knomeBASE

knomeBASE  provides geneticists with the informatics and tools they need to shortlist and validate candidate variants, genes, and pathways. knomeBASE is for geneticists and other researchers who desire to interpret genomes on their own—but lack sufficient informatics support. Researchers who seek a more comprehensive solution should consider knomeDISCOVERY.

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knomeBASE process

Our process starts with raw sequence data (client-supplied or Knome-supplied). We then review sequence quality, and run your sequence data through kGAP, our 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 as well as a comparison database for all studied genomes.

These easily queriable databases are staged and loaded into our proprietary software tools to enable clients to efficiently interpret next generation sequence data analysis.

These easily queriable databases are staged and loaded into proprietary desktop software tools designed to enable geneticists and molecular biologists to efficiently interpret multiple genomes.

Informatics

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Underlying the knomeBASE service is kGAP™, an informatics engine that automates the process of annotating, comparing and distilling whole genome sequence data—transforming raw sequence data into a format optimized for interpretation. Designed to process many genomes at once, kGAP completes in a day what would otherwise require months of effort and a team of specialists.

Standardizes sequence data

To allow the comparison of many genomes at once – even if sequenced at different times, under different specifications, or on different platforms – we convert raw sequence data into a standard diploid genome format (Human Genome Format, or .HGF), aligned to reference, that allows us to thoroughly capture simple and complex variants.

Annotates known and novel variants

kGAP is based on a database of known human allele-phenotype associations. Its state-of-the-art curation integrates, reconciles, and refines reference data from diverse sources (including public, proprietary, and project-specific) in order to yield accurate and detailed insights into sequence variants carried by each genome or exome under examination. In addition to analyzing previously annotated variants, kGAP offers crucial predictive insight into the potential functional effects of novel variants, prioritizing them for empirical follow-up based on a set of custom criteria that identifies leading candidates for plausible involvement in the phenotype of interest.

Distills data

For every genome, kGAP produces a compact, fully annotated, easily queriable database of variation. These databases are accessible through a robust API that enables the rapid development of new interpretation applications.

Once processed through kGAP, genomes can be quickly and flexibly interrogated by our software tools, including knomeVARIANTS and knomePATHWAYS, in order to identify the genetic variants, genes, and pathways most likely to govern the disease or drug response of concern.

Enables multi-genome comparison

Investigation often requires comparing many genomes to each other in order to identify alleles that are associated with a given phenotype, or to detect somatic variation. kGAP was built from the ground up for multi-genome comparison. It sifts through vast amounts of sequence data to identify alleles shared by particular subsets of genomes in a study, flagging variants most likely implicated in the phenotype of interest.

kGAP creates a single compact database (a Variable Site Comparison Database, or VSCDs) that summarizes the distribution of variants among all studied genomes, enabling the fast and flexible querying of multiple genomes.

knomeBASE deliverables

The deliverables for knomeBASE include your sequence data, annotated databases and our software tools, scripts, and libraries.

Enhanced data.  Your genomes are delivered on a secure hard drive and are accessible through an easy to use dashboard interface. Our user interface provides access to each individual genome or exome database, the comparison database that incorporates all samples in your study, and the tools required to ask genetic questions of your sequence data.

knomeVARIANTS™.  So that you can replicate our findings or test alternative hypotheses, we provide you with the software tools that we use to pinpoint candidate causal variants in your genomes. Our software includes a query interface, scripting libraries, and data conversion utilities. Simply identify cases vs. controls and a putative inheritance mode, and then add sensible filtering criteria to generate a list of candidate variants.

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.

Pricing

knomeBASE, including all of the deliverables listed above, is available with or without sequencing. For more information, please contact us at research@knome.com or call (617) 715-1000.