Biostatistics and Health Data Science Works

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Works authored by scholars from the Department of Biostatistics and Health Data Science, a dual department of the Richard M. Fairbanks School of Public Health and the IU School of Medicine.

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A Bayesian phase I/II biomarker-based design for identifying subgroup-specific optimal dose for immunotherapy
(Sage, 2022) Guo, Beibei; Zang, Yong; Biostatistics and Health Data Science, School of Medicine
Immunotherapy is an innovative treatment that enlists the patient’s immune system to battle tumors. The optimal dose for treating patients with an immunotherapeutic agent may differ according to their biomarker status. In this article, we propose a biomarker-based phase I/II dose-finding design for identifying subgroup-specific optimal dose for immunotherapy (BSOI) that jointly models the immune response, toxicity, and efficacy outcomes. We propose parsimonious yet flexible models to borrow information across different types of outcomes and subgroups. We quantify the desirability of the dose using a utility function and adopt a two-stage dose-finding algorithm to find the optimal dose for each subgroup. Simulation studies show that the BSOI design has desirable operating characteristics in selecting the subgroup-specific optimal doses and allocating patients to those optimal doses, and outperforms conventional designs.
A Bayesian Phase I/II Design to Determine Subgroup-Specific Optimal Dose for Immunotherapy Sequentially Combined with Radiotherapy
(Wiley, 2023) Guo, Beibei; Zang, Yong; Lin, Li-Hsiang; Zhang, Rui; Biostatistics and Health Data Science, Richard M. Fairbanks School of Public Health
Sequential administration of immunotherapy following radiotherapy (immunoRT) has attracted much attention in cancer research. Due to its unique feature that radiotherapy upregulates the expression of a predictive biomarker for immunotherapy, novel clinical trial designs are needed for immunoRT to identify patient subgroups and the optimal dose for each subgroup. In this article, we propose a Bayesian phase I/II design for immunotherapy administered after standard-dose radiotherapy for this purpose. We construct a latent subgroup membership variable and model it as a function of the baseline and pre-post radiotherapy change in the predictive biomarker measurements. Conditional on the latent subgroup membership of each patient, we jointly model the continuous immune response and the binary efficacy outcome using plateau models, and model toxicity using the equivalent toxicity score approach to account for toxicity grades. During the trial, based on accumulating data, we continuously update model estimates and adaptively randomize patients to admissible doses. Simulation studies and an illustrative trial application show that our design has good operating characteristics in terms of identifying both patient subgroups and the optimal dose for each subgroup.
A Contextual Approach to the Psychological Study of Identity Concealment: Examining Direct, Interactive, and Indirect Effects of Structural Stigma on Concealment Motivation Across Proximal and Distal Geographic Levels
(Sage, 2021) Lattanner, Micah R.; Ford, Jessie; Bo, Na; Tu, Wanzhu; Pachankis, John E.; Dodge, Brian; Hatzenbuehler, Mark L.; Biostatistics, School of Public Health
Psychological theories of identity concealment locate the ultimate source of concealment decisions within the social environment, yet most studies have not explicitly assessed stigmatizing environments beyond the immediate situation. We advanced the identity-concealment literature by objectively measuring structural forms of stigma related to sexual orientation (e.g., social policies) at proximal and distal geographic levels. We linked these measures to a new, population-based data set of 502 gay and bisexual men (residing in 44 states and Washington, DC; 269 counties; and 354 cities) who completed survey items about stigma, including identity-concealment motivation. Among gay men, the association between structural stigma and concealment motivation was (a) observed across three levels (city, county, and state), (b) conditional on one's exposure at another geographic level (participants reported the least motivations to conceal their identity if they resided in both cities and states that were lowest in structural stigma), and (c) mediated by subjective perceptions of greater structural stigma.
A Deep Language Model for Symptom Extraction From Clinical Text and its Application to Extract COVID-19 Symptoms From Social Media
(IEEE, 2022) Luo, Xiao; Gandhi, Priyanka; Storey, Susan; Huang, Kun; Biostatistics and Health Data Science, School of Medicine
Patients experience various symptoms when they have either acute or chronic diseases or undergo some treatments for diseases. Symptoms are often indicators of the severity of the disease and the need for hospitalization. Symptoms are often described in free text written as clinical notes in the Electronic Health Records (EHR) and are not integrated with other clinical factors for disease prediction and healthcare outcome management. In this research, we propose a novel deep language model to extract patient-reported symptoms from clinical text. The deep language model integrates syntactic and semantic analysis for symptom extraction and identifies the actual symptoms reported by patients and conditional or negation symptoms. The deep language model can extract both complex and straightforward symptom expressions. We used a real-world clinical notes dataset to evaluate our model and demonstrated that our model achieves superior performance compared to three other state-of-the-art symptom extraction models. We extensively analyzed our model to illustrate its effectiveness by examining each component’s contribution to the model. Finally, we applied our model on a COVID-19 tweets data set to extract COVID-19 symptoms. The results show that our model can identify all the symptoms suggested by CDC ahead of their timeline and many rare symptoms.
A descriptive study of the multidisciplinary healthcare experiences of inpatient resuscitation events
(Elsevier, 2023-01-06) Varner-Perez, Shelley E.; Shelley E., Kelly A. L.; Banks, Sarah K.; Burke, Emily S.; Slaven, James E.; Morse, Gregory J.; Whitaker, Myra K.; Cottingham, Ann H.; Ahmed, Rami A.; Biostatistics, School of Public Health
Background: In-hospital resuscitation events have complex and enduring effects on clinicians, with implications for job satisfaction, performance, and burnout. Ethically ambiguous cases are associated with increased moral distress. We aim to quantitatively describe the multidisciplinary resuscitation experience. Methods: Multidisciplinary in-hospital healthcare professionals at an adult academic health center in the Midwestern United States completed surveys one and six weeks after a resuscitation event. Surveys included demographic data, task load (NASA-TLX), overall and moral distress, anxiety, depression, and spiritual peace. Spearman's rank correlation was computed to assess task load and distress. Results: During the 5-month study period, the study included 12 resuscitation events across six inpatient units. Of 82 in-hospital healthcare professionals eligible for recruitment, 44 (53.7%) completed the one-week post-resuscitation event survey. Of those, 37 (84.1%) completed the six-week survey. Highest median task load burden at one week was seen for temporal demand, effort, and mental demand. Median moral distress scores were low, while "at peace" median scores tended to be high. There were no significant non-zero changes in task load or distress scores from weeks 1-6. Mental demand (r = 0.545, p < 0.001), physical demand (r = 0.464, p = 0.005), performance (r = -0.539, p < 0.001), and frustration (r = 0.545, p < 0.001) significantly correlated with overall distress. Performance (r = -0.371, p = 0.028) and frustration (r = 0.480, p = 0.004) also significantly correlated with moral distress. Conclusions: In-hospital healthcare professionals' experiences of resuscitation events are varied and complex. Aspects of task load burden including mental and physical demand, performance, and frustration contribute to overall and moral distress, deserving greater attention in clinical contexts.
A distinct symptom pattern emerges for COVID-19 long-haul: a nationwide study
(Springer Nature, 2022-09-23) Pinto, Melissa D.; Downs, Charles A.; Huang, Yong; El‑Azab, Sarah A.; Ramrakhiani, Nathan S.; Barisano, Anthony; Yu, Lu; Taylor, Kaitlyn; Esperanca, Alvaro; Abrahim, Heather L.; Hughes, Thomas; Giraldo Herrera, Maria; Rahamani, Amir M.; Dutt, Nikil; Chakraborty, Rana; Mendiola, Christian; Lambert, Natalie; Biostatistics, School of Public Health
Long-haul COVID-19, also called post-acute sequelae of SARS-CoV-2 (PASC), is a new illness caused by SARS-CoV-2 infection and characterized by the persistence of symptoms. The purpose of this cross-sectional study was to identify a distinct and significant temporal pattern of PASC symptoms (symptom type and onset) among a nationwide sample of PASC survivors (n = 5652). The sample was randomly sorted into two independent samples for exploratory (EFA) and confirmatory factor analyses (CFA). Five factors emerged from the EFA: (1) cold and flu-like symptoms, (2) change in smell and/or taste, (3) dyspnea and chest pain, (4) cognitive and visual problems, and (5) cardiac symptoms. The CFA had excellent model fit (x2 = 513.721, df = 207, p < 0.01, TLI = 0.952, CFI = 0.964, RMSEA = 0.024). These findings demonstrate a novel symptom pattern for PASC. These findings can enable nurses in the identification of at-risk patients and facilitate early, systematic symptom management strategies for PASC.
A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies
(Springer Nature, 2022) Li, Zilin; Li, Xihao; Zhou, Hufeng; Gaynor, Sheila M.; Selvaraj, Margaret Sunitha; Arapoglou, Theodore; Quick, Corbin; Liu, Yaowu; Chen, Han; Sun, Ryan; Dey, Rounak; Arnett, Donna K.; Auer, Paul L.; Bielak, Lawrence F.; Bis, Joshua C.; Blackwell, Thomas W.; Blangero, John; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer A.; Cade, Brian E.; Conomos, Matthew P.; Correa, Adolfo; Cupples, L. Adrienne; Curran, Joanne E.; de Vries, Paul S.; Duggirala, Ravindranath; Franceschini, Nora; Freedman, Barry I.; Göring, Harald H. H.; Guo, Xiuqing; Kalyani, Rita R.; Kooperberg, Charles; Kral, Brian G.; Lange, Leslie A.; Lin, Bridget M.; Manichaikul, Ani; Manning, Alisa K.; Martin, Lisa W.; Mathias, Rasika A.; Meigs, James B.; Mitchell, Braxton D.; Montasser, May E.; Morrison, Alanna C.; Naseri, Take; O'Connell, Jeffrey R.; Palmer, Nicholette D.; Peyser, Patricia A.; Psaty, Bruce M.; Raffield, Laura M.; Redline, Susan; Reiner, Alexander P.; Reupena, Muagututi'a Sefuiva; Rice, Kenneth M.; Rich, Stephen S.; Smith, Jennifer A.; Taylor, Kent D.; Taub, Margaret A.; Vasan, Ramachandran S.; Weeks, Daniel E.; Wilson, James G.; Yanek, Lisa R.; Zhao, Wei; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Rotter, Jerome I.; Willer, Cristen J.; Natarajan, Pradeep; Peloso, Gina M.; Lin, Xihong; Biostatistics and Health Data Science, School of Medicine
Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 TOPMed samples. We also analyze five non-lipid TOPMed traits.
A Highly Ordered, Nanostructured Fluorinated CaP-Coated Melt Electrowritten Scaffold for Periodontal Tissue Regeneration
(Wiley, 2021) Daghrery, Arwa; Ferreira, Jessica A.; de Souza Araújo, Isaac J.; Clarkson, Brian H.; Eckert, George J.; Bhaduri, Sarit B.; Malda, Jos; Bottino, Marco C.; Biostatistics, School of Public Health
Periodontitis is a chronic inflammatory, bacteria-triggered disorder affecting nearly half of American adults. Although some level of tissue regeneration is realized, its low success in complex cases demands superior strategies to amplify regenerative capacity. Herein, highly ordered scaffolds are engineered via Melt ElectroWriting (MEW), and the effects of strand spacing, as well as the presence of a nanostructured fluorinated calcium phosphate (F/CaP) coating on the adhesion/proliferation, and osteogenic differentiation of human-derived periodontal ligament stem cells, are investigated. Upon initial cell-scaffold interaction screening aimed at defining the most suitable design, MEW poly(𝝐-caprolactone) scaffolds with 500 µm strand spacing are chosen. Following an alkali treatment, scaffolds are immersed in a pre-established solution to allow for coating formation. The presence of a nanostructured F/CaP coating leads to a marked upregulation of osteogenic genes and attenuated bacterial growth. In vivo findings confirm that the F/CaP-coated scaffolds are biocompatible and lead to periodontal regeneration when implanted in a rat mandibular periodontal fenestration defect model. In aggregate, it is considered that this work can contribute to the development of personalized scaffolds capable of enabling tissue-specific differentiation of progenitor cells, and thus guide simultaneous and coordinated regeneration of soft and hard periodontal tissues, while providing antimicrobial protection.
A Multi-Center, Single Arm, Phase Ib study of Pembrolizumab (MK-3475) in Combination with Chemotherapy for Patients with Advanced Colorectal Cancer: HCRN GI14-186
(Springer, 2021) Herting, Cameron J.; Farren, Matthew R.; Tong, Yan; Liu, Ziyue; O’Neil, Bert; Bekaii-Saab, Tanios; Noonan, Anne; McQuinn, Christopher; Mace, Thomas A.; Shaib, Walid; Wu, Christina; El-Rayes, Bassel F.; Shahda, Safi; Lesinski, Gregory B.; Biostatistics and Health Data Science, Richard M. Fairbanks School of Public Health
Modified FOLFOX6 is an established therapy for patients with metastatic colorectal cancer (mCRC). We conducted a single-arm phase Ib study to address the hypothesis that addition of pembrolizumab to this regimen could safely and effectively improve patient outcomes (NCT02375672). The relationship between immune biomarkers and clinical response were assessed in an exploratory manner. Patients with mCRC received concurrent pembrolizumab and modified FOLFOX6. The study included safety run-in for the first six patients. The primary objective was median progression-free survival (mPFS), with secondary objectives including median overall survival, safety, and exploratory assessment of immune changes. To assess immunological impact, peripheral blood was collected at baseline and during treatment. The levels of soluble factors were measured via bioplex, while a panel of checkpoint molecules and phenotypically defined cell populations were assessed with flow cytometry and correlated with RECIST and mPFS. Due to incidences of grade 3 and grade 4 neutropenia in the safety lead-in, the dose of mFOLFOX6 was reduced in the expansion cohort. Median PFS was 8.8 months and median OS was not reached at data cutoff. Best responses of stable disease, partial response, and complete response were observed in 43.3%, 50.0%, and 6.7% of patients, respectively. Several soluble and cellular immune biomarkers were associated with improved RECIST and mPFS. Immunosuppressive myeloid and T cell subsets that were analyzed were not associated with response. Primary endpoint was not superior to historic control. Biomarkers that were associated with improved response may be informative for future regimens combining chemotherapy with immune checkpoint inhibitors.
A multistate transition model for statin‐induced myopathy and statin discontinuation
(Wiley, 2021) Zhu, Yuxi; Chiang, Chien-Wei; Wang, Lei; Brock, Guy; Milks, M. Wesley; Cao, Weidan; Zhang, Pengyue; Zeng, Donglin; Donneyong, Macarius; Li, Lang; Biostatistics and Health Data Science, Richard M. Fairbanks School of Public Health
The overarching goal of this study was to simultaneously model the dynamic relationships among statin exposure, statin discontinuation, and potentially statin-related myopathic outcomes. We extracted data from the Indiana Network of Patient Care for 134,815 patients who received statin therapy between January 4, 2004, and December 31, 2008. All individuals began statin treatment, some discontinued statin use, and some experienced myopathy and/or rhabdomyolysis while taking the drug or after discontinuation. We developed a militate model to characterize 12 transition probabilities among six different states defined by use or discontinuation of statin and its associated myopathy or rhabdomyolysis. We found that discontinuation of statin therapy was common and frequently early, with 44.4% of patients discontinuing therapy after 1 month, and discontinuation is a strong indicator for statin-induced myopathy (risk ratio, 10.8; p < 0.05). Women more likely than men (p < 0.05) and patients aged 65 years and older had a higher risk than those aged younger than 65 years to discontinue statin use or experience myopathy. In conclusion, we introduce an innovative multistate model that allows clear depiction of the relationship between statin discontinuation and statin-induced myopathy. For the first time, we have successfully demonstrated and quantified the relative risk of myopathy between patients who continued and discontinued statin therapy. Age and sex were two strong risk factors for both statin discontinuation and incident myopathy.

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