My chromosomes and me

The diagram to the left is a pictorial representation of 22 of my 23 chromosomes as provided by the personal genomics company 23andMe, which I sent samples of my DNA (mailing a tube full of spit) for analysis. The colors represent the likely geographic origins of my DNA, green blocks representing African origins, orange blocks representing Asian origins, and blue blocks representing European origins. In my case, the DNA of Asian origin most likely is Amerindian, a population whose genetic features is most like East Asian populations.

My family immigrated from Ecuador to the US when I was little. And I remember distinctly when the US Census form first came to our home in the space where we were asked to choose race we checked off "Other" and filled in "mestizo". We grew up thinking of ourselves as mestizo rather than belonging to any of the races listed as options in the form. Mestizos being people of both European and Amerindian ancestry, it was a conjecture apparent from one quick look at my family. The results of this DNA analysis done by 23andMe confirm this long held assertion of ours.

The genetic map I show here is only one type of data provided by 23andMe. The results provided to me online also tell me what traits I am likely to have based on my genetics. The company accurately predicted, for example, that I most likely have dark brown eyes and wavy hair. They predicted my blood type, and suggest I am only mildly lactose tolerant. What's interesting about the latter result is that lactose tolerance is a trait primarily determined by genetics, but the environment can have a role in influencing it (for example, by the nature of bacteria living in my intestines). The prediction is pretty good, as I can tolerate a glass of milk OK, but more than that gets me belly upset.

Since the genetic information gleaned from my DNA can be so useful in telling me about traits I know of or suspected, what can it tell me about traits I don't know about, in particular, medically relevant traits, such as propensity towards certain diseases or disorders, or responses to drugs? Though the results to such things are presented and clearly explained, they are always presented "assuming [my] European ethnicity". The company makes a call based on the sources of DNA in my genome (shown in the above diagram) and says I'm European. This is important because versions of genes that determine traits don't usually do it in isolation, they do it in the genomic context in which they exist. Meaning that one version of a gene X for trait A in one genome may cause trait B in another. This is due to combinations of different gene versions that can interact to determine what the trait.

Knowing that the nature of our genomes is tied to the ethnicity we belong to, and that this can affect interpretations of genetic data, how relevant is it to my data that I am Hispanic? Hispanics (or Latinos) run a whole spectrum of genomic signatures, from nearly 100% European, to nearly 100% Amerindian, to nearly 100% African, and the vast majority of populations are in between. So it seems that being Hispanic does not lend itself to increasing the predictive power of genetic signatures. In fact, it may be completely irrelevant, in contrast to more homogenous populations, such as, for example Ashkenazi Jews, Japanese, or Zulus.

Figure from the Bustamante lab website, showing the principal components underlying genetic variation in Latin American populations. Note that genetic variation constitutes a range determined by three sources of genetic variation: African, Native American (or Amerindian) and European.

Given that most health standards in the United States are based on a white population with DNA largely originating in Europe, how can health guidelines and recommendations be refined by personal genomics so they more accurately reflect our individual biologies? At the moment, it seems we have inadequate information or understanding of how to best use genetic information to make health decisions, some of which will vary depending on our genetic backgrounds, some of which will be more influenced by environmental conditions. Can a slightly lactose tolerant person like me, for example, improve lactose tolerance with a certain diet? Or would it be best for me to ignore the "got milk" campaign altogether and forgo milk in my diet? The role of ethnicity, genetics and health is one I hope to see explored in the years to come at scientific conferences and in research publications.

This post is part of the Diversity in Science Blog Carnival #18: Latino / Hispanic Health: Science and Advocacy. 

An un-extinction event in the Galapagos

When the word of new extinctions has become all too common, it's good to hear about when a species thought to be extinct is found to be alive.

'Extinct' Galapagos tortoise may still exist - BBC News

Well, at least the DNA says they're out there somewhere on Isabela Island.

And if they don't find the pure-breds, at least the newly identified hybrids can be used in a breeding program to bring back the Floreana Galapagos tortoise into existence and reintroduced into its native island, where it has not existed for 162 years.

Interesting how if this turns out to be true, it means that at some point the Floreana tortoise was an accidentally introduced invasive species on Isabela (and perhaps still is). In this case, turns out this may have been the salvation of the species!

I am what I eat

Me and some plantains, Portoviejo, Ecuador.

From the Hall of Human Origins, National Museum of Natural History, Washington DC.

Ecuador is one of the top producers of bananas and the largest exporter of this fruit*.  Plantain (which, like banana, is a domesticated and sterile hybrid of two species of plants from the genus Musa) is a prevalent staple in the cuisine of the Ecuadorian coastal region, eaten green or ripe, fried, baked, in soups, with ceviche, eaten with breakfast, lunch or dinner.  The wild ancestors of these fruits contain seeds, and like many inter-species hybrids, bananas and plantains are sterile, and in this case seedless, which is a desirable trait for an edible fruit.  How are they propagated then, with no seeds?  Bananas and plantains must be reproduced from cuttings of the underground stem. Since there is no sexual reproduction involved, there is very little genetic diversity among banana cultivars, and thus there is concern that this important crop plant can become vulnerable to disease and it would be difficult to generate resistant clones.  Efforts are underway to increase the genetic diversity of bananas and plantains to make this a stable food source for consumers and source of income for farmers.

*Ecuador also produced me, a long time ago.

Gay pride, genes and brains

This post is part of the Diversity in Science Pride Blog Carnival: Pride Month 2011 edition.

Having grown up very early on as both an avid student of Darwin’s ideas and an earnest follower of the Roman Catholic faith, puberty posed for me a painfully confounding paradox: how could a nice church-going boy who read biology text books for fun find himself attracted to the same sex, an implausible urge that both my religion and science deemed abnormal and maladaptive? Hormones and peer-pressure can make life a bit problematic for many teenagers, but for a gay one who made sense of his world through the lens of biology and Catholicism, life suddenly became unfathomably perplexing, and quite depressing.

But it was biology that would help rescue me from the emotional tailspin. It was in the early 1990s that two highly publicized studies came out on biology and sexual orientation. These were Simon LeVay’s brain structure studies and Dean Hamer’s genetic linkage studies of gay men.

LeVay published results in 1991 that indicated differences in the structure of a small part of the brain when comparing the brains of homosexual to heterosexual men. The difference was reported to be in the third Intersitial Nucleus of the Anterior Hypothalamus (INAH3). This small bundle of neurons was more than twice as large in heterosexual men as it was in homosexual men. The reduced size of INAH3 was also observed in heterosexual women.

Figure of the INAH3 region of the hypothalamus courtesy of simonlevay.com.


In 1993, Hamer and colleagues published a study of a linkage analysis among gay men. The report indicated that among the gay male subjects, there was a higher frequency of gay male uncles and cousins on the mother’s side than on the father’s side of the family, suggesting there might be maternal inheritance of genetic determinants of homosexuality. The study went on to test for X chromosome linkage among the gay subject, and found a linkage between homosexuality and a stretch of the X chromosome called Xq28.

Figure of the X chromosome and the Xq28 region courtesy of NCBI.

Both these studies resulted in a frenzy of media coverage, with headlines about “the gay brain” and “the gay gene” splashed across magazine covers and newspaper front pages. For a young student of biology, it was always thrilling when science made its way to the top stories in the news. But this time it was personal. These studies told me that there might be a biological basis for the variation in sexual behavior among humans. And that if it was in the genes and in the brain circuitry, and thus not a choice as many proposed, why struggle and suffer needlessly to change it?

Of course, these studies had their critics. The LeVay brain data showed a correlation, but did not clarify if the brain structure variations were the cause or result of homosexual behavior. And the Hamer study never actually pinpointed to a specific gene allele that determined sexual orientation, but to a whole region of the X chromosome, and while some studies recapitulated the results, others did not, as is often the case in studies on the genetic underpinnings of such complex traits as human behavior. Still, the studies came out at the right time for me to come out. Not only did the findings appeal to my scientific way of thinking, but they also brought the talk of sexual orientation out into the open, on the news, on the covers of mainstream magazines, and into the lab and the world of biology.

Of course the coming out process did not magically become a piece of cake for me. But as a young scientist in the making, Dean Hamer and Simon LeVay were heroes to me, and their timely publication of their results made an unintended but hugely positive difference in my life.