / Zaidi, Syed H; Harrison, Tabitha A; Phipps, Amanda I; Steinfelder, Robert; Trinh, Quang M; Qu, Conghui; Banbury, Barbara L; Georgeson, Peter; Grasso, Catherine S; Giannakis, Marios; Adams, Jeremy B; Alwers, Elizabeth; Amitay, Efrat L; Barfield, Richard T; Berndt, Sonja I; Borozan, Ivan; Brenner, Hermann; Brezina, Stefanie; Buchanan, Daniel D; Cao, Yin; Chan, Andrew T; Chang-Claude, Jenny; Connolly, Charles M; Drew, David A; Farris, Alton Brad; Figueiredo, Jane C; French, Amy J; Fuchs, Charles S; Garraway, Levi A; Gruber, Steve; Guinter, Mark A; Hamilton, Stanley R; Harlid, Sophia; Heisler, Lawrence E; Hidaka, Akihisa; Hopper, John L; Huang, Wen-Yi; Huyghe, Jeroen R; Jenkins, Mark A; Krzyzanowski, Paul M; Lemire, Mathieu; Lin, Yi; Luo, Xuemei; Mardis, Elaine R; McPherson, John D; Miller, Jessica K; Moreno, Victor; Mu, Xinmeng Jasmine; Nishihara, Reiko; Papadopoulos, Nickolas; Pasternack, Danielle; Quist, Michael J; Rafikova, Adilya; Reid, Emma E G; Shinbrot, Eve; Shirts, Brian H; Stein, Lincoln D; Teney, Cherie D; Timms, Lee; Um, Caroline Y; Van Guelpen, Bethany; Van Tassel, Megan; Wang, Xiaolong; Wheeler, David A; Yung, Christina K; Hsu, Li; Ogino, Shuji; Gsur, Andrea; Newcomb, Polly A; Gallinger, Steven; Hoffmeister, Michael; Campbell, Peter T; Thibodeau, Stephen N; Sun, Wei; Hudson, Thomas J.

In: NAT COMMUN, Vol. 11, No. 1, 20.07.2020, p. 3644.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Zaidi, SH, Harrison, TA, Phipps, AI, Steinfelder, R, Trinh, QM, Qu, C, Banbury, BL, Georgeson, P, Grasso, CS, Giannakis, M, Adams, JB, Alwers, E, Amitay, EL, Barfield, RT, Berndt, SI, Borozan, I, Brenner, H, Brezina, S, Buchanan, DD, Cao, Y, Chan, AT, Chang-Claude, J, Connolly, CM, Drew, DA, Farris, AB, Figueiredo, JC, French, AJ, Fuchs, CS, Garraway, LA, Gruber, S, Guinter, MA, Hamilton, SR, Harlid, S, Heisler, LE, Hidaka, A, Hopper, JL, Huang, W-Y, Huyghe, JR, Jenkins, MA, Krzyzanowski, PM, Lemire, M, Lin, Y, Luo, X, Mardis, ER, McPherson, JD, Miller, JK, Moreno, V, Mu, XJ, Nishihara, R, Papadopoulos, N, Pasternack, D, Quist, MJ, Rafikova, A, Reid, EEG, Shinbrot, E, Shirts, BH, Stein, LD, Teney, CD, Timms, L, Um, CY, Van Guelpen, B, Van Tassel, M, Wang, X, Wheeler, DA, Yung, CK, Hsu, L, Ogino, S, Gsur, A, Newcomb, PA, Gallinger, S, Hoffmeister, M, Campbell, PT, Thibodeau, SN, Sun, W & Hudson, TJ 2020, 'Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival', NAT COMMUN, vol. 11, no. 1, pp. 3644. https://doi.org/10.1038/s41467-020-17386-z

APA

Zaidi, S. H., Harrison, T. A., Phipps, A. I., Steinfelder, R., Trinh, Q. M., Qu, C., Banbury, B. L., Georgeson, P., Grasso, C. S., Giannakis, M., Adams, J. B., Alwers, E., Amitay, E. L., Barfield, R. T., Berndt, S. I., Borozan, I., Brenner, H., Brezina, S., Buchanan, D. D., ... Hudson, T. J. (2020). Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival. NAT COMMUN, 11(1), 3644. https://doi.org/10.1038/s41467-020-17386-z

Vancouver

Zaidi SH, Harrison TA, Phipps AI, Steinfelder R, Trinh QM, Qu C et al. Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival. NAT COMMUN. 2020 Jul 20;11(1):3644. https://doi.org/10.1038/s41467-020-17386-z

Bibtex

@article{69e5d7d7c59541bd83d14e8520b42cd7,
title = "Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival",
abstract = "Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR = 0.42, 95% CI: 0.21-0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR = 1.53, 95% CI: 1.21-1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features.",
keywords = "Colonic Neoplasms/genetics, Colorectal Neoplasms/genetics, High-Throughput Nucleotide Sequencing, Humans, INDEL Mutation, Mutation, Neoplasm Proteins/genetics, Prognosis, Tumor Suppressor Protein p53/genetics",
author = "Zaidi, {Syed H} and Harrison, {Tabitha A} and Phipps, {Amanda I} and Robert Steinfelder and Trinh, {Quang M} and Conghui Qu and Banbury, {Barbara L} and Peter Georgeson and Grasso, {Catherine S} and Marios Giannakis and Adams, {Jeremy B} and Elizabeth Alwers and Amitay, {Efrat L} and Barfield, {Richard T} and Berndt, {Sonja I} and Ivan Borozan and Hermann Brenner and Stefanie Brezina and Buchanan, {Daniel D} and Yin Cao and Chan, {Andrew T} and Jenny Chang-Claude and Connolly, {Charles M} and Drew, {David A} and Farris, {Alton Brad} and Figueiredo, {Jane C} and French, {Amy J} and Fuchs, {Charles S} and Garraway, {Levi A} and Steve Gruber and Guinter, {Mark A} and Hamilton, {Stanley R} and Sophia Harlid and Heisler, {Lawrence E} and Akihisa Hidaka and Hopper, {John L} and Wen-Yi Huang and Huyghe, {Jeroen R} and Jenkins, {Mark A} and Krzyzanowski, {Paul M} and Mathieu Lemire and Yi Lin and Xuemei Luo and Mardis, {Elaine R} and McPherson, {John D} and Miller, {Jessica K} and Victor Moreno and Mu, {Xinmeng Jasmine} and Reiko Nishihara and Nickolas Papadopoulos and Danielle Pasternack and Quist, {Michael J} and Adilya Rafikova and Reid, {Emma E G} and Eve Shinbrot and Shirts, {Brian H} and Stein, {Lincoln D} and Teney, {Cherie D} and Lee Timms and Um, {Caroline Y} and {Van Guelpen}, Bethany and {Van Tassel}, Megan and Xiaolong Wang and Wheeler, {David A} and Yung, {Christina K} and Li Hsu and Shuji Ogino and Andrea Gsur and Newcomb, {Polly A} and Steven Gallinger and Michael Hoffmeister and Campbell, {Peter T} and Thibodeau, {Stephen N} and Wei Sun and Hudson, {Thomas J}",
year = "2020",
month = jul,
day = "20",
doi = "10.1038/s41467-020-17386-z",
language = "English",
volume = "11",
pages = "3644",
journal = "NAT COMMUN",
issn = "2041-1723",
publisher = "NATURE PUBLISHING GROUP",
number = "1",

}

RIS

TY - JOUR

T1 - Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival

AU - Zaidi, Syed H

AU - Harrison, Tabitha A

AU - Phipps, Amanda I

AU - Steinfelder, Robert

AU - Trinh, Quang M

AU - Qu, Conghui

AU - Banbury, Barbara L

AU - Georgeson, Peter

AU - Grasso, Catherine S

AU - Giannakis, Marios

AU - Adams, Jeremy B

AU - Alwers, Elizabeth

AU - Amitay, Efrat L

AU - Barfield, Richard T

AU - Berndt, Sonja I

AU - Borozan, Ivan

AU - Brenner, Hermann

AU - Brezina, Stefanie

AU - Buchanan, Daniel D

AU - Cao, Yin

AU - Chan, Andrew T

AU - Chang-Claude, Jenny

AU - Connolly, Charles M

AU - Drew, David A

AU - Farris, Alton Brad

AU - Figueiredo, Jane C

AU - French, Amy J

AU - Fuchs, Charles S

AU - Garraway, Levi A

AU - Gruber, Steve

AU - Guinter, Mark A

AU - Hamilton, Stanley R

AU - Harlid, Sophia

AU - Heisler, Lawrence E

AU - Hidaka, Akihisa

AU - Hopper, John L

AU - Huang, Wen-Yi

AU - Huyghe, Jeroen R

AU - Jenkins, Mark A

AU - Krzyzanowski, Paul M

AU - Lemire, Mathieu

AU - Lin, Yi

AU - Luo, Xuemei

AU - Mardis, Elaine R

AU - McPherson, John D

AU - Miller, Jessica K

AU - Moreno, Victor

AU - Mu, Xinmeng Jasmine

AU - Nishihara, Reiko

AU - Papadopoulos, Nickolas

AU - Pasternack, Danielle

AU - Quist, Michael J

AU - Rafikova, Adilya

AU - Reid, Emma E G

AU - Shinbrot, Eve

AU - Shirts, Brian H

AU - Stein, Lincoln D

AU - Teney, Cherie D

AU - Timms, Lee

AU - Um, Caroline Y

AU - Van Guelpen, Bethany

AU - Van Tassel, Megan

AU - Wang, Xiaolong

AU - Wheeler, David A

AU - Yung, Christina K

AU - Hsu, Li

AU - Ogino, Shuji

AU - Gsur, Andrea

AU - Newcomb, Polly A

AU - Gallinger, Steven

AU - Hoffmeister, Michael

AU - Campbell, Peter T

AU - Thibodeau, Stephen N

AU - Sun, Wei

AU - Hudson, Thomas J

PY - 2020/7/20

Y1 - 2020/7/20

N2 - Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR = 0.42, 95% CI: 0.21-0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR = 1.53, 95% CI: 1.21-1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features.

AB - Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR = 0.42, 95% CI: 0.21-0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR = 1.53, 95% CI: 1.21-1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features.

KW - Colonic Neoplasms/genetics

KW - Colorectal Neoplasms/genetics

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - INDEL Mutation

KW - Mutation

KW - Neoplasm Proteins/genetics

KW - Prognosis

KW - Tumor Suppressor Protein p53/genetics

U2 - 10.1038/s41467-020-17386-z

DO - 10.1038/s41467-020-17386-z

M3 - SCORING: Journal article

C2 - 32686686

VL - 11

SP - 3644

JO - NAT COMMUN

JF - NAT COMMUN

SN - 2041-1723

IS - 1

ER -