Data Science Core

National Institute On Deafness And Other Communication Disorders

Investigators

Abstract

The Data Science Core (DSC), led by Dr. Hui Cheng and Dr. Andrew S. Aston, provides bioinformatics and biostatistics support across the research lifecycle, including study design, data analysis; figure generation and visualization; drafting methods and results; and coordinating revisions and responses to peer review for submitted manuscripts. In the last year, the DSC has provided the following services: Bioinformatics • Conduct single-cell RNA-seq and long-read RNA-seq analyses. Biostatistics • Advise investigators on appropriate computational/statistical tools for hypothesis testing and valid inference. • Ensure alignment with target journals’ statistical reporting guidelines. • Provide analyses including power/sample-size estimation; survival/time-to-event methods; multivariable modeling; clustering and heat maps; association analyses; intraclass correlation (ICC); linear mixed-effects regression; and logistic regression. • Interpret and report results; prepare publication-ready figures/tables; assist with manuscripts; and respond to reviewers’ comments. Data Management & Sharing • Support intramural investigators in developing, submitting, and complying with NIH Data Management and Sharing (DMS) Plans. • Communicate requirements, provide guidance, and train relevant staff to ensure ongoing compliance. Training • Provide one-on-one consultations and hands-on instruction for research fellows (postdoctoral, MRSP, and postbaccalaureate) in the effective, reproducible use of statistical and bioinformatics methods. NIDCD Projects Audiology Unit (Chief Research Audiologist: Gayla L. Poling, Ph.D.; Emeritus: Carmen C. Brewer, Ph.D.): The DSC collaborated with Drs. Gayla Poling and Carmen Brewer, Jen Chisholm (Audiologist) and Dr. Angie Garinis (Oregon Health & Science University) on a study to investigate the effects of amikacin (an ototoxic aminoglycoside) treatment on patients’ hearing. The study used four metrics (MAFTS, MSFTS, ASHA shift and CTCAE) to characterize the presence of ototoxicity. We fitted and selected the appropriate models for these different scales, and identified the effect of amikacin administration, previous amikacin treatment, primary diagnosis, and worse ear 4, 6, 8kHz pure tone average on patients’ outcome. Section on Human Genetics (Inna Anatolievna Belyantseva, PhD, MD; PI: Thomas B Friedman, PhD): The DSC collaborated with Drs Inna Belyantseva and Tracy Fitzgerald on a study that identifies taperin as a protein crucial for hearing by bundling F-actin at the pivot points of hair cell stereocilia. We designed and executed the mixed-effects modeling framework for ABR/VsEP outcomes (genotype, age, genotype×age; subject random effects; frequency for ABR) with Tukey-adjusted post-hoc contrasts. The model substantiated that TPRN deficiency causes progressive, high-frequency-first hearing loss while largely sparing vestibular function in this dataset. Audiology Unit (Chief Research Audiologist: Gayla L. Poling): The DSC collaborated with Julie Christensen, Drs. Gayla Poling and Joan Marini on a longitudinal audiometric study on the osteogenesis imperfecta patients to investigate the relationship between hearing loss and the COL1A1 or COL1A2 genotype. The mixed-effects model analysis found that COL1A1 variants were associated with progressive loss, while gradual hearing threshold recovery has been observed in COL1A2 variants. Auditory Development and Restoration Program (PI: Michael Hoa, M.D.): The DSC collaborated with Dr. Mike Hoa and Julia Telischi (Pre-doctoral IRTA fellow) on a longitudinal study evaluating the variability in cervical and ocular Vestibular Evoked Myogenic Potentials (cVEMP and oVEMP) testing over time in patients with Hearing Instability (HI) disorders to determine if variability in vestibular test results correlates to clinical presentation and disease status, and may offer additional objective information for clinicians when monitoring patient status and response to therapy. Projects with other NIH insitutes Center for Cancer Research, National Cancer Institute (PI: Vassiliki Saloura, M.D. Ph. D.): The DSC collaborated with Dr. Meiye Jiang and Dr. Valia Saloura on a project that led to a manuscript “Genomic profiling of chromatin factors in squamous cell carcinoma of the head and neck”. The study utilized the molecular profiles from 530 HNSCC tumor samples in the Cancer Genome Atlas, and characterized the mutationl, copy number and transcriptional alterations of 422 chromatin factors as well as their correlation with the “cold” tumor phenotype in HPV-negative and HPV-positive HNSCCs.