Published October 7, 2020
| Version 1.001
Dataset
Open
Expression-based polygenic score from the amygdala 5HTT gene network
Authors/Creators
- Merscher Sobreira de Lima, Randriely1
- Barth, Barbara2
- Mar Arcego, Danusa3
- José de Mendonça Filho, Euclides3
- Clappison, Andrew4
- Patel, Sachin4
- Wang, Zihan4
- Pokhvisneva, Irina4
- Britto Sassi, Roberto5
- B. C. Hall, Geoffrey6
- Kobor, Michael S.7
- Santana de Vasconcellos Bittencourt, Ana Paula8
- J. O'Donnell, Kieran3
- Meaney, Michael J.9
- Dalmaz, Carla1
- Pelufo Silveira, Patrícia3
- 1. Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- 2. Integrated Program in Neuroscience (IPN), McGill University, Montreal, QC, Canada
- 3. Department of Psychiatry, Faculty of Medicine, McGill University, Montreal, QC, Canada
- 4. Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, McGill University, Montreal, QC, Canada
- 5. Mood Disorders Program, Department of Psychiatry & Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
- 6. Department of Psychology, Neuroscience & Behaviour, McMaster University, Hamilton, ON, Canada
- 7. Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
- 8. Departamento de Ciências Fisiológicas, Universidade Federal do Espírito Santo, Vitoria, Brazil
- 9. Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
Description
This pipeline intends to facilitate the calculation of biologically informed polygenic scores from collected genomic data. This template can be adapted to create other expression-based polygenic risk scores. Data is 1) step by step description and 2) a list of genes that compose the gene network.
Files
5-HTT-ePRS.csv
Additional details
Related works
- Is supplement to
- Journal article: 10.3389/fnins.2020.00198 (DOI)
References
- de Lima RMS, Barth B, Arcego DM, et al. Amygdala 5-HTT Gene Network Moderates the Effects of Postnatal Adversity on Attention Problems: Anatomo-Functional Correlation and Epigenetic Changes. Front Neurosci-Switz. 2020;14(198).
- Silveira PP, Pokhvisneva I, Parent C, et al. Cumulative prenatal exposure to adversity reveals associations with a broad range of neurodevelopmental outcomes that are moderated by a novel, biologically informed polygenetic score based on the serotonin transporter solute carrier family C6, member 4 (SLC6A4) gene expression. Dev Psychopathol. 2017;29(5):1601-1617.
- Miguel PM, Deniz BF, Deckmann I, et al. Prefrontal cortex dysfunction in hypoxic-ischaemic encephalopathy contributes to executive function impairments in rats: Potential contribution for attention-deficit/hyperactivity disorder. The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry. 2017:1-14.
- Mulligan MK, Mozhui K, Prins P, Williams RW. GeneNetwork: a toolbox for systems genetics. In: Systems Genetics. Springer; 2017:75-120.
- Miller JA, Ding S-L, Sunkin SM, et al. Transcriptional landscape of the prenatal human brain. Nature. 2014;508(7495):199-206.
- Hari Dass SA, McCracken K, Pokhvisneva I, et al. A biologically-informed polygenic score identifies endophenotypes and clinical conditions associated with the insulin receptor function on specific brain regions. EBioMedicine. 2019;42:188-202.