SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study.

paper Primary Public

Authors: Saccone, Scott F; Bolze, Raphael; Thomas, Prasanth; Quan, Jiaxi; Mehta, Gaurang; Deelman, Ewa; Tischfield, Jay A; Rice, John P
Year: 2010
Journal: Nucleic acids research
PMID: 20529875
DOI: 10.1093/nar/gkq513
PMCID: PMC2896195

#	Section	Preview
0	INTRODUCTION	Due to corrections for multiple testing and limited sample sizes, genome-wide association studies…
1	INTRODUCTION	Even when there is only a single confirmed SNP, linkage disequilibrium (LD) with other SNPs can make…
2	INTRODUCTION	In these scenarios, the known biological properties of the variants can prove to be useful in…
3	INTRODUCTION	involve many false positives, care should be used in determining the thresholds, and a careful…
4	INTRODUCTION	We recently introduced the genomic information network (GIN) model for systematically incorporating…
5	METHODS — Genomic Information Networks	Given a list of SNPs and P-values from a statistical test for genetic association, the goal of the…
6	METHODS — Genomic Information Networks	A GIN prioritization score represents an order of magnitude change in P-value from a test for…
7	METHODS — Genomic Information Networks	the rankings are the same as by P-value alone [for more information see the discussion of normalized…
8	METHODS — Genomic Information Networks	Figure 1 shows a screenshot from SPOT displaying the GIN diagram for the SNP rs3762611, which is in…
9	METHODS — Genomic Information Networks	The process is repeated for all LD proxies. The highest scoring LD proxy is used to determine the…
10	METHODS — Genomic Information Networks	Following the convention introduced in (4), the ‘Gene’ node has a score of 1 for all genes and…
11	METHODS — Genomic Information Networks	We have incorporated information from the PolyPhen method of predicting the effect of an amino acid…
12	METHODS — Genomic Information Networks	The user may prioritize specific genes by providing gene symbols and prioritization scores as input…
13	METHODS — Genomic Information Networks	The final results of the GIN prioritization process may be viewed in an interactive table within the…
14	METHODS — Using SPOT	The main page consists of a web form for the primary user input. Users must first either upload a…
15	METHODS — Using SPOT	A number of methods can be used to specify genes and genomic regions. For example, the query…
16	METHODS — Programmatic architecture	MySQL (http://www.mysql.com) is used via the Perl DBI module (http://dbi.perl.org) to process and…
17	METHODS — Programmatic architecture	SPOT’s web interface makes use of different technologies and programming languages. From the user…
18	METHODS — Execution time	In the following runs of SPOT, the default LD settings were used so that LD proxies from the HapMap…
19	METHODS — Security	The results of a GWAS are sensitive information and SPOT takes several steps to ensure this…

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