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Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway
Authors
L. Bao
C.C., Benz
+56 more
A. Berger
A.H. Berger
B.P. Berman
R. Beroukhim
J.D. Campbell
J. Carrot-Zhang
M.A.A. Castro
J.C. Chang
A.D. Cherniack
H.Y. Choi
E.A. Collisson
J.S. Damrauer
A. Deshpande
S. Devarakonda
L. Ding
O. Elemento
I. Felau
G.F. Gao
G. Getz
R. Govindan
D. Haan
D.N. Hayes
T. Hinoue
K.A. Hoadley
M. Imielinski
E. Khurana
K. Kumar
D.J. Kwiatkowski
P.W. Laird
J.J.-K. Lee
W.-W. Liang
E.M. Liu
Y. Liu
M. Meyerson
S. Moorthi
K.L. Mungall
E. Rheinbay
A.G. Robertson
N. Robine
O. Shapira
T.C. Silva
J. Stuart
TCGA Research Network
W.D. Travis
T. Trieu
M.S. Tsao
J.N. Weinstein
C.K. Wong
L. Yang
X. Yao
C. Yau
J.C. Zenklusen
H. Zhang
B. Zhitomirsky
M. Zhou
M.C. Zody
Publication date
1 January 2021
Publisher
Elsevier B.V.
Doi
Cite
Abstract
RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(−) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of STK11 (n = 7) or KEAP1 (n = 3), and promoter mutations associated with the increased expression of ILF2 (n = 6). We also identify complex structural variations associated with high-level copy number amplifications. Moreover, an enrichment of focal deletions is found in TP53 mutant cases. Our results indicate that RPA(−) cases demonstrate tumor suppressor deletions and genome instability, but lack unique or recurrent genetic lesions compensating for the lack of RPAs. Larger WGS studies of RPA(−) cases are required to understand this important LUAD subset. © 2021 The AuthorsCarrot-Zhang et al. perform whole-genome characterization of lung adenocarcinomas (LUADs) lacking RTK/RAS/RAF pathway alterations (RPAs) and identify mutations or structural variants in both coding and non-coding spaces that define a unique entity of RPA(−) LUADs and potentially explain the underlying biology of this disease
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Last time updated on 11/12/2021