An Intelligent Search & Retrieval System (IRIS) and Clinical and Research Repository for Decision Support Based on Machine Learning and Joint Kernel-based Supervised Hashing

Large-scale, multi-site collaboration is becoming indispensable for a wide range of research and clinical activities in oncology. To facilitate the next generation of advances in cancer biology, precision oncology and the population sciences it will be necessary to develop and implement data management and analytic tools that empower investigators to reliably and objectively detect, characterize and chronicle the phenotypic and genomic changes that occur during the transformation from the benign to cancerous state and throughout the course of disease progression. To facilitate these efforts it is incumbent upon the informatics community to establish the workflows and architectures that automate the aggregation and organization of a growing range and number of clinical data types and modalities ranging from new molecular and laboratory tests to sophisticated diagnostic imaging studies. In an attempt to meet those challenges, leading health care centers across the country are making steep investments to establish enterprise-wide, data warehouses. A significant limitation of many data warehouses, however, is that they are designed to support only alphanumeric information. In contrast to those traditional designs, the system that we have developed supports automated collection and mining of multimodal data including genomics, digital pathology and radiology images. In this paper, our team describes the design, development and implementation of a multi-modal, Clinical & Research Data Warehouse (CRDW) that is tightly integrated with a suite of computational and machine-learning tools to provide actionable insight into the underlying characteristics of the tumor environment that would not be revealed using standard methods and tools. The System features a flexible Extract, Transform and Load (ETL) interface that enables it to adapt to aggregate data originating from different clinical and research sources depending on the specific EHR and other data sources utilized at a given deployment site.

Prevalence of SARS-CoV-2 IgG antibodies in health care workers at a tertiary care academic medical center - An assessment of occupational infection risk

Background

The purpose of this study was to assess the occupational SARS-CoV-2 infection risk among health care workers (HCW) at University of Kentucky HealthCare (UKHC) by evaluating the prevalence of SARS-CoV-2 antibodies.

Methods

This is a prospective cohort study of HCW at UKHC. SARS-CoV-2 IgG antibody seropositivity was measured in a CLIA-certified laboratory utilizing the Abbott Architect SARS-CoV-2 IgG antibody assay. Demographics and work type were self-reported by study participants via an emailed survey.

Results

The overall antibody positivity rate of HCW was 1.55% (5/322; 95% confidence interval: 0.65%-3.71%) at cohort entry. There were no differences in antibody positivity between those that worked directly with SARS-CoV-2 infected patients and those that did not. The antibody rate of positivity of patients during the same time period was similar, 1.8% (9/499; 95% confidence interval 0.94%-3.45%).

Conclusions

Antibody positivity was low and similar between HCW and patients tested during a similar time period. HCW positivity rates did not appear to be impacted by caring for known SARS-CoV-2 infected patients suggesting that appropriate use of personal protective equipment is effective in protecting individuals from transmission.

Real world clinicopathologic observations of patients with metastatic solid tumors receiving immune checkpoint inhibitor therapy: Analysis from Kentucky Cancer Registry

The state of Kentucky has the highest cancer incidence and mortality in the United States. High‐risk populations such as this are often underrepresented in clinical trials. The study aims to do a comprehensive analysis of molecular landscape of metastatic cancers among these patients with detailed evaluation of factors affecting response and outcomes to immune checkpoint inhibitor (ICI) therapy. We performed a retrospective analysis of metastatic solid tumor patients who received ICI and underwent molecular profiling at our institution.

Sixty nine patients with metastatic solid tumors who received ICI were included in the study. Prevalence of smoking and secondhand tobacco exposure was 78.3% and 14.5%, respectively. TP53 (62.3%), CDKN1B/2A (40.5%), NOTCH and PIK3 (33.3%) were the most common alterations in tumors. 67.4% were PDL1 positive and 59.4% had intermediate‐high tumor mutational burden (TMB). Median TMB (12.6) was twofold to fourfold compared to clinical trials. The prevalence of mutations associated with smoking, homologous recombinant repair and PIK3/AKT/mTOR pathway mutations was higher compared to historic cohorts.

PDL1 expression had no significant effect on radiologic response, but PFS improvement in patients with tumors expressing PDL1 trended toward statistical significance (median 18 vs. 40 weeks. HR = 1.43. 95%CI 0.93, 4.46). Median PFS was higher in the high‐TMB cohort compared to low‐intermediate TMB (median not reached vs. 26 weeks; HR = 0.37. 95%CI 0.13, 1.05). A statistically significant improvement in PFS was observed in the PIK3 mutated cohort (median 123 vs. 23 weeks. HR = 2.51. 95%CI 1.23, 5.14). This was independent of tumor mutational burden (TMB) status or PDL1 expression status. PIK3 mutants had a higher overall response rate than the wild type (69.6% vs. 43.5%, OR 0.34; p = 0.045). The results should prompt further evaluation of these potential biomarkers and more widespread real‐world data publications which might help determine biomarkers that could benefit specific populations.

Using residential histories in case-control analysis of lung cancer and mountaintop removal coal mining in Central Appalachia

Population-based ecological and cross-sectional studies have observed high risk for several cancers in areas of Central Appalachia where mountaintop removal coal mines operate. Case-control studies could provide stronger evidence of such relationships, but misclassification of exposure is likely when based on current residence, since individuals could have inhabited several residences with varying environmental exposures over many years. To address this, we used residential histories for individuals enrolled in a previous case-control study of lung cancer to assess residential proximity to mountaintop removal coal mining over a 30-year period, using both survey data and proprietary data from LexisNexis, Inc. Supplementing the survey data with LexisNexis data improved precision and completeness of geographic coordinates. Final logistic regression models revealed higher odds of high exposure among cases. These findings suggest that living in close proximity to mountaintop removal coal mining sites could increase risk for lung cancer, after adjusting for other relevant factors.

Abstract A001: Improving cancer germline testing in rural Appalachian populations with ORIEN

Background: Reduced access to treatment advances in rural populations contributes to increased cancer mortality. Rural Appalachian Kentucky is a geographically isolated population with a unique carcinogen exposure and a low frequency guideline-recommended germline testing. To improve testing rates, a return of germline results program for patients enrolled in the Total Cancer Care (TCC) protocol at Markey Cancer Center (MCC) was initiated. Methods: Pre-intervention testing rates were obtained from the electronic health record. Patient and physician focus groups were conducted to assess barriers to germline testing. Whole exome germline data from TCC patients enrolled in the Avatar subset is analyzed using standard bioinformatics pipeline for known, clinically significant mutations in the 59 American College of Medical Genetics (ACMG) genes where return of incidental germline findings is recommended and 21 pharmacogenetic genes. Results are reviewed by our Molecular Tumor Board and a recommendation for confirmatory clinical testing, if needed, is made to the treating physician. Results: Baseline rates of guideline recommended germline testing at MCC in 2018 was 20% of ovarian, 15% of breast, 9% of colon, 3% of pancreas and no metastatic prostate patients. Testing was infrequent in rural communities. Almost all patients who had testing recommended by their physician, had testing performed. Unaffected family members were also rarely tested. Physician focus groups at MCC identified lack of time and low perceived value of the testing as barriers. Rural physicians also identified lack of access to genetic counselors. Patient focus groups in the Appalachian region demonstrated poor quality internet and low knowledge and self- efficacy as major barriers to patients discussing genetic testing with family members. To overcome patient barriers, a preloaded audio card was developed to facilitate discussion with family members. The preloaded audio card was tested in a rural Appalachian community, demonstrating significantly improved knowledge and self-efficacy. To overcome physician barriers, a genetic counselor telemedicine clinic and standing order were initiated. To improve physician perception of test value, the ORIEN return of germline results project was initiated. Of the more than 2000 patients enrolled on TCC at MCC, approximately 40% are from Appalachia, 173 have appropriate consent and specimen availability for germline sequencing and 5 have had results returned. Data describing the first 3 months of this initiative, including frequency of mutations in patients and unaffected family members and acceptance of genetic counselor referrals by physicians, patients and family members will be presented. Conclusion: Rural Appalachian communities identified significant barriers to guideline recommended germline testing, however, ORIEN and the TCC protocol are novel methods to reduce these barriers and improve the rates of testing in both patients and their family members.

Citation Format: Jill Kolesar, Micheal Cavnar, Rachel Miller, Justine Pickarski, Shulin Zhang, Kannabiran Nandakumar, Marissa Schuh, Elizabeth Belcher, Eric Durbin, Ming Poi, Fred Ueland, Isaac Hands, Therese Bocklage, JC Jeong, Susanne Arnold, Mark Evers. Improving cancer germline testing in rural Appalachian populations with ORIEN [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr A001.

Identifying Smoking Status and Smoking Cessation Using a Data Linkage Between the Kentucky Cancer Registry and Health Claims Data

PURPOSE

Linkage of cancer registry data with complementary data sources can be an informative way to expand what is known about patients and their treatment and improve delivery of care. The purpose of this study was to explore whether patient smoking status and smoking-cessation modalities data in the Kentucky Cancer Registry (KCR) could be augmented by linkage with health claims data.

METHODS

The KCR conducted a data linkage with health claims data from Medicare, Medicaid, state employee insurance, Humana, and Anthem. Smoking status was defined as documentation of personal history of tobacco use (International Classification of Diseases, Ninth Revision [ICD-9] code V15.82) or tobacco use disorder (ICD-9 305.1) before and after a cancer diagnosis. Use of smoking-cessation treatments before and after the cancer diagnosis was defined as documentation of smoking-cessation counseling (Healthcare Common Procedure Coding System codes 99406, 99407, G0375, and G0376) or pharmacotherapy (eg, nicotine replacement therapy, bupropion, varenicline).

RESULTS

From 2007 to 2011, among 23,703 patients in the KCR, we discerned a valid prediagnosis smoking status for 78%. KCR data only (72%), claims data only (6%), and a combination of both data sources (22%) were used to determine valid smoking status. Approximately 4% of patients with cancer identified as smokers (n = 11,968) and were provided smoking-cessation counseling, and 3% were prescribed pharmacotherapy for smoking cessation.

CONCLUSION

Augmenting KCR data with medical claims data increased capture of smoking status and use of smoking-cessation modalities. Cancer registries interested in exploring smoking status to influence treatment and research activities could consider a similar approach, particularly if their registry does not capture smoking status for a majority of patients.

Late-Stage Melanoma: Be Sure to Screen Uninsured, Unmarried Men

OBJECTIVE

The purpose of this study was to assess for any associations between individual and social factors and late-stage melanoma in Kentucky from 1995 to 2013.

METHODS

The study combines three datasets: individual-level data from the Kentucky Cancer Registry, census tract-level data from the US Census, and county-level physician licensure data from the Kentucky Department for Public Health. The study population is described by all cases, early stage, and late stage. Logistic regression was used to evaluate the unadjusted associations between each covariate and early-stage and late-stage disease groups. All of the significant variables were assessed for interaction effect, and the significant interaction terms were used in the final model. Multiple logistic regression provided the final model of late-stage disease.

RESULTS

In this study population, a dramatic increase in melanoma incidence is seen from 1995 to 2013 with a threefold increase in the number of cases per year. Of the 10,109 cases reported, 13.6% have late-stage disease, with a mean age for all cases at 56.9 years and the majority being men. Late-stage cases are more commonly uninsured or insured with Medicaid or Medicare compared with cases with early-stage lesions. Having a spouse or partner is clearly protective from being diagnosed as having late-stage melanoma, whereas being uninsured or having Medicaid increases the odds of late-stage melanoma.

CONCLUSIONS

The incidence of melanoma is increasing dramatically. With no screening recommendation for the general population from the US Preventive Task Force, clinicians should focus on those at increased risk of late-stage melanoma: unmarried men who are uninsured or receiving Medicaid.

An inventory model for optimizing purchasing of intravenous fluids for hospitals: a case study

This paper deals with determining the optimal level of purchase of intravenous fluids for hospitals by utilizing inventory control concepts. Using the conceptual framework of the economic order quantity (EOQ) model, the hospital administrators can elicit the efficient materials management, thus reducing both the space and capital requirements without compromising the quality of services rendered.