Publications

All Publications


  • Higher Absolute Lymphocyte Counts Predict Lower Mortality from Early-Stage Triple-Negative Breast Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research Afghahi, A., Purington, N., Han, S. S., Desai, M., Pierson, E., Mathur, M. B., Seto, T., Thompson, C. A., Rigdon, J., Telli, M. L., Badve, S. S., Curtis, C., West, R. B., Horst, K., Gomez, S. L., Ford, J. M., Sledge, G. W., Kurian, A. W. 2018

    Abstract

    Tumor-infiltrating lymphocytes (TILs) in pre-treatment biopsies are associated with improved survival in triple-negative breast cancer (TNBC). We investigated whether higher peripheral lymphocyte counts are associated with lower breast cancer-specific mortality (BCM) and overall mortality (OM) in TNBC.Data on treatments and diagnostic tests from electronic medical records of two healthcare systems were linked with demographic, clinical, pathologic, and mortality data from the California Cancer Registry. Multivariable regression models adjusted for age, race/ethnicity, socioeconomic status, cancer stage, grade, neoadjuvant/adjuvant chemotherapy use, radiotherapy use, and germline BRCA1/2 mutations were used to evaluate associations between absolute lymphocyte count (ALC), BCM and OM. For a subgroup with TILs data available, we explored the relationship between TILs and peripheral lymphocyte counts.1,463 Stage I-III TNBC patients were diagnosed from 2000-2014; 1113 (76%) received neoadjuvant/adjuvant chemotherapy within one year of diagnosis. Of 759 patients with available ALC data, 481 (63.4%) were ever lymphopenic (minimum ALC <1.0 K/μL). On multivariable analysis, higher minimum ALC, but not absolute neutrophil count, predicted lower OM (hazard ratio [HR]: 0.23, 95% confidence interval [CI]: 0.16-0.35) and BCM (HR: 0.19, CI: 0.11-0.34). Five-year probability of BCM was 15% for patients who were ever lymphopenic versus 4% for those who were not. An exploratory analysis (N=70) showed a significant association between TILs and higher peripheral lymphocyte counts during neoadjuvant chemotherapy.Higher peripheral lymphocyte counts predicted lower mortality from early-stage, potentially curable TNBC, suggesting that immune function may enhance the effectiveness of early TNBC treatment.

    View details for DOI 10.1158/1078-0432.CCR-17-1323

    View details for PubMedID 29581131

  • Architecture and implementation of a clinical research data warehouse for prostate cancer EGEMS Seneviratne, M., Seto, T., Blayney, D. W., Brooks, J. D., Hernandez-Boussard, T. 2018
  • Changes in Prostate Specific Antigen Screening and Prostate Cancer Diagnosis After Guideline Changes The Journal of Urology Magnani, C. J., Li, K., Seto, T., McDonald, K. M., Blayney, D. W., Brooks, J. D., Hernandez-Boussard, T. 2018; 199 (4)
  • Utilization and effectiveness of multimodal discharge analgesia for postoperative pain management Journal of Surgical Research Desai, K., Carroll, I., Asch, S., Seto, T., McDonald, K. M., Curtin, C., Hernandez-Boussard, T. 2018; 228
  • Mining Electronic Health Records to Extract Patient-Centered Outcomes Following Prostate Cancer Treatment. AMIA ... Annual Symposium proceedings. AMIA Symposium Hernandez-Boussard, T., Kourdis, P. D., Seto, T., Ferrari, M., Blayney, D. W., Rubin, D., Brooks, J. D. 2017; 2017: 876–82

    Abstract

    The clinical, granular data in electronic health record (EHR) systems provide opportunities to improve patient care using informatics retrieval methods. However, it is well known that many methodological obstacles exist in accessing data within EHRs. In particular, clinical notes routinely stored in EHR are composed from narrative, highly unstructured and heterogeneous biomedical text. This inherent complexity hinders the ability to perform automated large-scale medical knowledge extraction tasks without the use of computational linguistics methods. The aim of this work was to develop and validate a Natural Language Processing (NLP) pipeline to detect important patient-centered outcomes (PCOs) as interpreted and documented by clinicians in their dictated notes for male patients receiving treatment for localized prostate cancer at an academic medical center.

    View details for PubMedID 29854154

  • A natural language processing algorithm to measure quality prostate cancer care Journal of Clinical Oncology Hernandez-Boussard, T., Kourdis, P., Dulal, R., Ferrari, M., Henry, S., Seto, T., McDonald, K., Blayney, D. W., Brooks, J. D. 2017; 35 (8_suppl): 232-232
  • Synergistic drug combinations from electronic health records and gene expression. Journal of the American Medical Informatics Association Low, Y. S., Daugherty, A. C., Schroeder, E. A., Chen, W., Seto, T., Weber, S., Lim, M., Hastie, T., Mathur, M., Desai, M., Farrington, C., Radin, A. A., Sirota, M., Kenkare, P., Thompson, C. A., Yu, P. P., Gomez, S. L., Sledge, G. W., Kurian, A. W., Shah, N. H. 2016

    Abstract

    Using electronic health records (EHRs) and biomolecular data, we sought to discover drug pairs with synergistic repurposing potential. EHRs provide real-world treatment and outcome patterns, while complementary biomolecular data, including disease-specific gene expression and drug-protein interactions, provide mechanistic understanding.We applied Group Lasso INTERaction NETwork (glinternet), an overlap group lasso penalty on a logistic regression model, with pairwise interactions to identify variables and interacting drug pairs associated with reduced 5-year mortality using EHRs of 9945 breast cancer patients. We identified differentially expressed genes from 14 case-control human breast cancer gene expression datasets and integrated them with drug-protein networks. Drugs in the network were scored according to their association with breast cancer individually or in pairs. Lastly, we determined whether synergistic drug pairs found in the EHRs were enriched among synergistic drug pairs from gene-expression data using a method similar to gene set enrichment analysis.From EHRs, we discovered 3 drug-class pairs associated with lower mortality: anti-inflammatories and hormone antagonists, anti-inflammatories and lipid modifiers, and lipid modifiers and obstructive airway drugs. The first 2 pairs were also enriched among pairs discovered using gene expression data and are supported by molecular interactions in drug-protein networks and preclinical and epidemiologic evidence.This is a proof-of-concept study demonstrating that a combination of complementary data sources, such as EHRs and gene expression, can corroborate discoveries and provide mechanistic insight into drug synergism for repurposing.

    View details for DOI 10.1093/jamia/ocw161

    View details for PubMedID 27940607

  • Use of Gene Expression Profiling and Chemotherapy in Early-Stage Breast Cancer: A Study of Linked Electronic Medical Records, Cancer Registry Data, and Genomic Data Across Two Health Care Systems. Journal of oncology practice / American Society of Clinical Oncology Afghahi, A., Mathur, M., Thompson, C. A., Mitani, A., Rigdon, J., Desai, M., Yu, P. P., de Bruin, M. A., Seto, T., Olson, C., Kenkare, P., Gomez, S. L., Das, A. K., Luft, H. S., Sledge, G. W., Sing, A. P., Kurian, A. W. 2016; 12 (6): e697-709

    Abstract

    The 21-gene recurrence score (RS) identifies patients with breast cancer who derive little benefit from chemotherapy; it may reduce unwarranted variability in the use of chemotherapy. We tested whether the use of RS seems to guide chemotherapy receipt across different cancer care settings.We developed a retrospective cohort of patients with breast cancer by using electronic medical record data from Stanford University (hereafter University) and Palo Alto Medical Foundation (hereafter Community) linked with demographic and staging data from the California Cancer Registry and RS results from the testing laboratory (Genomic Health Inc., Redwood City, CA). Multivariable analysis was performed to identify predictors of RS and chemotherapy use.In all, 10,125 patients with breast cancer were diagnosed in the University or Community systems from 2005 to 2011; 2,418 (23.9%) met RS guidelines criteria, of whom 15.6% received RS. RS was less often used for patients with involved lymph nodes, higher tumor grade, and age < 40 or ≥ 65 years. Among RS recipients, chemotherapy receipt was associated with a higher score (intermediate v low: odds ratio, 3.66; 95% CI, 1.94 to 6.91). A total of 293 patients (10.6%) received care in both health care systems (hereafter dual use); although receipt of RS was associated with dual use (v University: odds ratio, 1.73; 95% CI, 1.18 to 2.55), there was no difference in use of chemotherapy after RS by health care setting.Although there was greater use of RS for patients who sought care in more than one health care setting, use of chemotherapy followed RS guidance in University and Community health care systems. These results suggest that precision medicine may help optimize cancer treatment across health care settings.

    View details for DOI 10.1200/JOP.2015.009803

    View details for PubMedID 27221993

    View details for PubMedCentralID PMC4957259

  • Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer BREAST CANCER RESEARCH Afghahi, A., Forgo, E., Mitani, A. A., Desai, M., Varma, S., Seto, T., Rigdon, J., Jensen, K. C., Troxell, M. L., Gomez, S. L., Das, A. K., Beck, A. H., Kurian, A. W., West, R. B. 2015; 17

    View details for DOI 10.1186/s13058-015-0623-y

    View details for Web of Science ID 000359348400001

    View details for PubMedID 26265211

  • Breast Cancer Treatment Across Health Care Systems CANCER Kurian, A. W., Mitani, A., Desai, M., Yu, P. P., Seto, T., Weber, S. C., Olson, C., Kenkare, P., Gomez, S. L., de Bruin, M. A., Horst, K., Belkora, J., May, S. G., Frosch, D. L., Blayney, D. W., Luft, H. S., Das, A. K. 2014; 120 (1): 103-111

    View details for DOI 10.1002/cncr.28395

    View details for Web of Science ID 000328443000017

  • Oncoshare: lessons learned from building an integrated multi-institutional database for comparative effectiveness research. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium Weber, S. C., Seto, T., Olson, C., Kenkare, P., Kurian, A. W., Das, A. K. 2012; 2012: 970-978

    Abstract

    Comparative effectiveness research (CER) using observational data requires informatics methods for the extraction, standardization, sharing, and integration of data derived from a variety of electronic sources. In the Oncoshare project, we have developed such methods as part of a collaborative multi-institutional CER study of patterns, predictors, and outcome of breast cancer care. In this paper, we present an evaluation of the approaches we undertook and the lessons we learned in building and validating the Oncoshare data resource. Specifically, we determined that 1) the state or regional cancer registry makes the most efficient starting point for determining inclusion of subjects; 2) the data dictionary should be based on existing registry standards, such as Surveillance, Epidemiology and End Results (SEER), when applicable; 3) the Social Security Administration Death Master File (SSA DMF), rather than clinical resources, provides standardized ascertainment of mortality outcomes; and 4) CER database development efforts, despite the immediate availability of electronic data, may take as long as two years to produce validated, reliable data for research. Through our efforts using these methods, Oncoshare integrates complex, longitudinal data from multiple electronic medical records and registries and provides a rich, validated resource for research on oncology care.

    View details for PubMedID 23304372