Nucleic Acids Research, 2003, Vol. 31, No. 16 4910-4916
© 2003 Oxford University Press
Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map
1 Department of Biochemistry, 2 Center for Bioinformatics, 3 Genetics and Molecular Biology Graduate Program, 4 DNA Sequencing Core Facility and 5 Bimcore, Emory University School of Medicine, Atlanta, GA 30322, USA
*To whom correspondence should be addressed at Biochemistry Department, Emory University School of Medicine, 4133 Rollins Research Center, 1510 Clifton Road, N.E., Atlanta, GA 30322, USA. Tel: +1 404 712 9783; Fax: +1 404 727 3231; Email: sedevin{at}emory.edu
The authors wish it to be known that, in their opinion, the first two authors should be considered as joint First Authors
An international effort is underway to generate a comprehensive haplotype map (HapMap) of the human genome represented by an estimated 300 000 to 1 million ‘tag’ single nucleotide polymorphisms (SNPs). Our analysis indicates that the current human SNP map is not sufficiently dense to support the HapMap project. For example, 24.6% of the genome currently lacks SNPs at the minimal density and spacing that would be required to construct even a conservative tag SNP map containing 300 000 SNPs. In an effort to improve the human SNP map, we identified 140 696 additional SNP candidates using a new bioinformatics pipeline. Over 51 000 of these SNPs mapped to the largest gaps in the human SNP map, leading to significant improvements in these regions. Our SNPs will be immediately useful for the HapMap project, and will allow for the inclusion of many additional genomic intervals in the final HapMap. Nevertheless, our results also indicate that additional SNP discovery projects will be required both to define the haplotype architecture of the human genome and to construct comprehensive tag SNP maps that will be useful for genetic linkage studies in humans.
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