knomeDISCOVERY™
knomeDISCOVERY is a complete genome interpretation solution. It includes whole genome sequencing, project-driven curation, sophisticated informatics, and in-depth interpretation by Knome’s team of experienced geneticists. knomeDISCOVERY is for academic, pharmaceutical, and biotech researchers who seek to outsource the bioinformatics and genetics needed for whole genome studies of human disease or drug response.
Click here to download a detailed description. Clients who only require genome interpretation informatics and tools for geneticists should review knomeBASE.
knomeDISCOVERY process
Our process starts with raw sequence data (client-supplied or Knome-supplied). After thoroughly reviewing sequence quality, we call variants as needed and complete project-specific curation. We then run your sequence data through kGAP, our automated informatics engine.
kGAP richly annotates all known and novel variants—including allele frequencies, effects on protein structure and function, and phenotypic associations—based on integration of more than a dozen public and private data sources. In addition, kGAP creates a compact, easily queriable database of annotated genotypes for each genome––and a comparison database for all studied genomes.
These easily queriable databases let our geneticists flexibly shortlist the variants, genes, and pathways likely to underlie the disease or drug response under study. To do so, they use our proprietary software tools. Depending on the project, they may also perform or run:
• Project-specific algorithms and custom scripts
• Rare variant burden tests
• Whole genome-wide association tests
• Population structure analysis
• Non-odds ratio-related annotations
• Niche annotations
Upon project completion, our findings are compiled into a Client Project Report and delivered together with your enhanced sequence data and copies of our discovery-supportive software tools.
Process map (click to expand)
knomeDISCOVERY deliverables
Detailed project report. You receive a detailed report that summarizes our interpretation findings (including a shortlist of candidate causal variants, genes, and gene sets), documents our methodology, provides summary statistics with a quality assessment, and recommends for areas of further exploration.
Enhanced data. Your genomes are delivered on a secure hard drive and accessible through an easy to use dashboard interface. Just click to access standardized data sets in Human Genome Format (HGF) for each genome, Variable Site Databases for each genome, and a Variable Site Comparison Database for all genomes within a study.
knomeVARIANTS™. So that you can replicate our findings or test alternative hypotheses, we provide you with the query kit that we use to pinpoint candidate causal variants in your genomes. It includes a query interface, scripting libraries, and data conversion utilities. Simply identify cases vs. controls and a putative inheritance mode, then add sensible filter criteria to automatically generate a sorted shortlist of leading candidates.
knomePATHWAYS™. We also provide you with a visualization tool that overlays variants found in your genomes onto known gene interaction and coexpression networks. This application helps identify functional interactions between variants in distinct genes.
Demos of our software tools
Our software tools are designed to help geneticists interpret genomes. As part of knomeDISCOVERY, our geneticists use these tools to interpret your genomes and report their findings. We also make these tools available for your use. Click the images below to see knomeVARIANTS and knomePATHWAYS in action.
knomePATHWAYS: overlaying variants onto gene interaction networks in order to spot important patterns (part 1).
knomePATHWAYS: overlaying variants onto gene interaction networks in order to spot important patterns (part 2).
knomeVARIANTS: examining shared germline variants that may influence inherited cancer risk.
knomeVARIANTS: examining a genome for nonsense variants, selecting those in genes already implicated in a disease or other phenotype.
knomeVARIANTS: looking through a single genome to better understand drug response.
knomeVARIANTS: examining the genome of tumor and healthy tissue from the same person.
Pricing
knomeDISCOVERY, including all of the deliverables listed above (sequencing through interpretation), is available for $4,998 per whole genome (30x) and $2,500 per exome (30x). Specialized cancer enhancements (SV and CNV calls; COSMIC, SV, and CNV annotation) are available for an additional $1,000 per sample. For more information, please contact us at research@knome.com or call (617) 715-1000.
