BrainSEQ™ Consortium

Last updated on Tue, May 9, 2023
BrainSEQ at LIBD eQTL browser
Image credit: LIBD

The Lieber Institute and pharmaceutical companies AstraZeneca, Astellas, Eli Lilly and Company, Lundbeck, Johnson & Johnson, Pfizer Inc. and Roche are participating in an early-stage research consortium BrainSEQ™, with the goal of expanding knowledge around the genetic contribution to brain disorders in the hope of identifying potential new treatment options.

  • Utilizing LIBD’s unprecedented brain tissue repository to generate and analyze genomic data related to neuropsychiatric disorders.
  • Making data freely available to scientists worldwide.

As part of the BrainSEQ Consortium, Leonardo analyzed datasets from Phase I and II, either for the publications describing those phases or for re-analyses of the same data. As a team, we then adapted this code base for the BipSeq and MDDSeq projects, among other ones.

BrainSeq bulk
Leonardo Collado-Torres
Leonardo Collado-Torres
Investigator @ LIBD, Assistant Professor, Department of Biostatistics @ JHBSPH

#rstats @Bioconductor/🧠 genomics @LieberInstitute/@lcgunam @jhubiostat @jtleek @andrewejaffe alumni/@LIBDrstats @CDSBMexico co-founder

Publications

Genetic and environmental contributions to ancestry differences in gene expression in the human brain
Ancestral differences in genomic variation are determining factors in gene regulation; however, most gene expression studies have been …
Cite Project DOI Preprint Code
Genetic and environmental contributions to ancestry differences in gene expression in the human brain
Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes
Most studies of gene expression in the brains of individuals with schizophrenia have focused on cortical regions, but subcortical …
Preprint PDF Cite Project DOI
Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes
Transcriptional and genetic sex differences for schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus
Schizophrenia is a complex neuropsychiatric disorder with sexually dimorphic features, including differential symptomatology, drug …
Cite Project DOI Preprint Code
Transcriptional and genetic sex differences for schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus
Comment on: What genes are differentially expressed in individuals with schizophrenia? A systematic review
Following the recent review by Merikangas et al. summarizing differential gene expression in schizophrenia, we wanted to provide …
Cite Project DOI
Comment on: What genes are differentially expressed in individuals with schizophrenia? A systematic review
Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways
Recent genetic studies have identified variants associated with bipolar disorder (BD), but it remains unclear how brain gene expression …
Cite Project DOI URL Code
Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/Bioconductor-powered RNA-seq analyses
Background. RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with …
Preprint PDF Cite Code Dataset Project Slides DOI
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/Bioconductor-powered RNA-seq analyses
Developmental Profile of Psychiatric Risk Associated With Voltage-Gated Cation Channel Activity
Background. Recent breakthroughs in psychiatric genetics have implicated biological pathways onto which genetic risk for psychiatric …
PDF Cite Project DOI
Developmental Profile of Psychiatric Risk Associated With Voltage-Gated Cation Channel Activity
SynGAP isoforms differentially regulate synaptic plasticity and dendritic development
SynGAP is a synaptic Ras GTPase-activating protein (GAP) with four C-terminal splice variants: α1, α2, β, and γ. Although studies have …
Preprint PDF Cite Project DOI
SynGAP isoforms differentially regulate synaptic plasticity and dendritic development
Profiling gene expression in the human dentate gyrus granule cell layer reveals insights into schizophrenia and its genetic risk
Jaffe et al. profile the granule cell layer of the human hippocampus and find unique molecular associations for aging and genetic variation, as well as diagnosis with schizophrenia and its genetic risk, that were previously undiscovered in homogenate tissue.
PDF Cite Project DOI
Profiling gene expression in the human dentate gyrus granule cell layer reveals insights into schizophrenia and its genetic risk
Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia
The hippocampus formation, although prominently implicated in schizophrenia pathogenesis, has been overlooked in large-scale genomics …
Preprint PDF Cite Code Dataset Project DOI
Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia
Poster presented at ASHG2018, biodata18 and PSB2019
PDF Project
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia
Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome
This paper is on smoking and its relation to gene expression at different life stages. These genes are also related to autism spectrum disorder.
Preprint PDF Cite Code Project DOI Read for free
Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis
Genome-wide association studies have identified 108 schizophrenia risk loci, but biological mechanisms for individual loci are largely …
Preprint PDF Cite Project Project DOI
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis
BrainSeq Phase II: schizophrenia-associated expression differences between the hippocampus and the dorsolateral prefrontal cortex
Poster presented at SAGES2018
PDF Project
BrainSeq Phase II: schizophrenia-associated expression differences between the hippocampus and the dorsolateral prefrontal cortex