Round-up Feb 1 – Feb 18

Controversy

  • An opinion piece in STAT by Michael Joyner and Nigel Paneth against the genetic reductionism of precision medicine: “We are calling for an open debate, in all centers of biomedical research, about the best way forward, and about whether precision medicine is really the most promising avenue for progress. It is time for precision medicine supporters to engage in debate — to go beyond asserting the truism that all individuals are unique, and that the increase in the volume of health data and measurements combined with the decline in the cost of studying the genome constitute sufficient argument for the adoption of the precision medicine program.” Their piece references a 1999 lecture from Francis Collins. He explains the background to the Human Genome Project (“a public science initiative focused so sharply on the molecular essence of humankind was too intriguing and too promising to forgo”) and then lays out his vision for what we now call Personalized Medicine, including an imagined 2010 encounter where a young soker learns of his increased risk of lung cancer, which “provides the key motivation for him to join a support group of persons at genetically high risk for serious complications of smoking, and he successfully kicks the habit.”

Science

  • Race as a biological variable. A paper that finds differences in Alzheimer biomarkers between African-Americans and non-Hispanic whites: lower cerebrospinal fluid concentrations of tau, with results varying by APOE status. In addition to a race-by-biomarker interaction, this is a race-by-genotype interaction. They argue that these uncovered links mean that a) any attempts to use biomarkers in diagnosis should adjust for race, and b) hope for better treatment based on incorporating “race dependent biological mechanisms”.
  • A review of polygenic risk scores in psychiatry. Reviews use of GWAS for “increasingly informative individual-level genetic risk prediction” for psychiatric disorders, which are not yet ready for the clinic. Does a nice job of showing that the idea of summing up the effects of many genetic variants to explain a continuous phenotype goes back to the very beginning of the study of hereditary. “ To understand how to incorporate PRS into clinical practice for patients with heritable psychiatric disorders, studies will need to assess health outcomes for various behavioral interventions, treatment regimens, and/or differential diagnoses” They make an interesting observation as regards height: “prediction accuracy is not distributed evenly; it performs particularly poorly at the extreme short end of the height distribution, indicating a larger contribution of environmental factors, large-effect rare variants, and/or other factors in these individuals”
  • Polygenic scores are trained on cohorts of diagnosed individuals. A Danish study shows that polygenic scores for depression are also predictive in a general cohort. A score of one standard deviation above the mean gives a 30% increased chance of a diagnosis of depression.

Applications

  • A look at how consumer genetic testing companies market testing for Native American ancestry, focusing on the claimed links to identity. They wonder, whilst acknowledging it is beyond the scope of their paper, “Are companies changing consumer behavior, or are consumers already coming in with certain expectations of verifying tribal ancestry and using the results as a means to accomplish this goal?” (See this paper for qualitative interviews with 100 people looking at this question). The paper references that the US government required tribes in 1934 to have a minimum “blood quantum” for enrollment. There is clear, and problematic, precedent for the use of genetics/blood to define identities. Rewind the clock to 2013, and in giving the majority opinion against a Native American father in a complicated court case, Justice Alito choose to start with “This case is about a little girl (Baby Girl) who is classified as an Indian because she is 1.2% (3/256) Cherokee.”, seemingly drawing attention to the genetic component of her Indian-ness, and in particular that it was only 1.2% (I recommend the More Perfect podcast episode about this case). Reading more about these considerations convinces me of just how counterproductive it was for Elizabeth Warren to act upon Trump’s goad to be genetically tested to proof her claims of Native ancestry.
  • A piece on SpectrumNews, about the benefits of genetic testing. I was struck by this quote from the mother of a child who received a pathogenic finding when her daughter was an adolescent: “Instead of trying to change her behaviors, we’re modifying how we take care of her… It has given me a lot of relief knowing where her autism comes from, and that there was nothing I could have done differently.” Her daughter was the “way she is because of biology”. Routine genetic testing, if it had been available at the time could have saved her ”years of worry and guilt”.  
  • Antonio Regalado reports on a start-up working towards designer babies. One of the founders “is skeptical of the role regulations can play—a lesson he says he learned working with Bitcoin, a digital currency outside the control of any central bank.” I was alarmed at this: “Bishop told me none of the ethicists he e-mailed had ever gotten back to him.”
  • The FBI can now send a sample to FamilyTree, and they will sequence it and see if it matches anything in their database:
  • Speaking of polygenic scores, did you see that the Scripps has an App for that?
  • Some lovely visual explainers of the difference between NGS and genotyping from NYT.

Regulation/Ethics

  • Designing babies with high IQs may be far off, but selecting between embryos based on polygenic scores for IQ is more or less upon us (witness Genomic Prediction). Erik Parens, Paul Appelbaum, and Wendy Chung argue that profiling embryos for IQ would be unethical. Parents have two competing ethical obligations: to accept their children as they are, and to shape their children. The market is producing a “grotesque” pull towards the latter. “Placing limits on the genetic selection of embryos is one small way for our society to affirm the importance of achieving a balance between the ethical obligations to shape our children and to accept them as they are — and the importance of closing, rather than widening, the gap between the rich and the poor.” They argue for regulation, pointing out that the UK manages to do just that.
  • Ethics dumping? The Economist asks whether Deem — the American scientist who was He’s thesis advisor and who had same role in the notorious experiments — is guilty.

The Backstreet Boys have a new album called DNA. Why? Watch this cringeworthy explainer.

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