Projects

Genomics

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Genotyping is a process in which an individual’s DNA is examined to reveal specific traits and alleles. The eMERGE Network has undertaken many genotyping projects since the foundation in 2007.  The following describe the data sets created by the eMERGE Network. The Genomics Workgroup guides data QC and analysis throughout the Network. A listing of the eMERGE studies currently available on dbGaP can be found here. A list of phenotype data available can be found here. Please see the below tables for a break down of count by site and platform.

eMERGE I-III imputed data set (N = 83,717)

The eMERGE Network also uses data from participants that are genotyped by individual sites, and this individual level data is then combined to create a de-identified dataset used for analysis across the Network. All data are sent through a strict quality control protocol and imputed to guarantee consistency and quality. Recently the eMERGE I-III GWAS data were imputed off the Haplotype Reference Consortium (HRC reference) using the Michigan Imputation Server. This produced a dataset with over 83,000 samples that is linked to phenotypic information across the sites.

eMERGE exome chip data set (N = 12,330)

Five sites across the Network provided exome chip data at the beginning of Phase III. The exome chip genotype content is based on the deep sequencing of ~12,000 African Ancestry and European ancestry individuals to discover rare variants which are then typed on this chip.  The exome chip genotype also contains many of the variants associated with disease in the GWAS Catalog and a selection of common variants useful in controlling for genetic ancestry in association studies.

eMERGE PGx data set (N = 9,010)

eMERGE-PGx was a multi-site test of the concept that genetic sequence information can be coupled to electronic medical records (EMRs) for use in healthcare. This project focused on pharmacogenomics (PGx) – the idea that individual variation in drug response includes a genomic component. The Network used the PGRNSeq sequencing platform developed by the PGRN Network. PGRNSeq was developed in a cooperation between Deep Sequencing Resources at the Baylor College of Medicine and the University of Washington to fully characterize the genetic variation across human populations in 84 genes. Though this project completed during Phase II of the eMERGE Network, work is still ongoing. Sequencing and phenotype data are housed in SPHINX (Sequence, PHenotype Integration Exchange).

eMERGEseq data set (25,000)

Currently the Network has launched an effort to sequence DNA from 25,000 participants across the consortium. These genotypes are being sequenced on an eMERGE specific panel based off of ACMG 56 and the results will then be returned to the participants. Learn more about the eMERGEseq panel here.

eMERGE Whole Genome Sequencing data set (N = 1,800)

Nine hundred Whole Genome Sequencing (WGS) data are available from each CHOP (pediatric subjects) and Northwestern (adult subjects). These subjects are racially and ethnically diverse and include European, African and Hispanic ancestry.  All subjects also have electronic health record information at their respective site, allowing for potential genotype/phenotype analysis.

eMERGE Whole Exome Sequencing data set (N = 3,745)

Whole Exome Sequencing (WES) data are available from Columbia. This cohort includes patients identified from our Breast Cancer Family Registry (15%), Pulmonary Artery Hypertension cohort (2%), and the Pediatric Cardiac Genomics Consortium (83%).

 Data set counts

Data counts by site

 

In the News

Here's what's happening with eMerge:

31
AUG

An upcoming scheduled maintenance window is starting Tuesday, September 5th and ending Wednesday, September 6th. During this time, the RD Discover, SD Discover, Subject Locator and Record Counter applications...

25
JUL

The NIH/NHGRI has published IGNITE II RFAs which are linked below for your convenience.

  • Implementing Genomics in Practice (IGNITE) II: Pragmatic Clinical Trials – Clinical Groups...

22
JUN

CMS announced last week it will award up to $30 million in grant funding to clinical specialty societies, clinical professional organizations and independent research organizations to develop quality measures...

10
FEB

eMERGE is excited to share the results of the national multi-site survey it conducted to investigate public attitudes towards consent and data sharing in biobank research recently publish in AJHG.  For...