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Consumer genetics giant 23andMe has been granted a US patent for a technique to predict a baby’s traits based on the DNA of its putative parents. The company’s Family Traits Inheritance Calculator has been available to custo...
Consumer genetics giant 23andMe has been granted a US patent for a technique to predict a baby’s traits based on the DNA of its putative parents. The company’s Family Traits Inheritance Calculator has been available to customers for some years already and is said to offer ‘an enga ...
about 6 hours ago
Barbara Prainsack is at the Department of Social Science, Health & Medicine at King’s College London. Her work focuses on the social, regulatory and ethical aspects of genetic science and medicine.More than seven years ago, my coll...
Barbara Prainsack is at the Department of Social Science, Health & Medicine at King’s College London. Her work focuses on the social, regulatory and ethical aspects of genetic science and medicine.More than seven years ago, my colleague Gil Siegal and I wrote a paper about pre-marital genetic compatibility testing in strictly orthodox Jewish communities. We argued that by not disclosing genetic results at the level of individuals but exclusively in terms of the genetic compatibility of the couple, this practice gave rise to a notion of “genetic couplehood”, conceptualizing genetic risk as a matter of genetic jointness. We also argued that this particular method of genetic testing worked well for strictly orthodox communities but that “genetic couplehood” was unlikely to go mainstream.Then, last month, a US patent awarded to 23andMe – which triggered heated debates in public and academic media (see here, here, here, here and here, for instance) – seemed to prove this wrong. The most controversially discussed part of the patent was a claim to a method for gamete donor selection that could enable clients of fertility clinics a say in what traits their future offspring was likely to have. The fact that these “traits” include genetic predispositions to diseases, but also to personality or physical and aesthetic characteristics, unleashed fears that a Gattaca-style eugenicist future is in the making. Critics have also suggested that the consideration of the moral content of the innovation could or should have stopped the US Patent and Trademark Office from awarding the patent. Read the rest of this entry | Read comments
1 day ago
Myriad Genetics is once again embroiled in litigation over its BRCA-related patents. But this time Myriad is the defendant. Counsyl, Inc., a San Francisco-based company that focuses on genetic carrier testing, sued Myriad in U.S. Distric...
Myriad Genetics is once again embroiled in litigation over its BRCA-related patents. But this time Myriad is the defendant. Counsyl, Inc., a San Francisco-based company that focuses on genetic carrier testing, sued Myriad in U.S. District Court for the Northern District of California on September 20, 2013. As we noted in an earlier post, Myriad — as a plaintiff — has recently sued two small companies, Ambry and Gene By Gene, that have entered the BRCA testing market in response to the Supreme Court decision invalidating Myriad’s gDNA patent. Myriad presumably filed those suits — against vulnerable defendants — to send a message that it would maintain its testing monopoly by enforcing patent claims that had survived the earlier litigation. But it took the risk that the defendants might succeed in invalidating those surviving claims. Now, with the Counsyl suit, the BRCA controversy has entered a new stage, with a prospective competitor launching a preemptive strike against Myriad and its patents. This is not the usual patent suit, where the plaintiff accuses the defendant of infringement and seeks damages. Here, Counsyl is asking the court for a declaratory judgment that (1) eight specified Myriad patents (each with many claims) are invalid and (2) even if they are valid, Counsyl isn’t infringing them. Declaratory judgments are a common tactic in intellectual property disputes. A company that thinks it’s about to be sued for infringement — a prospective defendant, in other words — jumps the gun and asks a court to rule in advance on the defenses it would raise if it were sued for an infringement. If Myriad sued Counsyl for infringement, Counsyl would defend by saying what almost every infringement defendant says: the plaintiff’s patents aren’t valid, but even if they are, we’re not doing anything that infringes them. By filing the declaratory judgment action, Counsyl gets to choose both the time and the court that will rule on these issues. Not surprisingly, it picked its home court. Otherwise, the case will play out exactly like an infringement suit. Because of something called the compulsory counterclaim rule, if Myriad thinks that Counsyl is currently infringing, it must assert its infringement claim as a counter-suit in this litigation. One special hurdle that Counsyl will have to get over is an arcane constitutional law doctrine called standing. The Constitution does not permit the federal courts to decide hypothetical questions. To be eligible for a declaratory judgment ruling in advance of any infringement litigation, Counsyl must show that there is — right now — an actual controversy between it and Myriad. Most declaratory judgment plaintiffs satisfy this requirement by showing things like cease and desist letters from the patent owner. But there appears to be no evidence that Myriad has yet threatened Counsyl. In fact, Counsyl has told the media that it is not currently offering BRCA testing. Given these facts, it is very likely that one of Myriad’s first moves will be to ask the court to dismiss the suit for lack of standing. Given all this, it is hard to figure out why Counsyl chose to file suit now. On the one hand, the filing allows Counsyl to determine the time and place of the litigation (now, and in San Francisco rather than later, and in Utah, Myriad’s clear preference). On the other, the compulsory counterclaim rule insures that Myriad will assert any infringement claims that it currently has. Counsyl must have decided that the benefits — especially avoiding Utah —outweighed the risks. That would make particular sense if Counsyl was persuaded that it is not doing anything right now that could give rise to an infringement claim. If the case proceeds beyond the standing question, then the validity of Myriad’s patents will once again be at issue. All eight patents that Counsyl is challenging are also the subject of infringement claims in Myriad’s Ambry and Gene By Gene suits (which have been consolidated for trial
1 day ago
A group of European politicians have signed a declaration against plans to permit mitochondrial replacement (MR), also known as three-person or three-parent IVF. ? The technique allows parents affected by mutations in their mitochondri...
A group of European politicians have signed a declaration against plans to permit mitochondrial replacement (MR), also known as three-person or three-parent IVF. ? The technique allows parents affected by mutations in their mitochondrial DNA have a genetic child without passing on the defects ...
2 days ago
There has been a great deal of coverage this week of the new patent issued to genetic testing company 23andMe.  U.S. Pat No. 8,543,339 is entitled “Gamete donor selection based on genetic calculations” and is directed to methods for pred...
There has been a great deal of coverage this week of the new patent issued to genetic testing company 23andMe.  U.S. Pat No. 8,543,339 is entitled “Gamete donor selection based on genetic calculations” and is directed to methods for predicting traits for a child based on the DNA of candidate parents, and selecting a preferred donor based at least in part on the prediction. Some of the coverage (including an editorial in Genetics in Medicine) has suggested that the methods are “hugely ethically controversial” and “‘GATTICA’-like,” and could lead to a “design-your-own-baby DNA test” and “designer babies.”  Another popular genetic genealogy blogger, Roberta Estes, also addressed the patent on her blog earlier this week (“23andMe Patents Technology for Designer Babies”). 23andMe preemptively addressed the patent in their blog the Spittoon (“A 23andMe Patent”), and stated that “[t]he company never pursued the concepts discussed in the patent beyond our Family Traits Inheritance Calculator, nor do [they] have any plans to do so.” Too Much Hype? The negative hype surrounding the patent, however, is based entirely on the misguided theory of genetic exceptionalism (the belief that genetic information is special and must therefore be treated differently from other types of medical information), and is unwarranted. Here is a brief summary of my hypothesis, which I’ll get into in more detail below: People have been screening possible gamete donors for decades based on things like religion, ethnicity, education, height, weight, eye color, hair color, age, and personal/family medical history, among other things (notably, several of these things are proxies for genotype, and some even work better than genotyping); The difference between using the traditional traits/characteristics listed above for donor screening and the methods described in the 23andMe patent is that the patent involves the use of DNA to screen donors: accordingly, the outrage about this patent is based on genetic exceptionalism; and Genetic exceptionalism lends itself very easily to government regulation, and is therefore potentially unfavorable for anyone opposed to genetic paternalism (including, presumably, genetic genealogists). #1 – Selecting A Donor Without DNA Although some may disagree with points #2 and 3 above, point #1 is indisputable. People have been screening potential donors for at least 50-60 years based on one or more of the factors listed above.  Things such as personal and family health history have a very strong genetic component, and in almost every way are better predictors of health in offspring.  For better and for worse, DNA has not turned out to be the strong predictor scientists thought it would be. And even before gamete donation, there was the simple selection of mate based on appearances and behavior, which can be very closely tied to genotype. Regardless, there is no doubt that donors have been screened for decades.  However, I’ve never heard anyone suggest that donors should not be screened, or that there should be regulation of donor selection to prevent screening based on certain traits.  Indeed, none of the coverage has suggested that any screening be stopped, other than DNA-based screening.  At best, a few of the better articles have mentioned in passing that non-DNA factors are routinely used for donor selection. #2 – The Myth of Genetic Exceptionalism The 23andMe patent describes methods of using genotype (DNA) to predict the possible traits of a child and thus allows the selection of a particular donor based on the “best odds.”  How is that process different from selecting a donor with the highest level of education and hoping that it corresponds to intelligence in the child?  Or selecting a tall donor with dark hair in the hopes that the child will be tall with dark hair? Or selecting a thin donor in hopes that the child will be thin? The difference is likely only that many people believe that DNA is different or special, that sele
2 days ago
I suppose I knew this was coming ... but did not expect it so soon ... see the email I received below. Focus in particular on the part highlighted in yellow .... Dear Colleague, British Biotechnology Journal (BBJ) is an OPEN p...
I suppose I knew this was coming ... but did not expect it so soon ... see the email I received below. Focus in particular on the part highlighted in yellow .... Dear Colleague, British Biotechnology Journal (BBJ) is an OPEN peer-reviewed, OPEN access, INTERNATIONAL journal, inspired from the great OPEN Access Movement. We offer both Online publication as well as Reprints (Hard copy) options. Article Processing Charge is only 50 US$ as per present offer. This journal is at present publishing Volume 4 (i.e. Fourth year of operation). 2. Transparent and High standard Peer review: In order to maintain highest level of transparency and high standard of review, this journal presently follows highly respected and toughest Advanced OPEN peer-review system(Example Link1, Link2, Link3, Link4, Link5, Link6, Link7, Link8, Link9, Link10,Link11, etc). We hope that you will appreciate this Advanced OPEN peer-review system, which is expected to give doubtless scholarly benefit and impact to the authors in long run. Additionally we strongly encourage and promote “Post-publication Peer review” by ourcomment section. As per a recent report (Link) of Science journal (present Impact factor 31), one of our journal passed a stringent test of quality of Peer review by rejecting a fake article (Link1,Link2, Link3). We applaud the dedication and hard-work of our peer reviewers and editors to maintain the high standard of our journals. It was reported that only few journals (20), out of total 304 journals tested, rejected the fake article after substantial peer review. We are happy that our journal was among these few successful journals along with industry leaders like PLoS One, Hindawi, etc. We believe that the result of this experiment also proved the efficacy of our Advanced OPEN peer review and ‘post publication’ peer review system. Though the report is debated, as it did not include subscription journals, we normally support any effort to improve the quality and transparency of peer review. 3. Proposed Time Schedule: Submission to first editorial decision with review comments: 3 weeks Submission to publication: 6 weeks State-of-the-art ‘running issue’ concept gives authors the benefit of 'Zero Waiting Time' for the officially accepted manuscripts to be published. 4. Abstracting/indexing: Many respected abstracting/indexing services covered our journals. ISI Thomson Reuters (Only for ARRB) ProQuest (Screen shot) HINARI (United Nation's Database) CAB abstract (UK) EBSCOhost (USA) (Mail confirmation link) AGORA (United Nation's FAO database) Google scholar DOAJ SHERPA/RoMEO (UK) OARE (United Nations Environment Programme (UNEP), Yale University, etc.) Ulrich's Zentralblatt MATH (only for BJMCS) CrossRef Chemical Abstracts Service (“CAS”) (Mail confirmatiom link) For more information please visit here. 5. Authors’ profile: Considering high peer review standard, quality control, etc. our journals have been chosen by academicians of many famous universities, institutes, etc. A glimpse of authors’ profileis provided here. 6. Testimonials: Appreciation of our esteemed satisfied authors is the greatest inspiration behind the hard-work of our editorial team. Some of the testimonials are available here. 7. Article Processing Charge (or Publication Charge): Article Processing Charge (or Publication Charge): Manuscript submitted within 1st July, 13 -- 30th September, 2013 will be eligible for 90% discount on normal Article Processing Charge (APC) of 500 USD. (i.e. Effective APC: 50 USD). For more information visit here. 7.1. Reprints (Hard copy): Reprints (Hard copy) are also available at extra cost. For detailed information please see here (Reprint information link). 8. Sample papers: Antibacterial and Antiviral Activities of Essential Oils of Northern….. African Cassava: Biotechnology and Molecular Breeding to the Rescue Growth I
2 days ago
Just got pointed to this very interesting paper by one of the authors: Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering : Nature Communications : Nature Publishing Group. I really reall...
Just got pointed to this very interesting paper by one of the authors: Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering : Nature Communications : Nature Publishing Group. I really really love this new approach of doing QTL experiments where the quantitative trait being measured is the relative abundance of various microbes. The first paper of this kind I know of that did such a QTL analysis was Benson et al. 2010 in PNAS in mouse. There have been a few others using this approach (e.g., Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits) and I am sure we will see many many more. Basically this approach allows one to identify genes / polymorphisms / regions of the genome in a host that influence the relative abundance of specific microbes. And such information will be critical in understanding the interactions of microbial communities with hosts. -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. --------
4 days ago
I just love this paper ... The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria | eLife from the labs of Ruth Ley and Jill Banfield (1st author is Sara C. Di Rienzi...
I just love this paper ... The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria | eLife from the labs of Ruth Ley and Jill Banfield (1st author is Sara C. Di Rienzi). It represents a landmark study in something that has intrigued many microbial diversity / human microbiome researchers for many years. Early in the history of sequencing rRNA genes from human microbiome samples, researchers discovered something a bit weird - quite a few sequences were coming from what appeared to be close relatives of Cyanobacteria. This was weird because all known Cyanobacteria were thought to be photosynthetic and - well - there is not too much light in the human gut. Now - one possible explanation for this was that these sequences were coming from photosynthetic bacteria but these bacteria were not residents of the human gut but came via consumable items (i.e., food and drink). Perhaps they were actually from chloroplasts of something in the diet (after all - chloroplasts are derived versions of cyanobacteria). This idea was discussed at many meetings I attended. But there was no evidence for this. Another possibility was that there was in fact some light in the human gut - leaking through from the outside or being produced from the inside. And perhaps this was enough to do a little photosynthesis. Sound crazy? Well, not so crazy after reports of photosynthesis in the deep sea. A third possibility was that these sequences were coming from residents of the human gut that were related to (or even within) cyanobacteria but were not photosynthetic. More detail on possible explanations are in this new paper and in some of the material cited therein. Anyway - Ruth Ley has been discussion these unusual sequences for years and now in this paper her group and the group of Jill Banfield at Berkeley (along with some others) has used metagenomics and detailed assembly and phylogenetic analysis to reveal many new insights into these sequences. I could write much more about this. But, I think the paper really speaks for itself. And it is open access so anyone and everyone can check it out. And you should. It is wonderful. Fig 2 from Di Rienzi et al. -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. --------
5 days ago
The UK’s ambitious plan to sequence 100,000 whole genomes of NHS patients over the next 3-5 years, announced by the UK Prime Minister in December last year, sparked interest and curiosity throughout the UK genetics community. Undeterred ...
The UK’s ambitious plan to sequence 100,000 whole genomes of NHS patients over the next 3-5 years, announced by the UK Prime Minister in December last year, sparked interest and curiosity throughout the UK genetics community. Undeterred by the enormity of the task, a new company, Genomics England Limited (GeL), was set up in June of this year by the Department of Health, tasked with delivering the UK100K genome project. Yesterday, they held what I’m sure will be the first of many ‘Town Hall’ engagement events, to inform and consult clinicians, scientists, patients and the public on their nascent plans.So what did we learn? First, let’s be clear on the aims. GeL’s remit is to deliver 100,000 whole genome sequences of NHS patients by the end of 2017. No fewer patients, no less sequence. At its peak, GeL will produce 30,000 whole genome sequences per year. There’s no getting away from the fact that this is an extremely ambitious plan! But fortunately, the key people at GeL are under no illusions about the fact that theirs is a near impossible task. Read the rest of this entry | Read comments
5 days ago
Yesterday at around noon I was on a conference call for a large-scale disease genomics project. In the middle of the call, a NCBI database that we use to exchange data — dbGaP — went offline. The shutdown had apparently taken...
Yesterday at around noon I was on a conference call for a large-scale disease genomics project. In the middle of the call, a NCBI database that we use to exchange data — dbGaP — went offline. The shutdown had apparently taken effect. To say that dbGaP is important for the day-to-day operations of a large-scale […]
6 days ago