INTEGRATIVE ANALYSIS FOR LUNG ADENOCARCINOMA PREDICTS MORPHOLOGICAL FEATURES ASSOCIATED WITH GENETIC VARIATIONS
Open accessAbstract
Lung cancer is one of the most deadly cancers and lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. However, LUAD is highly heterogeneous due to genetic difference as well as phenotypic differences such as cellular and tissue morphology. In this paper, we systematically examine the relationships between histological features and gene transcription. Specifically, we calculated 283 morphological features from histology images for 201 LUAD patients from TCGA project and identified the morphological feature with strong correlation with patient outcome. We then modeled the morphology feature using multiple co-expressed gene clusters using Lasso-regression. Many of the gene clusters are highly associated with genetic variations, specifically DNA copy number variations, implying that genetic variations play important roles in the development cancer morphology. As far as we know, our finding is the first to directly link the genetic variations and functional genomics to LUAD histology. These observations will lead to new insight on lung cancer development and potential new integrative biomarkers for prediction patient prognosis and response to treatments.
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.
Integrity signals
Registry
Cites
Statistics
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.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
WGCNA: an R package for weighted correlation network analysis
Langfelder, P., & Horvath, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-559 · Cited by 27,252 · see citing works
Radiomics: extracting more information from medical images using advanced feature analysis
Lambin, P., Rios-Velazquez, E., Leijenaar, R., Carvalho, S., van Stiphout, R. G. P. M., Granton, P., Zegers, C. M. L., Gillies, R., Boellard, R., Dekker, A., et al. (2012) · European Journal of Cancer · doi:10.1016/j.ejca.2011.11.036 · Cited by 6,084 · see citing works
Comprehensive molecular profiling of lung adenocarcinoma
The Cancer Genome Atlas Research Network (2014) · Nature · doi:10.1038/nature13385 · Cited by 5,732 · see citing works
Lung cancer in never smokers – A review
Couraud, S., Zalcman, G., Milleron, B. J., Morin, F., & Souquet, P.-J. (2012) · European Journal of Cancer · doi:10.1016/j.ejca.2012.03.007 · Cited by 962 · see citing works
Systematic Analysis of Breast Cancer Morphology Uncovers Stromal Features Associated with Survival
Beck, A. H., Sangoi, A. R., Leung, S. C. Y., Marinelli, R. J., Nielsen, T. O., van de Vijver, M. J., West, R. B., van de Rijn, M., & Koller, D. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3002564 · Cited by 765 · see citing works
Russell, P. A., Wainer, Z., Wright, G. M., Daniels, M. G., Conron, M., & Williams, R. A. (2011) · Journal of Thoracic Oncology · doi:10.1097/jto.0b013e318221f701 · Cited by 624 · see citing works
Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling
Yuan, Y., Failmezger, H., Rueda, O. M., Ali, H. R., Gräf, S., Chin, S.-F., Schwarz, R. F., Curtis, C., Dunning, M. J., Bardwell, H., et al. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3004330 · Cited by 426 · see citing works
Qi, X., Xing, F., Foran, D. J., & Yang, L. (2011) · IEEE Transactions on Biomedical Engineering · doi:10.1109/tbme.2011.2179298 · Cited by 231 · see citing works
Self-citationRadiologic Implications of the 2011 Classification of Adenocarcinoma of the Lung
Austin, J. H. M., Garg, K., Aberle, D. R., Yankelevitz, D. F., Kuriyama, K., Lee, H., Brambilla, E. M., & Travis, W. D. (2012) · Radiology · doi:10.1148/radiol.12120240 · Cited by 227 · see citing works
Balsara, B., Sonoda, G., du Manoir, S., Siegfried, J. M., Gabrielson, E. W., & Testa, J. R. (1997) · PubMed · Cited by 154 · see citing works
Edwards, S., Roberts, C., McKean, M. E., Cockburn, J. S., Jeffrey, R. R., & Kerr, K. M. (2000) · Journal of Clinical Pathology · doi:10.1136/jcp.53.7.537 · Cited by 140 · see citing works
The SRY-HMG box gene, SOX4, is a target of gene amplification at chromosome 6p in lung cancer†
Medina, P. P., Castillo, S. D., Blanco, S., Sanz-García, M., Largo, C., Álvarez, S., Yokota, J., González‐Neira, A., Benitez, J. J., Clevers, H. C., et al. (2009) · Human Molecular Genetics · doi:10.1093/hmg/ddp034 · Cited by 114 · see citing works
Solis, L. M., Behrens, C., Raso, M. G., Lin, H. Y., Kadara, H. N., Yuan, P., Galindo, H., Tang, X., Lee, J. J., Kalhor, N., et al. (2011) · Cancer · doi:10.1002/cncr.26584 · Cited by 111 · see citing works
Texture feature coding method for classification of liver sonography
Horng, M., Sun, Y.-N., & Lin, X. (2002) · Computerized Medical Imaging and Graphics · doi:10.1016/s0895-6111(01)00029-5 · Cited by 93 · see citing works
Identification of frequent novel genetic alterations in small cell lung carcinoma.
Levin, N., Brzoska, P. M., Gupta, N., Minna, J. D., Gray, J. W., & Christman, M. F. (1994) · PubMed · Cited by 88 · see citing works
Biomarkers in the Lung Cancer Diagnosis: A Clinical Perspective
Li, X., ASMITANANDA, T., GAO, L., Gai, D., SONG, Z., Zhang, Y., Ren, H., YANG, T., Chen, T., & CHEN, M. (2012) · Neoplasma · doi:10.4149/neo_2012_064 · Cited by 73 · see citing works
Novel image markers for non-small cell lung cancer classification and survival prediction
Wang, H., Xing, F., Su, H., Stromberg, A. J., & Yang, L. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-310 · Cited by 69 · see citing works
Self-citationWang, C., Pécot, T., Zynger, D. L., Machiraju, R., Shapiro, C. L., & Huang, K. (2013) · Journal of the American Medical Informatics Association · doi:10.1136/amiajnl-2012-001538 · Cited by 47 · see citing works
Self-citationUpdate on biomarkers for the detection of lung cancer
Camps, C., Lewintre, E. J., Usó, & Sanmartín, E. (2012) · Lung Cancer Targets and Therapy · doi:10.2147/lctt.s23424 · Cited by 37 · see citing works
Conde, E., Angulo, B., Izquierdo, E., Paz-Ares, L. G., Belda-Iniesta, C., Hidalgo, M. M., & López‐Ríos, F. (2013) · Clinical & Translational Oncology · doi:10.1007/s12094-012-0983-z · Cited by 31 · see citing works
Mining Histopathological Images via Composite Hashing and Online Learning
Zhang, X., Yang, L., Liu, W., Su, H., & Zhang, S. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-10470-6_60 · Cited by 28 · see citing works
Self-citationPsf3 is a prognostic biomarker in lung adenocarcinoma
Hokka, D., Maniwa, Y., Tane, S., Nishio, W., Yoshimura, M., Okita, Y., Ohbayashi, C., Sakai, Y., Chen, X., & Hayashi, Y. (2012) · Lung Cancer · doi:10.1016/j.lungcan.2012.10.001 · Cited by 27 · see citing works
Acquirement of DNA copy number variations in non-small cell lung cancer metastasis to the brain
Li, F., Sun, L., & Zhang, S. (2015) · Oncology Reports · doi:10.3892/or.2015.4188 · Cited by 24 · see citing works
Computer-Assisted Diagnosis of Lung Cancer Using Quantitative Topology Features
Yao, J., Ganti, D., Luo, X., et al. (2015) · Lecture notes in computer science · doi:10.1007/978-3-319-24888-2_35 · Cited by 22 · see citing works
Chmielecki, J., Pietanza, M. C., Aftab, D. T., Shen, R., Zhao, Z., Chen, X., Hutchinson, K. E., Viale, A. J., Kris, M. G., Stout, T. J., et al. (2011) · Journal of Thoracic Oncology · doi:10.1097/jto.0b013e31823c5aee · Cited by 21 · see citing works
Digitized pathology: theory and experiences in automated tissue-based virtual diagnosis.
Kayser, K., Radziszowski, D., Bzdyl, P., Sommer, R., & Kayser, G. (2006) · PubMed · Cited by 19 · see citing works
Further evaluation of quantitative nuclear image features for classification of lung carcinomas
Thunnissen, E., Diegenbach, P. C., van Hattum, A. H., Tolboom, J. T. M., van der Sluis, D. M., Schaafsma, W., Houthoff, H. J., & Baak, J. P. A. (1992) · Pathology - Research and Practice · doi:10.1016/s0344-0338(11)80050-6 · Cited by 18 · see citing works
Adamson, R. T. (2013) · PubMed · Cited by 13 · see citing works
Flagged first, then by citations
Research works printed but not linked: 9
- [8]Robert PF Adamson T Am. J. Manag. Care. 19 2013 24494721
- [17]Kayser K Radziszowski D Bzdyl P Sommer R Kayser G Rom. J. Morphol. Embryol 2006 47 21 8 16838053
- [21]Zhu X IEEE 13th International Symposium on Biomedical Imaging (ISBI) 2016 2016 1173 1176 IEEE http://ieeexplore.ieee.org/document/7493475/
- [24]Xing F Yang L 2013 IEEE 10th International Symposium on Biomedical Imaging 2013 386 389 IEEE
- [27]Haralick RM Shanmugam K Dinstein I IEEE Trans. Syst. Man. Cybern 1973 3 610 621
- [28]Laws K Wiener TF 24th Annual Technical Symposium 1980 376 381 International Society for Optics and Photonics
- [29]Ojala T Pietikainen M Maenpaa T IEEE Trans. Pattern Anal. Mach. Intell 2002 24 971 987
- [33]Balsara BR Cancer Res 1997 57 2116 20 9187106
- [36]Levin NA Cancer Res 1994 54 5086 91 7923122
Cited by
Sorted by citations
AI in Medical Imaging Informatics: Current Challenges and Future Directions
Panayides, A. S., Amini, A., Filipovic, N. D., Sharma, A., Tsaftaris, S. A., Young, A., Foran, D., Do, N., Golemati, S., Kurc, T., et al. (2020) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2020.2991043 · Cited by 713 · see citing works
Self-citationIntegrating imaging and omics data: A review
Antonelli, L., Guarracino, M. R., Maddalena, L., & Sangiovanni, M. (2019) · Biomedical Signal Processing and Control · doi:10.1016/j.bspc.2019.04.032 · Cited by 81 · see citing works
A Review of Fusion Methods for Omics and Imaging Data
Huang, W., Tan, K., Zhang, Z., Hu, J., & Dong, S. (2022) · IEEE/ACM Transactions on Computational Biology & Bioinformatics · doi:10.1109/tcbb.2022.3143900 · Cited by 30 · see citing works
SPOP regulates the DNA damage response and lung adenocarcinoma cell response to radiation.
Dong, Y., Zhang, D., Cai, M., Luo, Z., Zhu, Y., Gong, L., Lei, Y., Tan, X., Zhu, Q., & Han, S. (2019) · PubMed Central · Cited by 25 · see citing works
Wu, Y., Liu, L., Shen, X., Liu, W., & Ma, R. (2021) · Cancer Management and Research · doi:10.2147/cmar.s281663 · Cited by 25 · see citing works
Lu, Z., Zhan, X., Wu, Y., Cheng, J., Shao, W., Ni, D., Han, Z., Zhang, J., Feng, Q., & Huang, K. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.06.026 · Cited by 18 · see citing works
Self-citationXu, S., Lu, Z., Shao, W., Yu, C. Y., Reiter, J. L., Feng, Q., Feng, W., Huang, K., & Liu, Y. (2020) · BMC Medical Genomics · doi:10.1186/s12920-020-00828-4 · Cited by 10 · see citing works
Self-citationCheng, J., Liu, Y., Huang, W., Hong, W., Wang, L., Zhan, X., Han, Z., Ni, D., Huang, K., & Zhang, J. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.623382 · Cited by 10 · see citing works
Self-citationSomatic genome alterations in relation to age in lung squamous cell carcinoma
Meucci, S., Keilholz, U., Heim, D., Klauschen, F., & Cacciatore, S. (2018) · Oncotarget · doi:10.18632/oncotarget.25848 · Cited by 3 · see citing works
- Authors
- WANG, C., SU, H., YANG, L., & HUANG, K.
- Affiliations
- The Ohio State University (US)
- University of Florida (US)
- Venue
- Biocomputing 2017
- Publisher
- WORLD SCIENTIFIC
- Published
- 2016-11-22
- Volume
- 22
- Pages
- 82-93
- PMC
- PMC5360185
- OpenAlex
- W2557229296
- Cited by
- 9
- References
- 27
- Citations by year
- 2022: 1 · 2021: 3 · 2020: 2 · 2019: 2 · 2018: 1
- FWCI
- 1.97
- Type
- conference paper
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Pacific Symposium on Biocomputing (PSB) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (U01CA188547)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Radiomics and Machine Learning in Medical Imaging
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Physical Sciences › Computer Science › Artificial Intelligence › AI in cancer detection
- Keywords
- lung adenocarcinoma, histomorphology, gene expression, copy number variation, co-expressed gene clusters, prognosis, histopathology image analysis, TCGA
- MeSH terms
- Adenocarcinoma of Lung, Adenocarcinoma, Algorithms, Multigene Family, Humans, Lung Neoplasms, Prognosis, Regression Analysis, Biomarkers, Tumor, Genetic Variation, Computational Biology, Gene Expression Profiling, Gene Regulatory Networks
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