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A journey through a Filipino genome

August 10, 2011 12:53pm
Science in the 20th century was the Age of Physics. The 21st century is the Age of Biology.

Just as the dawn of the last century saw many of the modern breakthroughs in physics —relativity and quantum mechanics being the two most prominent scientific advances— the end of the century saw science determine the structure of DNA, many of the basic processes that drive cells, and the beginnings of molecular biology and biotechnology. And the ascent of biology was capped by the completion early this century of the massive international effort to sequence the human genome —the 3 billion letters that make up all of our genes.

The effort to sequence the human genome took the international scientific community more than 11 years at a cost of over P130 billion. Determining our entire genetic code, and those of other species, has revolutionized the science of biology and has changed how we do research in medicine, agriculture, and the environment. It has spawned numerous applications —from new diagnostic tools, new drugs, and new crop varieties to innovations in biotechnology.

Armed with data on Filipino genomes, we can find out what genetic disorders are common in our people and which are rare, develop new diagnoses, and maybe find some life-saving cures.

In fact, we now know the genome sequences of about 1,000 humans on the planet, part of an international effort to understand how humans are different in their DNA. Among the Asian genomes that were sequenced are those from individuals in China, Japan, India and Vietnam. One thing, however, is lacking in this international effort. The genome sequence of a Filipino has never been read completely, and we still do not know what the Filipino genome looks like.

I don’t really study human genomes —most of my research is on the rice genome, to try to understand how rice has evolved and adapted as it spread across the world. But in some sense it doesn’t matter whether it’s rice or humans; many of the techniques we use to study DNA is the same. And although a Filipino genome has never been sequenced, I decided to do a quick scan of about 1 million letters of my own DNA and see what it looked like. So last June I had my DNA extracted and scanned on the Illumina human DNA chip by the personal genomics company 23andMe, and with the data they gave me I looked into my own genes.

The genome sequence of a Filipino has never been read completely, and we still do not know what the Filipino genome looks like.

One thing we can learn from our genome is our personal history —how our genes evolved and what that tells us about our ancestors. First of all, I looked for the portion of my DNA that comes from my mother. It is difficult to figure out which portions of the approximately 25,000 genes in my genome comes from my mother, but our cells contain mitochondria, small organs that have their own DNA that is inherited by all of us from our mothers.

My mother is from Pampanga, as are my grandparents on her side of the family. Looking at the DNA from my own mitochondria showed that it belongs to a group called B4. This type of DNA comes from Taiwan, where it arose about 13,000 years ago in aboriginal pre-Chinese groups on that island. Several thousand years ago, people from Taiwan started to migrate southwards to the Philippines, and afterwards east towards Polynesia. My specific mitochondria type, B4a1a1, arose from this Taiwanese DNA about 9,000 years ago as ancient migrants left that island. The genes in my Kapampangan mitochondria have come down across thousands of years from those early travelers that used the Philippines as a way station before crossing the Pacific Ocean.

Where my Y-chromosome is found in Asia, after spreading from its origin in China.Image ©23andMe.
Now for my father’s genes. Just as my mitochondrial DNA comes from my mother, my Y-chromosome is strictly inherited from my father. He was born in Manila in the late 1920s but his father is an Ilocano that hails from Cagayan Valley. My genome scan showed my Y-chromosome is classified as O3a3c1, which evolved about 30,000 years ago and is found among Chinese, Koreans, Malaysians and, yes, Filipinos. This Y-chromosome somehow made it to Northern Luzon, where my father’s male ancestors come from, either from China itself or maybe by early Filipinos who migrated to our archipelago from mainland Southeast Asia.

How about the other 45 chromosomes I have (22 pairs of regular ones plus the X-chromosome)? The DNA from these other chromosomes comes to us as a mixture from all our ancestors (both from our father’s and mother’s families) going back several hundreds of thousands of years. By comparing my genome with a database from people around the world, I find that I am a blend —71% Asian and 29% European— the latter of which I got from my Spanish paternal grandmother who was born in the last days of Spanish colonial rule in 1895.

My 22 chromosomes, showing genetic mixing from Asia and Europe. If a piece of the chromosome is one color, it comes from either Europe or Asia. Two colors indicate it is a mixture from ancestors both continents. Gray is where there is no information. The percentage of Asian and European pieces of my genome is also shown in the bottom.Image ©23andMe.
Finding out about my ancestry was only half the story. In my DNA I could also read what some of my genes told me about nearly 200 traits and possible diseases. I found out that I can drink alcohol just fine, but it takes longer for my body to break down caffeine. Genes for cholesterol and heart and kidney disease are fine, and I also have lowered risk for melanoma and certain types of cancers. My risk for asthma and migraines are higher.

Of course whether I get any of these diseases depends a lot on the environment, and we also know that there is still uncertainty over several of these genetic studies. In fact, there are a few things that don’t make sense —my genes tell me I should be slightly lactose intolerant and that I do not have a preference for sweet foods. Well I take in milk products just fine, and like many Filipinos I have a sweet tooth. It is clear there is still a lot we do not know about our own genes.

Looking at my own genome was a personal journey that told me more about who I am and where I came from. But it shouldn’t be just my journey —it should be a trip that every Filipino should be able to go on. It is time we study the Filipino genome so that we can get a full picture of what our genome looks like and what it tells us about ourselves. We can then reconstruct the history of Filipinos as written in our genes, find out how we are similar to each other and how we are different, our place among the peoples of the world, trace the migrations that have populated our archipelago over the last hundred thousand years.

And it will also help us to study diseases in the Philippines, since most human genetic studies are done with people of European descent; we really do not know if the same genes also affect the health of Filipinos. Armed with data on Filipino genomes, we can find out what genetic disorders are common in our people and which are rare, develop new diagnoses, and maybe find some life-saving cures.

By studying our genome, we can all embark on a journey of discovery with potential applications to our health.

With support from the Department of Science and Technology (DOST) and the University of the Philippines, we may be able to do these studies. After several years of planning by scientists in the Philippines and abroad, the Philippine Genome Center will be established this year. It will be a research center that will hopefully take the lead in the sequence and analysis of the genomes of the Filipino people, as well as other animal, plant, and microbial species across our country. Scientists can then look at genome information not only for medical research, but also to study disease-causing microbes, develop better forensic tools, breed better crops, and help conserve endangered species.

By studying our genome, we can all embark on a journey of discovery with potential applications to our health. It will cost us about P1 million for one person, and we should do it for several Filipinos from across the country. Which brings up a question we can all think about – who should be the first Filipinos whose genome we will sequence?

The above essay was written by Dr. Purugganan for GMA News Online. — HGS/YA/TJD, GMA News

Michael Purugganan is the Dorothy Schiff Professor of Genomics and the co-director of the Center for Genomics and Systems Biology at New York University, and is advising the Philippine Genome Center. He graduated from UP Diliman in 1985, and got his MA at Columbia and Ph.D. at the University of Georgia. He has been awarded a Sloan Young Investigator Award and a Guggenheim Fellowship, and honored by the Ayala Foundation/PhilDev Foundation. You can learn more about his genome research at
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