#génomique

Les très graves ratés de l’expérience chinoise des « bébés CRISPR »
▻http://theconversation.com/les-tres-graves-rates-de-lexperience-chinoise-des-bebes-crispr-1287

L’annonce de la naissance en Chine de Lulu et Nana, des jumelles dont le génome a été modifié en utilisant la technologie de l’édition du génome CRISPR/Cas9, a choqué le monde entier l’année dernière. Une année après cette annonce, Jiankui He, le scientifique chinois a l’origine de la naissance de ces bébés génétiquement modifies, a été condamné à trois ans de prison ferme et 380 000 euros d’amendes pour la pratique illégale de la médecine.

▻https://seenthis.net/messages/814993

#CRISPR #Hubris_scientifique #Génomique #Modification_génétique

Scientists Dodge FDA to Offer a $1 Million Anti-Aging Treatment in Colombia
▻https://onezero.medium.com/scientists-dodge-fda-to-offer-a-1-million-anti-aging-treatment-in-co

https://miro.medium.com/focal/1200/632/48/47/1*4-Mlq4CokGt88d4RRRsZPg.jpeg

Would you pay $1 million and fly to South America for a chance to live longer?

Libella Gene Therapeutics, a Kansas-based company that says it is developing a gene therapy that can reverse aging by up to 20 years, is hoping your answer is yes. In an interview with OneZero, the company says it is ready to give an experimental anti-aging therapy to older people at a clinic north of Bogota, Colombia. But that’s not all — it’s also charging people $1 million to participate. Scientists and ethicists say the company’s experiment is not only dubious but it also raises concerns about how anti-aging treatments should be tested in people.

The aim of Libella’s therapy is to lengthen a person’s telomeres, which sit at the tips of chromosomes like caps on the end of shoelaces. First discovered in the 1970s, telomeres have been linked to aging because they seem to shorten as a person gets older. By delivering a gene called TERT to cells, which in turn makes a telomere-rebuilding enzyme called telomerase, Libella thinks it can prevent, delay, or even reverse aging.

“I know what we’re trying to do sounds like science fiction, but I believe it’s a science reality,” Jeff Mathis, CEO of Libella Gene Therapeutics, tells OneZero.

The anti-aging field has drawn plenty of criticism for scams and overhyped products with no proven health benefits. Libella’s clinical trial listings also raise red flags. First among them is the fact that the company and its trials are located in different countries. Mathis, an occupational therapist who runs a rehabilitation practice in Manhattan, Kansas, says he chose Colombia for the trial because it was the “path of least resistance.” The company looked at eight different countries, and he says, “the easiest, the quickest, and the best way forward ended up being in Colombia.”

Leigh Turner, a bioethicist at the University of Minnesota who studies clinical trials that market unproven therapies, says he suspects the company chose to go outside the country to avoid the Food and Drug Administration, which oversees clinical trials in the United States. “Even though the company is based in the United States, they’ve managed to find a way to evade U.S. federal law by going to a jurisdiction where it’s easier to engage in this activity,” he tells OneZero.

Turner says the $1 million participation cost is alarming because most clinical trials are free. In fact, many pay people to participate because of the time commitment and the potential risks involved with receiving an experimental treatment. Andrews justifies the fee, saying it costs Libella “hundreds of thousands of dollars to produce enough of the gene therapy to treat one person.”

Some researchers in the field are concerned that putting a lot of telomerase into cells could make cells divide more quickly and promote tumor growth, says Austad. Previous research has linked longer telomeres to increased cancer risk, with scientists finding that cancer cells tend to have more telomerase that most normal cells. But telomere evangelists like Michael Fossel believe that shortened telomeres are a cause of age-related diseases like cancer and thus, lengthening them could help protect against these conditions.

How a dubious clinical trial was able to be registered into a government website in the first place has been a longstanding problem for the National Institutes of Health, which runs ClinicalTrials.gov. The website is the largest database of its kind and lists studies in more than 200 countries. It’s a tremendous resource for people with rare diseases, cancer, and those who have run out of treatment options, and physicians regularly refer their patients to the site.

But Turner says the site can be easily manipulated and taken advantage of because the process to register is automated. NIH does not screen studies that are submitted to the database, which allows companies to submit predatory and pay-to-participate studies on the site. This has been the case with many stem cell businesses marketing unproven therapies. “ClinicalTrials.gov can basically be used as a marketing platform,” Turner says.

Being registered on the site gives an air of legitimacy, and often patients can’t tell the difference between a scientifically sound clinical trial and one that’s suspicious. ClinicalTrials.gov listings also don’t include information about participation costs, so patients can’t tell if there’s a fee involved up-front.

#Pharmacie #Anti_âge #Arnaque #Vieillesse #Santé_publique #Génomique

Des mutations inquiétantes sur les bébés chinois génétiquement modifiés par CRISPR - UP’ Magazine
▻https://up-magazine.info/index.php/le-vivant/innovations-vertes/28764-des-mutations-inquietantes-sur-les-bebes-chinois-genetiquement-m

https://up-magazine.info/wp-content/uploads/2019/12/bebes-crispr.jpg

Les jumelles chinoises nées l’an dernier d’embryons génétiquement modifiés par les ciseaux moléculaires « CRISPR » ont probablement des mutations imprévues dans leur génome à la suite de cette manipulation. C’est un journaliste américain qui révèle cette information ce 3 décembre après avoir obtenu une version non publiée de l’étude détaillant l’expérience.

L’annonce avait choqué le monde en novembre 2018 : le scientifique He Jiankui avait révélé à Hong Kong qu’il avait modifié des embryons, dans le cadre d’une fécondation in vitro pour un couple, afin de tenter de créer une mutation de leurs génomes qui leur conférerait une immunité naturelle contre le virus du sida au cours de leur vie. Cette nouvelle avait provoqué un tollé car la procédure employée n’avait aucune justification médicale, présentait de graves dangers pour la santé et contrevenait aux règles éthiques les plus élémentaires.

LIRE DANS UP : Les Chinois auraient mis au monde deux bébés génétiquement modifiés par CRISPR

Des jumelles étaient nées, nommées Lulu et Nana, mais elles et leurs parents sont restés anonymes, et on ignore totalement ce qu’elles sont devenues.

L’expérience d’He Jiankui avait vivement été condamnée par la communauté scientifique internationale et les autorités de son pays, et l’affaire avait relancé les appels à une interdiction des « bébés Crispr ».
Le manuscrit de l’étude révélé

Un journaliste de la MIT Technology Review a reçu le manuscrit de l’étude que He Jiankui a tenté de faire publier par des revues scientifiques prestigieuses, et qui détaille sa méthode et ses résultats. Mais le texte de l’étude confirme ce que beaucoup d’experts suspectaient : selon des généticiens interrogés, il ne montre en réalité pas que la mutation tentée, sur une partie du gène CCR5, a effectivement réussi. L’étude affirme que la mutation accomplie est « similaire » à celle qui confère l’immunité, et non identique.
Des conséquences imprévisibles

En outre, des données incluses en annexe montrent que les jumelles ont subi des mutations ailleurs dans leur génome, et probablement différentes d’une cellule à l’autre, ce qui rend les conséquences imprévisibles.

« CRISPR » est une technique révolutionnaire de modification du génome inventée en 2012, bien plus simple et facile d’utilisation que les technologies existantes. Mais les ciseaux coupent souvent à côté de l’endroit ciblé, et les généticiens répètent que la technologie est encore loin d’être parfaite pour être utilisée à des fins thérapeutiques.

« Il y a énormément de problèmes dans l’affaire des jumelles CRISPR. Tous les principes éthiques établis ont été violés, mais il y a aussi un grand problème scientifique : il n’a pas contrôlé ce que CRISPR faisait, et cela a créé plein de conséquences imprévues », a dit le professeur de génétique Kiran Musunuru, de l’université de Pennsylvanie, dans un entretien récent à l’AFP.

Dans la MIT Technology Review, le généticien Fyodor Urnov déclare : « La recherche était toutefois incomplète et le manuscrit passe sous silence un point clé : les cellules prélevées sur les embryons au stade précoce pour les tester n’ont pas réellement contribué aux corps des jumeaux. Les cellules restantes, celles qui se multiplieraient et se développeraient pour devenir les jumeaux, auraient pu aussi avoir des effets hors cible, mais il n’y aurait eu aucun moyen de le savoir avant le début de la grossesse. » Il ajoute : « Une déformation flagrante des données réelles qui ne peut, encore une fois, être décrite que comme un mensonge flagrant. Il est techniquement impossible de déterminer si un embryon modifié « n’a présenté aucune mutation hors cible » sans détruire cet embryon en inspectant chacune de ses cellules. Il s’agit d’un problème clé pour l’ensemble du domaine de l’édition d’embryons, un problème que les auteurs balaient sous le tapis ici. »

#CRISPR #Hubris_scientifique #Génomique #Modification_génétique

How Earnest Research Into Gay Genetics Went Wrong | WIRED
▻https://www.wired.com/story/how-earnest-research-into-gay-genetics-went-wrong

https://media.wired.com/photos/5db73e6f60047600090d3ac2/191:100/w_1280,c_limit/science%2520-%2520GenePlaza%2520debacle%2520-%2520featured%2520art.jpg

Un excellent article sur les danger éthiques et sociaux de l’usage sans précaution des données génétiques, notamment les données massives obtenues soit par des actes volontaires (recherche d’ancêtres, et autres) soit au fil d’actes médicaux.

Anonymiser les données ne suffit pas à garantir qu’il n’y aura pas de conséquences fâcheuses pour l’ensemble de la société.

Un très bon papier.

In late spring 2017, Andrea Ganna approached his boss, Ben Neale, with a pitch: He wanted to investigate the genetics of sexuality. Neale hesitated. One of the top geneticists in the country, Neale and his colleagues at the Broad Institute, a pioneering biotech hub in Boston, had a decade earlier developed software that made it much easier for scientists to study the vast amounts of genetic data that were beginning to flood in. It was the kind of tool that helped illuminate a person’s risk of developing, say, heart disease or diabetes. And now, as Ganna was proposing, the approach could be applied to the foundations of behavior, personality, and other social traits that in the past had been difficult to study.

Ganna wanted to pounce on a new opportunity. A giant collection of carefully cataloged genomes, called the UK Biobank, was about to become available to researchers. A scientist could apply and then gain access to data from 500,000 British citizens—the largest public repository of DNA on the planet. To Ganna, the genetic origins of being gay or straight seemed like the kind of blockbuster question that might finally get an answer from a data set of this size.

Neale wasn’t so sure. As a gay man himself, he worried that such research could be misconstrued or wielded to advance hateful agendas. On the other hand, a better understanding of how genetics influences same-sex attraction could also help destigmatize it.

Then Ganna mentioned that another group was already pursuing the question using the UK Biobank: a geneticist named Brendan Zietsch, at the University of Queensland, and his colleagues. In 2008, Zietsch published a study suggesting that the genes straight people shared with their gay twins made them more successful at bedding heterosexual partners. Now he was going to further test this “fecundity hypothesis” with a much more powerful data set. He’d also proposed investigating the genetic associations between sexual orientation and mental health. Thinking his lab could add expertise coupled with caution to such a project, Neale agreed they should try to team up with Zietsch.

“Armed with the knowledge that this research was going to be done, I thought it was important that we try and do it in a way that was responsible and represented a variety of different perspectives,” he says, noting that, because there is so much genetic data to work with these days, collaborations in his field are commonplace “But it was also important to me personally, as a gay man, to get involved.”

From the outset, Neale expected some pushback and misunderstandings. That’s why he involved LGBTQ+ groups along the way, something not technically required for the kind of research he was doing. But he wasn’t prepared for scientists within his home institution to rise up and challenge the value and ethics of his work. And he was even less prepared for a company to exploit the results of the study—just a few weeks after it was published in the journal Science—to sell an app purporting to predict how attracted someone is to the same sex.

#Données_génétiques #Big_data #Ethique #Recherche #Hubris #Génomique #Homosexualité #Fausse_science

China Uses DNA to Track Its People, With the Help of American Expertise - The New York Times
▻https://www.nytimes.com/2019/02/21/business/china-xinjiang-uighur-dna-thermo-fisher.html

https://static01.nyt.com/images/2019/02/20/business/00chinadna-1-promo/00chinadna-1-facebookJumbo.jpg

Collecting genetic material is a key part of China’s campaign, according to human rights groups and Uighur activists. They say a comprehensive DNA database could be used to chase down any Uighurs who resist conforming to the campaign.

Police forces in the United States and elsewhere use genetic material from family members to find suspects and solve crimes. Chinese officials, who are building a broad nationwide database of DNA samples, have cited the crime-fighting benefits of China’s own genetic studies.

To bolster their DNA capabilities, scientists affiliated with China’s police used equipment made by Thermo Fisher, a Massachusetts company. For comparison with Uighur DNA, they also relied on genetic material from people around the world that was provided by Kenneth Kidd, a prominent Yale University geneticist.

On Wednesday, Thermo Fisher said it would no longer sell its equipment in Xinjiang, the part of China where the campaign to track Uighurs is mostly taking place. The company said separately in an earlier statement to The New York Times that it was working with American officials to figure out how its technology was being used.

Dr. Kidd said he had been unaware of how his material and know-how were being used. He said he believed Chinese scientists were acting within scientific norms that require informed consent by DNA donors.

China’s campaign poses a direct challenge to the scientific community and the way it makes cutting-edge knowledge publicly available. The campaign relies in part on public DNA databases and commercial technology, much of it made or managed in the United States. In turn, Chinese scientists have contributed Uighur DNA samples to a global database, potentially violating scientific norms of consent.

Cooperation from the global scientific community “legitimizes this type of genetic surveillance,” said Mark Munsterhjelm, an assistant professor at the University of Windsor in Ontario who has closely tracked the use of American technology in Xinjiang.

#Génomique #DNA_database #Chine #Surveillance #Consentement

James Watson Won’t Stop Talking About Race - The New York Times
▻https://www.nytimes.com/2019/01/01/science/watson-dna-genetics-race.html

https://static01.nyt.com/images/2019/01/01/science/01SCI-WATSON1/01SCI-WATSON1-facebookJumbo.jpg

It has been more than a decade since James D. Watson, a founder of modern genetics, landed in a kind of professional exile by suggesting that black people are intrinsically less intelligent than whites.

In 2007, Dr. Watson, who shared a 1962 Nobel Prize for describing the double-helix structure of DNA, told a British journalist that he was “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours, whereas all the testing says, not really.”

Moreover, he added, although he wished everyone were equal, “people who have to deal with black employees find this not true.”

Some scientists said that Dr. Watson’s recent remarks are noteworthy less because they are his than because they signify misconceptions that may be on the rise, even among scientists, as ingrained racial biases collide with powerful advances in genetics that are enabling researchers to better explore the genetic underpinnings of behavior and cognition.

“It’s not an old story of an old guy with old views,’’ said Andrea Morris, the director of career development at Rockefeller University, who served as a scientific consultant for the film. Dr. Morris said that, as an African-American scientist, “I would like to think that he has the minority view on who can do science and what a scientist should look like. But to me, it feels very current.’’

David Reich, a geneticist at Harvard, has argued that new techniques for studying DNA show that some human populations were geographically separated for long enough that they plausibly could have evolved average genetic differences in cognition and behavior.

But in his recent book, “Who We Are and How We Got Here,’’ he explicitly repudiates Dr. Watson’s presumption that such differences would “correspond to longstanding popular stereotypes’’ as “essentially guaranteed to be wrong.’’

Even Robert Plomin, a prominent behavioral geneticist who argues that nature decisively trumps nurture when it comes to individuals, rejects speculation about average racial differences.

“There are powerful methods for studying the genetic and environmental origins of individual differences, but not for studying the causes of average differences between groups,” Dr. Plomin writes in an afterword to be published this spring in the paperback edition of his book, “Blueprint: How DNA Makes Us Who We Are.”

#Racisme #Génomique #Watson

Most White Americans’ DNA Can Be Identified Through Genealogy Databases - The New York Times
▻https://www.nytimes.com/2018/10/11/science/science-genetic-genealogy-study.html

https://static01.nyt.com/images/2018/10/12/science/12DNA-print/13DNA-facebookJumbo.jpg

The genetic genealogy industry is booming. In recent years, more than 15 million people have offered up their DNA — a cheek swab, some saliva in a test-tube — to services such as 23andMe and Ancestry.com in pursuit of answers about their heritage. In exchange for a genetic fingerprint, individuals may find a birth parent, long-lost cousins, perhaps even a link to Oprah or Alexander the Great.

But as these registries of genetic identity grow, it’s becoming harder for individuals to retain any anonymity. Already, 60 percent of Americans of Northern European descent — the primary group using these sites — can be identified through such databases whether or not they’ve joined one themselves, according to a study published today in the journal Science.

Within two or three years, 90 percent of Americans of European descent will be identifiable from their DNA, researchers found. The science-fiction future, in which everyone is known whether or not they want to be, is nigh.

Their results were eye-opening. The team found that a DNA sample from an American of Northern European heritage could be tracked successfully to a third-cousin distance of its owner in 60 percent of cases. A comparable analysis on the MyHeritage site had similar results. (The analysis focused on Americans of North European background because 75 percent of the users on GEDmatch and other genealogy sites belong to that demographic.)

Some experts have raised questions about the study’s methodology. Its sample size was small, and it didn’t factor in that more than one match is often required to identify a suspect.

CeCe Moore, a genetic genealogist with Parabon, a forensic consulting firm, also expressed worry in an email that the Science paper may obscure the difficulty involved in puzzling out someone’s identity; it takes a highly skilled expert to build a family tree from the initial genetic clues.

Still, she said, the takeaway of the study “is not news to us.” In recent months Ms. Moore has been involved in a dozen murder and sexual assault cases that used GEDmatch to identify suspects. Of the 100 crime-scene profiles that her firm had uploaded to GEDmatch by May, half were obviously solvable, she said, and 20 were “promising.”

“I think it’s a strong and convincing paper,” said Graham Coop, a population genetics researcher at the University of California, Davis. In a blog post in May, Dr. Coop calculated just how lucky investigators had been in the Golden State killer case. He reached a statistical conclusion similar to Dr. Erlich’s: society is not far from being able to identify 90 percent of people through the DNA of their cousins in genealogical databases.

“This is this moment of, wow, oh, this opens up a lot of possibilities, some of which are good and some are more questionable,” he said.

In an alarming result, the Science study found that a supposedly “anonymized” genetic profile taken from a medical data set could be uploaded to GEDmatch and positively identified. This shows that an individual’s private health data might not be so private after all.

#Génomique #ADN #Vie_privée

New studies show how easy it is to identify people using genetic databases - STAT
▻https://www.statnews.com/2018/10/11/genetic-databases-privacy

https://www.statnews.com/wp-content/uploads/2018/10/AP_18123601803275-1024x576.jpg

n recent months, consumer genealogy websites have unleashed a revolution in forensics, allowing law enforcement to use family trees to track down the notorious Golden State Killer in California and solve other cold cases across the country. But while the technique has put alleged killers behind bars, it has also raised questions about the implications for genetic privacy.

According to a pair of studies published Thursday, your genetic privacy may have already eroded even further than previously realized.

In an analysis published in the journal Science, researchers used a database run by the genealogy company MyHeritage to look at the genetic information of nearly 1.3 million anonymized people who’ve had their DNA analyzed by a direct-to-consumer genomics company. For nearly 60 percent of those people, it was possible to track down someone whose DNA was similar enough to indicate they were third cousins or closer in relation; for another 15 percent of the samples, second cousins or closer could be found.

Yaniv Erlich, the lead author on the Science paper, said his team’s findings should prompt regulators and others to reconsider the assumption that genetic information is de-identified. “It’s really not the case. At least technically, it seems feasible to identify some significant part of the population” with such investigations, said Erlich, who’s a computer scientist at Columbia University and chief science officer at MyHeritage.

The Science paper counted 12 cold cases that were solved between April and August of this year when law enforcement turned to building family trees based on genetic data; a 13th case was an active investigation.

The most famous criminal identified this way: the Golden State Killer, who terrorized California with a series of rapes and murders in the 1970s and 1980s. With the help of a genetic genealogist, investigators uploaded a DNA sample collected from an old crime scene to a public genealogy database, built family trees, and tracked down relatives. They winnowed down their list of potential suspects to one man with blue eyes, and in April, they made the landmark arrest.

To crack that case, the California investigators used GEDmatch, an online database that allows people who got their DNA analyzed by companies like 23andMe and Ancestry to upload their raw genetic data so that they can track down distant relatives. MyHeritage’s database — which contains data from 1.75 million people, mostly Americans who’ve gotten their DNA analyzed by MyHeritage’s genetic testing business — works similarly, although it explicitly prohibits forensic searches. (23andMe warns users about the privacy risks of uploading their genetic data to such third party sites.)

“For me, these articles are fascinating and important and we shouldn’t shy away from the privacy concerns that these articles raise. But at the same time, we should keep in mind the personal and societal value that we believe that we are accruing as we make these large collections,” said Green, who was not involved in the new studies and is an adviser for genomics companies including Helix and Veritas Genetics.

He pointed to the potential of genomics not only to reunite family members and put criminals behind bars, but also to predict and prevent heritable diseases and develop new drugs.

As with using social media and paying with credit cards online, reaping the benefits of genetic testing requires accepting a certain level of privacy risk, Green said. “We make these tradeoffs knowing that we’re trading some vulnerability for the advantages,” he said.

#Génomique #ADN #Vie_privée

Are Genetic Testing Sites the New Social Networks? - The New York Times
▻https://www.nytimes.com/2018/06/16/style/23-and-me-ancestry-dna.html

https://static01.nyt.com/images/2018/06/07/style/00dna-04/00dna-04-facebookJumbo.jpg

At-home genetic testing services have gained significant traction in the past few years. 23andMe, which costs $99, has over five million customers, according to the company; AncestryDNA (currently $69), over 10 million.

The companies use their large databases to match willing participants with others who share their DNA. In many cases, long-lost relatives are reuniting, becoming best friends, travel partners, genealogical resources or confidantes.

The result is a more layered version of what happened when Facebook first emerged and out-of-touch friends and family members found one another. Children of long-ago casual sperm donors are finding their fathers. Adoptees are bonding to biological family members they’ve been searching for their entire lives.

The Genetic Global Village

Others who have their DNA tested are forming relationships not with specific people, but with their family’s places of origin.

One example is Leah Madison, 32, an education outreach coordinator for the Desert Research Institute in Reno, Nev. She was planning trips to Peru and Korea when she learned a year and a half ago from 23andMe that her family came from Greece, Italy and the Iberian Peninsula.

Over the winter she and her father went to the Iberian Peninsula for two weeks. She felt an ineluctable connection to the people as she ate their bread masterpieces, toured buildings by Antoni Gaudí and danced to flamenco music.

“I had a piece of paper that tells me I’m from Spain,” Ms. Madison said. “But then I went there and I noticed all these people have curly hair, and maybe that is where mine comes from?” Now she feels compelled to visit the other places as well.

Perhaps the most frustrating reality is when users don’t have any known connections at all. This can happen to people in certain ethnic groups, including Latinos and Asians, that thus far have fewer people using the services and a smaller database.

“Diversity in genetic research is a global problem,” said Joanna Mountain, the senior director of Research at 23andMe, adding that the company is offering free testing in some countries to begin to rectify that. “The results for Hispanics and Asians aren’t there yet, but they are coming,” said Jenn Utley, a family historian at Ancestry (the parent company of AncestryDNA). “The database keeps growing.”

#Génomique #Données_personnelles #Familles #23andme

Google Has Released an AI Tool That Makes Sense of Your Genome - MIT Technology Review
▻https://www.technologyreview.com/s/609647/google-has-released-an-ai-tool-that-makes-sense-of-your-genome

https://cdn.technologyreview.com/i/images/aiandgenomics.jpg?cx=0&cy=0&cw=2760&ch=1552&sw=1200

DeepVariant was developed by researchers from the Google Brain team, a group that focuses on developing and applying AI techniques, and Verily, another Alphabet subsidiary that is focused on the life sciences.

The team collected millions of high-throughput reads and fully sequenced genomes from the Genome in a Bottle (GIAB) project, a public-private effort to promote genomic sequencing tools and techniques. They fed the data to a deep-learning system and painstakingly tweaked the parameters of the model until it learned to interpret sequenced data with a high level of accuracy.

“The success of DeepVariant is important because it demonstrates that in genomics, deep learning can be used to automatically train systems that perform better than complicated hand-engineered systems,” says Brendan Frey, CEO of Deep Genomics.

The release of DeepVariant is the latest sign that machine learning may be poised to boost progress in genomics.

DeepVariant will also be available on the Google Cloud Platform. Google and its competitors are furiously adding machine-learning features to their cloud platforms in an effort to lure anyone who might want to tap into the latest AI techniques (see “Ambient AI Is About to Devour the Software Industry”).

#Génomique #Google #Deep_learning

How to Spend $1,900 on Gene Tests Without Learning a Thing - MIT Technology Review
▻https://www.technologyreview.com/s/609103/how-to-spend-1900-on-gene-tests-without-learning-a-thing

https://cdn.technologyreview.com/i/images/screen-shot-2017-10-17-at-4.32.54-pm.png?cx=250&cy=0&cw=4714&ch=2652&sw=1200

But instead of air purifiers, bacon toasters, and other electronic gadgets that no one really needs, people with money to burn can spend $149 on a scarf whose pattern is personalized using their genes, DNA diet apps, or even genetically influenced wine recommendations.

Eric Topol, an influential heart doctor and geneticist at the Scripps Research Institute in La Jolla, California, says he’s had enough. To Topol, too many of these apps amount to genetic astrology. “The data has no basis. It’s pseudoscience—complete, utter nothing,” he says. He calculated that a consumer could spend $1,900 on 17 apps and learn almost nothing of value.

Earlier this year, the U.S. Food and Drug Administration signaled that it would unwind what had been a de facto ban on a range of direct-to-consumer gene reports. What’s followed has been a quick expansion of gene tests that range from reasonable to downright silly.

Aside from Helix, many others are selling DNA tests, too. One, being advertised on TV, is “Soccer Genomics,” which promises a “personalized report that will help guide player development.” And for $99, a company called Orig3n will sell you a test that claims to predict your kid’s ability to learn languages. Last month, that company had to cancel a planned giveaway of DNA tests at a Baltimore Ravens game, after objections from state regulators.

Mais ils ne sont responsables de rien... un peu comme les plateformes et les fake-news... ce sont ceux qui y croient qui ont tort. Ben voyons.

In response to critics, Helix cofounder Justin Kao cautions against a “paternalistic” attitude toward what kind of information consumers should be able to spend their money on. “People should be able to choose how they want to interact and experience DNA-powered insights and decide for themselves what is of value to them,” he says.

#Génomique #Tests_génétiques #DTCtests #Arnaques

The rise and fall and rise again of 23andMe : Nature News & Comment
►http://www.nature.com/news/the-rise-and-fall-and-rise-again-of-23andme-1.22801

http://www.nature.com/polopoly_fs/7.46922.1507718105!/image/Wojcicki.jpg_gen/derivatives/nature_homepage/Wojcicki.jpg

23andme has always been the most visible face of direct-to-consumer genetic testing, and it is more formidable now than ever before. In September, the company announced that it had raised US$250 million: more than the total amount of capital raised by the company since its inception. Investors estimate that it is worth more than $1 billion, making it a ’unicorn’ in Silicon Valley parlance — a rare and valuable thing to behold. But for scientists, 23andme’s real worth is in its data. With more than 2 million customers, the company hosts by far the largest collection of gene-linked health data anywhere. It has racked up 80 publications, signed more than 20 partnerships with pharmaceutical firms and started a therapeutics division of its own.

“They have quietly become the largest genetic study the world has ever known,” says cardiologist Euan Ashley at Stanford University, California.

Scientists, meanwhile, were dubious. Family history was and is still a more powerful indicator than genes are for predicting the risk of most diseases. “The evidence is increasingly strong that the benefits of direct-to-consumer testing for these kinds of indications are somewhere between small and zero,” says Stanford University lawyer and ethicist Hank Greely, a long-time critic of the company.

#Génomique #23andme

Une plateforme pour la génomique personnelle | InternetActu.net
►http://www.internetactu.net/a-lire-ailleurs/une-plateforme-pour-la-genomique-personnelle
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Centralisation comme décentralisation posent des problèmes. Et dans tous les domaines (monnaie, données personnelles d’usage,...)

23andMe a-t-il du souci à se faire ? Une nouvelle génération d’entreprises se consacrant à la génomique personnelle est en train de voir le jour, et parmi elles Helix, à laquelle la Technology Review a consacré un récent article. Helix utilise une technique de « vrai » séquençage de l’ADN, et non de génotypage comme le fait aujourd’hui 23andMe, et se montre en mesure de fournir, pour 80$, une lecture de l’exome, c’est-à-dire une portion de l’ADN bien plus importante que celle proposée aujourd’hui par la société d’Anne Wojcicki. Mais pour la revue du MIT, l’originalité d’Helix tient à ce qu’elle appelle un App store pour l’ADN. En effet, explique l’article, les compagnies de génomique classique fonctionnent en une seule étape. On envoie sa salive, puis on reçoit les résultats une bonne fois pour toutes. Helix se veut une plateforme ouverte à des développeurs externes qui fabriqueront des applications susceptibles de donner certaines informations précises sur le contenu de notre génome. Par exemple, la société Exploragen se propose d’analyser les rythmes de sommeil. Insitome de son côté va découvrir la proportion de gènes néandertaliens au sein d’un ADN…

Évidemment, comme tout ce qui touche à ce domaine très controversé, des questions d’éthique et de risque se posent (comme le fait de devoir payer un loyer à vie pour pouvoir accéder à notre propre code génétique et bénéficier des avancées de la médecine, comme s’en inquiète le professeur de marketing, Christophe Benavent sur son blog). Lorsque tous les résultats sont concentrés au sein d’une même société, on peut à la limite tenter d’avoir un peu de contrôle. Mais dans un système décentralisé, qui va vérifier le sérieux des applications ?

#Génomique

Une plateforme pour la #génomique personnelle
►http://www.internetactu.net/a-lire-ailleurs/une-plateforme-pour-la-genomique-personnelle

23andMe a-t-il du souci à se faire ? Une nouvelle génération d’entreprises se consacrant à la génomique personnelle est en train de voir le jour, et parmi elles Helix, à laquelle la Technology Review a consacré un récent article. Helix utilise une technique de « vrai » séquençage de l’ADN, et non de (...)

#A_lire_ailleurs #Services #bodyware

Gene Editing for ‘Designer Babies’? Highly Unlikely, Scientists Say - The New York Times
▻https://www.nytimes.com/2017/08/04/science/gene-editing-embryos-designer-babies.html

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Here is what science is highly unlikely to be able to do: genetically predestine a child’s Ivy League acceptance letter, front-load a kid with Stephen Colbert’s one-liners, or bake Beyonce’s vocal range into a baby.

That’s because none of those talents arise from a single gene mutation, or even from an easily identifiable number of genes. Most human traits are nowhere near that simple.

“Right now, we know nothing about genetic enhancement,” said Hank Greely, director of the Center for Law and the Biosciences at Stanford. “We’re never going to be able to say, honestly, ‘This embryo looks like a 1550 on the two-part SAT.’”

Even with an apparently straightforward physical characteristic like height, genetic manipulation would be a tall order. Some scientists estimate height is influenced by as many as 93,000 genetic variations. A recent study identified 697 of them.

Talents and traits aren’t the only thing that are genetically complex. So are most physical diseases and psychiatric disorders. The genetic message is not carried in a 140-character tweet — it resembles a shelf full of books with chapters, subsections and footnotes.

So embryonic editing is unlikely to prevent most medical problems.

But about 10,000 medical conditions are linked to specific mutations, including Huntington’s disease, cancers caused by BRCA genes, Tay-Sachs disease, cystic fibrosis, sickle cell anemia, and some cases of early-onset Alzheimer’s. Repairing the responsible mutations in theory could eradicate these diseases from the so-called germline, the genetic material passed from one generation to the next. No future family members would inherit them.

A composite image showing the development of embryos after injection of a gene-correcting enzyme and sperm from a donor with a genetic mutation known to cause hypertrophic cardiomyopathy. Credit Oregon Health & Science University

But testing editing approaches on each mutation will require scientists to find the right genetic signpost, often an RNA molecule, to guide the gene-snipping tool.

#génomique #designer_baby #thérapeutique_génique #CRISPR

Biopunk : Subverting Biopolitics – The New Inquiry
▻https://thenewinquiry.com/biopunk-subverting-biopolitics

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My own work has also taken a political and critical approach to working with biotechnology. With Stranger Visions, in 2012, I created portraits of strangers from their abandoned DNA. I began by collecting genetic artifacts I found in public: hair, cigarette butts, chewed-up gum. I learned how to extract DNA, how to sequence it, and how to analyze it to generate a portrait of what someone might look like based on an interpretation of their DNA, utilizing scientific research ranging from the established to the speculative. I 3-D printed the portraits life size, in full color, and exhibited these alongside documentation of the artifact, where and when it was collected, and what I analyzed.
Stranger Visions (installation view)

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The work was meant to call attention to the vulnerability of the body to new forms of surveillance and to predict the future direction of forensic DNA phenotyping—the profiling of a person’s outward characteristics from their DNA. At the time there were clear signals this research was happening, but it hadn’t been publicly discussed.

Two years later the prediction came true with the launch of Parabon Nanolabs DNA “Snapshot”, offering genomic mugshots to police around the country. The danger of offering stereotypes based primarily on sex and ancestry predictions is that a black box algorithm in the hands of the police can become a new form of racial profiling which appears to have the authority of real genetic evidence.

Most recently, I worked with Chelsea Manning. Subject to a strict policy of visitation and representation, Chelsea’s image had been suppressed since her sentencing and gender transition in 2013. She realized that DNA could give her a kind of visibility or presence that she had been stripped of for years. Chelsea didn’t want to appear too masculine in the portraits. I realized it was a perfect opportunity to highlight the reductionism of DNA phenotyping. Instead of producing one portrait to represent her, I generated two: one that was algorithmically gender “neutral” and one parameterized “female.” I presented the two portraits side by side to focus attention on the limitations of this technique even in regards to a genetic trait considered “legible.”

Just as the libertarian fraction of the cyberpunks fantasizes about the singularity putting the mind into software, biopunk-driven positivism fantasizes about DNA code being the instructions for life itself. “We have discovered the secret of life.” This was how Watson and Crick bragged about their discovery of the DNA double helix after poaching the work of their colleague Rosalind Franklin. Code is the ultimate dream.

#Génomique #biopunk #23andme #surveillance
So let’s imagine what happens as this runs its course. What will evolve from biohacking, taking into consideration what we have said so far?

Boom in human gene editing as 20 CRISPR trials gear up | New Scientist
▻https://www.newscientist.com/article/2133095-boom-in-human-gene-editing-as-20-crispr-trials-gear-up

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The CRISPR genome editing revolution continues to advance at an astounding pace. As many as 20 human trials will be under way soon, mostly in China, New Scientist has learned.

One of these trials will involve the first-ever attempt to edit cells while they are inside the body. The aim is to prevent cervical cancers by using CRISPR to target and destroy the genes of the human papillomavirus (HPV) that cause tumour growth. This study is due to begin in July at the First Affiliated Hospital of Sun Yat-Sen University in China.

Gene therapy, which involves adding extra genes to cells, was first used to cure people in 1990, but it is mainly useful for treating rare genetic disorders. In contrast, gene-editing, which involves altering existing genes inside cells, promises to treat or cure a much wider range of conditions, from HIV infection to high blood cholesterol.

The HPV trial, meanwhile, will break new ground. Instead of editing cells outside the body, a gel containing DNA coding for the CRISPR machinery will be applied to the cervix. The CRISPR machinery should leave the DNA of normal cells untouched, but in cells infected by HPV, it should destroy the viral genes, preventing them from turning cancerous.

“Targeting HPVs seems a sensible approach if they can deliver the genome-editing components to sufficient numbers of cells,” says Robin Lovell-Badge of the Crick Institute in the UK.

#génomique #médecine
“It is tricky to do these experiments in animals as they are not infectable by HPV,” says Bryan Cullen of Duke University Medical Center in North Carolina, whose group also hopes to use gene editing to get rid of HPV. But there is a risk of off-target mutations leading to cancer, he warns.

23andMe Is Making Its First Foray into At-Home Research, to Study Pain - MIT Technology Review
▻https://www.technologyreview.com/s/607928/23andme-is-making-its-first-foray-into-at-home-research-to-study-p
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Une expérience médicale menée at home par les usagers de 23andMe. Une certaine conception de la médecine, dont l’entreprise est familière.

“It was uncomfortable and slightly painful, but nothing like wearing wet gloves and shoveling snow for an hour at 10 below zero,” says Pardy, who lives in northwest Vermont. Most people can stand to keep their hands in near-freezing water for at least 100 seconds, according to 23andMe.

The experiment Pardy did is known as a cold pressor test, and it’s one of many used to gauge a person’s tolerance to pain. It’s part of a new study 23andMe announced earlier this month to study the genetic links of pain tolerance, and it represents the company’s first foray into at-home research.

23andMe has previously launched studies on medical conditions like depression, fertility problems, and irritable bowel disease, using surveys to ask participants about things like their health history, lifestyle, and diet (see “23andMe Pulls Off Massive Crowdsourced Depression Study”). The new study also includes two surveys about pain tolerance and pain history, but this is the first time the company has asked people to do an experiment on their own and report the results.

Carrie Northover, director of research services for 23andMe, says the goal of the study is to “understand genetic factors associated with experiencing pain and response to medications that help alleviate pain.” Previous research has suggested that multiple genetic factors are at play in chronic pain, and that certain groups of people report pain more often than others.

Ajay Wasan, vice chair for pain medicine at the University of Pittsburgh Medical Center, says the cold pressor test is only one way to measure pain. There are a range of other tests, including ones that measure a person’s tolerance to heat, pin pricks, and pressure.

“The problem is no one single experimental pain test maps really well to overall pain sensitivity and doesn’t have high correlation to someone’s clinical chronic pain or their response to treatment,” he says.

#médecine #génétique #23andMe #génomique

Drugs companies unite to mine genetic data - FT.com
▻http://www.ft.com/intl/cms/s/0/4d1792fe-d2f1-11e4-b7a8-00144feab7de.html#axzz3VchnVvVj

Several of the world’s biggest pharmaceuticals companies have formed a partnership with Genomics England in the first step towards using genetic data from NHS patients in medical research.
GlaxoSmithKline and AstraZeneca, the two biggest UK drugs groups, will team up with rivals, including Roche of Switzerland and AbbVie and Biogen of the US, to mine information from a government project to decode the genomes of 100,000 patients with cancer and rare diseases.

La génomique personnelle dans la tourmente
▻http://internetactu.blog.lemonde.fr/2013/12/20/la-genomique-personnelle-dans-la-tourmente/#xtor=RSS-32280322

Face à une telle situation, le débat peut se dérouler à plusieurs niveaux. L’un, philosophique, concerne le droit des individus à se connaître eux-mêmes, quels que soient les risques auxquels ils s’exposent via cette connaissance. L’autre aspect, ce sont les habituelles tractations administratives et commerciales. Enfin des polarisations politiques viennent parasiter le débat. Comme souvent dans ces domaines, les différents niveaux s’entremêlent allègrement.

#23andMe #ADN #Biologie #Diagnostic_(médecine) #Génomique #Innovation #Médecine #États-Unis

La FDA est allée un peu vite sur 23&Me - Quartz
▻http://qz.com/167178/new-evidence-shows-the-fda-was-wrong-to-halt-23andme-testing

Selon une étude menée par le chercheur en génétique Robert C Green et l’avocat spécialisé en bioéthique Nita Farahany, la seule chose qu’on devrait exiger de 23&Me est d’être honnête sur les limites de leur tests de santé. Les chercheurs ont montré que la plupart des clients de 23&Me sont allé prendre les conseils d’un médecin avant de prendre des mesure. 58% des 1000 clients de 23&Me interrogés n’ont rien fait du tout de leurs résultats génomiques. Sur les 42% qui ont pris des décisions sur la base des informations de santé de 23&Me, seuls 2% ont changé de régimes de médicament sans consulter un médecin. La majorité des clients ont fait des changement basés sur leur alimentation, l’exercice ou les vitamines. Une autre étude a montré que les tests n’étaient la plupart pas très utiles et que la plupart des (...)

#ADN #génomique

Analysis of huge data sets will reshape health care
▻http://www.usatoday.com/story/news/nation/2013/11/24/big-data-health-care/3631211

Electronic medical records and decisions by governments and companies to share data have made for smarter decision-making that can save money and provide better care, experts say.

Though the rewards of such data use are great, so are the privacy concerns, Hide said. “We have opened a pandora’s box, and it makes the NSA’s problems look trivial.”

If made public, genomic data could lead to employment discrimination, as some people might not be hired for jobs because of potential health problems that could raise an employer’s insurance costs.

There have been cases in which health and insurance information has been released accidentally. The industry must do better, Sengupta said.

“We treat privacy now as a legal issue with a disclaimer,” Sengupta said. “We need to have privacy built in. Technology created the problems, but technology can also fix it.”

#big_data #santé #génomique #vie_privée

Quand Google Books permet de comprendre notre génome culturel « InternetActu.net
►http://www.internetactu.net/2011/06/20/quand-google-books-permet-de-comprendre-notre-genome-culturel

l’étude de l’évolution de la #culture nécessitait quelque chose comme un génome, une base de #données si puissante qu’elle permettrait à de telles analyses d’être faites rapidement, sur toutes sortes de sujets, pas seulement les verbes irréguliers. Et on a remarqué que certains des livres très obscurs que nous utilisions apparaissaient sur #Google_Books. On a fait le lien.” Et voici comment Harvard et Google Books se mettent à travailler ensemble.

#recherche #génomique #livres #Numérisation

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