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Robert West
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Personalized Medicine Evangelist
Personalized Medicine Evangelist

1,073 followers
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Can Genomics Contribute to Clinical Understanding of Chronic Human Disease, and Facilitate Progress Toward Treatments?

I explore this possibility in a guest post series on the blog of one of Health 2.0's premier patient advocates, Kelly Young (aka @rawarrior), using Rheumatoid Arthritis as a model disease to address the question.

Bottom line for those who don't want to read the whole story? The glass is half-full.

Part 1: An Introduction to the Genetics of Rheumatoid Arthritis (RA)
http://bit.ly/mQFY1e

Part 2: Direct to Consumer (DTC) Genetics of RA
http://bit.ly/on2SMs

Part 3. Fundamental Studies of RA Genetics & Genomics
http://bit.ly/qMbtKY

This series is intended to facilitate the bench-to-bedside translation, and who better to receive the information available than e-Patients themselves?

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This is interesting. And I note - it is also kind of funny since the announcement of the new HHMI/Wellcome journal seemed to be taking a dig at Nature and PLOS Biology and so what do they do? Hire someone who used to work at Nature and PLoS Biology.

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Follow-up on the "sequencing old people" project by Complete Genomics, and a new entrant in the genome interpretation space
Some interesting tidbits on the Complete Genomics deal with Scripps to sequence 1,000 healthy elderly people (I can't bring myself to use the term "wellderly" in any context other than an ironic one).

Firstly, from an email exchange with Complete Genomics publicist Lisa Osborne. I was puzzled by the decision by Complete to do this sequencing free of charge, so I asked:

Will the company be charging academic researchers for access to the data? If not, what is the goal of this project from a commercial perspective?

The reply:

By providing Scripps with this sequencing data at no charge, we are enabling them to allocate their resources towards further analysis and annotation of the data via Cypher Genomics. Complete Genomics will then provide this annotated data to the genomics community through a new service offering – the Wellderly Genomics Reference Resource.

Due to the constraints of the Wellderly Project participant consent forms, Complete Genomics cannot make this genomic data publicly available. Any customer who is provided access to this data will also have to agree to a number of privacy and legal restrictions in order to be able to use it.

We plan to make the Wellderly Genomic Reference Resource available to our customers as a genomic information service. Specific pricing to access this resource has yet to be determined. Customers will be provided with different tiers of service depending on the type of institution they represent (not for profit vs. for profit, for example) and the type of data they need to access. We anticipate having more details to share around the data access model and related fee structure by the end of Q4.

Well, that answers that question. As a kind of "hyper-control" group, this cohort may well have some value to academic and biotech researchers, although whether they'll be prepared to pay fees that make Complete's investment worthwhile remains to be seen. (It's worth noting that attempts to make money by generating genetic data do not have a good track record in the profitability stakes, but that doesn't mean it's impossible, or indeed that this is Complete's primary goal with this project.)

Osborne's answer raises a second question: who or what are Cypher Genomics? Turns out I missed this paragraph in the Scripps/Complete press release:

Another valuable aspect of the Reference Resource will be the addition of Cypher Genomics clinical annotations to the sequencing datasets. Cypher Genomics is a project headed by Drs. Schork and Topol, as well as STSI faculty member Dr. Ali Torkamani and STSI industry liaison Dr. Ashley Van Zeeland. STSI has developed and plans to commercialize this software suite for annotating genomic variant lists with clinically relevant pathway and disease prediction information.

Very interesting - yet another new entrant to the genome interpretation space, just a couple of week's after the launch of Stanford-based Personalis. The Cypher website contains no useful information yet, so we'll have to wait and see what emerges about this company over the next few months.

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Metagenomics and Personalized Medicine
.....host-gene-microbial interactions are major determinants for the development of these multifactorial chronic disorders and, thus, for the relationship between genotype and phenotype. We also explore how genome-wide association studies (GWAS) on autoimmune and inflammatory diseases are uncovering mechanism-based subtypes for these disorders. Applying these emerging concepts will permit a more complete understanding of the etiologies of complex diseases and underpin the development of both next-generation animal models and new therapeutic strategies for targeting personalized disease phenotypes....
http://www.cell.com/abstract/S0092-8674(11)01063-4
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CELL. Human Genetics: Special Focus

http://bit.ly/pFR5xs

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A few initial thoughts on 23andMe's new $999 exome product:

1. The company steers clear of the FDA's baleful gaze by (at least initially) offering raw data only with no analysis.

2. This is for hardcore beta testers only. A raw exome sequence with no interpretation requires some serious data-wrangling to extract useful data from. Even existing open-access interpretation tools like Promethease will provide fairly overwhelming data.

3. The offer is open only to existing customers. That has two benefits: the one they emphasise on their site is that it selects for people with at least some experience in looking at genetic data. A more important (but unstated) benefit is that the customers' chip data will provide a comparison data-set for exome quality control.

4. We shouldn't forget that Knome has been offering both genome and exome sequencing DTC (along with interpretation) for a long time. However, my sense is that they've attracted relatively few customers. I suspect 23andMe will be able to rope in a substantially larger customer base even at a comparable price point, leveraging their marketing and community-building strengths.

5. Still, no question that the number of people willing to fork out $999 for a non-clinical-grade exome is pretty small.

6. At Genomes Unzipped we'll be looking to get hold of at least one of these exomes, as well as providing some suggestions on ways in which the raw data can be used. Exciting times for those of us who've spent the last few years working with sequence data...
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