How do I know ‘my sequence’ is really mine?

by jurvetson

Celebrity genomics without the Y chromosome: Glenn Close has her genome sequenced
[Via Genetic Future]

Zoe McDougall from Oxford Nanopore points me to a press release from Illumina announcing a new era of celebrity genomics:

Illumina, Inc. (NASDAQ:ILMN) today announced that it has sequenced the DNA of American actress Glenn Close, the first publicly named female to have her DNA sequenced to full coverage. The service was completed in Illumina’s CLIA certified and CAP accredited laboratory utilizing Illumina’s Genome Analyzer technology and following the established process shown at http://www.everygenome.com/. Ms. Close’s DNA was sequenced to an average depth greater than 30 fold, providing information on SNP variation and allowing for the analysis of other structural characteristics of the genome such as insertions, deletions and rearrangements. Specifically, over 95% of the known genome was reported, including over 12 million genotype calls on previously documented SNPs. In addition, 379,000 SNPs previously not reported in any public database were found.

While there’s nothing new about celebrity genomics, previous examples have largely been “scientific celebrities” (such as Jim Watson and Craig Venter) – so Close is the first genome with broader celebrity status, and also the first named individual without a Y chromosome to rack up her 6 billion base pairs. That’s of negligible interest scientifically, but there’s no doubt this will dramatically increase the public profile of whole genome sequencing.
(Added in edit: I’ve just been reminded by Misha Angrist that technically Close isn’t the first named female to be sequenced – a press release back in May 2008 announced the sequencing of Dutch geneticist Marjolein Kriek, although we’re yet to see an actual publication of those data and the quality of the sequence is unclear.)

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One worry I have with commercial DNA sequencing companies – how do I really know that the DNA sequence they give me is really mine? At this point, a company gets several 10s of thousands of dollars ($48,000 currently) and hands me a sequence.

What sort of validation is present to make sure that they really performed what they say they perform (30-fold depth, etc.)? How can I be certain they do not just make up some sequence and give it to me? How can I be certain the sequence is really mine?

I looked around on Illumina’s site some and could not find anything about the validation of its protocols, what it does to maintain the trust of its customers that it is actually providing what it says it does, or just what its quality control process is?

Now, Illumina is unlikely to be doing anything fraudulent here. It is simply not going to benefit them at all. But I wonder about what happens as the price drops and other companies entire the field. What happens when they appear on infomercials? How can we make sure they are all ethical and dot the actual sequencing?

I am sure this will be all regulated and validated but even that could fail. Look at the forensic labs that were doing work that determined a person’s guilt or innocence yet failed miserably at actually providing the correct data.

Perhaps when each of us has our own sequence, we can get together as families and compare each other’s genome. Comparison will inform us whether the sequences follow Mendelian inheritance or not.

This is not something that is going to slow things down. I just worry what happens when someone selling nutriceuticals right now decides to offer their own sequencing program. What is the process for validatation?

How technology allows new questions to be asked and answered

from Wikipedia

Sequencing genome of entire family reveals parents give kids fewer gene mutations than was thought
[Via EurekAlert! - Biology]

(University of Utah Health Sciences) Researchers at the University of Utah and other institutions have sequenced for the first time the entire genome of a family, enabling them to accurately estimate the average rate at which parents pass genetic mutations to their offspring and also identify precise locations where parental chromosomes exchange information that creates new combinations of genetic traits in their children.

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Until recently, the ability to sequence the genomes of 4 individuals was pretty much out of reach. The cost was too high and the time needed was also pretty high.

But sequencing technologies have improved to rapidly that now a genome can be sequenced in months for less that $10,000. So now we can get at questions that used to be really hard but the technology now makes much easier.

Sequencing the DNAs of a family permits us to really understand not only how many mutations are passed from parent to child, but also almost all the intriguing steps of how DNA is exchanged between chromosomes in an event called crossing over. This is an important aspect of increasing genetic diversity is sexual animals.

Now we know the exact location of these events. Cool.

Simple solutions to complex problems seldom succeed

by r-z

More maize ethanol may boost greenhouse gas emissions
[Via Eureka! Science News]

In the March issue of BioScience, researchers present a sophisticated new analysis of the effects of boosting use of maize-derived ethanol on greenhouse gas emissions. The study, conducted by Thomas W. Hertel of Purdue University and five co-authors, focuses on how mandated increases in production of the biofuel in the United States will trigger land-use changes domestically and elsewhere. In response to the increased demand for maize, farmers convert additional land to crops, and this conversion can boost carbon dioxide emissions.

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Changing land use practices will remove any positive effects of using corn for biofuels. ‘The researchers’ main conclusion is stark: these indirect, market-mediated effects on greenhouse gas emissions “are enough to cancel out the benefits the corn ethanol has on global warming.”

These sorts of analyses will be necessary in order to actually find ways to make biofuels a net positive. We shall see.

And perhaps dinosaurs were just as unusual as chickens

by jaybergesen

Half-cock chicken mystery solved
[Via BBC News | Science/Nature]

Researchers in Edinburgh say they have solved the mystery of why some chickens hatch out half-male and half-female.

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How chickens and birds develop sexually seems very different than how mammals do. So it is possible for a chicken to develop with both male and female cells in it. Weird.

New models for the news

by baligraph

Is the Future Of News Dependent On The Generosity Of Billionaire Philanthropists?
[Via Xeni @ Blogging.la]

James Rainey, at the The Los Angeles Times, reports on the “Bay Area News Project” financed with $5 million by Warren Hellman, a local philanthropist.

The project has a CEO with a $400,000 salary and its editor, Jonathan Weber, used to run the Industry Standard, a popular magazine during the dotcom era.

Bay Area News Project has high hopes, few employees – latimes.com

When the Bay Area News Project launches its website in late spring or early summer, it will be just the latest — and perhaps the most ambitious — nonprofit venture among a string of similar start-ups.
…
“On the one hand, you want to have big ambitions,” Weber explained from his office, a stylish but spartan space donated by a San Francisco law firm. “On the other hand, you don’t want to be presumptuous about what you can do with a small newsroom.
…
The project will have to rely on paid interns from one of its partners, UC Berkeley and the Graduate School of Journalism, to provide some of that coverage. The university also intends to bring an R&D component.
…
Weber has committed to covering public institutions like government, education and the law. But he conceded in a recent meeting with freelance writers that even this civic mandate would be an enormous challenge. And with a couple of other editors likely to come on board in a week or two, he’s yet to hire another editorial employee.
…
“I think that in some ways we are kind of entering a Golden Age of journalism,” Weber said, “because the barriers to entry have been largely removed.”

Foremski’s Take: The great thing about emerging new media business models, is if one media organization figures it out – we all figure it out – we can all adapt and adopt a similar model. It’s win-win.

But I don’t see the Bay Area News Project being able to do that, for several reasons:

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New business models, particularly for things like news, will have to be constructed. A pure non-profit has some possibility but I tend to favor something like a low profit limited liability corporation (L3C). It has the possibility of bringing together the best aspects of both for-profit and non-profi entity.

I wrote about this last year for another type of news media organization, Xconomy. This news outlet targets very specific, high value news in biotech and high tech in a limited number of cities in the country. They have a continuing stream of underwriters and partners to help pay. They also put on events and panels to connect people and ideas. This is another model worth examining.