Human endogenous retroviruses linked to neurodegenerative disorders

Content: This repository contains code used for the manuscript Duarte et al., 2024 (Duarte R.R.R., Nixon D.F., Powell T.R. Ancient viral DNA in the human genome linked to neurodegenerative diseases. Brain, Behavior, and Immunity, 2024, https://doi.org/10.1016/j.bbi.2024.10.020).

Related content:
- How to perform a retrotranscriptome-wide association study (rTWAS): https://rodrigoduarte88.github.io/neuro_rTWAS/. Reference: Duarte, R.R.R., Pain, O., Bendall, M.L. et al. Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions. Nat Commun 15, 3803 (2024). https://doi.org/10.1038/s41467-024-48153-z. 

- 1000 Genomes Project: https://www.internationalgenome.org/
Reference: The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015). https://doi.org/10.1038/nature15393.
- FUSION software: https://github.com/gusevlab/fusion_twas
Reference: Gusev, A., Ko, A., Shi, H. et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet 48, 245–252 (2016). https://doi.org/10.1038/ng.3506.
- FOCUS software: https://github.com/bogdanlab/focus
Reference: Mancuso, N., Freund, M.K., Johnson, R. et al. Probabilistic fine-mapping of transcriptome-wide association studies. Nat Genet 51, 675–682 (2019). https://doi.org/10.1038/s41588-019-0367-1.

Acknowledgements: Research reported in this publication was supported by the National Institutes of Health (NIH) under award number R21 HG011513 to T.R.P., D.F.N. and R.R.R.D., and a Psychiatry Research Trust grant to T.R.P. and R.R.R.D. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. T.R.P. is supported by an MRC (UKRI) New Investigator Research Grant (MR/W028018/1). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. This research is also part-funded by the National Institute for Health and Care Research (NIHR) Maudsley Biomedical Research Centre at South London and Maudsley National Health Service (NHS) Foundation Trust and King’s College London. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care.