Updates to the human germline editing saga

• News that various US based academics knew about He’s plans. The New York Times outlines that various American academics knew what He was planning, but kept silent, mostly because they didn’t know what to do about research happening in China, and/or because they thought they had dissuaded He from discontinuing. Meanwhile, STAT reports that Deem, He’s US based thesis advisor was listed as the last author of the manuscript He submitted to Nature (which declined to review it). The extent of his involvement is unclear. And the Associated Press broke the news that He had informed Nobel winning geneticist Mello about the pregnancy in April.
• The NASAM report, that I covered here, stopped short of calling for a moratorium. He seemed to think that he was not contravening it. This has lead to renewed calls for a clearer stance. Debate continues over whether a moratorium is the correct response. The New York Times editorial team issued a statement against a moratorium, and in favor of diversifying the deciders and engaging the public. “It may be impossible to prevent truly rogue actors, but it is possible to slow them down without stopping everyone else.” Jennifer Doudna opposes a moratorium, Feng Zhang supports one.
• A larger question looms about the relevant role of scientists in this debate. In an opinion piece in STAT, Are scientists’ reactions to ‘CRISPR babies’ about ethics or self-governance?, the authors make a strong case for the latter: “We believe that the alarm being sounded by the scientific community isn’t really about ethics. It’s about protecting a particular form of scientific self-governance, which the “ethics” discourse supports.” “Scientists articulated more concern about maintaining their authority to unilaterally transform human biology than a willingness to have a public debate about the ethics of whether — and under what conditions — such transformation should take place.” A Hastings Report article outlines the differences in opinion being expressed by scientists about the relevant roles of scientists and society in the future of the technology.

Controversy

• In a long piece in the New York Times Magazine on paleogenomics, takehomes here,  Gideon Lewis-Kraus points to the field’s major and recent successes, but also highlights how some archeologists fear that it traffics in “grand intellectual narratives” that history warns us against. This is an indication of culture wars between geneticists and others.

Science

• A study that doubled the number of microbial genomes available (150,000) by producing data from metagenomic studies including those covering non-Westernized countries. They grouped their ~150,000 new sequences in to 5000 “species bins”, 77% of which were novel. The new sequences dramatically increase the mappability of samples to 87%.
• A fine grained (682bp) map of where crossovers occur on chromosomes, from Decode. The CEO of Decode, and author, Dr Stefansson (source): “The classic premise of evolution is that it is powered first by random genetic change. But we see here in great detail how this process is in fact systematically regulated – by the genome itself and by the fact that recombination and de novo mutation are linked. We have identified 35 sequence variants affecting recombination rate and location, and show that de novo mutations are more than fifty times more likely at recombination sites than elsewhere in the genome. Furthermore, women contribute far more to recombination and men to de novo mutation, and it is the latter that comprise a major source of rare diseases of childhood. What we see here is that the genome is an engine for generating diversity within certain bounds. This is clearly beneficial to the success of our species but at great cost to some individuals with rare diseases, which are therefore a collective responsibility we must strive to address”
• Polygenic score for lifespan, explaining 1% of the phenotypic variance, which is 5% of the heritability. Those in the top 10% of the score can expect, on average, to live 5 years longer than those in the bottom 10%.
• GWAS for risk tolerance and risky behaviors, with genetic overlaps found between different “risky” phenotypes, and with various personality traits.

Applications

• Following the successful completion of Genomics England’s 100,000 genomes project, healthy patients will soon be able to pay for genetic tests through the NHS. The NHS has, up until this point, been free at the point of service. Fears of a ‘two tier system” are weighed against the idea that “Every genome sequenced moves us a step closer to unlocking life-saving treatments.”
• Ongoing issues with patients getting access to their own data from testing companies.
• Data sharing issues are also a hot topic in the research space, see this opinion piece that all publicly available data should be completely open access. Advances will be made each easier with improvements to tracking the ways in which data can be used in a fixed format. That is the purpose of the GA4GH’s Data Use Ontology, now open for comment.
• Identical twins tried out various ancestry kits and received somewhat different results.
• A silicon valley startup offering tumor genetic testing and personalized therapy recommendations — for dogs. The idea is that the dogs could be treated with therapies for humans, under something akin to compassionate use programs.
• An editorial in Nature calls on the WHO to integrate genomic testing of cholera to help fight outbreaks. This new-ish field is called genomic phylogeography.

Regulation

• More powers for DNA forensics. As of the beginning of January, the Rapid DNA Act comes into force. Rapid DNA machines sitting inside police stations allow police officers to obtain sequence results in 90 minutes. The Act allows for police to upload this data to CODIS, the National DNA database, and look for matches to e.g. previous crime scenes.

In other news: The preprint server for biology BioRxiv, just turned five. In 2018, about 1711 preprints were posted per month, and in October there were over 1 million downloads. A project called the Rxvist allows users to see which preprints are generating the most twitter attention. I have added this to my bookmarks, and will be using it to help inform this round-up from henceforth!