Is Anyone Familiar With Knome And Their Kgap Software?

Question

[Travis]

I was just reading about these guys and their services. They're talking about automated analysis of hundreds of genomes simultaneously (including association studies etc) and at scarily low costs. Has anyone had any dealings with them or their data? I'm just wondering if the claims they make about the software are solid or what shortcomings they might have.

[Casey Bergman]

How could anyone have anything bad to say about the company that sequenced Ozzy Osbourne's genome: http://thechart.blogs.cnn.com/2011/04/15/dna-day-the-osbournes-geneticist/

Answer 1

[Nathan Pearson]

Hi Travis (and all),

Knome's Director of Research here. As such, I'm not a client, so will leave it to others to speak from that viewpoint. But to fill in a bit on what we do, running securely on the Cloud, kGAP aligns, assembles, and calls variants from the raw data generated for a work order; richly annotates each resulting genome/exome; and wraps them into a jointly queriable dataset, which we deliver with simple software tools for quickly and flexibly browsing the data. Our website videos ('2 Minute Genomes') show how to use those tools.

As part of the service, we deliver our own shortlists of suspect variants, genes, and gene sets, to help clients make sense of the data and follow up empirically. To make those lists, we filter variants by sensible criteria such as functional class (effects on protein sequence and, by predictive algorithms, function), distribution among cases/controls/reference populations (per expectations of rarity/novelty, inheritance mode, penetrance, etc.), and, as appropriate, gene function (including reported site- and gene-associated phenotypes). For the last, we leverage project-driven curation: while samples are being sequenced, we curate project-relevant publications, to ensure that our database of genotype-phenotype associations is up-to-date when we get the data back and bounce each genome off our reference data. Our curators work in Bangalore (as suggested in Arvktr's answer), and our Cambridge team builds and runs our pipeline and end-user tools, analyzes all project-generated data, and handles all other tasks.

Hope that helps a bit. Happy to answer any further questions: npearson [at] knome.com.

Best,

Nathan Pearson Director of Research Knome, Inc.

[Travis]

So kGAP's job is effectively done at the point of sequence annotation?

Answer 2

[Arvktr]

Knome was in the news in 2007 for their million dollars personalized genome sequencing. As of late 2010, Knome was using BGI in china for the sequencing and outsourced the data curation and analysis to a company in India. Maybe they are using BGI's cloud service and the 4000+ bioinformaticians who work there.

Answer 3

[Nathan Pearson]

Travis wrote: 'So kGAP's job is effectively done at the point of sequence annotation?'

Close. kGAP actually annotates each genome separately, and -then- wraps them together into one jointly queriable comparative database file. The joint and single-genome databases ship together, along with the KDK query app (which works on both types) and the KnomePathways protein interaction query app.

Notably, each single-genome database file carries a bit more detail (e.g., genotype-, sex-, and reference population-specific ranges of odds ratio estimates and p-values for previously phenotype-implicated sites) than the joint database does, as the latter would have to 'accordion' to carry such fine data for every genome in the order, ballooning file sizes. Both files can be useful, though researchers often dig into the joint file first, as variant distribution among samples is generally key to analysis, at least in the first pass.

Nathan