As I understand it, the contest is technology-driven to get 100 genomes in 30 days. The benefits to us in the genetics community is 100 excellent genomes sequenced many times over, from 105 year-olds who act as supercontrols for age-related diseases. We also get a software contest so we get better browsers. I think if the 100 centenarians can be taken from 10 different projects, then we can leverage the projects via the shared controls and get more data sharing and trust

As described in the editorial “Towards a medical grade human genome sequence”, we are pleased to collaborating with the $10 Million Archon Genomics X PRIZE (AGXP) to develop a set of standards and procedures to help with judging the prize contest. Your comments are needed but should not be limited to this aim alone because the contest is just the beginning of this standard-setting project. For examples, it is likely that the very kinds of genome variation browser and related software that are needed to evaluate the sequencing effort are the spin-off product the community really needs to make medical genomics a reality.

The draft validation protocol is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the AGXP competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches.

Alexander Zaranek et al. have in response posted an intriguing set of suggestions to simplify, improve and reduce costs of validating the AGXP. We encourage readers to examine that article and help us decide whether the suggestions should be substituted or incorporated into the Protocol.

Thomas Perls and Nir Barzilai have now made the exciting suggestion that the AGXP use the genomes of 100 survivors of age-related diseases (over 105 years old) as the sample set for the contest. They list a number of reasons why such a set of genomes would add considerable scientific knowledge as opposed to 100 random genomes.

Comments can be submitted via Nature Precedings, or can be sent directly to the corresponding author of the validation protocol: Larry Kedes kedes[at]usc.edu. Alternatively, you may prefer to email this Nature Genetics blog at freeassociation[at]nature.com. In the latter case, please let the moderator (Myles Axton) know how you wish your comments to be posted here. They can be either attributed or anonymous, provided you let us know your email address and real name.

Dear Myles:

I truly enjoyed reading the following statements in your editorial (43:page 85) 

First…“for the parallel study of mechanisms of evolution, both the mechanisms of speciation and those operating in adaptation at the population level in the course of domestication history and agricultural improvement.” 

Second. “…we remain at heart a journal of genetic variation.” 

I admire your commitment to the above principles. 

Darwin was inspired by domestication of plants and animals by farmers and animal fanciers, and he asked how variation was molded by nature. 



The great triumvirate – Fisher, Haldane and Wright were not only inspired by Darwin, but also intimately associated with plant and animal breeding. That is why their work is so practical, meaningful, endearing and enduring. Perhaps it may not be an exaggeration if I mention that to a large extent, we are yet to transcend the limits (should we call it the Fisher-Haldane-Wright limit?) set by these visionaries.

 The later ones such as Kimura, Ohta, Nei, Mather, McClintock, Beadle to name a few, were all trained in plant breeding. Similarly, Lush, Robertson, Cockerham, Henderson et al. were animal breeders. Examples such as the origin of cultivated wheat, cotton and sunflower are exhilarating. Indeed, these discoveries absolutely dwarf the present craze in structural/copy number variation – Please don’t mention this to Evan Eichler or Jim Lupski! 



Single genes could transform and even destroy agriculture and livestock. I am sure humans are no different from these general phenomena. These views must be addressed in our own times. 

It is a pleasure to witness this wonderful progress and to see a journal committed to advance these fundamental principles of biology. 



Sincerely yours

- Raju Govindaraju

Dr Raju Govindaraju takes me to task for skipping from 1906 to 1919 without crediting the advances in genetics from the field of plant breeding. It is a fascinating history deserving of books rather than just a paragraph in an editorial. I thank him for his comments:

“I congratulate you on your Editorial titled, “In praise of maize.” (Nature Genetics 42: 1031). It is heartening to note that Nature Genetics is finally taking a look at other organisms and questions (in addition to human GWAS!) that also throw light on human genetics and health.

I would like to make the following remarks on your editorial:

1. Although the title rhymes well…perhaps “In praise of crops,” or plants (Arabidopsis or yeast or other plants are not crops) or something similar would have been more appropriate.

2. The sentence “The discipline (i.e., the science of genetics – I suppose) ….current genetic methods…” is misleading as it glosses over many important points, and gives the impression all of that happened only after 1919.

a. The big intellectual boost for genetics came in the 1910’s using plants are: Inbreeding and hybrid corn (East, Shull, Jones); pure line theory, gene, genotype, phenotype (Beans; Wilhelm Johanssen); size inheritance (Tobacco; East); size and shape in plants (Emerson); wheat color (Nilsson Ehle) etc.

Fisher’s monumental work of 1918 was the predecessor of his 1925 work. The latter introduced “how to do experiments” with replication, randomization and local control. Harvard awarded him an honorary degree citing this work. In other words, “the big boost” happened prior to 1919. Only “Modern Synthesis” happened following Fisher’s 1925 work in the early 30’s (Fisher, Haldane and Wright and others later)c. Rothamstead’s focus on maize research was minimal. They focused largely on the application of fertilizers and crop yields.

Thank you for your interest.

Regards,

D.R. Govindaraju"

It is interesting to see how new views are building up as more authors join the initiative to develop the draft standards paper. It is also fascinating to see them experiment with new tools and services for a diverse author group. There is now an active discussion page for authors and referees of the standards paper at Wikigenes. A collection of relevant supporting papers has been assembled on Mendeley. It would be great if the corresponding authors have time to submit a revised draft to Nature Precedings before the authoring deadline so that we can see how the reference copy has evolved.

Now there is another way to make your contribution to the standards document “Principles for the post-GWAS functional characterisation of risk loci” described in the previous post, automatically becoming a co-author in the process. Wikigenes creator Robert Hoffmann has set up a splash page, introducing the paper and a link to the editable version at Wikigenes.

We do not anticipate problems in assigning authorship and author roles since it is obvious whether you have contributed conceptual input or corrected punctuation. Corresponding author Ian Mills and editor Myles Axton will check and if necessary edit author names and roles for the final version to be submitted for publication after December 20th 2010.

To follow changes of the article you can subscribe to the following feed

https://www.wikigenes.org/e/pub/e/84.rss?all=1

If you have problems with the feed please address your queries to Wikigenes, not to Free Association blog, bearing in mind this is an experiment.

A group of researchers funded by the NIH Post-GWAS Initiative have produced a draft standards document for the cancer genomics field entitled “Principles for the post-GWAS functional characterisation of risk loci” that can be found in preprint form at Nature Precedings archive. This document is intended for publication as a Perspective in Nature Genetics. Because field-specific criteria supported by broad consensus are more likely to be useful, we have decided to invite all stakeholders to become co-authors or peer referees of this document in place of editorially supervised peer review. This is very much an experiment, some editorial judgment may be needed, or formal expert review may or may not be needed in this case.

Background on the journal’s involvement in developing field-specific standards by soliciting community consensus can be found in two Editorials, “Discussing Standards” and “On beyond GWAS”.

To become a contributor you have several options:

1) Comment using the Nature Precedings comment function.

2) Email your comments and text to the corresponding authors at snpfunction(at)gmail.com whether or not you want to be considered for co-authorship.

3) Post your comments to the Nature Genetics blog freeassociation(at)natureny.com letting the moderator know whether you want your comments to be attributed to you or anonymous.

4) Although our aim is consensus, substantial distinct and dissenting perspectives may need to be submitted as preprints to Nature Precedings. These can be combined into a themed Collection of preprints that will not preclude their eventual publication in journals, for example as Correspondence.

Substantial conceptual contributions and substantial contributions to the writing of the submitted document will be acknowledged with authorship in the final document if submitted before the community review deadline, December 20th 2010. If you wish to contribute to the document as a referee only, you may stipulate that you do not want co-authorship.

Hello,

Thank you for contacting the 23andMe Team. Our apologies for the delay responding to your email inquiry. At this time we do not report on Neanderthal SNP’s.

Best regards,

The 23andMe Team

Editorials June 2006-May 2009

2004-6 Editorials

The Journal’s Standards

GWAS and CNV associations for neuropsychiatric studies

MIAME compliant transcriptome data

Transparent papers are cited better

Contributor ID and attribution

Incentives to make data public

The Human Variome Project 1, 2

Microattribution reviews

Corresponding authors and consortium authorship

Publisher metadata and PubMed

Advances in fields of genetics

Human methylome

Malaria genomic resources

GWAS for prostate cancer

eQTLs

Transcriptional networks

RNA isoforms

Agricultural genomics

CNV detection

de novo CNV

Conferences

ASHG 2006

Nephrogenetics 2007

GCD07

GCD08

ICG2008 1, 2

Social and Political

Preserving diverse science during NIH budget cuts

US research competitiveness

EU funding for research

Arab genomics

Genetic nondiscrimination legislation

Genetics for developing nations

Encouraging creative research

Personal genomics 1, 2

Darwin’s legacy

History of the journal

Limits of scientific analogies

My thanks to the delegates of the second Genomics of Common Diseases Conference:

Many thanks to all of you, the participants, a highly interconnected network of collaborators and competitors who form a core area of Nature Genetics’s content. You are our readers, authors and referees. That core, like the journal, is expanding internationally. Just as, when we send your research to review, we try to add a new referee alongside those experienced and calibrated experts we have relied upon to produce papers that are useful research tools; I hope that you will be able to extend your networks of excellence in a similar manner.

It is fascinating to see these collaborative networks built by the NHGRI, the Broad, and Wellcome, extend internationally to address diseases that are of local concern: malaria, HIV, tuberculosis, diabetes and cancer. As the techniques develop, these long-range collaborations can meet with success.

But, I know from lab visits in many countries that building local capacity matters a great deal to developing and emerging nations. As DNA sequencing becomes cheaper and the tools of discovery become reliable commodities, it is populations with particular characteristics and demographics that are crucial. Here I would cite the success of the Pan-Asian SNP initiative from Singapore in mobilizing the participation of regional collaborators, the new genome centers of Mexico, South Africa and several nations in the Arab world, building centers of excellence to address genetic problems of local significance. These patterns of collaboration go beyond the paradigm of long-range collaboration with established experts in developed countries to build sutainable capacity with immediate neighbors.

For a developing nation, making an essential contribution to the global understanding of our shared human genome is an important source of pride. With the new concentration on genomics come beneficial coat-tail effects: education and provision of primary health care. So, I hope you will join me in a toast to international collaboration with a commitment to capacity building, in the hope that we can make some of these common diseases less common.