Search

The adaptation of high-throughput sequencing (HTS) to the B cell receptor (BCR) and T cell receptor (TCR) has made it possible to characterize the Adaptive Immune Receptor Repertoire (AIRR) at unprecedented depth. These AIRR sequencing (AIRR-seq) studies offer tremendous potential to increase the understanding of adaptive immune responses in vaccinology, infectious disease, autoimmunity, and cancer. The increasingly wide application of AIRR-seq is leading to a critical mass of studies being deposited in the public domain, offering the possibility of novel scientific insights through secondary analyses and meta-analyses. However, effective sharing of these large-scale data remains a challenge. The AIRR Community has proposed MiAIRR (Minimal Information about Adaptive Immune Receptor Repertoire), a standard for reporting AIRR-seq studies. The MiAIRR standard has been operationalized using the National Center for Biotechnology Information (NCBI) repositories. Submissions of AIRR-seq data to the NCBI repositories typically use a combination of web-based and flat-file templates and include only a minimal amount of terminology validation. As a result, AIRR-seq studies at the NCBI are often described using inconsistent terminologies, limiting scientists’ ability to access, find, interoperate, and reuse the data sets. In order to improve metadata quality and ease submission of AIRR-seq studies to the NCBI, we have leveraged the software framework developed by CEDAR (Center for Expanded Data Annotation and Retrieval), which develops technologies involving the use of data standards and ontologies to improve metadata quality. The resulting CEDAR-AIRR (CAIRR) pipeline enables data submitters to: i) create web-based templates whose entries are controlled by ontology terms, ii) generate and validate metadata, and iii) submit the ontology-linked metadata and sequence files (FASTQ) to the NCBI BioProject, BioSample, and Sequence Read Archive (SRA) databases. Overall, CAIRR provides a web-based metadata submission interface that supports compliance with the MiAIRR standard. This pipeline is available at http://cairr.miairr.org, and will facilitate the NCBI submission process and improve the metadata quality of AIRR-seq studies.

As the use of positron emission tomography-computed tomography (PET-CT) has increased rapidly, there is a need to retrieve relevant medical images that can assist image interpretation. However, the images themselves lack the explicit information needed for query. We constructed a semantically structured database of nuclear medicine images using the Annotation and Image Markup (AIM) format and evaluated the ability the AIM annotations to improve image search. We created AIM annotation templates specific to the nuclear medicine domain and used them to annotate 100 nuclear medicine PET-CT studies in AIM format using controlled vocabulary. We evaluated image retrieval from 20 specific clinical queries. As the gold standard, two nuclear medicine physicians manually retrieved the relevant images from the image database using free text search of radiology reports for the same queries. We compared query results with the manually retrieved results obtained by the physicians. The query performance indicated a 98 % recall for simple queries and a 89 % recall for complex queries. In total, the queries provided 95 % (75 of 79 images) recall, 100 % precision, and an F1 score of 0.97 for the 20 clinical queries. Three of the four images missed by the queries required reasoning for successful retrieval. Nuclear medicine images augmented using semantic annotations in AIM enabled high recall and precision for simple queries, helping physicians to retrieve the relevant images. Further study using a larger data set and the implementation of an inference engine may improve query results for more complex queries.

Quantitative and semantic information about medical images are vital parts of a radiological report. However, current image viewing systems do not record it in a format that permits machine interpretation. The ePAD tool can generate machine-computable image annotations on 2D images as part of a radiologist's routine workflow. The tool has been evaluated in image studies with good results. Since ePAD currently only provides 2D visualization and annotation of images, we developed a plugin to ePAD for the visualization of volumetric image datasets, using the three planes: axial, frontal and sagittal. A study with 6 radiologists was carried out to determine the best interface for also marking 3D ROIs. Video prototypes were created for 3 options: join pixels based on intensity similarity, detect borders around image features, and paint ROIs using a spheric 3D cursor. The 3D cursor was the preferred option. We present these results and also show the final 3D cursor implementation.

There are two key challenges hindering effective use of quantitative assessment of imaging in cancer response assessment: 1) Radiologists usually describe the cancer lesions in imaging studies subjectively and sometimes ambiguously, and 2) it is difficult to repurpose imaging data, because lesion measurements are not recorded in a format that permits machine interpretation and interoperability. We have developed a freely available software platform on the basis of open standards, the electronic Physician Annotation Device (ePAD), to tackle these challenges in two ways. First, ePAD facilitates the radiologist in carrying out cancer lesion measurements as part of routine clinical trial image interpretation workflow. Second, ePAD records all image measurements and annotations in a data format that permits repurposing image data for analyses of alternative imaging biomarkers of treatment response. To determine the impact of ePAD on radiologist efficiency in quantitative assessment of imaging studies, a radiologist evaluated computed tomography (CT) imaging studies from 20 subjects having one baseline and three consecutive follow-up imaging studies with and without ePAD. The radiologist made measurements of target lesions in each imaging study using Response Evaluation Criteria in Solid Tumors 1.1 criteria, initially with the aid of ePAD, and then after a 30-day washout period, the exams were reread without ePAD. The mean total time required to review the images and summarize measurements of target lesions was 15% (P < .039) shorter using ePAD than without using this tool. In addition, it was possible to rapidly reanalyze the images to explore lesion cross-sectional area as an alternative imaging biomarker to linear measure.We conclude that ePAD appears promising to potentially improve reader efficiency for quantitative assessment of CT examinations, and it may enable discovery of future novel image-based biomarkers of cancer treatment response.

Medical imaging plays an important role in the diagnosis, prognosis and treatment of cancer. Quantitative and qualitative data about medical images are vital components of a radiological report and are very important to the oncologist that requests the radiological exams. However, traditional methods to register these data are inefficient and error prone. The use of unstructured free text in radiology reports makes it impossible to perform even simple calculations, such as changes in lesion dimensions. It also makes the aggregated analysis of many reports difficult. Free text reports lack a reference to the image regions of the finds they refer to and are not machine-computable. This paper proposes a method to provide support for collaborative work among radiologists and oncologists (providing care or taking part in clinical trials) using an imaging web tool, ePAD, to generate structured radiology reports that can be machine-computable. It also shows how ePAD uses Rad Lex ontology terms and the Annotation and Image Markup (AIM) language (and templates) to generate the reports.