Data Exploration In Biomedical Research

By means of this “dynamic” article, we would like to share with you the most interesting and/or promising approaches to the use of EDA techniques we come across with in our daily surveillance of the matter.

Since we started up with Butler Scientifics, the number of scientific publications and clinical trials underlying the increasingly relevant role of Exploratory Data Analysis (EDA) in their studies has grown substantially.

For us this trend is both encouraging and challenging. It is encouraging as it means scientists are becoming more comfortable at relying on exploratory analysis, while it is challenging for the rising number of dimensions and new approaches that come to light every day, opening paths that need to be taken care of.

Jul 2019, Sports, Cannabis Use, PEACE Survey, Clustering, Exploratory Factor Analysis

"The Athlete PEACE Survey examined cannabis use patterns and subjective effects to cannabis in a community-based cohort of adult athletes. Cluster analysis was used to determine cannabis user phenotypes and exploratory factor analysis (EFA) was used to create subjective effects factors. Associations between cannabis user phenotype clusters and the subjective effects factors were explored using multivariate analysis. "

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Jun 2019, Mendelian Diseases, Variant Combinations, ORVAL Study, Integrative Machine Learning

"This online platform integrates innovative machine learning methods for combinatorial variant pathogenicity prediction with visualization techniques, offering several interactive and exploratory tools, such as pathogenic gene and protein interaction networks, a ranking of pathogenic gene pairs, as well as visual mappings of the cellular location and pathway information."

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Jun 2018, Psychology, Sleep Quality, Questionnaires, Exploratory Factor Analysis

"The objective was to shorten the Pittsburgh Quality Sleep Index (PSQI) for young adults. Nonparametric correlation analysis (Spearman's rho) was conducted between the global sleep scores of the shortened and original surveys."

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(HIGH IMPACT) May 2018, Oncology, HER2-Negative Advanced Breast Cancer, Exploratory Biomarker Analysis

"Here we report updated efficacy and safety data, together with exploratory biomarker analyses, from the MONALEESA-2 study."

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(HIGH IMPACT) Apr 2018, Oncology, Colorectal Cancer, Electronic Medical Records

"We conducted an exploratory post-hoc analysis of RAISE trial and a retrospective, observational analysis of electronic medical record (EMR) data to determine and verify the association of neutropaenia, baseline absolute neutrophil count (ANC) and survival."

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Mar 2018, Cardiology, Hypertension, Correlational Analysis

"We explored the relationship of sample size, trial duration, baseline blood pressure, and number of treatment arms to placebo/drug response and efficacy outcome measures."

Open Access Article

Feb 2018, Neuroscience, Dementia, Edinburgh Feeding Evaluation (EdFED), Exploratory Factor Analysis

"A version of EdFED culturally adapted to Spanish was obtained. An additional three-factor structure was tested using an exploratory factorial analysis performed with a subsample that was later verified by confirmatory factor analysis in the remaining sample."

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Jan 2018, Hematology, Genetics, Activation-induced deaminase (AID), Machine Learning

"Integrative analysis of the molecular features of mutated genes coupled to machine learning has produced a powerful predictive tool for AID targets."

Open Access Article

Dec 2017, Hematology, Mantle Cell Lymphoma, Subgroup Analysis

"Here we present the long-term follow-up data and results of preplanned subgroup exploratory analyses to evaluate the potential impact of demographic factors, baseline clinical characteristics and prior therapies on PFS."

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Nov 2017, Chronic Pain, Adverse Events, Data Mining

"We used the US FDA's Adverse Events Reporting System (FAERS) database to conduct exploratory analysis on the demographics of those who reported painkiller-related AEs, examine the AEs most commonly associated with different types of painkillers, and identify potential safety signals."

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Oct 2017, Neuroscience, Huntington's Disease, Linear Regression

"This exploratory study aimed to evaluate, for the first time, whether multidisciplinary rehabilitation can slow further deterioration of disease-related brain changes and related cognitive deficits in individuals with manifest Huntington's Disease."

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Sept 2017, Oncology, Glioblastoma, Clinical Trial, Exploratory Efficacy

"The exploratory objective of this study was to evaluate expression of factors associated with tumor angiogenesis using a multiples cytokine assay among participants undergoing therapy with AMG 386 with response to therapy and development of resistance."

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(HIGH IMPACT) Jul 2017, Neurology, Acute Stroke, Efficacy Analysis

"Our aim was to test for a treatment-by-ipsilateral atherosclerotic stenosis interaction in a subgroup analysis of patients in the Acute Stroke or Transient Ischaemic Attack Treated with Aspirin or Ticagrelor and Patient Outcomes (SOCRATES) trial."

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(HIGH IMPACT) Jun 2017, Oncology, AKT1 Mutations, Predictive Biomarkers, Survival Analysis

"In an exploratory biomarker analysis, imbalance of the AKT1 E17K-mutant allele ... was associated with longer progression-free survival as was the presence of coincident PI3K pathway hotspot mutations.

This study provides the first clinical data that AKT1 E17K is a therapeutic target in human cancer."

Read More / Related Poster (2015)

(HIGH IMPACT) May 2017, Oncology, Non-Small-Cell Lung Cancer, Phase II Trial

"This article reports the results from the phase II of AURA project, a study that treats patients with advanced NSCLC who have already received at least one course of specific anti-cancer treatment but the tumour has started to re-grow following that treatment.

Patient-reported outcomes comprised an exploratory objective..."

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(HIGH IMPACT) May 2017, Cardiology, Migraine, Ischemic Stroke, Multivariable Logistic Regression

"The objective of this study is to evaluate whether patients with migraine are at increased risk of perioperative ischemic stroke and whether this may lead to an increased hospital readmission rate.

Exploratory outcomes included post-discharge stroke and strata of neuroanatomical stroke location."

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(HIGH IMPACT) May 2017, Oncology, Epidermal Growth Factor Receptor, Cox Regression

"We performed an individual patient data meta-analysis to examine the impact of first-generation epidermal growth factor receptor (EGFR tyrosine kinase inhibitor (TKI) therapy on overall survival (OS) in advanced non-small cell lung cancer (NSCLC)."

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Apr 2017, Burns, Scarring, POSAS, Exploratory-Confirmatory Design

"Exploratory Factor Analysis was used initially to identify the number of factors within the tool, then Confirmatory Factor Analysis using structural equation modelling explored areas of misfit within each factor and whether the model provided a predictable structure to capture patient perception of scar severity."

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(HIGH IMPACT) Mar 2017, Chemistry, Materials Genome Initiative, Machine Learning, Integrated Analysis

"We used information on 'dark' reactions collected from archived laboratory notebooks from our laboratory, and added physicochemical property descriptions using cheminformatics techniques.

We used the resulting data to train a machine-learning model to predict reaction success."

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(HIGH IMPACT) Feb 2017, Oncology, Palliative Care, PCA, Exploratory Factor Analysis

"This is the largest quantitative study ever done looking at perceptions of palliative care provision among health professionals.