Ming-Chin Lin

A Characterization of Local LOINC Mapping for Laboratory Tests in Three Large Institutions

OBJECTIVES We characterized the use of laboratory LOINC® codes in three large institutions, focused on the following questions: 1) How many local codes had been voluntarily mapped to LOINC codes by each institution? 2) Could additional mappings be found by expert manual review for any local codes that were not initially mapped to LOINC codes by the local institution? and 3) Are there any common characteristics of unmapped local codes that might explain why some local codes were not mapped to LOINC codes by the local institution? METHODS With Institutional Review Board (IRB) approval, we obtained deidentified data from three large institutions. We calculated the percentage of local codes that have been mapped to LOINC by personnel at each of the institutions. We also analyzed a sample of unmapped local codes to determine whether any additional LOINC mappings could be made and identify common characteristics that might explain why some local codes did not have mappings. RESULTS Concept type coverage and concept token coverage (volume of instance data covered) of local codes mapped to LOINC codes were 0.44/0.59, 0.78/0.78 and 0.79/0.88 for ARUP, Intermountain, and Regenstrief, respectively. After additional expert manual mapping, the results showed mapping rates of 0.63/0.72, 0.83/0.80 and 0.88/0.90, respectively. After excluding local codes which were not useful for inter-institutional data exchange, the mapping rates became 0.73/0.79, 0.90/0.99 and 0.93/0.997, respectively. CONCLUSIONS Local codes for two institutions could be mapped to LOINC codes with 99% or better concept token coverage, but mapping for a third institution (a reference laboratory) only achieved 79% concept token coverage. Our research supports the conclusions of others that not all local codes should be assigned LOINC codes. There should also be public discussions to develop more precise rules for when LOINC codes should be assigned.

Metadata mapping and reuse in caBIG

BackgroundThis paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facilitate the building domain models. This is examined in the context of an existing system, the National Cancer Institute (NCI)s cancer Biomedical Informatics Grid (caBIG™). The goal is to demonstrate the deployment of open source tools that can be used to effectively map models and enable the reuse of existing information objects and CDEs in the development of new models for translational research applications. This effort is intended to help developers reuse appropriate CDEs to enable interoperability of their systems when developing within the caBIG™ framework or other frameworks that use metadata repositories.ResultsThe Dice (di-grams) and Dynamic algorithms are compared and both algorithms have similar performance matching UML model class-attributes to CDE class object-property pairs. With algorithms used, the baselines for automatically finding the matches are reasonable for the data models examined. It suggests that automatic mapping of UML models and CDEs is feasible within the caBIG™ framework and potentially any framework that uses a metadata repository.ConclusionThis work opens up the possibility of using mapping algorithms to reduce cost and time required to map local data models to a reference data model such as those used within caBIG™. This effort contributes to facilitating the development of interoperable systems within caBIG™ as well as other metadata frameworks. Such efforts are critical to address the need to develop systems to handle enormous amounts of diverse data that can be leveraged from new biomedical methodologies.

Outcomes of Induction Chemotherapy for Head and Neck Cancer Patients: A Combined Study of Two National Cohorts in Taiwan.

AbstractThe use of induction chemotherapy (CT) is controversial. We compared the survival of head and neck cancer patients receiving docetaxel- or platinum-based induction CT before concomitant chemoradiotherapy (CCRT) with the survival of those receiving upfront CCRT alone.Data from the National Health Insurance and cancer registry databases in Taiwan were linked and analyzed. We enrolled patients who had head and neck cancer between January 1, 2002 and December 31, 2011. Follow-up was from the index date to December 31, 2013. We included head and neck patients diagnosed according to the International Classification of Diseases, Ninth Revision, Clinical Modification codes 140.0–148.9 who were aged >20 years, at American Joint Committee on Cancer clinical cancer stage III or IV, and receiving induction CT or platinum-based CCRT. The exclusion criteria were a cancer history before head and neck cancer diagnosis, distant metastasis, AJCC clinical cancer stage I or II, receipt of platinum and docetaxel before radiotherapy, an age <20 years, missing sex data, docetaxel use during or after RT, induction CT for >8 weeks before RT, induction CT alone before RT, cetuximab use, adjuvant CT within 90 days after RT completion, an RT dose <7000 cGy, curative head and neck cancer surgery before RT, nasopharyngeal cancer, in situ carcinoma, sarcoma, and head and neck cancer recurrence.We enrolled 10,721 stage III–IV head and neck cancer patients, with a median follow-up of 4.18 years (interquartile range, 3.25 years). The CCRT (arm 1), docetaxel-based induction CT (arm 2), and platinum-based CCRT (arm 3; control arm) groups comprised 7968, 503, and 2232 patients, respectively. Arm 3 was used to investigate mortality risk after induction CT. After adjustment for age, sex, clinical stage, and comorbidities, the adjusted hazard ratios (aHRs) (95% confidence interval [CI]) for overall death were 1.37 (1.22–1.53) and 1.44 (1.36–1.52) in arms 2 and 3, respectively. In a disease-specific survival rate analysis, aHRs (95% CI) of head and neck cancer-related death were 1.29 (1.14–1.46) and 1.47 (1.38–1.56) in arms 2 and 3, respectively.Compared with CCRT alone, docetaxal- or platinum-based induction CT did not improve survival but increased the risk of all-cause and head and neck cancer-related death.

A Prospective Randomized Study of Brain Tissue Oxygen Pressure-Guided Management in Moderate and Severe Traumatic Brain Injury Patients

The purpose of this study was to compare the effect of PbtO2-guided therapy with traditional intracranial pressure- (ICP-) guided treatment on the management of cerebral variables, therapeutic interventions, survival rates, and neurological outcomes of moderate and severe traumatic brain injury (TBI) patients. From 2009 to 2010, TBI patients with a Glasgow coma scale <12 were recruited from 6 collaborative hospitals in northern Taiwan, excluding patients with severe systemic injuries, fixed and dilated pupils, and other major diseases. In total, 23 patients were treated with PbtO2-guided management (PbtO2 > 20 mmHg), and 27 patients were treated with ICP-guided therapy (ICP < 20 mmHg and CPP > 60 mmHg) in the neurosurgical intensive care unit (NICU); demographic characteristics were similar across groups. The survival rate in the PbtO2-guided group was also significantly increased at 3 and 6 months after injury. Moreover, there was a significant correlation between the PbtO2 signal and Glasgow outcome scale-extended in patients from 1 to 6 months after injury. This finding demonstrates that therapy directed by PbtO2 monitoring is valuable for the treatment of patients with moderate and severe TBI and that increasing PaO2 to 150 mmHg may be efficacious for preventing cerebral hypoxic events after brain trauma.

Tamoxifen and the Risk of Parkinson's Disease in Female Patients with Breast Cancer in Asian People: A Nationwide Population-Based Study

Purpose Whether tamoxifen affects the risk of neurodegenerative disease is controversial. This nationwide population-based study investigated the risk of Parkinsons disease (PD) associated with tamoxifen treatment in female patients with breast cancer using Taiwans National Health Insurance Research Database. Methods A total of 5,185 and 5,592 female patients with breast cancer who did and did not, respectively, receive tamoxifen treatment between 2000 and 2009 were included in the study. Patients who subsequently developed PD were identified. A Cox proportional hazards model was used to compare the risk of PD between the aforementioned groups. Results Tamoxifen did not significantly increase the crude rate of developing PD in female patients with breast cancer (tamoxifen group, 16/5,169; non-tamoxifen group, 11/5,581; p=0.246). Tamoxifen did not significantly increase the adjusted hazard ratio (aHR) for subsequently developing PD (aHR, 1.310; 95% confidence interval [CI], 0.605–2.837; p=0.494). However, tamoxifen significantly increased the risk of PD among patients followed up for more than 6 years (aHR, 2.435; 95% CI, 1.008–5.882; p=0.048). Conclusion Tamoxifen treatment may increase the risk of PD in Taiwanese female patients with breast cancer more than 6 years after the initiation of treatment.