It is common and advised practice in biomedical research to validate experimental or observational findings in a population different from the one where the findings were initially assessed. This practice increases the generalizability of the results and decreases the likelihood of reporting false-positive findings. Validation becomes critical when dealing with high-throughput experiments, where the large number of tests increases the chance to observe false-positive results. In this article, we review common approaches to determine statistical thresholds for validation and describe the factors influencing the proportion of significant findings from a 'training' sample that are replicated in a 'validation' sample. We refer to this proportion as rediscovery rate (RDR). In high-throughput studies, the RDR is a function of false-positive rate and power in both the training and validation samples. We illustrate the application of the RDR using simulated data and real data examples from metabolomics experiments. We further describe an online tool to calculate the RDR using t-statistics. We foresee two main applications. First, if the validation study has not yet been collected, the RDR can be used to decide the optimal combination between the proportion of findings taken to validation and the size of the validation study. Secondly, if a validation study has already been done, the RDR estimated using the training data can be compared with the observed RDR from the validation data; hence, the success of the validation study can be assessed.

Supplementary data are available at Bioinformatics online.

Molecular classification of breast cancer into clinically relevant subtypes helps improve prognosis and adjuvant-treatment decisions. The aim of this study is to provide a better characterization of the molecular subtypes by providing a comprehensive landscape of subtype-specific isoforms including coding, long non-coding RNA and microRNA transcripts. Isoform-level expression of all coding and non-coding RNAs is estimated from RNA-sequence data of 1168 breast samples obtained from The Cancer Genome Atlas (TCGA) project. We then search the whole transcriptome systematically for subtype-specific isoforms using a novel algorithm based on a robust quasi-Poisson model. We discover 5451 isoforms specific to single subtypes. A total of 27% of the subtype-specific isoforms have better accuracy in classifying the intrinsic subtypes than that of their corresponding genes. We find three subtype-specific miRNA and 707 subtype-specific long non-coding RNAs. The isoforms from long non-coding RNAs also show high performance for separation between Luminal A and Luminal B subtypes with an AUC of 0.97 in the discovery set and 0.90 in the validation set. In addition, we discover 1500 isoforms preferentially co-expressed in two subtypes, including 369 isoforms co-expressed in both Normal-like and Basal subtypes, which are commonly considered to have distinct ER-receptor status. Finally, analyses at protein level reveal four subtype-specific proteins and two subtype co-expression proteins that successfully validate results from the isoform level.

This study aimed to analyze medication adherence and persistence among open-angle glaucoma patients in Korea. A retrospective study was conducted using the Korean National Health Insurance (NHI) claims database from 2016 to 2019. Newly diagnosed open-angle glaucoma patients who were prescribed with the intraocular pressure (IOP)-lowering eyedrops were included. Adherence was measured using the medication possession ratio (MPR), and persistence was measured using the duration of therapy during the 24 month follow-up period. During the study period, 14,648 open-angle glaucoma patients were identified, and 3118 (21.3%) and 4481 patients (30.6%) were adherent to and persistent with their glaucoma treatment, respectively. The mean MPR was 48.8%, and the mean duration of therapy was 357.2 days. Logistic regression analysis showed that patients who are older, female, using prostaglandins as the index medication, and visiting secondary or tertiary hospitals were significantly associated with greater rates of adherence (odds ratio (OR) = 1.21, 1.12, 1.27, and 1.73, respectively) and persistence (OR = 1.11, 1.17, 1.16, 1.17, and 1.36, respectively) during the study period. Patients with open-angle glaucoma in Korea had substandard medication adherence and discontinued their treatment. Ophthalmologists should pay more attention to younger, male patients to improve adherence.