Summary
The TCGA Lung Phenotype Research Group is part of the CIP TCGA Radiology Initiative focused on analyzing images from the TCGA-LUAD and TCGA-LUSC (coming soon) 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
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.
Note: Findings using TCGA-LUSC data (not currently available on TCIA) may be published freely, but per TCGA Guidelines formal permission requests are still required to submit publications using TCGA-LUAD data until 5/30/2013. More info at http://cancergenome.nih.gov/abouttcga/policies/publicationguidelines.
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
There 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.
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