Summary

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According to the TCGA page on lung adenocarcinomaLUAD, researchers hope to make the following types of discoveries about lung adenocarcinoma ( LUAD ) and lung squamous cell carcinoma (LUSC):

• Pinpoint gene changes that divide squamous and adenocarcinoma tumors into molecular subgroups.
• Distinguish patterns of gene changes between adenocarcinoma and squamous cell carcinomaLUAD and LUSC.
• Distinguish genomic changes between smokers and non-smokers.

Starting or Joining a Research Project

We are not yet hosting calls in support of TCGA lung based research projects (TCGA-LUAD, TCGA-LUSC) but are currently looking for additional interested group members. Please contact us at cancerimagingarchive@mail.nih.gov if you would like to inquire about setting up a new research project, join an existing project, or be otherwise kept in the loop as this effort moves forward.

Group Projects

This is a listing of ongoing projects.  If you are working with the TCGA lung data hosted on TCIA please let us know and we would be happy to add a section describing your project here.

• Coming soon

Publications

Research and Publications

Per TCGA and TCIA Guidelines, formal permission requests are still required to submit publications using TCGA-LUAD data. Please see the following links for more information about the freedom-to-publish criteria for these data sets:

Please contact us at help@cancerimagingarchive.net if you have any questions about these policies.

TCGA Lung Marker Paper and Image Source Sites (ISS)

Imaging Source Site (ISS) Groups will be populated and governed by participants from institutions that have provided imaging data to the archive for a given cancer type. Modeled after TCGA analysis groups, ISS groups are given the opportunity to publish a marker paper for a given cancer type per the guidelines in the table above. This opportunity will generate increased participation in building these multi-institutional data sets as they become an open community resource. Current TCGA-LUAD source sites include:

• Washington University in St. Louis
• UPMC

This group has not yet been established. We will provide a point of contact for the group from the ISS site(s) as soon as possible to address scientific questions or requests to collaborate with their groupThere are currently no imaging based publications for TCGA-LUAD or TCGA-LUSC that we are aware of.  Please notify us at cancerimagingarchive@mail.nih.gov if you know of publications utilizing these TCIA collections.

References

The following links contain publications from the main TCGA project , as well as their posted publication guidelines.:

• TCGA Publications
• TCGA Publication Guidelines

In addition, this section contains papers, presentations, and videos from the genomics/clinical perspectives which may be of interest to the lung imaging group.

• Li, Y., Zhang, L., Ball, R.L., Liang, X., Li, J., Lin, Z. and Liang, H. (2012) Comparative analysis of somatic copy-number alterations across different human cancer types reveals two distinct classes of breakpoint hotspots. Hum Mol Genet. 21(22):4957-4965. View PubMed abstract
• Sproul, D., Kitchen, R.R., Nestor, C.E., Dixon, J.M., Sims, A.H., Harrison, D.J., Ramsahoye, B.H. and Meehan, R.R. (2012) Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns. Genome Biol. 13(10):R84. Read the full article
• Greulich, H., Kaplan, B., Mertins, P., Chen, T.H., Tanaka, K.E. Yun, C.H., Zhang, X., Lee, S.H., Cho, J., Ambrogio, L., et al. (2012) Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2. Proc Natl Acad Sci U S A. 109(36):14476-14481. View PubMed abstract
• Liu, P., Morrison, C., Wang, L., Xiong, D., Vedell, P., Cui, P., Hua, X., Ding, F., Lu, Y., James M, et al. (2012) Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing. Carcinogenesis. 33(7):1270-1276 . View PubMed abstract
• Shinjo, K., Okamoto, Y., An, B., Yokoyama, T., Takeuchi, I., Fujii, M., Osada, H., Usami, N., Hasegawa, Y., Ito, H., et al. (2012) Integrated analysis of genetic and epigenetic alterations reveals CpG island methylator phenotype associated with distinct clinical characters of lung adenocarcinoma. Carcinogenesis. 33(7):1277-1285. View PubMed abstract
• Andreopoulos, B. and Anastassiou, D. (2012) Integrated analysis reveals hsa-miR-142 as a representative of a lymphocyte-specific gene expression and methylation signature. Cancer Inform. 11 61-75. Read the full article
• Zhuang, J., Jones, A., Lee, S.-H., Ng, E., Fiegl, H., Zikan, M., Cibula, D., Sargent, A., Salvesen, H., Jacobs, I.J., et al. (2012) The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer. PLoS Genet. 8(2):e1002517. Read the full article
• Yao, C., Li, H., Shen, X., He, Z., He, L. and Guo, Z. (2012) Reproducibility and concordance of differential DNA methylation and gene expression in cancer. PLoS One. 7(1):e29686. Read the full article
• Lin, K., Taylor, J.R. Jr., Wu, T.D., Gutierrez, J., Elliott, J.M., Vernes, J.M., Koeppen, H., Phillips, H.S., de Sauvage, F.J. and Meng, Y.G. (2011) TMEFF2 is a PDGF-AA binding protein with methylation-associated gene silencing in multiple cancer types including glioma. PLoS One. 6(4):e18608. Read the full article

TCGA 2nd Annual Symposium

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