Round-up March 17th – April 3rd

A review from some GSK scientists arguing for integrating genetic based drug-efficacy into clinical trails, despite the fact that at GSK they have done 17 such GWAS and not found anything clinically actionable. They argue that “only a minority of truly efficacious drugs are likely to have clinically meaningful genetic predictors of efficacy” http://www.nature.com/nrg/journal/v17/n4/full/nrg.2016.12.html

The European Society of Human Genetics has published some musings on expanded carrier screening, which also serves as a useful survey of carrier screening http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2015271a.html.

  • “Since the stated aim of reproductive screening (including carrier screening) here is not prevention, but rather the provision of options for reproductive decision making, appropriate pre-test information and voluntary decision making becomes an essential requirement rather than a mere side-constraint: without this, the screening cannot fulfil its aim.”
  • Success of programs should be judged on whether “informed choice and reproductive decision making” is optimized (not by birth prevalence of affected children)
  • They suggest that the risk of information overload may limit the type of tests that should be performed.
  • Consent as one of the most challenging issues, and the possibility of “generic consent” should be explored

Some more commentary on the Athena case, highlighting the risk that cases such as this could prevent the fledgling genetic testing field from  really getting off the ground: http://techonomy.com/2016/03/lawsuit-underscores-risk-of-thinking-genetic-tests-authoritative/.

Sequenom’s patent for non-invasive prenatal testing has been struck down, with lower courts citing the influence of the Supreme Court’s “sweeping language” in the Mayo v Prometheus. This case struck down a patent for a personalized medicine based approach to setting drug dosage level https://en.wikipedia.org/wiki/Mayo_Collaborative_Services_v._Prometheus_Laboratories,_Inc. Sequenom will now. appeal to the Supreme Court: https://www.genomeweb.com/molecular-diagnostics/sequenom-files-petition-supreme-court-review-decision-invalidating-nipt-patent

23andMe will be launching “Genotyping Services for Research” in Q2, whereby they will genotype and provide 23andMe accounts to participants in trials. Engaging those involved with research trails is seen as a challenge for many studies, and this is an easy way to give something back to them. https://www.genomeweb.com/molecular-diagnostics/23andme-running-genotyping-research-service-pilot-projects-launch-slated-q2

Qiagen have teamed up with Intel to offer a complete highly-scalable genetic testing pipeline, announcing analysis of a whole genome for $22. Note: “analysis” means variant calling: https://www.qiagenbioinformatics.com/wp-content/uploads/2016/03/White-Paper-Final-Version.pdf

Craig Venter has made a bacteria with 473 genes, which is considered an “MVP” of a genome. 149 of these genes have no known function (though are essential). http://www.sciencemag.org/news/2016/03/synthetic-microbe-lives-less-500-geneshttp://www.theatlantic.com/science/archive/2016/03/the-quest-to-make-synthetic-cells-shows-how-little-we-know-about-life/475053/

A programming language for DNA: http://www.nature.com/news/biology-software-promises-easier-way-to-program-living-cells-1.19671

Some analysis of PacBio’s threat to Illumina: http://www.fool.com/investing/general/2016/03/18/is-this-the-biggest-threat-yet-to-illumina.aspx

Risks in the genetic testing industry, a summary of a set of interviews with genetics professionals. Main risks linked to lack of physician education and pace of technology development: http://www.nature.com/gim/journal/vaop/ncurrent/full/gim201616a.html

A study using the 150k participants in the UK BioBank have quantified the lifespan reduction of having certain SNPs: http://www.eurekalert.org/pub_releases/2016-03/uoe-igc033016.php

Large GWAS meta-analysis of the genetics of cannabis use finds no significant SNPs, but four genes: http://www.nature.com/tp/journal/v6/n3/full/tp201636a.html

On secondary findings, and how not to over interpret them: http://www.nature.com/gim/journal/vaop/ncurrent/full/gim201619a.html

The case continues to grow that the genetic code may be more flexible than we think, with extra codons shown to code for selenocysteine, the 21st amino acid (i.e. just outside the canonical set of 20): https://www.sciencedaily.com/releases/2016/03/160331134413.htm

Making the case for individuals owning their health data, and the risk of the “unpatient”: http://www.nature.com/nbt/journal/v33/n9/full/nbt.3340.html

 

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