FDA slows down CRISPR

Gene Editing Promise Stalled at FDA

The FDA is currently claiming regulatory authority over gene-edited livestock based on a decades-old administrative decision related to older transgenic biotechnology, where a foreign gene is inserted into an animal’s genome. Gene editing is making simple changes or deletions within an animal’s native genome.

NPPC is pushing for regulatory oversight by the USDA. The USDA has already established the right regulatory framework by adopting a risk-based approach to reviewing potential genetic changes in plants. It easily could adapt that approach for livestock and regulate gene-edited animals under the Animal Health Protection Act. 

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One-stop shopping for your gene-editing needs

Brand new CRISPR/Cas9 Platform: One-stop Gene Knockout/knockin Service for Precise Gene Editing

New York, Mar 25th, 2019 - Creative Biogene, as a leading provider focuses on offering professional products and services to accelerate gene research, recently announces the brand new CRISPR/Cas9 Platform, which provides comprehensive gene editing services and products. With talented and experienced scientists, Creative Biogene can offer more reliable and professional service to support gene editing projects.

Read the whole press release here …

Cornell sequences student genomes

What’s in Your DNA? Cornell Genomics Class Provides Students Free 23andMe Testing

“The first-ever sequencing of the human genome cost $2.7 billion. Today, the service 23andMe offers personal genome sequencing for less than $200. And for students enrolled in Cornell’s personal genomics class, it’s free.

Prof. Charles Aquadro, molecular biology and genetics, has been teaching Molecular Biology and Genetics 1290: Personal Genomics and Medicine: Why Should You Care About What’s in Your Genes for seven years now, following his hugely successful Cornell University Genetic Ancestry Project, a collaboration that traced the ancestry of over 200 Cornell undergraduates in the spring of 2011.”

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Funding for European NGS projects

European Genomics Collaborative Issues First Call for Proposals

“NEW YORK (GenomeWeb) — The European Advanced Infrastructure for Innovative Genomics (EASI-Genomics) today issued a first call for proposals for a range of projects that will be able to take advantage of the group's next-generation sequencing technologies and services.

EASI-Genomics, which is funded with €10 million ($11.3 million) under the European Union's Horizon 2020 program, is tasked with providing free access to NGS technologies and genomic services to researchers from industry and academia. It was launched earlier this year and aims to support between 150 and 300 projects over the next four years.“

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George Smith on what's to gain from looking into the genomes of extinct furry elephants

Decoding a Mammoth with George Church

Join Harvard DNA pioneer George Church and Chris Smith in conversation as they discuss gene cloning, DNA sequencing, decoding the mammoth genome, the risks posed by fossil viruses lurking in extinct genomes, the prospects of xenotransplantation, and safety of gene therapy, and the risks of human CRISPR. The discussion was recorded on March 15th, live in front of a studio audience at the Hello Tomorrow Summit, in Paris, 2019...

Watch the video here …

The Possibility of Computational DNA

Reprogrammable DNA

“Researchers from the California Institute of Technology and Harvard University have shown that it is possible to reprogram a DNA-based computer, Wired reports.

The team, led by Caltech's Erik Winfree, reports in Nature that it developed and validated a set of 355 DNA tiles that they could then reprogram into a range of six-bit algorithms. In particular, the team says it constructed 21 circuits that perform algorithms that copy, sort, elect a leader, and generate random patterns, among other tasks, with an error rate of less than 1 in 3,000. This, they add, suggests "molecular self-assembly could be a reliable algorithmic component within programmable chemical systems.“

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What happens when a super-power, not start up, has your genome

What Will China Do With Your DNA?

China’s Fourth Magic Weapon, Part III: Bioweapons

by Steven Mosher (Epoch Times)

“Editor’s Note: In Parts I and II, Steven Mosher wrote about the Chinese Communist Party’s program to collect the DNA of all Chinese citizens. This was, he suggested, an effort to develop a fourth “magic weapon” of control over the Chinese population. The first three “magic weapons,” outlined by President Xi Jinping in a September 2014 speech, are “the People’s Liberation Army, propaganda, and United Front tactics.”

But this effort also extends beyond China’s borders. Here, in Part III, Mosher discusses ways in which the CCP is able to collect foreign DNA and how it might be able to profit from, or even weaponize, the genetic information it acquires from analyzing it.“

Chinese American scientists express concerns about profiling

Racial profiling harms science

“On behalf of the Society of Chinese Bioscientists in America (SCBA), the Chinese American Hematologist and Oncologist Network (CAHON), and the Chinese Biological Investigators Society (CBIS), we write to express our concerns about the recent political rhetoric and policies that single out students and scholars of Chinese descent working in the United States as threats to U.S. national interests [e.g., (1) and pp. 6–7 in (2)]. These developments have led to confusion, fear, and frustration among these highly dedicated professionals, who are in danger of being singled out for scape-goating, stereotyping, and racial profiling. U.S. policies must avoid targeting, as Representative Judy Chu (D–California) put it, “an entire ethnic group of people for suspicion that they're spies for China” (3).”

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CRISP documentary reviewed in Ars Technica

New documentary has a good time asking how gene editing might change the world

Here's a poorly kept secret: the internal chatter at a given research and scientific institution is typically more interesting than what emerges on the public record. Published papers and newspaper interviews don't come with the banter, pop-culture references, or sheer wit that pumps through most nerds' veins.

I thought back to all that nerd humor when I reflected on Human Nature, a documentary about gene editing and CRISPR that had its world premiere at South by Southwest 2019. There's a lot of ground to cover on such a topic, and the film, co-produced by Dan Rather, does quite well by identifying existing research and studies, then grounding them with context and equal parts optimism and pessimism. But Human Nature is also the rare science film that isn't afraid to let its smart talking heads be funny, dorky, or just plain sharp.

Google AI variant caller goes deep on rice genomes

Analyzing 3024 rice genomes characterized by DeepVariant

“Rice is an ideal candidate for study in genomics, not only because it’s one of the world’s most important food crops, but also because centuries of agricultural cross-breeding have created unique, geographically-induced differences. With the potential for global population growth and climate change to impact crop yields, the study of this genome has important social considerations.

This post explores how to identify and analyze different rice genome mutations with a tool called DeepVariant. To do this, we performed a re-analysis of the Rice 3Kdataset and have made the data publicly available as part of the Google Cloud Public Dataset Program pre-publication and under the terms of the Toronto Statement.

We aim to show how AI can improve food security by accelerating genetic enhancement to increase rice crop yield. According to the Food and Agriculture Organization of the United Nations, crop improvements will reduce the negative impact of climate change and loss of arable land on rice yields, as well as support an estimated 25% increase in rice demand by 2030.”

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Standardized Germline Variant Calling Performance Metrics

GA4GH Benchmarking Team Releases Best Practices for Comparing Germline Variant Calls

NEW YORK (GenomeWeb) – Members of the benchmarking team of the Global Alliance for Genomics and Health have developed methods for producing standardized performance metrics for benchmarking small germline variant calls.

The GA4GH Benchmarking team brings together participants from research institutes, technology companies, government agencies, and clinical laboratories. It includes researchers from the National Institute of Standards and Technology (NIST), Illumina, Ontario Institute for Cancer Research, DNAnexus, and others.

As explained in a Nature Biotechnology paper published yesterday, the methods that they have developed address challenges associated with standardizing metrics like recall and precision, comparing different representations of variant calls, and stratifying performance by variant type and genome context. The team has made the code used for the benchmarking available in Github.

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Chinese gene editing therapies are developing

China’s race to test ‘mutation-free’ gene-editing technology on cancer patients

BEIJING — China could be just over a year away from clinical trials of a new gene-editing therapy with an unprecedented high level of safety, according to a team of Chinese scientists involved in the research programme.

The scientists said the research, based on groundbreaking work published in the journal Science earlier this month, could help save the lives of many patients battling deadly diseases including cancer.

The existing genome-editing method works like a shotgun, breaking up a large numbers of genome strands and sometimes missing its intended target, causing unnecessary damage to cells.

The new tool under development in China targets and swaps individual “letters” in the DNA with extreme precision, avoiding cuts to the strands and significantly reducing the risk of unexpected mutations.

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Why don't we make heritable gene editing available to everybody?

We should not fear 'editing' embryos to enhance human intelligence, says leading geneticist George Church

One of the world’s leading geneticists says it will only be a matter of time before the genes of  human embryos are ‘edited’ to enhance their health and intelligence – and it is something we should embrace rather than fear.

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Goals for improving cancer treatment in children

Ushering in the next generation of precision trials for pediatric cancer

Steven G. DuBois, Laura B. Corson, Kimberly Stegmaier, and Katherine A. Janeway

Science (Review article)

Abstract—Cancer treatment decisions are increasingly based on the genomic profile of the patient’s tumor, a strategy called “precision oncology.” Over the past few years, a growing number of clinical trials and case reports have provided evidence that precision oncology is an effective approach for at least some children with cancer. Here, we review key factors influencing pediatric drug development in the era of precision oncology. We describe an emerging regulatory framework that is accelerating the pace of clinical trials in children as well as design challenges that are specific to trials that involve young cancer patients. Last, we discuss new drug development approaches for pediatric cancers whose growth relies on proteins that are difficult to target therapeutically, such as transcription factors.

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Ed Yong gets punny about evolution in the Atlantic

This Is a Truly Lousy Experiment About Evolution

By placing feather-eating lice on white, black, and gray pigeons, researchers showed how the parasites change color to better blend in.

“Believing that it is always best to study some special group, I have, after deliberation, taken up domestic pigeons,” wrote one Charles Darwin in On the Origin of Species. Four years earlier, Darwin had taken to raising pigeons in his own dovecote, hobnobbing with other pigeon fanciers, and carefully measuring the birds. In the diverse breeds, with their fantails, feather-duster feet, and frilly backs, Darwin saw validation for his ideas about evolution. If people could artificially select for such astonishing diversity in just a few generations, nature was surely capable of far more over longer timescales.

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Important reminder that your genome is your property

Your invaluable genome

Genomic data is the currency of a new era of medicine that promises incredible advances. Here, bioinformatician Nana Mensah explains why…

In the race for greatest medical revolution of the 21st century, genomics is undoubtedly a frontrunner. Those outside of the field, however, might still find themselves wondering: 'what's all the fuss about?' There are many reasons why genomics is revolutionary, but data is at the root of it all. As genomics is used more and more in mainstream care, it becomes ever more important to understand the great power and value of this new kind of data, writes Nana Mensah.

From cell to computer

While the word ‘genome’ refers to the entire sequence of DNA of an individual organism, the term ‘genomic data’ refers to its digital representation – a large data file resulting from the sequencing process.

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UK Research and Innovation awards £45 million to EMBL’s European Bioinformatics Institute (EMBL-EBI)

Funding awarded for bioinformatics infrastructure

UK Research and Innovation (UKRI) has awarded £45 million to EMBL’s European Bioinformatics Institute (EMBL-EBI), to enhance the institute’s technical and building infrastructure. The funding, which comes from the UKRI’s Strategic Priorities Fund, will support EMBL-EBI’s existing and emerging data resources, including in areas of major interest, such as genomics and bioimaging.

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We'll need AI to deal with coming wave of genome data

Getting smart about artificial intelligence

By: Alison Cranage, Science writer

“Genomics is set to become the biggest source of data on the planet, overtaking the current leading heavyweights – astronomy, YouTube and Twitter. Genome sequencing currently produces a staggering 25 petabytes of digital information per year. A petabyte is 1015 bytes, or about 1,000 times the average storage on a personal computer. And there is no sign of a slowdown.”

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Moratorium on heritable genome editing covered by MIT Technology Review

CRISPR experts are calling for a global moratorium on heritable gene editing

After the first International Summit on Human Gene Editing in December 2015, a statement was released. The organizers were unanimous in agreeing that the creation of genetically modified children was “irresponsible” unless we knew for sure it was safe.

Well, a fat lot of good that did. As MIT Technology Review revealed in November last year, Chinese scientist He Jiankui edited embryos to create two genetically engineered babies. Other groups are now actively looking to use the technology to enhance humans.

This has prompted some of the biggest names in gene editing (some of whom signed the 2015 statement) to call for a global moratorium on all human germline editing—editing sperm or egg cells so that the changes are hereditary.

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Also, we suggest reading the whole Rewriting Life series at the MIT Technology Review.

Conflict over proposed heritable genome editing moratorium covered in Science

New call to ban gene-edited babies divides biologists

John Cohen sums up the conflict nicely in Science

A prominent group of 18 scientists and bioethicists from seven countries has called for a global “moratorium” on introducing heritable changes into human sperm, eggs, or embryos—germline editing—to make genetically altered children. The group, which published a commentary in Naturetoday, hopes to influence a long-standing debate that dramatically intensified after China’s He Jiankui announced in November 2018 that he used the genome editor CRISPR to try to alter the genes of babies to be resistant to the AIDS virus.

Their call, which is endorsed in the same issue of Nature by Francis Collins, director of the U.S. National Institutes of Health, is a departure from statements issued by two global summits on genome editing in 2015 and 2018, a 2017 report from the U.S. National Academies of Sciences, Engineering, and Medicine (NASEM), and a 2018 report from the United Kingdom’s Nuffield Council on Bioethics. None has banned human germline editing, and most have stressed that it holds promise to help correct some heritable diseases. All have warned against using germline editing for cognitive or physical “enhancement” of people. Scientists including Nobel laureate David Baltimore of the California Institute of Technology in Pasadena remain opposed to a moratorium. Even in the wake of the He incident, Baltimore, who helped organize the summits, denounced such a ban as “draconian” and “antithetical to the goals of science.”

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