Genetic Neuroscience: How Human Genes and Alleles Shape Neuronal Phenotypes

The goal of this collaborative, interdisciplinary project is to develop powerful, generalizable approaches for discovering how risk variants for psychiatric disorders shape neurobiological processes at multiple levels of analysis, and to identify the processes whose dysregulation underlies disease.

Induced pluripotent stem cells (iPSCs) were used towards the development of these new experimental and inferential systems bridging gaps between human genetics and experimental biology. The largest publicly available collection of iPSCs (2607 lines) has been generated from 2184 donors by the California Institute for Regenerative Medicine (CIRM). To expand our donor collection, an additional 44 iPSC donors from the McLean_Levy cohort were identified. We wish to share the available SNP data for 2167 CIRM lines and whole genome sequence data generated at the Broad Institute for 473 of the CIRM and 44 McLean_Levy iPSC donors. These data can be used to identify (for experiments) lines with specific genotypes of interest and lines from donors with high or low polygenic risk scores for phenotypes of interest. The data can also be used to identify acquired mutations in the iPSC lines. The CIRM iPSC lines are available through Fujifilm Cellular Dynamics iPSC Repository (https://www.fujifilmcdi.com/cirm-ipsc-products/). The McLean_Levy lines are available through the NIMH Repository & Genomics Resource (https://www.nimhgenetics.org/).

Additional project data registered with the study includes data from an iPSC line derived from an SMA patient (n=1), as well as single-cell RNA sequence data and supplemental processed genomic datasets in support of project publications.

Molecular Datasets

• Single-cell RNA-seq: 10X Genomics, Illumina NovaSeq
• Supplemental "cell village" pooled genomic sequence data: Illumina NextSeq
• Whole Genome Genotyping: Infinium Global Screening Array-24 Kit, Illumina HumanCore chip
• Whole Genome Sequencing: Illumina NovaSeq

• Study Weblinks:
  • CIRM iPSC Repository at FCDI
  • CIRM iPSC Catalog Search Tool
  • High-dimensional phenotyping to define the genetic basis of cellular morphology
  • Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages
  • bioRxiv preprint: Mapping genetic effects on cellular phenotypes with “cell villages”
  • Stanley Center Stem Cell Resource
  • NIMH Repository & Genomics Resource
• Study Design:
  • Case-Control
• Study Type:
  • Case-Control
  • Cohort
  • eQTL
  • Family
  • Genotype/Expression array
  • Sequencing
  • Single Cell Analysis
  • Stem Cell Lines
  • Whole Genome Sequencing

• PubMed
• MeSH
• Gene
• PMC

• Primary Phenotype: Psychiatric Disorders
• Neurodevelopmental Disorders
• Neurodegenerative Diseases
• Muscular Atrophy, Spinal

• LRP1
• NRXN1
• SMN1
• SMN2

• Funding Sources
  • U01MH115727. National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
  • Stanley Center Philanthropic Gift. Broad Institute, Cambridge, MA, USA.
• Principal Investigators
  • Steve McCarroll. Broad Institute, Cambridge, MA, USA.
  • Ralda Nehme. Broad Institute, Cambridge, MA, USA.
  • Kevin Eggan. Broad Institute, Cambridge, MA, USA.