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Our Filipino genome

We are our genomes, or at least a good part of who we are is engraved in our DNA. It was about a decade ago that the sequence of the human genome was released, the completion of a monumental 11-year international effort costing over P130 billion. Knowing the sequence of the human genome — the more than three billion letters that make up our DNA, including our approximately 25,000 genes — has revolutionized biology, and the science of genomics has changed research in medicine, agriculture and the environment.

Today, we roughly know the genome sequences of about 1,000 humans on the planet, part of an international effort to understand how humans differ in their DNA. But as far as I know the genome sequence of a Filipino has never been read completely, and we still remain largely ignorant of what our genes look like. Will we be able to read our genetic past in order to understand our present? Are we able to explain who and what we are based on our DNA?

I became curious and decided to use myself as a guinea pig by reading about one million letters of my own genome. So last June I had my DNA extracted from my saliva and scanned on the Illumina human DNA chip. I got the results a few weeks later, and armed with this data I peered into my genes.

The first thing I wanted to see was what my genome told me about my ancestors, and my first stop was the mitochondrial genome. Our mitochondria are small organs within our cells that contain DNA inherited by all of us from our mothers. My mitochondrial DNA is a legacy given to me from the female Kapampangan ancestors on my mother’s side.

My genome scan shows that the DNA in my mitochondria belongs to a group called B4, which evolved about 13,000 years ago in the aboriginal pre-Chinese groups of Taiwan. My specific mitochondria type, B4a1a1, split off from this Taiwanese DNA about 9,000 years ago as ancient migrants left that island and started going south and east toward the Philippines and Polynesia. The genes in my Kapampangan mitochondria are a clear legacy of that ancient migration.

Just as my mitochondrial DNA comes from my mother, my Y-chromosome is strictly inherited from my father. My father was born in Manila in the 1920s but his father hails from Cagayan Valley. My genome scan showed my Y-chromosome is classified in the group O3, a very Asian Y-chromosome. This is an old line that started to evolve about 30,000 years ago and is found among Chinese, Koreans, Malaysians and, yes, Filipinos. My particular Y-chromosome, called O3a3c1 appears to have left China around 265 AD, spreading to Yunnan, Tibet, mainland Southeast Asia, and clearly the Ilocos region of Luzon, from where my father’s male ancestors come from.

Then there are the other chromosomes I have, which are a mixture of genetic pieces from all my ancestors. Comparing my genome with a database from people around the world, I find I am clearly Asian, but that large chunks of my DNA, about 29 percent, are European — thanks to my Spanish paternal grandmother Maria Aldeguer. Like many Filipinos, my genome displays that blend of Asia and Europe that is the genetic legacy of our colonial heritage.

I also found out about some of my own genetic traits. My genome scan confirmed my eye color as brown, my hair is slightly curly and I am above average in height for a Filipino.

My DNA says I am not resistant to malaria and will have a higher propensity for male pattern baldness (how depressing). According to my genes I digest caffeine more slowly than most (which may explain why I can get wired from a single espresso), and that if I were to take up heroin there is a good possibility I will get addicted. If I contract hepatitis C I have a reduced chance of responding to treatment. I have a higher risk of getting asthma or migraines, but I have lower genetic risk for melanoma, multiple sclerosis and some types of cancers. 

Of course, my genes are only half the story — whether or not I get any of these diseases depends heavily on the environment as well. But it’s good to know I should pay extra attention to certain potential problems to my health.

I learned a lot about myself by looking at my own DNA, and wouldn’t it be great if we could see what the genomes of other Filipinos look like? We could then study the genetic history of Filipinos, showing how we are similar to each other and how we are different, how we are related to the other peoples of the world, and trace the migrations that have populated our archipelago over the last hundred thousand years. We can figure out what genetic disorders are common in Filipinos, develop new diagnoses and maybe find some life-saving cures.

We may soon be able to do all this. With support from DOST and the University of the Philippines, the Philippine Genome Center will be launched this year. It will be a research center that will usher in the study of the genomes of Filipinos as well as other animal, plant and microbial species across the Philippines. It will allow Philippine researchers to mine genome information not only for medical research, but study disease-causing microbes, develop better forensic tools, breed better crops and help conserve endangered species.

With the establishment of the Philippine Genome Center, the study of our genome is about to become a reality. Today, it will cost us only P1 million to sequence a human genome, and so who will be the first Filipino whose DNA we sequence?

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Michael Purugganan is the co-director of the Center for Genomics and Systems Biology and the Dorothy Schiff professor of Genomics at New York University. He graduated BS Chemistry at UP Diliman in 1985, and went to the US to get an MA at Columbia and Ph.D. at the University of Georgia. He has been awarded a Sloan Young Investigator Award, a Guggenheim Fellowship, honored by the Ayala Foundation/PhilDev Foundation and is a member of PAASE. You can learn more about his impractical research at http://puruggananlab.bio.nyu.edu/

 

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