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We’re all mutants now

Enlarge / We might all be mutants now, but don't break out the spandex just yet.

The field of study called population genetics played a critical role in the development of modern biology, helping unite Mendelian genetics and Darwinian evolution into one coherent framework. In most genetics classes, though, it typically gets plowed through in a simplified form in a single lecture. I suspect this is because it involves a lot of math, and most biologists like being in the field precisely because it's generally possible to avoid all but the simplest math.

Nevertheless, population genetics has some critical insights to offer in the area of modern genomics, as evidenced by a paper that appeared in this week's edition of Science. Some population geneticists have looked into the results of the search for mutations in genome data. Their conclusion: the human population explosion has led to the appearance of many new, rare mutations in the human population, and it's throwing all the math off, which has some serious implications for medical research.

At the simplest level, population genetics can help us predict how often a mutation should be present in a specific population. Feed its equations things like the population size, how harmful or beneficial the mutation is, the typical mutation rate, and so forth, and it will spit out a nice prediction of what the final frequency of the mutation should be. It nicely demonstrates why even harmful mutations stick around at low levels in a population, even as evolution is doing its best to get rid of them.

Read more on Ars Technica…


We’re all mutants now

Enlarge / We might all be mutants now, but don't break out the spandex just yet.

The field of study called population genetics has played a critical role in the development of modern biology, helping unite Mendelian genetics and Darwinian evolution into one coherent framework. In most genetics classes, though, it typically gets plowed through in a simplified form in a single lecture. I suspect this is because it involves a lot of math, and most biologists like being in the field precisely because it's generally possible to avoid all but the simplest math.

Nevertheless, population genetics has some critical insights to offer in the area of modern genomics, as evidenced by a paper that appeared in this week's edition of Science. Some population geneticists have looked into the results of the search for mutations in genome data. Their conclusion: the human population explosion has led to the appearance of many new, rare mutations in the human population, and it's throwing all the math off, which has some serious implications for medical research.

At the simplest level, population genetics can help us predict how often a mutation should be present in a specific population. Feed its equations things like the population size, how harmful or beneficial the mutation is, the typical mutation rate, and so forth, and it will spit out a nice prediction of what the final frequency of the mutation should be. It nicely demonstrates why even harmful mutations stick around at low levels in a population, even as evolution is doing its best to get rid of them.

Read more on Ars Technica…


Nanopore tech brings rackmounted genome machines, USB-based DNA sensors

The DNA sequencing systems on the market produce their output by synthesizing new DNA in a way that allows them to read the identity of the base that's added. There have been a few ideas floated around that involved reading the bases directly from existing molecules, but the technical challenges of doing so have kept anyone from bringing these technologies to market. Now, a company called Oxford Nanopore has announced that it will be selling a DNA-reading machine before the year is over. Not only does this represent an entirely new sequencing technology, but the systems will be sold as rack-mounted hardware that can be clustered.

The basic principle behind nanopore sequencing is pretty simple (we've got more detail if you're interested). An external voltage forces DNA molecules to snake their way through a narrow protein pore embedded in a membrane. As each base passes through, its distinct chemical properties cause changes in the voltage difference across the membrane. By tracking the local voltage changes, it's possible to identify each base as it slides through the pore.

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Genome of extinct human relative placed on Amazon web services

It has been nearly 200 years since we became aware of the Neanderthals, an extinct form of humans that once shared Europe and Asia with the modern humans. But it has been less than two years since we discovered that the Neanderthals were not the only archaic modern human around at the time. In short order, researchers in Germany produced a draft of the Denisova genome, which showed that the ancestors of some modern human populations had interbred with the Denisovans at some point in the past.

However, the genome sequence that was published in 2010 was only a draft, which is expected to contain errors and areas of very poor coverage. The folks at the Max Planck Institute have continued sequencing away, though, and have greatly expanded their coverage of the Denisova genome; they're apparently preparing a paper to describe the expanded sequence right now. But to keep the research community from waiting for the paper to clear peer review, they've decided to release the sequence, both on the Max Planck website and through Amazon's web services. The release includes both the raw sequence itself, as well as alignments to the human and chimp genomes.

To protect their ability to publish a paper, the Max Planck team is releasing the sequence under a license that prohibits anyone else from doing an analysis of the complete genome. But anyone interested in looking at specific genes is able to do their analysis without waiting. People interested in doing something in between these two extremes are invited to get in touch with Svante Pääbo, who is directing the work, to sort out an agreement.

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Fierce competition on the road to the $1,000 genome

Although the focus on CES is on consumer technology, it's not unusual to see announcements for products that companies will use to provide services to consumers. Even by that standard, one of the announcements made at the show this year was rather unusual, since it was for a consumer service that's not quite there yet: personal genomics. Right now, two companies are pushing hard to become the first to be able to produce a human genome for $1,000.

The first is Ion Torrent, now part of the Life Technologies conglomerate. We covered their sequencing technology back when they were a startup. In short, it copies DNA one base pair at a time and registers which base was added by a silicon chip. Each chip is an array of sensors, with each sensor reading the results from a small population of identical DNA molecules. (The use of a population is important, because it cuts down on the noise and error rate. Things can go wrong with one molecule, but the problem will be swamped out by the signal from all the molecules that do the right thing.)

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Mendeley API Battle: open genetics-sharing tool declared victorious

In March, the platform-agnostic research management tool, Mendeley, announced an API Battle, held in conjunction with the Public Library of Science. The goal was to spur the community into developing neat apps that use the database that powers Mendeley. Apps were judged by a panel that included Tim O'Reilly (of O'Reilly Media) and Amazon CTO Werner Vogels, based on the following criteria: API key usage, whether or not it goes viral, how much the app contributes to collaboration and transparency, and general coolness.

Late last week (December 1st) the winners were announced, and 1st place went to openSNP, a community-driven project for publicly sharing personal genetic data (such as an individual's 23andMe results). You can read an interview with the winners over at Mendeley's blog. PaperCritic and rOpenSci were the runners-up.

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