Douglas C. Wallace
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Genetic databanks
GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).
More on 23andMe
23andMe Opens Research Portal to Outside Investigators in Effort to Advance Genomics Knowledge November 07, 2012
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By Turna Ray
In an effort to advance research that uncovers new associations between genes and diseases, direct-to-consumer genetic testing firm 23andMe has launched a new research platform that it will open up to a select group of outside investigators who then can bolster the company's findings with their own.
23andMe this week announced that it will accept applications from a "limited number" of academic researchers who propose new ideas for analyzing the company's data. These projects can seek to use 23andMe's data in a number of ways, including identifying new gene-disease associations, exploring new phenotypes linked to established gene markers, looking for pharmacogenomic associations, or honing in on the frequency of rare mutations in the larger population.
"Our primary objective with the research portal is to speed the discovery process so that new genetic discoveries can advance understanding of human genetics and biology," 23andMe spokesperson Catherine Afarian told PGx Reporter.
"We wanted to find a way to connect … researchers from all over the world with different areas of specialty to our vast amounts of data," Afarian added. "We believe the Research Portal can do this efficiently and the potential for discoveries is really exciting."
The data included in the portal will be gleaned from 23andMe's direct-to-consumer genotyping service, called the Personal Genome Service. Researchers chosen to participate in the beta version of the Research Portal will have access to genotype-phenotype data collected from 23andMe's PGS customers who have consented to submit their data for research or from participants of company-sponsored studies. The data will be de-identified and provided under a protocol approved by an institutional review board.
According to information provided by 23andMe about its Research Portal Beta Program, selected researchers will gain access to genome-wide association analysis summaries for 50 phenotypes. 23andMe will provide information about its genotyping platform, details about the chosen phenotypes the company collects, and demographic characteristics represented in the data.
"The 50 phenotypes that will be included have not yet been selected," Afarian said. "They will be chosen in partnership with organizations participating in the beta development of the Research Portal."
Eventually, 23andMe hopes that the beta effort will grow from 50 phenotypes to hundreds. As this beta project progresses, the firm will add additional features to the portal that will allow researchers to make more "sophisticated queries and analyses."
Only researchers who work for non-commercial public or private institutions can apply to gain access to 23andMe's research portal. 23andMe will grant collaborators non-exclusive access to the aggregate-level data in the portal for six months. The data "cannot be distributed, shared, or sold to third parties," 23andMe states in an online description of the beta project.
If researchers wish to publish their findings, they must do so in open-access scientific journals and follow 23andMe's publication best practices. "Currently those best practices only allow for the publication of summary statistics for up to 10,000 SNPs," the company stated. Additionally, 23andMe will not cover the cost of additional data collection from research participants, if a collaborators' research proposal requires it.
However, the data emerging from these research collaborations will not show up in public databases. Afarian noted that submissions to public databases are not allowed by its IRB-approved protocols.
23andMe's spokesperson highlighted that the company is working to grow public knowledge of gene-disease associations in other ways. "23andMe already favors publishing in open-access journals and regularly posts to pre-print servers," Afarian said. "The company also posts its research findings on its own website … and incorporates findings into the reports that are provided to customers of the PGS."
In a recent paper published in the European Journal of Human Genetics, policy experts urged payors and health regulatory bodies to instate regulations that would require genetic testing companies to share genotype-phenotype interpretation data in public databases. This type of open environment, the paper's authors said, is critical to improving knowledge of how gene variants are linked to diseases, particularly as whole-genome sequencing technologies uncover more and more markers that we know little about (PGx Reporter 11/2/2012).
Likewise, the American College of Medical Genetics and Genomics this week released a position statement urging payors, regulators, and genetic testing providers to work on mechanisms for ensuring that the interpretation of genomic variants be shared in publicly available resources.
Separate from the Research Portal beta project, 23andMe does "hope to make significant contributions to the understanding of variants of unknown significance," Afarian said. "Our work with exomes is also still in the very early stages and we are in the process of understanding how best to manage this data."
Last year, 23andMe launched an exome sequencing pilot project that offered customers a chance to get 50 million DNA bases sequenced for $999. At the American Society of Human Genetics Meeting this week, the company will present a poster on how it is handling some of the data challenges associated with its exome sequencing effort.
Researchers interested in gaining access to 23andMe's data in the Research Portal have until Dec.14 to submit their applications.
Turna Ray is the editor of GenomeWeb's Pharmacogenomics Reporter. She covers pharmacogenomics, personalized medicine, and companion diagnostics. E-mail her here or follow her GenomeWeb Twitter account at @PGxReporter.
Wayne Pfeiffer Suggestions
Hi Doug,
Here is information on 23andMe:
http://en.wikipedia.org/wiki/23andMe
Note the following:
"In June 2011, 23andMe announced it had accumulated a database of more than 100,000 individuals."
These data are not generally available, but you might be able to get access to an anonymized version of some of them if you were able to interest someone at 23andMe to collaborate with you.
A data set of fewer individuals, but with more detail on each, is being generated by the 1000 Genomes Project:
http://en.wikipedia.org/wiki/The_1000_Genomes_Project
These data will be publicly available and are just being rolled out. However, I don't know how useful they might be for what you want to do.
Regards, Wayne
CHOP Philadelphia
http://www.chop.edu/doctors/wallace-douglas-c.html http://stokes.chop.edu/publications/press/?ID=566 Doug Wallace
NEW: 267 425 3034 - Abigail
215 590 3800 <Doug Wallace> wallace1@chops.email.edu <Dmitria Chalkias> chalkiad@chops.email.edu (works for chops, lives/does the work at UCI) Postdoctoral Scholar at CHOP Research Institute, Center of Mitochondrial and Epigenomic Medicine
OLD:
267 425 3054 Doug
215 595 3034 Madeline and Doug Wallace
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Contact Us
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New integrations
Publications
Wallace, Douglas C. 2010. The epigenome and the mitochondrion: bioenergetics and the environment. Genes & Development 24(15): 1571-3
- Why Do We Have a Maternally Inherited Mitochondrial DNA? Insights from Evolutionary Medicine. 2007. Douglas Wallac
- Abstract
The human cell is a symbiosis of two life forms, the nucleus-cytosol and the mitochondrion. The nucleus-cytosol emphasizes structure and its genes are Mendelian, whereas the mitochondrion specializes in energy and its mitochondrial DNA (mtDNA) genes are maternal. Mitochondria oxidize calories via oxidative phosphorylation (OXPHOS) to generate a mitochondrial inner membrane proton gradient (DeltaP). DeltaP then acts as a source of potential energy to produce ATP, generate heat, regulate reactive oxygen species (ROS), and control apoptosis, etc. Interspecific comparisons of mtDNAs have revealed that the mtDNA retains a core set of electron and proton carrier genes for the proton-translocating OXPHOS complexes I, III, IV, and V. Human mtDNA analysis has revealed these genes frequently contain region-specific adaptive polymorphisms. Therefore, the mtDNA with its energy controlling genes may have been retained to permit rapid adaptation to new environments.
Douglas C. Wallace. 2009. Mitochondria, bioenergetics, and the epigenome in eukaryotic and human evolution. Cold Spring Harb Symp Quant Biol. 2009;74:383-93. Epub 2009 Dec 2.
Douglas C. Wallace. 2010.
Douglas C. Wallace. 2010. Bioenergetics, the origins of complexity, and the ascent of man — PNAS. Published online before print May 5, 2010, doi: 10.1073/pnas.0914635107 PNAS May 11, 2010 vol. 107 no. Supplement 2 8947-8953.
- Author Affiliations. Organized Research Unit for Molecular and Mitochondrial Medicine and Genetics and Departments of Ecology and Evolutionary Biology, Biological Chemistry, and Pediatrics, University of California, Irvine, CA 92697-3940
- Abstract. Complex structures are generated and maintained through energy flux. Structures embody information, and biological information is stored in nucleic acids. The progressive increase in biological complexity over geologic time is thus the consequence of the information-generating power of energy flow plus the information-accumulating capacity of DNA, winnowed by natural selection. Consequently, the most important component of the biological environment is energy flow: the availability of calories and their use for growth, survival, and reproduction. Animals can exploit and adapt to available energy resources at three levels. They can evolve different anatomical forms through nuclear DNA (nDNA) mutations permitting exploitation of alternative energy reservoirs, resulting in new species. They can evolve modified bioenergetic physiologies within a species, primarily through the high mutation rate of mitochondrial DNA (mtDNA)–encoded bioenergetic genes, permitting adjustment to regional energetic environments. They can alter the epigenomic regulation of the thousands of dispersed bioenergetic genes via mitochondrially generated high-energy intermediates permitting individual accommodation to short-term environmental energetic fluctuations. Because medicine pertains to a single species, Homo sapiens, functional human variation often involves sequence changes in bioenergetic genes, most commonly mtDNA mutations, plus changes in the expression of bioenergetic genes mediated by the epigenome. Consequently, common nDNA polymorphisms in anatomical genes may represent only a fraction of the genetic variation associated with the common “complex” diseases, and the ascent of man has been the product of 3.5 billion years of information generation by energy flow, accumulated and preserved in DNA and edited by natural selection.
- Keywords: Evolution - mitochondria - natural selection - human origins - common diseases
- Charles Darwin and Albert Russel Wallace hypothesized that the environment acts on individual variation via natural selection to create new species (1, 2). However, nothing in the concept of natural selection requires that biological systems should evolve toward ever greater complexity. Yet, throughout the more than 3.5 billion years of biological evolution (3), life has generated ever more complex forms. What, then, drives increasing biological complexity, and what are its implications for the ascent of man?
- Section: Bioenergetics and the Origin of Biological Complexity
- In a thermodynamically isolated system, complex structures decay toward randomness. However, in nonequilibrium systems, the flow of energy through the system generates and sustains structural complexity, and nonhomogeneous structures embody information (4, 5).
Maps: Not by Wallace
Homo Sapiens Events
L. David Roper' Homo Sapiens Events (www.roperld.com) (roperld@vt.edu)
The climate data here is very interesting: current global warming a major trend as against solar insolation and against rise in human population.
Ancestries of Satyaji Kaivalya SYAHIN
see Matri genome map
see Patri genome map
http://www.kaisyahin.id.au/ft/Geno/ft_fathers_matri.html
http://www.kaisyahin.id.au/ft/Geno/WorldMigrations.jpg
Eurasian Adam Neville Map
Mitochondrial Eve 150,000 ybp Africa -> Europe
Mitochondrial Eve 150,000 ybp Africa -> Asia
Other references
Pritchard, Jonathan K. 2010. How We Are Evolving: New analyses suggest that recent human evolution has followed a different course than biologists would have expected. – Scientific American Magazine September 22, 2010. In Brief:
- As early Homo sapiens spread out from Africa starting around 60,000 years ago, they encountered environmental challenges that they could not overcome with prehistoric technology.
- Many scientists thus expected that surveys of our genomes would reveal considerable evidence of novel genetic mutations that have recently spread quickly throughout different populations by natural selection—that is, because those who carry the mutations have greater numbers of healthy babies than those who do not.
- But it turns out that although the genome contains some examples of very strong, rapid natural selection, most of the detectable natural selection appears to have occurred at a far slower pace than researchers had envisioned.
Peeples, Lynne. 2009 Did Lactose Tolerance First Evolve in Central, Rather Than Northern Europe? Tolerance for cow's milk may have arisen in the Neolithic period among the Linearbandkeramik culture of central Europe, not with the Lutefisk-lovers of Scandinavia – Scientific American Magazine | August 28, 2009
Hawkes, . 2009. Human Evolution II: Recent Evolution; and "Becoming Human" NOVA Preview November 03, 2009 – Scientific American Magazine – Science Talk
Swaminathan, Nikhil. 2006. African Adaptation to Digesting Milk Is "Strongest Signal of Selection Ever" December 11, 2006 – News –Scientific American Magazine
Swaminathan, Nikhil. 2008. When Incest Is Best: Kissing Cousins Have More Kin ...biotechnology company deCODE genetics say that when third and fourth... Scientific American Magazine February 08, 2008
Swaminathan, Nikhil. 2007. Not Milk? Neolithic Europeans Couldn't Stomach the Stuff ...direct evidence of the evolution of lactase-persistence (the ability to... –Scientific American Magazine February 27, 2007 – News
Biello, David. 2007. Culture Speeds Up Human Evolution: Scientific American. Analysis of common patterns of genetic variation reveals that humans have been evolving faster in recent history. Scientific American | December 10, 2007
Harmon, Katherine. 2009. (News Blog:) How fast are humans mutating? Humans seem to have accelerated the pace of just about everything from... . Scientific American | August 27, 2009.
Editor in Chief John Rennie 2009. Introduction to Special Issue. The Evolution of Evolution Scientific American Magazine | January 07, 2009 – Science Talk
Stix, Gary. 2008. The Migration History of Humans: DNA Study Traces Human Origins Across the Continents: DNA furnishes an ever clearer picture of the multimillennial trek from Africa all the way to the tip of South America. Scientific American Magazine | July 07, 2008.
Jeffrey L. Ward maps
Ruiz-Pesini, E., Lott, M.T., Procaccio, V., Poole, J., Brandon, M.C., Mishmar, D., Yi, C., Kreuziger, J., Baldi, P., and Wallace, D.C. 2007. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Research 35 (Database issue):D823-D828. URL: http://www.mitomap.org. http://freepages.genealogy.rootsweb.ancestry.com/~ncscotts/GG/mt_DNA.htm
- The Cradle of Humanity - © 2005 Jeffery L. Ward ENLARGE TO 150
- [mtDNA Migrations Map - © 2002 MITOMAP
- [mtDNA Migrations Map-1 - © 2005 FTDNA
- [mtDNA Migrations Map-2 - © 2006 FTDNA
- [mtDNA Migrations Map-2 (revised) - © 2006 FTDNA
- [mtDNA Migrations Map - © 2006 NYTimes
