List all: genes, pathways, drugs

Sequence and Phenotype Integration Exchange (SPHINX) is a web-based tool for exploring data for hypothesis generation, especially around drug response implications of genetic variation across the eMERGE Network.
Sites Samples Variants Genes Pathways Drugs
eMERGEseq 10 15,745 43,575 788 12,216 1,840
PGRNseq 9 9,010 60,034 413 7,452 2,020
Total (unique) 12 24,755 100,990 1,138 13,434 2,514

Last update: 8/13/2018

The eMERGE-PGx project was a multi-center pilot of implementing pharmacogenetic sequencing in clinical practice to improve health care. SPHINX is a searchable catalog of observed inherited variants in a 24,755 subject population, large enough to reflect even rare variation. The participants’ constitutional DNA was sequenced using the PGRNseq assay, a targeted megabase of sequence in 82 PGx genes, genes identified as important for pharmcogenomics.

The eMERGEseq project was one of the major aims of the eMERGE Network during Phase III. It is aimed to identify rare variants with presumed major impact on function in a cohort of 25,000 participants across the Network. The Network created an eMERGE specific sequencing platform that is used to sequence participants at the individual sites. Baylor College of Medicine Human Genome Sequencing Center (HGSC) and Partners Healthcare with Broad Institute (the two sequencing centers) worked with the Clinical Annotation Workgroup and the Network sites to identify and validate an impactful set of genes and single nucleotide variants (SNVs) that allow for clinically actionable, pathogenic variants to be returned while providing researchers with the data needed to aid in genomic discovery. This resulted in a panel consisting of 109 genes and 1,551 SNVs.

What can I do with SPHINX?

See the lists of genes, drugs, and pathways in the catalog

Search the catalog of variants by:

  • Gene
  • Drug interactions
  • Pathway
  • Chromosome position
  • rsID (SNVid)

See for each gene:

  • Observed single nucleotide variants
  • Pathways involved
    • Other genes in each pathway
    • Other variants in each pathway
  • Drug interactions
    • Other genes with that drug interaction
    • Other variants with that drug interaction

See for each variant:

  • rsID (SNVid), where known
  • Allele frequencies by European, African and Asian ancestry
  • Variant category or “Type” (from SNPeff)
  • Link to dbSNP and PharmGKB, where available

Questions?

The sites participating in eMERGE and the eMERGE-PGx project include:

  • Children's Hospital of Philadelphia
  • Cincinnati Children's Hospital Medical Center with Boston Children's Hospital
  • Essentia Rural Health with Marshfield Clinic and The Pennsylvania State University
  • Geisinger
  • Kaiser Permanente Washington with University of Washington
  • Mayo Clinic
  • Mount Sinai School of Medicine
  • Northwestern University
  • Vanderbilt University Medical Center

Sites participating in the eMERGEseq project include:

  • Children's Hospital of Philadelphia
  • Cincinnati Children's Hospital Medical Center with Boston Children's Hospital
  • Columbia University
  • Geisinger
  • Harvard University
  • Kaiser Permanente Washington with University of Washington
  • Mayo Clinic
  • Meharry Medical College
  • Northwestern University
  • Vanderbilt University Medical Center

References


eMERGE Network acknowledgement text

If data from the PGx project are used, please cite:

The eMERGE Network was initiated and funded by NHGRI through the following grants: U01HG006828 (Cincinnati Children’s Hospital Medical Center/Boston Children’s Hospital); U01HG006830 (Children’s Hospital of Philadelphia); U01HG006389 (Essentia Institute of Rural Health, Marshfield Clinic Research Foundation and Pennsylvania State University); U01HG006382 (Geisinger Clinic); U01HG006375 (Group Health Cooperative/University of Washington); U01HG006379 (Mayo Clinic); U01HG006380 (Icahn School of Medicine at Mount Sinai); U01HG006388 (Northwestern University); U01HG006378 (Vanderbilt University Medical Center); U01HG006385 (Vanderbilt University Medical Center serving as the Coordinating Center); and U01HG004438 (CIDR) serving as a Sequencing Center.

If data from the eMERGEseq project are used, please cite:

This phase of the eMERGE Network was initiated and funded by the NHGRI through the following grants: U01HG8657 (Group Health Cooperative/University of Washington); U01HG8685 (Brigham and Women’s Hospital); U01HG8672 (Vanderbilt University Medical Center); U01HG8666 (Cincinnati Children’s Hospital Medical Center); U01HG6379 (Mayo Clinic); U01HG8679 (Geisinger Clinic); U01HG8680 (Columbia University Health Sciences); U01HG8684 (Children’s Hospital of Philadelphia); U01HG8673 (Northwestern University); U01HG8701 (Vanderbilt University Medical Center serving as the Coordinating Center); U01HG8676 (Partners Healthcare/Broad Institute); and U01HG8664 (Baylor College of Medicine)