Summary
The TCGA-LUAD Phenotype Research Group is part of the CIP TCGA Radiology Initiative focused on analyzing images from the TCGA-LUAD collections. Multiple modalities of images which correlate to the lung tissue data in the TCGA Data Portal are continuing to be gathered for submission to TCIA. In the mean time a group is beginning preliminary discussions around research methods and goals.
According to the TCGA page on lung adenocarcinoma, 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 carcinoma
- Distinguish genomic changes between smokers and non-smokers
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 cancerimagingarchive@mail.nih.gov if you have any questions about these policies, or would like to join our mailing list and be kept in the loop about new data releases and other related news as this effort moves forward.
TCGA-LUAD 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, these groups are given the opportunity to publish a marker paper for a given cancer type per the aforementioned publication policy. It is hoped that this will generate increased participation in the building of these multi-institutional data sets that become an open community resource. Current TCGA-LUAD source sites include:
- Washington University in St. Louis
References
The following links contain publications from the main TCGA project, as well as their posted publication guidelines.
In addition, this section contains papers, presentations, and videos from the genomics/clinical perspectives which may be of interest to TCGA-LUAD researchers.
- 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