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Study Description

POPRES version 1 and 2

Technological and scientific advances, stemming in large part from the Human Genome and HapMap projects, have made large-scale, genome-wide investigations feasible and cost-effective. These advances have the potential to dramatically impact drug discovery and development by identifying genetic factors that contribute to variation in disease risk as well as drug pharmacokinetics, treatment efficacy, and adverse drug reactions. In spite of the technological advancements, successful application in biomedical research would be limited without access to suitable sample collections. To facilitate exploratory genetic research, we have assembled a DNA resource from a large number of subjects participating in multiple studies throughout the world. This resource was initially genotyped using the Affymetrix 500K SNP panel. This project includes nearly 6,000 subjects of African American, East Asian, South Asian, Mexican, and European origin.

POPRES version 3

The discovery and development of novel drugs is challenging and with high attrition rates. Selection of the right target and optimal indications for novel therapeutics represent key decision points in this process, and are often hampered by our limited understanding of the biology of the target in humans. Building a robust body of knowledge of variation within drug target genes has in several cases increased the probability of success for novel therapeutics. Our knowledge of variation within drug target genes and their influence on traits of medical interest is still very limited. In an effort to fill this gap, we resequenced the exons of 202 known or suspected drug target genes in over 16,000 well-phenotyped individuals. A total of 863,883 bases were targeted, including 351 kb of coding and 323 kb of untranslated exon regions. The sequenced subjects included 3,381 from two studies that were part of the Population Reference Sample (POPRES) project: CoLaus (N = 2,059) and LOLIPOP (N = 1,322). Genotyping data generated through the targeted next generation sequencing is available through the dbGaP.

  • Study Types: Population, Control Set
  • dbGaP estimated ancestry components using GRAF-pop
  • Number of study subjects that have individual level data available through Authorized Access: 8012

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

POPRES version 1 and 2

The POPRES collection includes subjects from ten individual collections. These collections are a mix of unrelated population samples and healthy controls, and are described in Nelson et al. (PMID: 18760391).

POPRES version 3

POPRES includes unrelated subjects from two population-based studies: CoLaus (Preisig et al. 2009; PMID: 19292899) and LOLIPOP (Kooner et al. 2008; PMID: 18193046). CoLaus Study: subjects included are participants in the PsyCoLaus follow-on study of psychiatric traits and/or extremes of several selected cardiovascular disease-associated traits. There was an overlap of 460 subjects between these two selections. LOLIPOP: Subjects included are a random selection of Indian Asians or European whites selected for overlap with previous genome-wide genotyping studies, European whites selected as extremes from several cardiovascular disease-related traits and subjects of other non-European ancestry.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Genotyping Affymetrix Mapping250K_Nsp 262264 33767 Affymetrix 500K Set comprises Mapping250K_Nsp and Mapping250K_Sty Arrays
Whole Genome Genotyping Affymetrix Mapping250K_Sty 238304 33766 Affymetrix 500K Set comprises Mapping250K_Nsp and Mapping250K_Sty Arrays
Targeted Sequencing Illumina Genome Analyzer IIX N/A N/A Paired 76bp reads
Exome Capture Roche NimbleGen High Density 2.1M Human Exome Array N/A N/A
Selected publications
Diseases/Traits Related to Study (MESH terms)
Links to Related Resources
Authorized Data Access Requests
Study Attribution