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Q&A: UIC's Rick Kittles on Using Arrays to Study Disease in African Americans


kittles.jpgName: Rick Kittles

Title: Associate professor of medicine, epidemiology, and biostatistics, University of Illinois at Chicago

Professional background: 2010-present, associate professor of medicine, epidemiology, and biostatistics, University of Illinois at Chicago; 2003-present, scientific director, African Ancestry; 2006-2010, associate professor of medicine, University of Chicago; 2004-2006, professor of molecular virology, immunology, and medical genetics, Ohio State University; 1998-2004, co-director, medical genetics, Howard University.

Education: 1998 — PhD, biological sciences, George Washington University; 1989 — BS, biology, University of Rochester

Rick Kittles is one of the foremost biologists studying the genetics of African American populations today.

This year so far, Kittles has been a co-author on 10 publications, including several studies identifying genetic markers that put African Americans at additional risk of developing prostate or colon cancer. He also is the co-founder of African Ancestry, a firm that provides customers with information about their origins.

Though Kittles has used microarrays for over a decade, he said that until recently most of the whole-genome genotyping arrays available were of little use, as they contained variation mostly related to populations of European descent. According to Kittles, that has changed with Affymetrix's recent introduction of an African-American population-focused array for association studies.

Kittles discussed his adoption of the chip at the International Congress on Human Genetics meeting in Montreal last month. BioArray News interviewed Kittles this week about his efforts. Below is an edited transcript of the interview.

What spurred your interest in population genetics?

What really got me excited about genetics in particular was the mitochondrial Eve story. The use of mitochondrial DNA to explore human origins and ancestry was fascinating. I had a strong interest in genetic anthropology that brought me to population genetics. At the same time that I started working in graduate school in genetics, population genetics in particular, I started looking at how we could use population genetic models to explore the genetics of human disease.

When did you start using newer technologies like microarrays?

It was around 1999 and 2000. I remember I was working on a project where we had access to the Affymetrix 10K data and we were looking at SNPs and ancestry informative markers.

The technology has obviously evolved since then. In Montreal, you discussed using the Axiom array from Affymetrix

The whole story of those arrays is fascinating and the technology is fascinating. A lot of it was spurred by the Human Genome Project and then, once those SNPs were identified, there was the SNP Consortium and databases that arose and dbSNP came about … A lot of that information that was on those early arrays was really useful for European populations, but in terms of African Americans, the resources were rather limited. So the sequence data, the SNP data, even the HapMap, to some extent early on was limited. Up until the Axiom array came out, the bulk of the arrays that had been designed have pretty decent coverage for whites, but very poor for African descent and other populations. That says something about where the technology and the mindset were. The bulk of the research was on European populations, and you really can't criticize that, but at the same time there was a big hole in terms of coverage.

There were tens of thousands of SNPs on those chips that were monomorphic or uninformative for African American populations, and so as a research tool, they were rather poor.

What did you do all this time until the population-specific chips came along?

It wasn't clear in the very beginning. We knew there was a lot more variation in Africans, but we didn't know that what we had was limited in terms of the resources. As we did more and more it became clear that we were wasting money and time. That is why I started to get excited over the last three years where there was focus from some companies that wanted to design arrays specific to certain populations. Gone were the days of saying that our business model is to just focus on European populations, because, to some extent that is what they were doing. They were saying, 'It is not going to be fruitful to us as a product to sell a specific African chip.' But it is exciting that Affymetrix has put some real effort into creating chips for specific populations. There were increasing murmurs in the research community about this issue.

Some researchers, though, have argued that the new high-density arrays or next-generation sequencing could be a better route than population-focused chips.

As someone who studies specific populations of non-European descent, I want to use a resource focused on that population. Of course I could use NGS, and a lot of people are going in that direction, but the reality is that it is still quite expensive. These arrays are much more cost effective than sequencing. If you understand and believe in the coverage of these arrays, you will know that they have strong utility. I haven't seen many good high-density arrays. I think it is different when one says, 'I am going to start from scratch and build a good array in this population,' in comparison with saying, 'I will add more SNPs to what I already have.' Those are two different approaches.

During your talk you mentioned that there are some issues when it comes to studying African Americans from different regions of the country. For example, you mentioned that there is higher admixture with European populations in Seattle, while less in places like South Carolina. How have you addressed that issue in designing your studies?

There are two levels to that issue. One is genetic admixture. When I talk about populations in Seattle versus South Carolina, I am talking about the level of European genetic ancestry, as there is a lot more admixture in Seattle African Americans versus in South Carolina African Americans. Their genetic substructures are different. The other form of stratification is the ethnic stratification within African Americans due to regional differences depending on where enslaved Africans came from and where they were sent. Some alleles are different between Nigerians and Africans from Senegal. We see that difference in certain communities, especially in the rural south. So what do we do? We try to broaden the content on the arrays so we can capture that diversity. We haven't quantified that yet. I am working with David Reich [at Harvard Medical School] looking at high-resolution GWAS data from different African American communities across the US to see if there are some different haploypes that might reflect regional ancestry. That is what I mean by ethnic stratification.

You have recently published papers related to colon cancer and prostate cancer. Can you provide an update on your research activities related to oncology?

I am looking for risk alleles for prostate and colon cancer, looking for inherited predisposition. There are several issues and some sad commentaries about prostate cancer. We are about 10 years behind breast cancer, where we have BRCA1 and BRCA2, but we are nowhere near that with prostate, and prostate disproportionately impacts African Americans. Once you talk about health disparities, you have a political spin to it. My focus is on inherited predisposition. We have identified several common variants with modest to low effect sizes. There hasn't been any group that has found the gene yet for prostate cancer. It's a lot more heterogeneous than breast or colon cancer and there are multiple pathways. It's just a complex cancer to study.

You are the scientific director of African Ancestry. How has the African American community reacted to the availability of this kind of genetic information?

They have been quite excited. The community sees the science and technology as exciting because it answers a question that is near and dear to them and it has been very educating to the black community. Some have suggested that our efforts have increased genetic literacy among African Americans by exposure to simple genetics that is occurring from genetic testing. It has been nothing but wins across the board. It has also brought African Americans closer to understanding research. With exposure to ancestry testing, they want to know what is going on with disease.

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