A prudent path forward for genomic engineering and germline gene modification

Dog-whistle sinophobia exists, but I think it’s attenuating, in consequence of more of China getting online and visible. Chinese science really isn’t the amoral wildcard which some people enjoy fantasizing about, and the internet is forcing this into the light.

The internet reduces some fears, while increasing others, largely trending towards accurate views. The discussion of a worldwide CRISPR framework before it has become doable is encouraging.

CONCLUSIONS. At the dawn of the recom- binant DNA era, the most important lesson learned was that public trust in science ul- timately begins with and requires ongoing transparency and open discussion. That les- son is amplified today with the emergence of CRISPR-Cas9 technology and the im- minent prospects for genome engineering. Initiating these fascinating and challenging discussions now will optimize the decisions society will make at the advent of a new era in biology and genetics. ■

Understanding the Flynn Effect

A charming and fairly inclusive monograph by Bob Williams, notable for aiming to make a distinction between the Flynn effect and the putative Jensen effect.

First time I see anything by Williams, but it speaks to the nature of the publishing system that this summary could as easily have been printed in a number of primary review journals, yet it was not.

vidya_282-283_BW_reprint

Quality control and conduct of genome-wide association meta-analyses

The future of great bio belongs to those who can administrate.

An analytical framework for optimizing variant discovery from personal genomes

Might be worth it to switch to novalign…

http://www.nature.com/ncomms/2015/150225/ncomms7275/full/ncomms7275.html

Embryo Editing divides scientists

In private conversations, I never seem to encounter this division.

Cyranoski_2015_Embryo_editing_divides_scientists

Embryo Selection for Cognitive Enhancement: Curiosity or Game-changer?

Science Fiction, until it happens.
http://onlinelibrary.wiley.com/doi/10.1111/1758-5899.12123/full

Genetic contributions to variation in general cognitive function

Interesting new paper out, overseen by Ian Deary.

Slightly inconsistent phenotyping, but clearing 50k+ samples makes this the best cohort yet.

Hits focused on just 3 haploblocks:

 

Accuracy vs Sensitivity

Complete Genomics vs Illumina, in other words.

Even most bioinformaticians aren’t going to have much familiarity with the topic. But as BGI starts to crank out more and more CG genomes, this comparison is going to loom large. Most of the data in the wild is currently Illumina, but that can’t stay the case forever; the CG data pool is going to grow rapidly, as BGI starts to shift all of their capacity into their acquisition.

The theme that seems to emerge again and again is the accuracy of CG vs the sensitivity of Illumina. And with “sensitivity”, I’m afraid I mean “infestation with false positives”. 

	Number tested	Validated	Validation rate
Both platforms	20	20	100%
Illumina-specific	15	2	13.3%
CG-specific	18	17	94.4%

http://www.completegenomics.com/blog/Comparing-Performance-Data–Taking-a-Different-Perspective–140765443.html

http://www.nature.com/nbt/journal/v30/n1/abs/nbt.2065.html

http://mendeliandisorder.blogspot.com/2012/03/cliff-reid-on-cg-vs-illumina.html

If a fitting complement of CG controls can be located to offset Illumina control bias, the shift in our experimental design towards CG for cases may prove to be a large accuracy boon.

BGI CGL GATA LAMP

Distributing several thousand genomes securely is hard.

Our Hong Kong BGI branch already has a fairly mature mechanism of distribution, for GATA sets whose security requirements match or exceed our own. But it’s a lot of work.

We’re currently storing the data inside a locked room, within a locked safe in the locked room, on encrypted RAID, and accessed only in a very indirect fashion. I anticipate that most high-end military security is far less diligent. But it’s a lot of work.

 

Fake IQ-Association Hits, and their Causes

http://www.denimandtweed.com/2013/03/false-discovery-how-not-to-find-genetic.html?spref=fb

I am impressed by this very accessible takedown by Yoder, popular science writing at its best. Sometimes, simplicity is both adequate and brilliant; Yoder explains so unpretentiously that I’ve shared his article to a swath of people with various backgrounds.

I hope the recent coverage of our project hasn’t catalysed copycatting – though in retrospect, I suppose the coverage can’t help but have had an encouraging effect, especially here in China. As Yoder demonstrates, some of these bids are perhaps somewhat openly cynical in motive.

Less critically, I’m reminded of the paper one year ago by Stein et al, with their excellent methodology for establishing SNP association with cranial volume, and then half-paragraph one-sentence by-the-way inference of association with IQ, which then promptly got blown up with yet another wave of “first IQ hit?” attention, which got forwarded to us a lot. I don’t believe that the paper authors had intended this.