A science blog with Eric Berger





Let me introduce you to the Beery Family.

Alexis and Noah Beery have gone through a lot to live normal lives. (K.C. Alfred)

As I report today in a story just published, for what may be the first time anywhere, scientists and physicians in Houston have used whole genome sequencing to diagnose an ailment and change medical care for the better.

This is a big step forward if you consider it was only last year that for the first time geneticists sequenced a person’s entire genome to identify the genetic cause of a disease.

The Beerys’ is a heart-rending story:

For every day of his first six years of life, Noah Beery drooled and threw up large amounts of what he ate. And he was the healthy twin.

His sister, Alexis, would wake multiple times at night and endure tremors for hours at a time. By midmorning she could no longer exert herself even to sit up. An initial diagnosis of cerebral palsy at age 2 proved false when the twins’ condition continued to deteriorate.

When the children were 6, doctors diagnosed them with a relatively rare genetic disorder. Treatment helped but did not cure them. When Alexis was 12 she nearly died after she stopped breathing. Paramedics had to revive her twice.

But for me the real news here is the fact that we’re beginning to see the promise of genetics and medicine. It comes as a result of two things.

First, over the last decade, geneticists have worked very doggedly to understand the genome, and associate gene mutations with disease. Richard Gibbs estimates we’re about 30 percent along with completing this task. Next comes figuring out the combinations of gene mutations that lead to common diseases like cancer.

Secondly the costs of doing who genome sequencing have continued to fall rapidly. The following graphic shows the declining costs of a full genome:


Put those two factors together and the type of breakthrough we’ve seen with the Beery family is going to become more and more commonplace.

There are a lot of fears out there about the proliferation of genetic information and what that means for our privacy. But it strikes me that it’s becoming increasingly clear that the health benefits of sequencing are going to be immense. And worth it.

Welcome to the era of personalized medicine.

Eric Berger

12 Responses

  1. JohnD says:

    This is a good story; thank you!

    Of course, there will be more to the story – epigenetics. As we’ve seen with the FADS2 gene and the mouse experiments (not to mention cloned animals), epigenetics has a very strong influence on the expression of genes and so will have a very strong influence on the outcome of gene therapy.

    • Eric Berger says:

      Yes, epigenetics will play a big role and is another emerging piece of the complex picture. Thankfully this is one area of science where technology is coming along that’s commensurate with the need to not only sequence all of this information, but to organize the data into a meaningful picture.

  2. craig says:

    Maybe this development will help offset tne trend by doctors pressured to see ever more patients during a given day to offset lowered medicare/insurance company payments which has resulted in the typical office vist going something like “Hi Doc, By Doc Say what?” anymore.

  3. Bill in Houston says:

    At the same time doctors are leaving private practice and joining hospital systems because of the unknown reach of Obamacare. Both my GP and my cardiologist are now employees of the Memorial Hermann system. MH offers better protection for them.

  4. David says:


    Your first two links aren’t really epigenetics in the sense that a geneticist would understand them. The third is.

    Variation and mutation in genes will certainly interact with environment, and those interactions can be incredibly significant–but that’s gene:environment interaction, not epigenetics. Two of the biggest success stories in prevention of intellectual disability are really environmental modifications: The biggest is iodine, and while there may be a genetic predisposition to hypothyroidism, goiter and attendant issues with brain development, we don’t even think about it in the West since we iodinated the salt. This has prevented millions cases of low IQ or intellectual disability, but developing countries lag behind here.

    The second success story is PKU. Look at your diet soda can–it warns PKU patients about the aspartame. Through newborn screening, we have identified patients with mutations in phenylalanine hydroxylase and made sure that they get a diet that has low levels of phenylalanine. Not the most pleasant diet, by the way–and aspartame is a dipeptide, with phenylalanine as one of the two amino acids. But the diet prevents a very severe disorder that usually includes a very low IQ. The change in diet allows these children to live normal lives, despite their mutation.

    These are old, old stories. In its simplest definition, epigenetics is a modification to a gene that can both be inherited and affect the output of the gene. Sometimes environment can play a role in this change. In some fascinating examples in mice, diet in grandparents modify gene expression in the grandchild. But it’s only quasi stable, so it’s not quite Lamarckian! Epigenetics has become a “sexy” term, so everyone throws it around, but it’s not used properly in your second link.

    • JohnD says:


      Really? Then why did the geneticists who wrote the second paper title it “Genetic polymorphisms in methyl-group metabolism and epigenetics: Lessons from humans and mouse models”? And why is the FADS2 link frequently used as an example of epigenetic influence? These are examples of epigenetics.

    • David says:

      My only point is that the term epigenetics has gotten appropriated to mean pretty much anything to do with genes or their expression, including variation! To a geneticist, it has a much more specific meaning. Of course you may use it as you please.

      Dr. Zeisel is a pediatrician and a nutritionist. His very distinguished CV doesn’t include any genetics training that I can find. He is very interested in one carbon metabolism, and dietary choline and folate and their influences on health. He likes the idea that choline deprivation is unhealthy due to effects on nuclear DNA, but it is also likely to be unhealthy for many reasons. When I wrote the above, I had only looked at the abstract of the paper you cite. It doesn’t really address anything to do with the DNA, even if he tosses in the word epigenetic. Now I’ve looked at the paper and it’s a breezy review, mostly about genetic variation in folate metabolism and how that might affect individual’s responses to choline/folate nutrition (not epigenetics), and then a paragraph that is an appropriate description of how prior exposure to excess (or lack) of choline in the diet can effect gene expression in mice and rats–citing the same studies in mice that I mentioned above. A scan of the 235 papers listed on his CV shows one study that actually finds some DNA effects in brains of mouse embryos that developed in mothers starved of choline during their gestation. If you massively perturb one-carbon metabolism, it’s likely that you’ll change how DNA and histones are methylated, and this might well alter gene expression. Choline is essential. Not having dietary choline is bad. Some of the effect might be through altering gene expression. Part of this effect is epigenetic at the limit case. Showing an effect with smaller variation is tougher, but it might be there.

      We supplement bread with folic acid to reduce neural tube defects. The mechanism isn’t well understood, but it works–maybe through altering gene expression, maybe through the many many other cellular and developmental processes that depend on one carbon metabolism. My only point is that while it’s sexy to call this “epigenetic”, it isn’t exactly clear.

      To a geneticist, changes in gene expression in response to the presence of nutrients or other environmental influences does not qualify as an epigenetic effect unless it’s a quasi-permanent change that can be inherited by daughter cells. A significant fraction(~15%) of genes express at different levels during the day, responding to internal oscillators that sync with light exposure. Is this epigenetic? Control of gene expression is a major topic in modern biology, and the vast majority of mechanisms that alter gene expression are not considered “epigenetic”.

      Ok, let’s turn to reference one. The FADS2 gene carries a polymorphic variant that Caspi et al proposed might alter response to breast milk’s influence on IQ. Setting aside the extreme difficulty with accurate assessment of IQ (and the quite small variation, 5 or 6 points in the normal range) and parent reports of breast feeding, this study clearly has nothing to do with epigenetics. It is an example (if accurate) of genotype interacting with environment (nutrition). To their credit, the authors don’t use the term “epigenetic” anywhere in the paper. By the way, a follow up paper with a larger cohort published last year could not replicate this effect They found that children of all genotypes showed a benefit of breast milk ( In any case even if there’s a differential response to breast milk, it’s not “epigenetic”. It’s genetic. As both papers agree that there is a response of IQ to breast feeding, that might be explained by nutrition, but several other hypotheses come to mind.

      Genes interact with environment. Genes do all kinds of interesting things. They don’t all qualify as epigenetic.

    • Lou says:


      The problem with breast milk is that it often lacks vitamin D and vitamin D has a profound effect on genes (over 2,000 if I recall). It is crucial to brain development and function. Now as a result of poor research by gov’t agencies in vitamin D, we now have a widespread problem in vitamin D deficiency. They currently recommend only 600 IU a day. Why is it that a clinical study showed that lactating mothers need to take at least 6,400 IU a day to be able to produce vitamin D rich breast milk? Isn’t that a major clue that we really need that much vitamin D?

      You can see the list of health problems brought on by lack of vitamin D – Amazing that a single nutrient (actually a prohormone that your body converts into powerful steroid like effect hormone that acts as gene regulator) can prevent and fix so many health problems?

    • JohnD says:


      And I am using the term as a geneticist would. See Holliday, R., Mechanisms for the control of gene activity during development, Biol Rev Camb Philos Soc. 1990 Nov;65(4):431-71.


      And is it your experience that editors will allow people with no knowledge of a subject to publish on it?


      No, to some geneticists, that is how it is defined. To others (including the person who first used the term in the literature), it has a broader definition.

    • Reggie says:

      Who’s touchier about criticism: JohnD or Lebron James? It is utterly impossible that JohnD could be mistaken (slightly or wholly) about any SciGuy blog topic. Don’t y’all realize that yet?

    • TomTom1978 says:

      So you’re basically saying COWBOYs IQ problem is a lack of iodine?

    • Bill in Houston says:

      @ TomTom1978

      I bet Lou thinks it comes from a lack of Vitamin D. Me, I think he might have been dropped as a child.