knomeBASE automatically annotates, compares and distills human whole genome data, freeing geneticists from informatics to focus on discovery
CAMBRIDGE, Mass.--(BUSINESS WIRE)--Knome Inc., the human genome interpretation company, today announced the release of knomeBASE, an informatics service that transforms raw sequence data from human genomes into a format optimized for interpretation by geneticists seeking to understand the basis of human disease or drug response. Designed to enable the comparison and interpretation of large numbers of whole genomes, knomeBASE annotates, compares and distills raw sequence data-addressing the primary informatics challenges that often bottleneck the process of interpreting multiple genomes.
"Our geneticists have been interpreting whole human genomes since early 2008"
As part of the knomeBASE service, clients receive a genome discovery kit (knomeGDKTM)-a suite of software tools, scripts and libraries that give geneticists unprecedented flexibility to query multiple genomes and visualize gene interaction networks across multiple genomes.
"Our geneticists have been interpreting whole human genomes since early 2008," said Jorge Conde, Knome's CEO. "Since then, we've engaged in multi-genome interpretation projects for researchers in 18 countries-primarily for cancer, drug response, rare disease and common disease. In the process, we've had a team of top software engineers creating the industrial-strength informatics pipeline and applications needed to solve real-world genome interpretation problems. With knomeBASE, we are making the battle-tested pipeline and tools we've used internally available to all geneticists."
knomeBASE addresses many of the bioinformatics challenges facing geneticists engaged in whole genome studies. These challenges generally fall into three categories: annotation, comparison and distillation.
* Annotation: to annotate known and novel variants, Knome has invested thousands of hours in curating and harmonizing reference data from more than a dozen sources, including dbSNP, PubMed, 1000 Genomes, ENSEMBL, RefGene, HGMD, SIFT, HPRD, KEGG and Reactome- yielding a deep database of functionally relevant information on human sequence variants.
* Comparison: to enable robust, simultaneous comparisons between many genomes, knomeBASE first converts raw sequence data into a standard genome format that thoroughly captures simple and complex variants. This allows genomes or exomes sequenced at different times, under different methods, and by different platforms (such as Illumina (ILMN) and Complete Genomics (GNOM)) to be compared to one another.
In addition, for all genomes in a study, knomeBASE creates a compact database that summarizes the distribution of variants among all studied genomes-allowing users to quickly and flexibly query multiple genomes in order to shortlist candidate causal variants, genes and gene networks.
* Distillation: to allow desktop interpretation, knomeBASE distills raw whole genome sequence data (typically ~200 GB) into a compact, easily queriable database (~9 GB) that details:
o Genotypes at known and novel variable sites in the human genome, including base substitutions and short indels;
o Call confidence, including reference matching and no-calls;
o Variant frequencies in appropriate populations;
o Gene IDs and associated phenotypes; site-associated phenotypes, with estimated odds ratio ranges and p-values;
o Variant specific effects on protein sequence and function (predicted); and
o Gene-to-gene interactions.
These databases are small enough to be managed on a desktop computer, yet robust enough to provide all of the information needed for interpretation. Further, they are easily accessed through a published API and set of libraries, allowing geneticists to create their own domain-specific applications and scripts.
The software tools delivered with knomeBASE include knomeVARIANTSTM-a GUI-based query interface that lets geneticists quickly and flexibly find suspect variants among many genomes, and knomePATHWAYSTM, a gene interaction visualization tool that lets users find sets of genes enriched for suspect variants in one set of genomes versus another.
"The genomics revolution has been slowed by a dearth of downstream analysis tools and services," said James D'Augustine, chief technology officer of Knome. "Researchers are flooded with sequence data and need help making sense of it all. knomeBASE breaks new ground by transforming raw sequence data into an interpretation-ready format that lets geneticists leverage their domain expertise to make sophisticated queries of many whole genomes at once without requiring a support team of bioinformaticians and software engineers."
knomeBASE is an informatics service that transforms raw sequence data from human genomes into a format optimized for comparison and interpretation. The service accepts whole genome data from all major platforms, including Illumina and Complete Genomics-automatically annotating, comparing and distilling sequence information so that geneticists can quickly identify the variants, genes and pathways that govern the phenotype of interest. As part of knomeBASE, clients also receive easy-to-use genome interpretation tools, libraries, and scripts that enable flexible querying, rapid hypothesis generation, data visualization, and custom software development. knomeBASE is priced at $750 per whole genome or exome, with academic and volume discounts available.
About Knome Inc.
Knome is a life sciences company that specializes in the interpretation of human genomes. Knome supports geneticists with the informatics and tools needed to investigate the genetic basis of human disease and drug response. In addition, the company provides researchers and families with end-to-end genome interpretation solutions. Underlying Knome's services is kGAPTM, an interpretation engine that automates the process of annotating, comparing and distilling whole genome sequence data. For more information, please visit www.knome.com.
Dan Budwick, 973-271-6085
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