“tracks the web technology ecosystem commonly referenced as “Web 2.0.” We collect facts and figures about new web products, startup companies, key startup employees, and the funding dollars powering their growth.”
3. 23andMe is a pioneering web-based, personalized genomics startup (founded in April, 2006) with a high-tech service, a definitely “Web 2.0″ website & investors most Web 2.0 startups only dreaming of.
Gábor Zsurka, scientist and developer made another upgrade on our favorite human mitochondrial DNA visualization tool, MitoWheel: this time allele frequencies at polymorphic positions are included in the sequence bar in the form of a gray bar above or below a nucleotide representing the number of individuals carrying the SNP.
This is really cool as it is a definite step to turn MitoWheel into a tinkering, engineering, mtDNA hacking tool besides its core science mission:
“This can help you to design reliable PCR primers for the human mitochondrial genome. After all, you don’t want your primer’s 3′-end sitting right on a very frequent polymorphism (risking that under certain conditions you will not be able to amplify a PCR fragment from a subset of individuals).” Source: MitoWheel Blog.
- compare GenBank’s circa 3000 fully sequenced human mitochondrial genome to the revised Cambridge Reference Sequence mutation by mutation
- by harnessing the power of the colorful group view and using the +, - mutation operators (see detailed introduction) you can dig deeply into phylogenetics and haplogroups
The idea of doing biological experiments with current biotechnological methods and conducting research projects at home is quite new. There are already many names in use referring to the same concept: bioDIY, home biology, biotech DIY, garage biology.
We have a detailed case example which can be considered as the first registered, high profile biotech DIY activity starting the era of useful garage biology: Recently Hugh Rienhoff amplified his daughter’s DNA at home to help doctors figure out her genetic disorder. From the Nature cover article:
“So he bought a used PCR machine, a microcentrifuge, some small-volume pipettes and a brand new gel box. All told, the equipment cost him about $2,000. With these simple tools and some sequence-specific DNA primers of his own design, he could pick the relevant genes out of his daughter’s genome and amplify them enough for sequencing. Freezing the samples and packing the tiny tubes on ice, Rienhoff sent them off for sequencing at about $3.50 a pop. He prepared upwards of 200.”
In my coming series I’d like to examine the following conditions of a mass biotech DIY movement: acquiring skills, affordable kits, tools, hardware, motivations, business opportunities and impact.
acquiring the how to skills:
- good education tools, protocols, videos, howto-s on the web
- short intensive academic or industrial lab courses available for every citizen
- cheap kits: based on the Rienhoff example, a very basic home lab can be set up out of 2-3000 dollars, which is the price of a good laptop.
says Mr. Rienhoff in an email: I bought all the equipment used from a local vendor who buys equipment at auction and from universities. All the gear is at least ten years old so it was very used and low throughput. But given that my project was incredibly focused I did not need the more sophisticated equipment.
To learn more, researchers need to collect thousands of genetic profiles – and the health data connected with each of them – to find correlations between the two. That leads to a second goal of 23andMe – to collect a large database of genetic information and then come back to you over time with invitations to provide specific health data and participate in research.
We’re not asking you to do this for purely altruistic reasons - either on our part or on yours. We’re a profit-seeking company, even though our founders and employees – and directors! – all share the vision of better understanding of everyone’s genomic make-up. As for you, the research results your data help produce could translate directly into benefits for you, or at least for your children, grandchildren and friends.
Now imagine a world (2009?) in which 23andMe genotype profiles could be uploaded to your Google Health profile with one click (see picture).
For historical reasons the standard human mitochondrial sequence, the Revised Cambridge Reference Sequence (rCRS) is a reconstruction of a single European individual’s mtDNA and contains several rare alleles. That’s why many times a usual mtDNA sequence alignment must appeal to phylogenetic historical reconstructions. The rCRS nevertheless provides a uniform nucleotide numbering scheme (0-16569). On the other hand, as there are thousands of high-quality, full-length mitochondrial sequences are now available, Robert Carter thought that it is time to construct and analyze a comprehensive human mitochondrial consensus sequence and published his efforts in Nucleic Acid Research, March, 2007: Mitochondrial diversity within modern human populations The sequence itself available as a supplementary material but with the permission of the author I copy it into this post below.
According to Robert Carter:
So far, all feedback has been good. By introducing the idea of “poly-x” sites (see later), I successfully created a technique that avoids all pre-conceived ideas about genetic history. This also allows one to effectively deal with indels, something that many authors have avoided in the mtDNA literature.
Briefly, 827 sequences were used, a master sequence alignment was created in BioEdit and BioPerl was used for all calculations using the rCRS asa template for nucleotide numbering. Read the rest of this entry »
One strategy (call it Life Extension Gets Personal) to raise awareness for the idea and technology of healthy life extension is to publicly encourage life extension “coming outs” on behalf of mainstream celebrities. In order to get an academic legitimacy for LE (which is one of the most important aim of Pimm) I am interested specially mainstream or at least well established scientific celebrities. To accomplish this project a man needs to identify target persons to interview (finding hints that the person is positive about LE), contacting these persons and publish the final piece somewhere.
As a first target Craig Venter, the genomics pioneer seemed unconventional and free minded enough to approach with the idea of a LE blogterview. On the other hand I found definite signs of his interest in longevity and life extension suggesting that if Craig Venter had been given a technological-medical chance to extend his healthy lifespan significantly he would definitely not like to die due to accumulating functional declines associated with aging within the next, say hundred years. Maybe I am wrong here, maybe I am not but to figure this situation out I translated these signs into the following blogterview questions and tried to contact him in early December, 2007. So far I reached only his nice and diplomatic PR agent, who said that maybe we have a chance to get the blogterview done in the near future. Till we get there below please find my targeted questions to Craig Venter:
1. Once I’ve read somewhere but was unable to recall later that one particular motivation behind the sequencing of your own genome was your serious life extension commitment and the belief that genomics has something to say about life expectancy. Is it true? If yes, what is the story of your life extension commitment? Is it a commitment for moderate or maximum life extension? In A Life Decoded I’ve found only one paragraph in your molecular biography explicitly on Long Life about the I405V of the CETP gene but no more hint to this important topic.
2. What do you think about Aubrey de Grey’s SENS approach? You’ve been one of the judges on the The SENS Challenge Prize organized by the Technology Review in 2005 for those “who could prove that SENS was “so wrong that it is unworthy of learned debate.” ? Who got the point there?
3. What do you think about the mitochondrial theory of aging? I was a little surprised when I’ve found that your circa 16.5kb mitochondrial DNA sequence was not published in the PLOS Biology paper: The Diploid Genome Sequence of an Individual Human Obviously it is not part of the diploid genome but I expected it at least as an appendix as those 37 genes and D-loop region can give important genetic information. Have your mitochondrial genome been sequenced already?
4. In a recent Rolling Stone interview you are saying that “There is probably nothing more important to study about human biology than stem cells.” What do you think about regenerative medicine’s role in a robust and healthy life extension technology? Read the rest of this entry »
When I had worked on my MSc thesis in biology on the relation of human mitochondrial mutations and aging the paper I used most frequently was Sequence and organization of the human mitochondrial genome by Anderson et al. published in Nature, 1981. The reason was simple: it is more of a database than a hypothesis driven article with the published 16.569 base pair sequence of the circular human mitochondrial genome (L-strand) containing 37 genes and a bigger non-coding, regulatory region. Throughout my work I had to use it as a basic reference. The sequence is a reconstruction of a single European individual’s mtDNA and contains several rare alleles. Nice figure isn’t it?
I’ve just realized with the help of genomics pioneer and warrior Craig Venter’s recent molecular autobiography Life decoded, that the brilliant two time Nobel laureate, sequencing urfather Frederick Sanger is also a coauthor of the paper. Here comes Venter: Read the rest of this entry »
Have you ever asked any important but infrequently asked questions? Have you ever heard about the first personal genome service by the biotech startup 23andMe? Here is an inF.A.Q. addressed to this company:
According to the cool 23andMe genetics educator:
According to the peer review literature this is not necessarily the case and sometimes (rarely I admit) things in your cells can happen otherwise or more scientifically (mitochondrial recombination can occur):
When 23andMe’s Maternal Ancestry Tree service is tracing the genetic path of their customers, the microarray employees are identifying their haplotypes based on the differences in the mitochondrial DNA. The company is using SNPs (single nucleotide variants) unusually both from genes in the compact mitochondrial coding region (around 15.5kb) as well as within the circa 1kb large hypervariable region to give a detailed ancestry assignment. 23andMe examines few thousand places (over 2000 says Mr. Bettinger) on the mitochondrial DNA out of the total 600,000 SNPs.
But.
In the above case the 28 year old man’s blood and muscle differed at 18 positions which allowed assignment of the two sequences to separate European mtDNA haplogroups, H and U5, former being the same as the mother’s haplotype, while the haplotype of the patient’s muscle mtDNA was identical to that of his father’s and uncle’s blood. I wonder whether 23andMe’s Illumina chips can help make things clear in cases like this. (solution: let’s sequence the whole mito genome instead of a couple thousand basepairs). So as the first step in my mission to support the mission of 23andMe to support the mission of academic research I’d like to suggest putting a short tail on the possibility of paternally inherited mtDNA in the cool 23andMe genetics education material. Read the rest of this entry »
“We are all from the same seed” - Kara Swisher summarizes what she heard from Linda Avey, co-founder of web based personal genome service 23andMe in the video interview below. Linda and the other founder Anne Wojcicki just talked about the company’s ancestry, genetic comparison and similarity seeking services, the ones that will technologically turned into a social networking service later based on shared genotypes backed by the genetical connectedness of all people (in this case all 23andMe customers). I called this idea the social networking XY.0 yesterday.
Linda’s thought was the following: “If genetics has the basis to bring people together, rather than differentiate them, that’s gonna be really interesting.” (Thanks Deepak for finding the videos)
In a recent Nature report by talented journalist Erika Check Hayden called So similar, yet so different we can find the following expert opinions on the very same topic that is commercialized and envisioned now by 23andMe (citing lengthy here, emphasis by me): In his 2000 State of the Union Address, President Bill Clinton chose to emphasize something he had recently heard from a genome researcher: that humans are all, irrespective of race, 99.9% the same genetically. “Modern science,” he told his country’s legislators, “has confirmed what ancient faiths have always taught: the most im
When I had worked on my MSc thesis in biology on the relation of human mitochondrial mutations and aging the paper I used most frequently was 
