NHLBI Exome Sequencing Project (ESP) Exome Variant Server Home Data Browser Data Usage and Release How to Use What's New Contact and FAQ Downloads If you have any questions regarding EVS and ESP data, please check the FAQ list first before sending an email. FAQ What is the difference between the current ESP6500 data release and the previous ESP5400 data release? [-] The current, also the final data release (ESP6500) of the ESP exome sequencing project includes the majority of the exomes in the previous ESP5400 release and an additional ~1100 new exomes. When new exomes were added, we examined the kinship among the samples and removed the samples showing first-degree to third-degree relatedness. As a result, limited exomes in the ESP5400 release were excluded from the ESP6500 release. The final set of exomes are from all the unrelated samples. The SNP calls were re-generated by analyzing all the unrelated exomes simultaneously. Is the ESP5400 data release still accessible? [-] There is no plan to host two different versions of the EVS web interface for both the ESP6500 and the ESP5400 because it can cause confusion for users. If the ESP5400 dataset is preferred by your ongoing projects for any reason, you still can get the bulk download of the ESP5400 release at the following URLs, ESP5400.snps.txt.tar.gz ESP5400.snps.vcf.tar.gz ESP5400.coverage.all_sites.txt.tar.gz ESP5400.coverage.seq_blocks.txt.tar.gz How do I obtain a user account to access ESP data? [-] The NHLBI ESP Exome Variant Server (EVS) is publicly available and no account is needed. Simply click on the "Data Browser" tab to begin your search. You can also download the allele counts and frequencies for the entire dataset by selecting the "Downloads" tab. What data is currently being served on the EVS? [-] The current version dataset is comprised of a set of 2203 African-Americans and 4300 European-Americans unrelated individuals, totaling 6503 samples (13,006 chromosomes). Are the samples in the ESP6500 clinical patients or healthy controls? [-] The samples included in the ESP6500 were selected from the populations listed on the "Home" tab. Information about these populations can be found through dbGaP. In general, ESP samples were selected to contain controls, the extremes of specific traits (LDL and blood pressure), and specific diseases (early onset myocardial infarction and early onset stroke), and lung diseases. Cohort or phenotype information about any particular individual CAN NOT BE RELEASED. The goal of the ESP dataset is to release the frequency counts of specific variants without regard to phenotype. How can I obtain the phenotype and genotype data associated with the data on the EVS? [-] Sample level data including genotypes and phenotypes are not available on the EVS and may only be obtained from dbGaP. All of the phenotype and genotype data are moving into dbGaP. The ESP samples and genotypes listed here are available in dbGaP. Is there a centralized mechanism through which I can apply for access to all of the data included in the ESP6500? [-] Due to the organization of dbGaP, data are grouped by cohort. Therefore, at the present there is no centralized way to access phenotype data for the entire data set. The ESP is working with dbGaP and other groups to consider more global release formats in the future. Have any of the ESP variants been validated by Sanger sequencing? [-] Large scale validation of the variants was not performed. However, sequencing validation of a small number of singleton (~200) and high frequency SNP calls (~800) was performed and reported in Tennessen et. al. as published in Science online May 21, 2012 (PMID: 22604720). None of the INDEL calls was validated, In general, the INDEL calls are less robust than the SNP calls and have a higher false positive rate. When applying the ESP data to research studies, users are advised to keep this difference in mind. What capture technology was used during exome sequencing? [-] Samples were sequenced at two centers - the University of Washington and the Broad Institute. At the University of Washington exome capture was performed using Roche/Nimblegen capture, and at the Broad using Agilent reagents. What calling algorithm was used to generate the ESP6500 data? [-] All SNP data were called simultaneously at the University of Michigan (Abecasis Laboratory). The Michigan SNP calling pipeline is available here. All INDEL data were analyzed at the Broad Institute (by the Genome Sequencing and Analysis group) using the GATK variation discovery pipeline following the guidelines in the GATK best practices v4. Which version of the dbSNP build contains the variants from the NHLBI ESP project? [-] The dbSNP build-134 contains a subset of the SNPs from the NHLBI-ESP project. The complete set of the SNP calls from the NHLBI ESP project is included in the dbSNP build-138. Some of the earlier submission entries in the build 134 are updated or removed in the build 138. The INDEL calls from the NHLBI ESP project are experimental, and are not submitted to the dbSNP yet. Contact us: evsserver@uw.edu Privacy Terms