knomeDISCOVERY

knomeDISCOVERY is an end-to-end genome interpretation solution. It includes whole genome or exome sequencing, sophisticated informatics, and in-depth custom interpretation by Knome’s team of experienced geneticists and bioinformaticians.

knomeDISCOVERY is for academic, pharmaceutical, and biotech researchers who seek to outsource the bioinformatics and genetics needed for whole genome or exome studies of human disease or drug response. Clients who only require annotation and interpretation tools should consider knomeBASE.

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knomeDISCOVERY science team

The team at Knome is your collaborative partner in next generation sequence interpretation. Our experienced scientists are here to assist at any stage of the process, from project design and sample selection to data mining and interpretation. As designers of Knome’s analysis pipeline and expert users of Knome’s proprietary interpretation tools, we execute highly customized projects in order to meet your specific scientific needs. Our broad range of experience includes personal genomics, genetic studies of rare medical disorders, adverse drug response studies, cancer studies and many others–from small single genome or exome studies to projects involving over 1,000 whole human genomes.

knomeDISCOVERY process

Our process starts with raw sequence data (client-supplied or Knome-supplied). We call variants as needed. Once we complete our quality control process, we run your sequence data through kGAP, our informatics engine.

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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 harmonized databases let our geneticists flexibly shortlist the variants, genes, and pathways likely to underlie the disease or drug response under study using our proprietary software tools. Depending on the project, our interpretation team may also utilize:

• Project-specific algorithms and custom scripts
• Rare variant burden tests
• Whole genome-wide association tests
• Population structure analysis
• Niche or custom annotations

Upon project completion, our findings are compiled into a Client Project Report and delivered together with your sequence data, annotated databases, and a copy of our discovery-supportive software tools.

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.  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 several of the Knome-developed software tools that we use to pinpoint candidate causal variants in your genomes. These tools includes knomeVARIANTS. Simply identify cases vs. controls and a putative inheritance mode, 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

knomeDISCOVERY, including all of the deliverables listed above is available with or without sequencing included. Specialized cancer enhancements (SV/CNV analysis and COSMIC database comparison) are available at additionalcost. For more information, please contact us at research@knome.com or call (617) 715-1000.