Google invests into DNAnexus: aging-driven big data bioinformatics without the Hadoop Ecosystem?

First time DNAnexus made me think a little about what they can achieve was when they came up with an alternative search and browse interface for the complete Sequence Read Archive (SRA) database. They came to the ‘rescue’ as NCBI discontinued SRA in 2011 although later they’ve changed their mind, so SRA is still up and running there.… Continue reading Google invests into DNAnexus: aging-driven big data bioinformatics without the Hadoop Ecosystem?

Aging-centric genetic health database in California: 100k people, ~65yrs, 700k SNPs, telomeres too

Kaiser Permanente alongside with UCSF plans for genetic analyses of an unprecedented 100,000 older Californians, the Technology Review writes in Massive Gene Database Planned in California The effort will make use of existing saliva samples taken from California patients, whose average age is 65. Their DNA will be analyzed for 700,000 genetic variations called single-nucleotide… Continue reading Aging-centric genetic health database in California: 100k people, ~65yrs, 700k SNPs, telomeres too

Mapping neurons without glial cells ~ SNP genotyping w/o whole sequencing?

Nature’s Journal Club column is usually a good & always a short read providing exciting angles on scientific topics/papers from good researchers. Recently ‘neuroscientist’ Dave Featherstone argued for a broader approach to brain mapping by not restricting it only to the connectome between neurons. Neurons are making up less than 10% of the human brain… Continue reading Mapping neurons without glial cells ~ SNP genotyping w/o whole sequencing?

Visualize 23andMe haplogroup defining SNPs with Mitowheel!

Last Friday 23andMe came up with Haplogroup Tree Mutation Mapper which is the first experimental feature that can be instantly tested by biogeek customers (a large portion of  the company’s customer base) in its freshly launched technology sandbox 23andMe Labs that is much like Google Labs. Haplogroup Tree Mutation Mapper “shows you which particular mutations… Continue reading Visualize 23andMe haplogroup defining SNPs with Mitowheel!

Practical DNA: Hugh Rienhoff’s got a story to tell

After the Nature cover article Hugh Rienhoff and the story of My Daughter’s DNA is now covered by Wired magazine. I wrote about Hugh (a fellow SciFoo Camper) as an example of any future bioDIY effort in The conditions of a mass biotech DIY movement and now the Wired piece gives us more context and details… Continue reading Practical DNA: Hugh Rienhoff’s got a story to tell

Nature Personal Genomics Very Special

The newest Nature issue concentrates on personal genomics and its consequences via many types of articles some of them with free access. I only read 1 piece so far by Erika Check Hayden, who has the exclusive freedom at Nature to always pick the best stories and write on any of them, but being a… Continue reading Nature Personal Genomics Very Special

Golden day for 23andMe: Time’s 2008 Invention of the Year

This is a golden day for 23andMe despite all crisis worries: Mountain View, CA (PRWEB) October 30, 2008 — TIME Magazine announced today that the Personal Genome Service™ from 23andMe, Inc. has been named 2008’s Invention of the Year. 23andMe was chosen as the year’s most significant invention for its exceptional work in making personal… Continue reading Golden day for 23andMe: Time’s 2008 Invention of the Year

Mountain View – Budapest: 20 days to get my 23andMe profile!

I ordered my first commercial genetic profile from 23andMe on the 9th of September online, FedExed my 2 ml saliva from Budapest to 23andMe, Mountain View on the 12th of September. I got the results today. That said within 3 weeks since the birth of the idea I purchased more than 500 000 SNPs of… Continue reading Mountain View – Budapest: 20 days to get my 23andMe profile!

Just ordered my 23andMe kit for $399+shipping!

It was time for me to enter personally into the age of commercialized-personalized genetics/genomics and not just to talk about it! New price, new customers! Here is my suggestion to the sales department of 23andMe! 23andMe Democratizes Personal Genomics With New Analytical Platform

Halcyon Molecular: whole genome sequencing well under $1000?

Halcyon Molecular is a quite ambitious startup,  don’t you think? What we do: Halcyon Molecular is developing an ultra-low-cost DNA sequencing technology. Our single molecule approach does not require PCR amplification and will allow for megabase read lengths with simultaneous determination of methylation pattern. We aim to sequence entire human genomes de novo for well… Continue reading Halcyon Molecular: whole genome sequencing well under $1000?

Innovation stop: “All they’ve done is created an extra billing event for the doctor”

It’s my first real encounter with a situation in which the officials of the state of California are clearly against innovation for financial reasons obvious enough (is enough): Wired Science, Alexis Madrigal, upcoming BioBarCamper: Exclusive: DNA Tester Reveals Cease-and-Desist Letter Wired.com has obtained a copy of the cease-and-desist letter sent to Navigenics by the state… Continue reading Innovation stop: “All they’ve done is created an extra billing event for the doctor”

Dear StartupSearch: Is 23andMe a web-based startup or not?

1. A start-up is a company with a limited operating history (Wikipedia). 2. Startup search “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… Continue reading Dear StartupSearch: Is 23andMe a web-based startup or not?

Mitowheel now helps you design PCR primers for mitochondrial DNA!

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… Continue reading Mitowheel now helps you design PCR primers for mitochondrial DNA!

Mitowheel upgrade: phylogenetics in motion

Gábor Zsurka has built some killer functions into Mitowheel, the human mitochondrial DNA visualization tool: – 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… Continue reading Mitowheel upgrade: phylogenetics in motion

The conditions of a mass biotech DIY movement

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… Continue reading The conditions of a mass biotech DIY movement

Biotechies at O’Reilly ETech, March 3 – 6, San Diego

The O’Reilly Emerging Technology Conference (ETech) is on and this year they had a growing number of biotech related sessions. Fellow SciFoo Campers like Hugh Rienhoff and Timo Hannay, Makers like Phil Torrone and Limor Fried, Brain Hackers like Ed Boyden are visiting and many more.

The second goal of 23andMe: using customer’s real health data later

Esther Dyson‘s honest post on getting the genotype-health risk correlation statistics right on The Spittoon blog: What You Can Do for 23andMe (and Future Generations) 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… Continue reading The second goal of 23andMe: using customer’s real health data later

The human mitochondrial consensus genome sequence by Robert Carter

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… Continue reading The human mitochondrial consensus genome sequence by Robert Carter

Craig Venter and the life extension drive: blogterview questions

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… Continue reading Craig Venter and the life extension drive: blogterview questions

The first human genome project: mitochondrial DNA, 16.6kb, 1981, Cambridge

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… Continue reading The first human genome project: mitochondrial DNA, 16.6kb, 1981, Cambridge

inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa?

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… Continue reading inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa?

23andMe: Genetics brings people together, rather than differentiate

“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… Continue reading 23andMe: Genetics brings people together, rather than differentiate