Tag Archives: gene editing

SummitGeneEdit

What’s the Answer? (Dare we edit the human race?) #GeneEditSummit

SummitGeneEditThis week’s question is a biggie. And there’s no answer yet. But that is the topic of the National Academies big event this week, International Summit on Human Gene Editing. I have been glued to this for the whole time and didn’t spend much time looking for questions this week. And I’ll be watching the final day today. You can find the agenda and livestream at that link now, and the recordings will be available later.

A very good summary of the meeting so far came from STAT News today, and that’s where I got the title. So the closest thing you’ll get to an answer right now is that. And you will see that mostly there are just more questions at this point. Hat tip to Tim Caufield.

In that STAT piece, you will also see the reference to Sarah Gray’s powerful moment. It’s less than a minute, but it had me weeping at my desk. I had already heard Sarah and her son’s story on Radiolab. Hat tip to Michelle Meyer for that connection after Sarah’s comment:

In case you missed it, it’s hard to link to exactly where it is in the videos. It doesn’t have a way to get you to a spot like Youtube. So I’ve taken the clip out here. You can link to the full video collection at the National Academies site here. Go to Day 1, Part 3, 2:01:30 for the part with her comment for the best version. I just offer this short screengrab clip because I think that reading her comment doesn’t have the same impact and you should see it. Take a minute.

In case you can’t watch the video, the quote from STAT:

She implored the meeting, “If you have the skills and the knowledge to eliminate these diseases, then frickin’ do it!”

I have nothing to add to that, except to say I stand with Sarah.

Quick links:

Summit site: http://www.nationalacademies.org/gene-editing/Gene-Edit-Summit/index.htm

Agenda document:  http://www.nationalacademies.org/cs/groups/genesite/documents/webpage/gene_168809.pdf

Reference on the summit:
Reardon, S. (2015). Human-genome editing summit to sample global attitudes Nature DOI: 10.1038/nature.2015.18879

SNPpets_2

Friday SNPpets

This week’s SNPpets includes, well, actual pets this week. BGI is selling edited pigs. Welcome to the future. There’s more future, too–see the tweet by Timothy Read about where NGS sequencing will go. And I, for one, welcome our new “smart toilet” overlords. NCBI is cleaning up some of the past (finally). The top 10 useful bioinformatics skills list is compiled. The wrap up of 1000 Genomes project. And a heated discussion of authorship as it pertains to software projects was really interesting. And more….


SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


And see what you can get with your sequence from Mick:

Friday SNPpets

This week’s SNPpets include The Economist and C&EN cover gene editing in different but useful ways, new software for metagenomics, stranded RNA-Seq, the new CDC Public Health Genomics Knowledge Base, IGB paper, Docker getting attention in biology, FDA precision medicine workshops, a nice popular press version of the ExAc (Exome Aggregate Consortium) story,  and the heresy of Keith Robison who doesn’t hate Excel enough.


Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


https://twitter.com/chris_dag/status/641672663493033984

Video Tip of the Week: CRISPRdirect for editing tools and off-target information

Great RCSB PDB molecule-of-the-month page on CRISPR

Great RCSB PDB molecule-of-the-month page on CRISPR

Genome editing strategies are certainly a hot topic of late. We were astonished at the traffic that the animation of the CRISPR/Cas-9 process recently drew to the blog. There’s a huge amount of potential for novel types of studies and interventions in human disease situations–but I’m already seeing applications in agriculture coming along. There’s an edited canola available in Canada already. China has edited wheat for disease resistance. There’s a project underway to remove horns from cattle–by merely snipping out a bit of sequence with TALENs/ZNF strategies. They’ve already created cattle with edited myostatin too.

To accompany this work, new software tools have been developed to help design target sequences and evaluate potential off-target situations. Both TALEN target software tools exist, and CRISPR tools exist. For this post I’ll be focusing on just one of the CRISPR tools, but I’ll list a few others as well. Some sites have incorporated both options in their software tools. Some will have a small range of species, some have larger sets. So part of choosing a tool is asking about the genomes it supports. In future Tips we may explore some of the others. There is something of a flood of these tools coming along, and I’ll continue to explore them.

This week’s focus is CRISPRdirect. A Japanese group has created this tool for generating a guide sequence and for evaluating potential off-target activity. This introductory video (with music, and with English annotations to convey the features) will give you an overview of the functions.

It seems to be an easy-to-use interface, with effective organization of the results. They have a nice range of species to examine–not only some of the mammalian genomes, but fish, chicken, worm, plants, and yeast too. There’s a graphical viewing component and an easy export option as well.

So I’ve come across a few tools in my search, but if you have favorites please feel free to add them below in the comments. I’m going to continue to look into these tools and will be looking to highlight others in the future.

Quick link:

CRISPRdirect: http://crispr.dbcls.jp/

A few links to other tools I’ve been looking at:

E-TALEN: http://www.e-talen.org/E-TALEN/

E-CRISP: http://www.e-crisp.org/E-CRISP/

TAL Effector Nucleotide Targeter 2.0: https://tale-nt.cac.cornell.edu/

Prognos: http://baolab.bme.gatech.edu/Research/BioinformaticTools/prognos.html

ZiFiT Targeter software (TALEN/ZNF/CRISPR support): http://zifit.partners.org/ZiFiT/

COSMID: https://crispr.bme.gatech.edu/

CRISPY (specific for CHO cells): http://staff.biosustain.dtu.dk/laeb/crispy/

Reference:

Naito Y., K. Hino, H. Bono & K. Ui-Tei (2014). CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites, Bioinformatics, DOI: http://dx.doi.org/10.1093/bioinformatics/btu743