Genomic variants like SNPs or small InDels are of major interest to biologists and clinicians alike. Identification of the relevant variants within a genome is crucial for the understanding of molecular mechanisms and diagnostics of rare or common diseases.
GeneGrid enables you to reduce the millions of variants generated by today's NGS experiments to the few or even the single relevant one(s) with a few clicks.
What is GeneGrid?
Annotate your variants with information content ranging from statistical scores to in-depth knowledge from public and proprietary sources.
Use GeneGrid to interactively explore your data and identify relevant information within minutes - no matter if you are looking at one individual or a group of patients.
Benefit from Genomatix' first-in-class literature knowledge - constantly distilled from millions of biomedical publications and life science journals.
Take your research one step ahead by seamlessly interpreting your findings within a pathway context using Genomatix Pathway System.
GeneGrid annotates your variants with information from established sources including allele frequencies from the 1000 genomes project, NHLBI GO-ESP, effect predictors like SIFT, conservation scores like phyloP and many more.
Moreover GeneGrid uses the richness of Genomatix' proprietary ElDorado genome annotation that combines RefSeq, Ensembl and GenBank for the most comprehensive transcript collection available. This enables users to focus on truly known exonic regions .
Gene-to-disease associations from carefully-selected, curated resources like OMIM, ClinVar and Genomatix proprietary LitInspector database make GeneGrid the tool of choice for clinical researchers.
Reference: Data Sources
GeneGrid supports the analysis of a variety of scientific scenarios.
The trio analysis determines Mendelian inheritance patterns and does also detect compound heterozygous events.
More complex data analysis strategies like case/control studies or the comparison of an arbitrary selection of samples can also be addressed by GeneGrid. Case and control groups can be easily formed from all available samples and subsequently analyzed by the software.
More details: Tutorial
Report generation & Data export
The relevant results of any analysis can be summarized in a comprehensive report in PDF format. This includes affected genes, evidence on gene-disease correlations, statistical scores, etc.
Moreover GeneGrid seamlessly integrates into existing pipelines by exporting results in standard VCF format or as tab-separated text file.
Sample report: Tutorial NMNAT1 (PDF)
All underlying annotation background for any chosen variant is immediately shown alongside the overview table. Protein effects an be examined at the transcript level, gene descriptions can accessed, or the best-associated diseases for a gene can be obtained.
Users that want to go to the primary source of evidence can quickly link to the primary entry in the source database or repository (e.g., variant data from dbSNP or disease information in OMIM or ClinVar).
Integration with Genomatix Pathway System (GePS)
GeneGrid allows you to directly transfer genes affected by variants into the full scope of Genomatix Pathway System.
Find associated pathways, diseases, tissues, transcription factors based on the statistical ranking of your list of genes and easily extend or modify the generated networks to get the full biological context.
For in-depth visualization, GeneGrid links out to Genomatix' Genome Browser. All available genomic annotation in the immediate environment of any variant can be viewed.
Optionally, by importing the original BAM file, alignments can be inspected down to single nucleotide level for inspecting aspects like coverage and read variability.
|Number of variants2||Up to 10,000||Up to 1,000,000||More than 1,000,000|
|Best suited for||Targeted sequencing and gene panels||Exome sequencing||Whole genome sequencing|
per sample, price in credits1
|10/per sample||100/per sample||500/per sample|
|Storage for annotated sample
per sample/per month, price in credits1
|1/per month||2/per month||5/per month|
|Genomatix proprietary literature annotation||Included||Included||Included|
|Storage for comparison study
per comparison/per month, price in credits1
|5/per month||5/per month||5/per month|
Available after manual filtering step
|Genomatix Genome Browser||Free||Free||Free|
|Genomatix Pathway System (GePS)||Free||Free||Free|
Example calculation: Performing a trio analysis with an input VCF file containing 3 samples from exome sequencing is available for 300 credits.
1. All services are paid with credits. Please contact our sales team for your quote.
2. This number is automatically determined by the number of rows in your input VCF file.
At Boston Children's Hospital CLARITY challenge (using GeneGrid for the analyses):
[...] the Genomatix team was considered to be the only group to correctly identify
the putative mutation in all three families.
Bio-IT World, November 7, 2012
[...] Genomatix's automated literature search tool, LitInspector was noted by judges
and other teams alike as being best in class - and some teams mentioned a desire
to utilize such methods in their own pipelines.
Brownstein, Catherine A., et al. "An international effort towards developing standards for best practices in analysis, interpretation and
reporting of clinical genome sequencing results in the CLARITY Challenge." Genome biology 15.3 (2014): R53.