Applied Biosystems SNPbrowser™

Category Genomics>Genetic Data Analysis/Tools

Abstract Applied Biosystems SNPbrowser Software is a tool that facilitates the intuitive selection of human SNPs and associated TaqMan® SNP Genotyping Assays.

It includes visualization of Single Nucleotide Polymorphisms (SNPs) integrated with the physical genome maps, linkage disequilibrium (LD) maps, and putative haplotype block information.

The LD and haplotype block information is generated from genotypes of over three (3) million SNPs validated by either Applied Biosystems or the International HapMap project in a total of five major populations.

Note: This extensive testing resulted in a unique dataset of 650 million genotypes, which can be exported to a file even if unassociated with Applied Biosystems product offerings.

SNPbrowser Software contains a library of over six (6) million human SNPs, facilitating the knowledge-driven design of association and fine mapping studies through the selection of the most informative SNPs for meaningful and powerful study results.

The software features assay product associations for over three (3) million TaqMan® SNP Assays and 5.6 million SNPlex System-compatible SNPs available from the Applied Biosystems online store.

The TaqMan SNP Genotyping Assay set features a large selection of TaqMan Validated, Pre-Designed, and non-synonymous Coding SNP Genotyping Assays that are easily identifiable in the SNPbrowser views.

The software features the complete high quality HapMap SNP set from the International HapMap SNP project, including over three (3) million SNP assays, offering an offline version of this data that can be supplemented with user specific SNPs of interest.

SNPbrowser Software supports association and fine mapping study designs by offering a wide variety of tools to search, view, export SNP information, and purchase assays for available SNPs.

When selecting genomic regions to view, users can apply filter criteria such as product associations and SNP minor allele frequency values by populations.

The software’s Map View also shows gene structure, haplotype blocks, and LD values. Views can be customized and saved as user preferences for future use. The software allows for multiple window views for comparing SNP selection methodologies.

SNPbrowser also features SNP wizards that perform back end calculations to optimize and streamline SNP selections in regions of interest. These include a tagging SNP selection wizard and SNP density selection wizard.

An extensive Help Text file is provided within the tool to assist in familiarizing users of the extensive functionality offered.

Applied Biosystems and HapMap Linkage Disequilibrium Maps -- Underlying SNPbrowser Software’s visualization tool is a vast amount of data including highly informative metric linkage disequilibrium maps. This information can be used to select a reduced set of highly informative SNPs needed for a genetic association study.

Linkage disequilibrium (LD) refers to the fact that particular alleles at nearby variant sites can co-occur by chance more often than is expected. The existence of linkage disequilibrium means that genetically-linked SNP markers can be used to discover nearby causative mutations that increase susceptibility to disease or adverse drug reactions.

The degree of allelic association is expressed in linkage disequilibrium units (LDUs), which represent distances proportional to the strength of LD. LDUs are analogous to the centi-Morgan units that are commonly used for linkage studies because they provide locations for markers with distances that are additive.

These units provide a more appropriate metric than physical distance to select appropriately spaced subsets of SNP markers for genetic association studies.

Two (2) separate databases of validated SNP genotypes, generated for four (4) distinct populations each, are included in SNPbrowser Software.

Every time SNPbrowser is launched, the user may select which data set will be used as the backbone information in computing LD maps, putative haplotype blocks, statistical study power, and Tag SNP selections. These two (2) databases are:

1) Applied Biosystems LD Map Database -- During the development of the TaqMan Validated SNP Genotyping Assays, Applied Biosystems generated the genotype data necessary to empirically create this map.

The underlying data was derived from over 160,000 SNPs in 45 distinct individuals from two to four populations including Caucasian, African American, Japanese and Chinese.

2) HapMap Project LD Map Database -- For this data set, the underlying SNP genotype data was obtained from the International HapMap Project for over 3.2 million high quality SNPs genotyped in 44 to 60 unrelated individuals from four (4) populations including Yorubans, Caucasian, Japanese and Chinese.

SNPbrowser Software enables users to locate SNPs of interest by supporting search options with respect to chromosomal regions, genes, or by entering specific search terms including gene identifiers, SNP identifiers or chromosomal locations. A batch search option provides a direct route to locating SNPs of interest.

Filters can be applied and saved to customize the results views based on specific needs. These include SNP product associations, minor allele frequency values, populations, LD maps, and haplotype (LD) blocks, LMS markers, tagging SNP designations, LDU density and disease allele associations.

To support independent researchers, SNPbrowser Software enables the import of SNPs from outside sources and incorporates them into the view with those in the SNPbrowser database.

Tools for Tagging SNP Selection and Optimizing Marker Coverage -- SNPbrowser Software enables the selection of tagging SNPs with the inclusion of the tagging SNP selection wizard.

Different methods have been proposed to select optimal subsets of SNPs, or “tagging” SNPs, based on the empirical pattern of LD for a given population and genomic region.

SNPbrowser Software incorporates three (3) tagging SNP algorithms to facilitate the selection of tagging SNPs and eliminate SNPs providing redundant genetic information.

These methods include genotype correlation, pair-wise r2 and haplotype R2, and aim to retain the statistical power of association achieved for a study while reducing the number of SNPs actually genotyped.

Calculations are performed on-the-fly based on the validated SNPs within a selected genomic region, and tagging SNPs are identified on the view. Tagging SNP selection results can be exported to a tab delimited file that can be configured to include all validated SNPs, independent of product associations.

Through the visualization of physical distances, haplotype block boundaries, and linkage disequilibrium units in the SNPbrowser Software, researchers can determine if gaps exist in their validated SNP collection for the region of interest.

SNPbrowser’s SNP density wizard assists in filling in these gaps by facilitating SNP selections that are evenly spaced between genetic locations and density within regions. Alternatively, you can select SNPs in a picket-fence pattern using kilobase spacing.

Power Calculations -- Statistical power is used for finding disease susceptibility mutations, using SNP genotyping data generated by either Applied Biosystems or HapMap databases.

It has been estimated based on the empirical genotype data obtained from the respective reference population panels. Statistical power is provided on a per gene basis, including 10 kb up and downstream of the transcribed region.

Power calculations are extremely useful at the beginning of association studies to answer questions like:

1) Do you have enough SNPs for the genes that you’re trying to study?

2) Do you need more samples?

3) Where do you need to supplement with additional SNPs?

Features of SNPbrowser Software v4.0 --

1) Customized adjacent SNP masking - filter SNPlex™ assays for adjacent SNPs up to +/- 15 bp from target SNPs;

2) Updated SNP gene annotation - new HapMap, dbSNP, transcript, and gene annotations;

3) Additional TaqMan® SNP Genotyping Assays for new SNPs in the public database;

4) Updated pre-screened SNPlex™ Genotyping System-compatible SNPs;

5) Now includes TaqMan Drug Metabolism Genotyping Assays; and

6) All assays are linked to the Applied Biosystems online store.

System Requirements

Contact manufacturer.


Manufacturer Web Site SNPbrowser

Price Contact manufacturer.

G6G Abstract Number 20158R

G6G Manufacturer Number 100301