Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 200

The DOI matches its Crossref record; 16 of the 16 references it cites were found in a registry or an index.

Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events

Open access
Liu, Jinfeng, Lee, William, Jiang, Zhaoshi, Chen, Zhongqiang, Jhunjhunwala, Suchit, Haverty, Peter M., Gnad, Florian, Guan, Yinghui, Gilbert, Houston N., Stinson, Jeremy, Klijn, Christiaan, Guillory, Joseph, Bhatt, Deepali, Vartanian, Steffan, Walter, Kimberly, Chan, Jocelyn, Holcomb, Thomas, Dijkgraaf, Peter, Johnson, Stephanie, Koeman, Julie, Minna, John D., Gazdar, Adi F., Stern, Howard M., Hoeflich, Klaus P., Wu, Thomas D., Settleman, Jeff, de Sauvage, Frederic J., Gentleman, Robert C., Neve, Richard M., Stokoe, David, Modrusan, Zora, Seshagiri, Somasekar, Shames, David S., Zhang, Zemin·2012·Genome Research
DOI 10.1101/gr.140988.112
Open this paper in CoChat — free account

Abstract

Lung cancer is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole-genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and three lung tumor/normal pairs. Overall, our data show that cell line models exhibit similar mutation spectra to human tumor samples. Smoker and never-smoker cancer samples exhibit distinguishable patterns of mutations. A number of epigenetic regulators, including KDM6A, ASH1L, SMARCA4, and ATAD2, are frequently altered by mutations or copy number changes. A systematic survey of splice-site mutations identified 106 splice site mutations associated with cancer specific aberrant splicing, including mutations in several known cancer-related genes. RAC1 b, an isoform of the RAC1 GTPase that includes one additional exon, was found to be preferentially up-regulated in lung cancer. We further show that its expression is significantly associated with sensitivity to a MAP2K (MEK) inhibitor PD-0325901. Taken together, these data present a comprehensive genomic landscape of a large number of lung cancer samples and further demonstrate that cancer-specific alternative splicing is a widespread phenomenon that has potential utility as therapeutic biomarkers. The detailed characterizations of the lung cancer cell lines also provide genomic context to the vast amount of experimental data gathered for these lines over the decades, and represent highly valuable resources for cancer biology.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/gr.140988.112

Cites

16 of 16 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 16 references

Cited by

See all 200

Metadata

Authors
Liu, J., Lee, W., Jiang, Z., Chen, Z., Jhunjhunwala, S., Haverty, P. M., Gnad, F., Guan, Y., Gilbert, H. N., Stinson, J., Klijn, C., Guillory, J., Bhatt, D., Vartanian, S., Walter, K., Chan, J., Holcomb, T., Dijkgraaf, P., Johnson, S., Koeman, J., Minna, J. D., Gazdar, A. F., Stern, H. M., Hoeflich, K. P., Wu, T. D., Settleman, J., de Sauvage, F. J., Gentleman, R. C., Neve, R. M., Stokoe, D., Modrusan, Z., Seshagiri, S., Shames, D. S., & Zhang, Z.
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2012-10-02
Volume
22
Issue
12
Pages
2315-2327
ISSN
1088-9051 (ISSN-L)
DOI
10.1101/gr.140988.112
OpenAlex
W2148351505
Cited by
200
References
16
Type
posted content
Language
en
Open access
hybrid

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. https://app.cochat.ai/papers/10.1101/gr.140988.112
The paper
Liu, J., Lee, W., Jiang, Z., Chen, Z., Jhunjhunwala, S., Haverty, P. M., Gnad, F., Guan, Y., Gilbert, H. N., Stinson, J., Klijn, C., Guillory, J., Bhatt, D., Vartanian, S., Walter, K., Chan, J., Holcomb, T., Dijkgraaf, P., Johnson, S., . . . Zhang, Z. (2012). Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Research. https://doi.org/10.1101/gr.140988.112

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.