A Query Tool for Investigator Access to the Data and Images of the National Lung Screening Trial

The National Cancer Institute (NCI), in conjunction with blinded university, provides a mechanism to enable public access to the study data, CT radiology images, and pathology images from the National Lung Screening Trial (NLST). Access to the data and images is through the NCI-sponsored, blinded university-hosted The Cancer Imaging Archive (TCIA), a repository of more than 40 study collections of cancer images. Once access to the NLST data has been granted by NCI, a Query Tool within TCIA is used to access the NLST data and images. The Query Tool is a simple-to-use menu-driven database application designed to quickly pose queries and retrieve/save results (from 53,452 NLST participants), download CT images (~20 million available), and view pathology images (~1200 available). NLST study data are contained in 17 Query Tool tables with ~370 variables to query. This paper describes Query Tool design, functionality, and usefulness for researchers, clinicians, and software developers to query data, save query results, and download/view images.     

Between Prevention and Therapy: Gio Batta Gori and the National Cancer Institute��s Diet, Nutrition and Cancer Programme, 1974�C1978

This paper explores the origins of the Diet, Nutrition and Cancer Programme (DNCP) of the National Cancer Institute (NCI) and its fate under its first director, Gio Batta Gori. The DNCP is used to explore the emergence of federal support for research on diet, nutrition and cancer following the 1971 Cancer Act, the complex relations between cancer prevention and therapeutics in the NCI during the 1970s, the broader politics around diet, nutrition and cancer during that decade, and their relations to Senator George McGovern’s select committee on Nutrition and Human Needs. It also provides a window onto the debates and struggles over whether NCI research should be funded by contracts or grants, the nature of the patronage system within the federal cancer research agency, how a director, Gio Gori, lost patronage within that system and how a tightening of the budget for cancer research in the mid-to-late 1970s affected the DNCP.     

非小细胞肺癌影像学特征与基因表达间相关性的探索性研究

影像基因组学通过挖掘肿瘤的影像和基因组学间的关联性,将两者的优势互补,以此指导不同患者个体化治疗方案的制定、预后评估、疗效检测等。针对非小细胞肺癌(NSCLC),建立其CT影像定量特征与基因表达之间的映射。首先,将对应的CT影像中肿瘤区域进行分割和特征提取,选用66种三维定量特征作为肿瘤区域影像特征集;然后,利用基因组学数据分析流程,在原始基因数据经过预处理、聚类后,获取其第一主成分作为具有相似表达谱基因聚类结果的代表;最后,运用基因芯片显著性分析算法探寻两者之间的相关性,并进行基因集的富集分析和预测模型的建立。对癌症图像归档数据库(TCIA)中的26例NSCLC影像数据和基因表达综合数据库(GEO)中相对应的基因数据进行分析,共得到126组成对的显著关联(q<0.05)。将所得结果中的29组元基因建立预测模型,并通过TCIA中更新的211组数据,对其中10组预测准确率大于70%且预测的元基因有生物学意义的预测模型进行验证,最终预测准确率为35.48%～80.85%,10个预测模型中有6个的准确率在70%以上。实验结果表明,特定的影像特征或其组合可以作为基因表达的影像标记物。     

The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation Model

Knowledge contained within in vivo imaging annotated by human experts or computer programs is typically stored as unstructured text and separated from other associated information. The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation information model is an evolution of the National Institute of Health’s (NIH) National Cancer Institute’s (NCI) Cancer Bioinformatics Grid (caBIG®) AIM model. The model applies to various image types created by various techniques and disciplines. It has evolved in response to the feedback and changing demands from the imaging community at NCI. The foundation model serves as a base for other imaging disciplines that want to extend the type of information the model collects. The model captures physical entities and their characteristics, imaging observation entities and their characteristics, markups (two- and three-dimensional), AIM statements, calculations, image source, inferences, annotation role, task context or workflow, audit trail, AIM creator details, equipment used to create AIM instances, subject demographics, and adjudication observations. An AIM instance can be stored as a Digital Imaging and Communications in Medicine (DICOM) structured reporting (SR) object or Extensible Markup Language (XML) document for further processing and analysis. An AIM instance consists of one or more annotations and associated markups of a single finding along with other ancillary information in the AIM model. An annotation describes information about the meaning of pixel data in an image. A markup is a graphical drawing placed on the image that depicts a region of interest. This paper describes fundamental AIM concepts and how to use and extend AIM for various imaging disciplines.     

Open Source Software Projects of the caBIG™ In Vivo Imaging Workspace Software Special Interest Group

The Cancer Bioinformatics Grid (caBIG?) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG? In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research.     

Shape Priors for Segmentation of the Cervix Region Within Uterine Cervix Images

The work focuses on a unique medical repository of digital uterine cervix images (“cervigrams”) collected by the National Cancer Institute (NCI), National Institute of Health, in longitudinal multiyear studies. NCI together with the National Library of Medicine is developing a unique web-based database of the digitized cervix images to study the evolution of lesions related to cervical cancer. Tools are needed for the automated analysis of the cervigram content to support the cancer research. In recent works, a multistage automated system for segmenting and labeling regions of medical and anatomical interest within the cervigrams was developed. The current paper concentrates on incorporating prior-shape information in the cervix region segmentation task. In accordance with the fact that human experts mark the cervix region as circular or elliptical, two shape models (and corresponding methods) are suggested. The shape models are embedded within an active contour framework that relies on image features. Experiments indicate that incorporation of the prior shape information augments previous results.     

Incidental health information use and media complementarity: a comparison of senior and non-senior cancer patients

OBJECTIVE: This study compares the health information and media usage patterns of older adults diagnosed with cancer with their younger adult counterparts and is based theoretically in media complementarity theory [Dutta-Bergman MJ. Complementarity in consumption of news types across traditional and new media. J Broadcast Electron 2004;48:41-60; Dutta-Bergman MJ. Interpersonal communication after 9/11 via telephone and Internet: a theory of channel complementarity. New Media Soc 2004;6:659-73] and health information seeking and scanning research [Shim M, Kelly B, Hornik R. Cancer information scanning and seeking behavior is associated with knowledge, lifestyle choices, and screening. J Health Commun 2006;11:157-72]. METHODS: A secondary analysis of the Health Information National Trends Survey (HINTS) II data collected by the National Cancer Institute (NCI) is performed to investigate differences in the health information behavior of younger and older adult cancer patients. The sample size was 401, with 260 non-senior cancer patients and 141 senior cancer patients. RESULTS: Younger adults diagnosed with cancer were more likely to gain information about health incidentally through their use of the Internet and to seek health information for others on the Internet than senior cancer patients. Complementarity of active health information seeking and incidental health information use online was supported with senior cancer patients, while complementarity of incidental health information use between traditional media channels and the Internet was partially confirmed with younger adults. CONCLUSION: This study reveals similarities and differences in the health information and media usage behavior of younger and older adults diagnosed with cancer. It also provides partial support for media complementarity theory. PRACTICE IMPLICATIONS: The Internet is not a panacea for health information. Health professionals need to provide written instructions to older adult cancer patients because they do not rely on the Internet for information about their illness and/or treatment.     

Research on cancer diagnosis in Malaysia: current status

Cancer is a major morbidity and mortality concern in Malaysia. Based on National Cancer Registry data, the Malaysian population is estimated to bear a cancer burden of about 40,000 new cases per year, and a cumulative lifetime risk of about 1:4. Cancer research in Malaysia has to consider needs relevant to our population, and resources constraints. Hence, funding bodies prioritise cancers of high prevalence, unique to our community and posing specific clinical problems. Cancer diagnosis is crucial to cancer management. While cancer diagnosis research largely aims at improvements in diagnostic information towards more appropriate therapy, it also impacts upon policy development and other areas of cancer management. The scope of cancer diagnosis upon which this paper is based, and their possible impact on other R&D areas, has been broadly categorized into: (1) identification of aetiological agents and their linkages to the development of precancer and cancer (impact on policy development, cancer prevention and treatment), (2) cancer biology and pathogenesis (impact on cancer prevention, treatment strategies and product development), (3) improvements in accuracy, sensitivity and specificity in cancer detection, monitoring and classification (impact on technology development) and (4) prognostic and predictive parameters (impact on treatment strategies). This paper is based on data collected by the Working Group on Cancer Diagnosis Research for the First National Conference on Cancer Research Coordination in April 2004. Data was collated from the databases of Institutions/Universities where the authors are employed, the Ministry of Science, Technology and Innovation (MOSTI) and targeted survey feedback from key cancer researchers. Under the 7th Malaysia Plan, 76 cancer projects were funded through the Intensified Research in Priority Areas (IRPA) scheme of MOSTI, amounting to almost RM15 million of grant money. 47(61.8%) of these projects were substantially in cancer diagnosis, accounting for 65.6% (RM 9.7 million) of cancer project funds. The 8th Malaysia Plan saw a change in research strategy. The IRPA agency fielded several top-down projects which encouraged a multicentre and multidisciplinary approach. This resulted in larger funding per project i.e. RM32 million for 49 projects. There was also a surge of interest in drug development and natural products. Because of this shift in direction, cancer diagnosis projects constituted only 51% of IRPA-funded cancer projects. Nonetheless funding for cancer diagnosis research has exceeded that of the 7th Malaysia Plan, being RM12.5 million by March 2004. The majority of such research is carried out at the Universities, engaging a large number of young scientists and postgraduate students (51 MSc and 21 PhD). A lot of research findings presented at scientific meetings have not yet been published and there is a glaring shortage of patents and commercialization of research findings (such as creation of test kits). Because diagnosis is very much a part of clinical practice, many researchers felt satisfied and confident that their work will be translated into practice and will significantly improve diagnostic services in Malaysia. National guidelines and consensus development on at least three malignancies i.e. breast cancer, oral cancer and lymphoma, have substantial basis in local R&D work. Problems encountered in research included (1) insufficient funding to realize research objectives, (2) lack of local expertise (most research assistants are inexperienced BSc graduates with no or minimal research experience), (3) inadequate technical support from vendors during equipment failure, (4) inexperienced Institutional development units to assist in product development, (5) lack of venture capital for commercialization of findings, and (6) inadequate incentives to undertake research. Researchers pointed out that plans to promote research should include the establishment of (1) regional and national cancer tissue banks, (2) a National Cancer Research Institute, (3) a dedicated cancer research fund, (4) a registry of cancer researchers, (5) national research coordinators, (6) improved coverage by the National Cancer Registry, (7) more international collaboration, (8) a better career structure for researchers, (9) improved Institutional support for product realization, and (10) better recognition for cancer researchers.     

The tissue microarray data exchange specification: A document type definition to validate and enhance XML data

Background  

The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format. Each tissue core within an array has separate data including digital images; therefore an organized, common approach to produce, navigate and publish such data facilitates viewing, sharing and merging TMA data from different laboratories. The AIDS and Cancer Specimen Resource (ACSR) is a HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers HIV-related malignancies and uninfected control tissues in microarrays (TMA) accompanied by de-identified clinical data to approved researchers. Exporting our TMA data into the proposed API specified format offers an opportunity to evaluate the API specification in an applied setting and to explore its usefulness.     

The caBIG terminology review process

The National Cancer Institute (NCI) is developing an integrated biomedical informatics infrastructure, the cancer Biomedical Informatics Grid (caBIG^®), to support collaboration within the cancer research community. A key part of the caBIG architecture is the establishment of terminology standards for representing data. In order to evaluate the suitability of existing controlled terminologies, the caBIG Vocabulary and Data Elements Workspace (VCDE WS) working group has developed a set of criteria that serve to assess a terminology’s structure, content, documentation, and editorial process. This paper describes the evolution of these criteria and the results of their use in evaluating four standard terminologies: the Gene Ontology (GO), the NCI Thesaurus (NCIt), the Common Terminology for Adverse Events (known as CTCAE), and the laboratory portion of the Logical Objects, Identifiers, Names and Codes (LOINC). The resulting caBIG criteria are presented as a matrix that may be applicable to any terminology standardization effort.     

The tissue micro-array data exchange specification: a web based experience browsing imported data

Background  

The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary.     

A novel web informatics approach for automated surveillance of cancer mortality trends

Cancer surveillance data are collected every year in the United States via the National Program of Cancer Registries (NPCR) and the Surveillance, Epidemiology and End Results (SEER) Program of the National Cancer Institute (NCI). General trends are closely monitored to measure the nation’s progress against cancer. The objective of this study was to apply a novel web informatics approach for enabling fully automated monitoring of cancer mortality trends. The approach involves automated collection and text mining of online obituaries to derive the age distribution, geospatial, and temporal trends of cancer deaths in the US. Using breast and lung cancer as examples, we mined 23,850 cancer-related and 413,024 general online obituaries spanning the timeframe 2008–2012. There was high correlation between the web-derived mortality trends and the official surveillance statistics reported by NCI with respect to the age distribution (ρ = 0.981 for breast; ρ = 0.994 for lung), the geospatial distribution (ρ = 0.939 for breast; ρ = 0.881 for lung), and the annual rates of cancer deaths (ρ = 0.661 for breast; ρ = 0.839 for lung). Additional experiments investigated the effect of sample size on the consistency of the web-based findings. Overall, our study findings support web informatics as a promising, cost-effective way to dynamically monitor spatiotemporal cancer mortality trends.     

Training, credentialing and re-credentialing for the performance of a thyroid FNA: a synopsis of the National Cancer Institute Thyroid Fine-Needle Aspiration State of the Science Conference

The National Cancer Institute (NCI) sponsored the NCI Thyroid Fine-Needle Aspiration (FNA) State of the Science Conference on October 22-23, 2007 in Bethesda, MD. The 2-day meeting was accompanied by a permanent informational website and several on-line discussion periods between May 1 and December 15, 2007 (http://thyroidfna.cancer.gov). This document summarizes matters regarding training for the performance of thyroid FNA via palpation; training for the performance of thyroid FNA via ultrasound imaging, and credentialing/re-credentialing for the performance of a thyroid FNA. (http://thyroidfna.cancer.gov/pages/info/agenda/)     

Image Data Sharing for Biomedical Research—Meeting HIPAA Requirements for De-identification

Data sharing is increasingly recognized as critical to cross-disciplinary research and to assuring scientific validity. Despite National Institutes of Health and National Science Foundation policies encouraging data sharing by grantees, little data sharing of clinical data has in fact occurred. A principal reason often given is the potential of inadvertent violation of the Health Insurance Portability and Accountability Act privacy regulations. While regulations specify the components of private health information that should be protected, there are no commonly accepted methods to de-identify clinical data objects such as images. This leads institutions to take conservative risk-averse positions on data sharing. In imaging trials, where images are coded according to the Digital Imaging and Communications in Medicine (DICOM) standard, the complexity of the data objects and the flexibility of the DICOM standard have made it especially difficult to meet privacy protection objectives. The recent release of DICOM Supplement 142 on image de-identification has removed much of this impediment. This article describes the development of an open-source software suite that implements DICOM Supplement 142 as part of the National Biomedical Imaging Archive (NBIA). It also describes the lessons learned by the authors as NBIA has acquired more than 20 image collections encompassing over 30 million images.     

Indications for thyroid FNA and pre-FNA requirements: a synopsis of the National Cancer Institute Thyroid Fine-Needle Aspiration State of the Science Conference

The National Cancer Institute (NCI) sponsored the NCI Thyroid Fine-Needle Aspiration (FNA) State of the Science Conference on October 22-23, 2007 in Bethesda, MD. The 2-day meeting was accompanied by a permanent informational website and several on-line discussions between May 1 and December 15, 2007 (http://thyroidfna.cancer.gov). This document summarizes the indications for performing an FNA of a nodule discovered by physical examination or an imaging study; the indications for using ultrasound versus palpation for guidance when performing a thyroid FNA; the issues surrounding informed consent for thyroid FNA; and the information required on a requisition form that accompanies a thyroid FNA specimen. (http://thyroidfna.cancer.gov/pages/info/agenda/)     

The NCI Thesaurus quality assurance life cycle

The National Cancer Institute Enterprise Vocabulary Services (NCI EVS) uses a wide range of quality assurance (QA) techniques to maintain and extend NCI Thesaurus (NCIt). NCIt is a reference terminology and biomedical ontology used in a growing number of NCI and other systems that extend from translational and basic research through clinical care to public information and administrative activities. Both automated and manual QA techniques are employed throughout the editing and publication cycle, which includes inserting and editing NCIt in NCI Metathesaurus. NCI EVS conducts its own additional periodic and ongoing content QA. External reviews, and extensive evaluation by and interaction with EVS partners and other users, have also played an important part in the QA process. There have always been tensions and compromises between meeting the needs of dependent systems and providing consistent and well-structured content; external QA and feedback have been important in identifying and addressing such issues. Currently, NCI EVS is exploring new approaches to broaden external participation in the terminology development and QA process.     

Evidence‐based evaluation of the risks of malignancy predicted by thyroid fine‐needle aspiration biopsies

A National Cancer Institute (NCI) “Thyroid Fine‐Needle Aspiration (FNA) State of the Science Conference” recently proposed standardized nomenclature and “risks of malignancies” associated with various diagnostic categories. We evaluated the evidence levels of the data used by NCI to predict malignancy risks and whether those estimates had clinical validity in our patient population. Eight hundred seventy‐nine patients underwent thyroid FNA during 2006. FNA diagnoses were translated into NCI diagnostic categories, and 2‐year follow‐up retrospective information was obtained. Four percentages of malignancies were calculated for each diagnostic category using follow‐up information from FNA, thyroidectomy, both, and all patients as denominators. 95% confidence intervals (CI) were estimated for all proportions, and results were analyzed with chi‐square statistics. “Relative risk” calculations were performed using the percentage of malignancies in the entire population under study as a denominator. Most of the studies cited by the NCI provided incomplete and variable level III evidence based mainly on surgical follow‐up. Among our patients, the percentages of malignancies calculated with follow‐up data from all patients as the denominator were similar to the “risk estimates” proposed by the NCI, but estimates based on surgical follow‐up overestimated the probability of thyroid malignancy for patients with FNA diagnosis of “benign” and “follicular lesions of undetermined significance” (FLUS). Relative risk and 95% CI calculations suggested that the NCI classification could be simplified into three categories: “benign,” “FLUS + neoplasm,” and “suspicious + malignant.” Diagn. Cytopathol. 2010. © 2009 Wiley‐Liss, Inc.     

An efficient architecture to support digital pathology in standard medical imaging repositories

In the past decade, digital pathology and whole-slide imaging (WSI) have been gaining momentum with the proliferation of digital scanners from different manufacturers. The literature reports significant advantages associated with the adoption of digital images in pathology, namely, improvements in diagnostic accuracy and better support for telepathology. Moreover, it also offers new clinical and research applications. However, numerous barriers have been slowing the adoption of WSI, among which the most important are performance issues associated with storage and distribution of huge volumes of data, and lack of interoperability with other hospital information systems, most notably Picture Archive and Communications Systems (PACS) based on the DICOM standard.This article proposes an architecture of a Web Pathology PACS fully compliant with DICOM standard communications and data formats. The solution includes a PACS Archive responsible for storing whole-slide imaging data in DICOM WSI format and offers a communication interface based on the most recent DICOM Web services. The second component is a zero-footprint viewer that runs in any web-browser. It consumes data using the PACS archive standard web services. Moreover, it features a tiling engine especially suited to deal with the WSI image pyramids. These components were designed with special focus on efficiency and usability. The performance of our system was assessed through a comparative analysis of the state-of-the-art solutions. The results demonstrate that it is possible to have a very competitive solution based on standard workflows.