Two new ArrayTrack libraries for personalized biomedical research.
BACKGROUND
Recent advances in high-throughput genotyping technology are paving the way for research in personalized medicine and nutrition. However, most of the genetic markers identified from association studies account for a small contribution to the total risk/benefit of the studied phenotypic trait. Testing whether the candidate genes identified by association studies are causal is critically important to the development of personalized medicine and nutrition. An efficient data mining strategy and a set of sophisticated tools are necessary to help better understand and utilize the findings from genetic association studies.


METHODS
SNP (single nucleotide polymorphism) and QTL (quantitative trait locus) libraries were constructed and incorporated into ArrayTrack, with user-friendly interfaces and powerful search features. Data from several public repositories were collected in the SNP and QTL libraries and connected to other domain libraries (genes, proteins, metabolites, and pathways) in ArrayTrack. Linking the data sets within ArrayTrack allows searching of SNP and QTL data as well as their relationships to other biological molecules. The SNP library includes approximately 15 million human SNPs and their annotations, while the QTL library contains publically available QTLs identified in mouse, rat, and human. The QTL library was developed for finding the overlap between the map position of a candidate or metabolic gene and QTLs from these species. Two use cases were included to demonstrate the utility of these tools. The SNP and QTL libraries are freely available to the public through ArrayTrack at http://www.fda.gov/ArrayTrack.


CONCLUSIONS
These libraries developed in ArrayTrack contain comprehensive information on SNPs and QTLs and are further cross-linked to other libraries. Connecting domain specific knowledge is a cornerstone of systems biology strategies and allows for a better understanding of the genetic and biological context of the findings from genetic association studies.
Z-Tech Corporation, ICF International company at NCTR, National Center for Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079, USA. Zhihua.xu@fda.hhs.gov
Joshua
J
Xu
Carolyn
C
Wise
Vijayalakshmi
V
Varma
Hong
H
Fang
Baitang
B
Ning
Huixiao
H
Hong
Weida
W
Tong
Jim
J
Kaput
D000818:Animals; D035843:Biomedical Research; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D046228:Microarray Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D057285:Precision Medicine / Q000379:methods*; D040641:Quantitative Trait Loci; D051381:Rats; D017422:Sequence Analysis, DNA