SNP databases and pharmacogenetics: great start, but a long way to go.
With the recent publication of the human genome project there has been an explosion of data available for pharmacogenetic research. Web-based databases containing information on single nucleotide polymorphisms (SNPs) are readily accessible to researchers, but there has been little comment on their utility. We used seven major international databases to identify SNPs in 74 genes involved in drug pathways. Very little overlap was seen among the databases, with only eight out of a putative 893 SNPs ( approximately 1%) common to the most commonly used databases. Problems with false positives, secondary to a high degree of homology in gene families, were also observed. These studies suggest researchers limiting their studies to one database would miss a great deal of information. Effort to update compilation databases, such as HGVbase, GeneSNP, PharmGKB, and HOWDY, and the aggressive removal of false positives from all databases is required if these resources are to facilitate the intended growth in pharmacogenetics research.
Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
Sharon
S
Marsh
Pui
P
Kwok
Howard L
HL
McLeod
D000595:Amino Acid Sequence; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D004358:Drug Therapy / Q000379:methods / Q000639:trends; D005796:Genes / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010597:Pharmacogenetics / Q000379:methods* / Q000639:trends; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid