What sequence data does Knome’s genome interpretation engine accept?

kGAP accepts sequence data from all major sequencing platforms, including Ilumina, Complete Genomics, and Life Technologies.

Do I have to be a bioinformatician or geneticist to be a client?

No. While an understanding of genomics is important, a bioinformatics education is certainly not required to work with us. Our clients are either 1) geneticists who seek our tools and informatics services in order to more quickly and acurately interpret genomes (knomeBASE) or 2) academic, medical, and pharmaceutical researchers who seek to outsource both the bioinformatics and genetics involved in identifying the basis of human disease and drug response (knomeDISCOVERY).

What types of customers does Knome have?

Our clients are primarily 1) pharmaceutical researchers seeking to understand individual variation in drug response, 2) researchers seeking to understand the genetic underpinnings of a disease or many diseases, and 3) physicians and families with a motivated interest in better understanding an individual’s health risks, carrier risks, and/or pharmacogenomic profile.

What kinds of research questions can Knome help answer?

Broadly speaking, we can help answer any question that involves trying to trace known human phenotypic variation to known or unknown sequence variation in the genome. The phenotypic/genotypic variation in question may distinguish one person from another (as in many diseases or adverse reactions), or one tissue from another within the same person (as in tumors).

How is Knome different than sequencing platform companies?

Our core strength is in providing whole genome downstream interpretation services. Knome is “technology platform agnostic,” meaning that we accept sequencing data produced by all commercially available sequencing platforms–including Illumina, Life Technologies’ SOLiD and Roche 454.

How is Knome different from 23andMe or Navigenics?

23andMe and Navigenics use a SNP chip-based data to look at less than 1/5,000th, or 0.02%, of the genome. On the other hand, we interpret whole human genomes, a more intensive and complicated process that allows us to “see” the genetic variants that drive the vast majority of disease risk and drug response.

Does Knome provide its services to researchers outside the USA?

Yes, we work closely with researchers in many countries.

Can Knome provide a service quote to build into my grant application?

Yes, we are happy to provide service quotes and other documentation to supplement researchers’ grant applications.

Yes, we have recently completed several cancer-related projects and have developed specialized cancer-related enhancements to our pipeline. Please contact us for additional details.

Can I use Knome to study non-human genome sequences?

Not today. That said, recognizing the scientific importance of studying genomes across various organisms, we plan to expand our scope to include microbial genomes in the future. Our experience in studying human tumor genomes should serve us well in that regard, as tumors and microbial infections tend to be genetically mixed, posing challenges to conventional genome intrepretation pipelines. Our bioinformatics team is currently building advanced tools to meet these challenges and to help researchers dissect the complex genetic interactions between microbes and their human hosts.

Do you provide sequencing services—like Illumina or Complete?

We outsource sequencing. We focus our technologists on building human genome interpretation tools and services. That said, we have extensive experience in managing sequencing projects for our clients. This experience is valuable as we know how to avoid common pitfalls and "rookie errors." We also get volume pricing from sequencing providers.

Does Knome report on indel variation?

Yes, our calling algorithms allow increasingly precise characterization of insertion/deletion variation in the human genome.

Does exome interpretation yield useful data on parts of the genome outside the exome?

Yes, exome capture methods typically greatly enrich the pool of sequenced DNA for exonic regions, but still carry many copies of non-exonic segments of the genome.

Can Knome compare the genomes of cells from different (e.g., tumor versus non-tumor) tissues in the same person?

Yes, we are able to compare the genomes of cells from different tissues in the same person.

Can Knome take care of the ‘background intrepretations’ of exomes and genomes for participants in my research study?

Yes, we have the staff, expertise, and automated tools needed to generate basic health profiles for every participant in a sequencing-based research study, letting you focus your energy fully on questions directly related to the main phenotype under study. Knome’s valuable background interpretation avoids wasting the wealth of data generated by high-throughput individual genome sequencing and can add useful incentives for both affected and healthy people to participate in your study.

For what variants do you look?

Our tools can identify short substitutions, insertions, and deletions, as well as segmental copy number variants, inversions, translocations, and other long structural variants. Moreover, we call and report complex variants, such as tandem substitutions that may be annotated as separate dbSNP entries, but together as one variant in a particular genotype-phenotype association paper; mitochondrial and HLA haplotypes (called inferentially, by arrangement), relevant in many phenotype studies; etc.