The Hall Lab

CLARITE version 2 has been released. Full release notes are available in the documentation, but the main improvement is support for genotype data and simplification of the analysis functions to better support a variety of association and interaction tests.
Support for genotype data is possible though the use of Pandas-Genomics, another project of the Hall Lab.

The Hall Lab published a study in PLoS Genetics featuring the lab’s novel genetic encoding method: EDGE. Using EDGE, we identified a novel genetic interaction associated with age-related cataract that no other method identified. EDGE shows promise for identifying nonadditive genetic effects in biomedical data.

Hall, Molly A., et al. “Novel EDGE encoding method enhances ability to identify genetic interactions.” PLoS genetics 17.6 (2021): e1009534.

New publication from our collaboration with Dr. Jennie Noll (Human Development and Family Studies) on risk for obesity in women who have experienced sexual abuse:

Li J, Hall MA, Shalev I, Schreier H, González-Zarzar T, Marcovici I, Putnam F, Noll J. (2021) Hypothalamic-pituitary-adrenal axis dysregulation and risk for obesity in sexually abused females. Psychoneuroendocrinology: 129, 105254

Kristin Passero (Hall Lab PhD student) and Molly Hall organized the session “What about the environment? Leveraging multi-omic datasets to characterize the environment’s role in human health” for the Pacific Symposium on Biocomputing with environmental health research experts Dr. Chirag Patel (Harvard Medical School), Dr. Arjun Manrai (Harvard Medical School), Dr. Kimberly McAllister (National Institute of Environmental Health Sciences), and Dr. Shefali Setia Verma (University of Pennsylvania).

Kristin published an introduction to the session and gave an introductory talk as well. Hall Lab MD/PhD student, Morris Aguilar, also gave a talk on his metabolomics research.

The Hall Lab is presenting at the 2020 ASHG virtual conference. Please see the following posters:

• 2045 John McGuigan Automated machine learning for rare variant analysis of response to antiretroviral therapy in persons living with HIV.
• 2418 Morris Aguilar Secondary Metabolomic Analysis of Breast Cancer Nanoparticle Chemotherapy: Fatty Acid Metabolism Perturbation With Newly Quantified Metabolites and High Fidelity Classification Models
• 2715 Jiayan Zhou Interactions between genes and fatty acids for cardiac-related traits in LURIC cohort
• 3508 Nicole Palmiero Environment-wide association study of the phenome to evaluate complexity of the exposome
• 3539 Molly Hall Metabolomics reveals novel biomarkers in children who experienced maltreatment

Jiayan Zhou’s first first-author paper titled “Investigation of gene-gene interactions in cardiac traits and serum fatty acid levels in the LURIC Health Study” was published in PLoS one.

Morris Aguilar’s paper was accepted at the Pacific Symposium on Biocomputing (PSB), which will be presented January 2021, titled “Semi-automated NMR Pipeline for Environmental Exposures: New Insights on the Metabolomics of Smokers versus Non-smokers”