Tag Archive for 'Nature'

The ENCODE project: lessons for scientific publication

The ENCODE Project has this week released the results of its massive foray into exploring the function of the non-protein-coding regions of the human genome. This is a tremendous scientific achievement, and is receiving plenty of well-deserved press coverage; for particularly thorough summaries see Ed Yong’s excellent post at Discover and Brendan Maher at Nature.

I’m not going to spend time here recounting the project’s scientific merit – suffice it to say that the project’s analyses have already improved the way researchers are approaching the analysis of potential disease-causing genetic variants in non-coding regions, and will have an even greater impact over time. Instead, I want to highlight what a tremendous feat of scientific publication the project has achieved.
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Friday Links

Hong Kong researchers have reported the first attempt to perform large-scale genetic analysis of an unborn child from the blood of its mother. The technique takes advantage of the fact that foetal DNA is found in small quantities in maternal blood; however, analysing this DNA is complicated by the fact that it is heavily contaminated by DNA from the mother (in a ratio of around 9:1). This means that while it is possible to identify the fraction of the foetus’ genome derived from the father, determining whether or not a specific variant has been inherited from the mother is extremely challenging.

Contrary to some media reports, the researchers didn’t succeed in (or attempt) sequencing of the foetus’ entire genome. Rather, they genotyped the parents at ~900,000 sites of common variation, and then estimated the foetus’ genotype at a fraction of those sites using next-generation sequencing of DNA extracted from the mother’s blood. Truly comprehensive analysis of the foetal genome would first require high-accuracy genome sequences of both parents, as well as extremely deep (and thus expensive) sequencing of maternal blood DNA. It seems likely thatin the immediate future foetal DNA analysis will be restricted mostly to targeted examination of specific disease mutations (a far more tractable problem), providing non-invasive detection of severe disease mutations in early pregnancy for at-risk families. [DM]

Over at Genomics Law Report, Unzipper Dan Vorhaus uses revelations from the WikiLeaks cables about US plans to obtain DNA and other biometric data from key world leaders to explore the currently muddy laws around surreptitious DNA testing. [DM]
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