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Genetic Neuroscience: How Human Genes and Alleles Shape Neuronal Phenotypes

Convergent Neurosciencephs002032.v1.p1dbGapdbGap FHIR

Description

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). We wish to share the available SNP data for 2166 CIRM lines and whole genome sequence data generated at the Broad Institute for 299 of the CIRM 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/].

Additional project data registered with the study includes WGS 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

  • Whole Genome Genotyping: Illumina HumanCore chip - Whole Genome Sequencing: Illumina Novaseq - Single-Cell RNA-Seq: 10X Genomics, Illumina Novaseq - Supplemental "cell village" pooled genomic sequence data: Illumina Nextseq

Stats

4Cohorts
2,547Samples
2,548Participants
6.91 TBSize

Summary

Consent CodesGRU, NA, DS-SMA-MDS
DiseasesUnspecified, spinal muscular atrophy, CIRM iPSC Repository
AccessControlled Access, Consortium Access Only
Study DesignTBD, Case-Control, Prospective Longitudinal Cohort
Data TypesTBD, Whole Genome, Single Cell RNAseq, Pooled Genomic Seq

Applying For Access

dbGaP FAQdbGaP Access Request Video Tutorial

Terra Workspaces

This study has been divided into the following workspaces by consent codes and optionally the originating laboratory.

Terra Workspace NameConsent CodeDiseaseAccessStudy DesignData TypeSamplesParticipantsSize (TB)
AnVIL_NIMH_Broad_ConvergentNeuro_McCarroll_Eggan_CIRM_GRU_VillageDataGRUUnspecifiedTBDTBD000.10
AnVIL_NIMH_Broad_ConvergentNeuro_McCarroll_Eggan_CIRM_GRU_WGSNA--Case-ControlWhole Genome3803806.77
AnVIL_NIMH_Broad_ConvergentNeuro_McCarroll_Eggan_Finkel_SMA_DS_WGSDS-SMA-MDSspinal muscular atrophyProspective Longitudinal CohortWhole Genome010.02
AnVIL_NIMH_CIRM_FCDI_ConvergentNeuro_McCarroll_Eggan_GRU_ArraysGRUCIRM iPSC RepositoryCase-ControlSingle Cell RNAseq, Pooled Genomic Seq2,1672,1670.02