NCBI retiring HapMap Resource

June 16, 2016

A recent computer security audit has revealed security flaws in the legacy HapMap site that require NCBI to take it down immediately. We regret the inconvenience, but we are required to do this. That said, NCBI was planning to decommission this site in the near future anyway (although not quite so suddenly), as the 1,000 genomes (1KG) project has established itself as a research standard for population genetics and genomics. NCBI has observed a decline in usage of the HapMap dataset and website with its available resources over the past five years and it has come to the end of its useful life. 

The figure below shows the number of unique IP addressing accessing HapMap relative to the 1KG website has been declining over the past three years. Data was analyzed over three week sections for the peak usage months (January, March and November).  Please note, this is usage for NCBI only, and many users access 1KG data from EBI. 
 
HapMap Usage Graph

Figure 1: HapMap vs 1KG usage over the past three years exemplified during the peak usage months.

The original mission statement of the International HapMap Project was to develop a haplotype map of the human genome, HapMap, which would describe the common patterns of human DNA sequence variation. Through this research millions of SNPs were discovered and many GWAS studies used this dataset in research for disease association. This project was a necessary stepping stone for the 1KG project which utilizes many of the same populations.  While this project was an impactful start for the scientific community, the HapMap Project has lost momentum in research. This statement from Buchanan et al. 2012 seems to have come to pass.

 “The number of novel variants is constantly increasing and many believe that the 1000 Genomes Project
could potentially overshadow the utility of HapMap.”

Please visit the 1000 Genomes Project resources for access to current and best data (genotypes, sequences and genome mapping) at http://www.1000genomes.org/, or through the NCBI Browser: https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/. The archived HapMap data will continue to be available via FTP from ftp://ftp.ncbi.nlm.nih.gov/hapmap/. Questions on these changes should be addressed to the NCBI Help Desk

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Last updated: 2016-06-16T14:55:08-04:00