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Oncology Times:
doi: 10.1097/01.COT.0000291801.55516.6e
International HapMap Project

Pioneering Gene Variation Map Will Help Create Framework to Assess Cancer Risk

Eastman, Peggy

Free Access

BETHESDA, MD—An international collaboration to develop a map of the common patterns of DNA sequence variation in 80% to 90% of the human genome should become a key resource for cancer researchers and, ultimately, oncologists, according to speakers at a workshop here.

The aim of the workshop, which was jointly sponsored by the National Cancer Institute and the National Human Genome Research Institute (NHGRI), was to explore ways to link human genetic variation with cancer risk assessment, detection, prevention, and treatment.

Known as the International HapMap Project, the collaboration—which began in October 2002—includes scientists from the United States, Japan, the United Kingdom, Canada, China, and Nigeria.

The project is named HapMap after the term haplotype, a set of associated single nucleotide polymorphism (SNP) alleles in a region of a chromosome. About 10 million somewhat common SNPs—sites in the genome where the DNA sequences of many people differ by a single base—are thought to exist in human populations.

While the DNA sequences of any two unrelated people are about 99.9% the same, it is the 0.1% that contain the genetic variants that determine differences in cancer risk and response to therapy.

This past November the HapMap project publicly released data on 13 million genotypes from 145,554 SNPs. The hope is to publicly release a wealth of similar data over the next two years.

Consistent with the concept that modern human beings had a common origin in Africa, research so far shows that most haplotypes are shared among populations on different continents and that very few individual alleles are specific to any one population, noted Lynn B. Jorde, PhD, Professor of Human Genetics at the University of Utah School of Medicine.

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Replication, Validation

While HapMap research on SNPs is exciting cutting-edge work, other speakers emphasized that in order to pursue the application of common genetic polymorphisms to cancer-association studies in human populations, the HapMap work has to be replicated and validated.

It also cannot take the place of ongoing research on candidate cancer-risk genes, those genes in which variation could influence cancer susceptibility or patient outcome, said Stephen Chanock, MD, Senior Investigator in NCI's Center for Cancer Research, Advanced Technology Center, Division of Cancer Epidemiology and Genetics.

“We can't forget the importance of candidate genes. Never leave candidate genes behind.” And, he added, “No real SNP study stands by itself; it has to be validated. Validation of genotypes for study is very important.”

This is particularly true because different researchers might reach different conclusions on the nature of variation in a particular gene, noted David Hunter, ScD, Professor of Epidemiology and Nutrition at the Channing Laboratory of Harvard School of Public Health.

NCI's interest in the HapMap includes hoped-for progress on the following issues, said Peter Greenwald, MD, DrPH, Director of NCI's Division of Cancer Prevention:

▪ Identification of populations at high risk of developing cancer.

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▪ Identification of high-risk populations that might benefit from clinical cancer prevention trials.

▪ Prediction of which cancers are aggressive and likely to progress and which are not.

▪ Prediction of response to cancer therapy, including which cancer patients are likely to respond to a given drug and which are not.

▪ Identification of those cancer patients at risk for adverse reactions to clinical interventions.

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‘Skeleton of Human Diversity’

The HapMap can be thought of as “a skeleton of human diversity,” Dr. Chanock said. As it reveals its mysteries, “The real question is going to be how we apply all these data.”

The HapMap is an answer to the question posed by those who asked “What next?” when the Human Genome Project was completed in 2003, said NHGRI Director Francis Collins, MD, PhD, in a keynote address at the workshop.

He noted that while there has been good scientific progress in finding genes for Mendelian forms of cancer such as retinoblastoma, there has been much less progress across all disorders, including cancer, in finding complex human polygenic traits.

“It is an indication of just how far we have to go,” Dr. Collins said, noting that while family linkage studies have contributed enormously to an understanding of disease risk, there are lots of genetic variants that will not be seen in linkage studies.

“The opportunity to go after them is going to be very exciting,” he said.

Because a person's disease-risk profile is not determined by genes alone, but by gene-environment interaction, Dr. Collins said a strong case can now be made for a large-scale prospective cohort study involving 500,000 Americans and extending over a decade.

“Such an effort would go a long way towards generating the kind of dataset that could be used in an unbiased way to assess gene-environment interactions and genotype relative risks for specific variations,” he said.

“These opportunities are challenging, but the payoff in terms of our understanding of the causes of the common forms of cancer could be unprecedented.”

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Legislation to Prohibit Genetic Discrimination

Dr. Collins put in a plea for legislation to prohibit genetic discrimination as more and more information on human genetic variation becomes available publicly.

Practically speaking, Dr. Collins said it would be far too expensive to go on a scientific gene hunt for all of the most common 10 million human SNPs.

The HapMap, which he said he thinks of as a shortcut, is an attempt “to come up with a better strategy if we're going to be realistic.”

Dr. Collins said that to form the HapMap, 270 anonymous blood samples of human DNA are being collected, from the:

▪ Yoruba people in Ibadan, Nigeria.

▪ Japanese in Tokyo.

▪ Han Chinese in Beijing.

▪ US residents with ancestry from Northern and Western Europe collected by the Centre d'Etude du Polymorphisme Humain (CEPH).

No clinical information will be collected.

The 10 participating HapMap centers that will analyze these samples have divided up the human genome according to their capacities and expertise in order to make the international project feasible, said Dr. Collins.

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Genotyped for at Least 1 Million SNPs

To develop the HapMap, the collected samples will be genotyped for at least one million SNPs across the human genome, he said.

A chromosome region may contain many SNPs, but only a few “tag” SNPs can provide most of the data on the pattern of genetic variation in that chromosomal region.

“The real output of this project is going to be the haplotype tag SNPs,” Dr. Collins said. “How many of these tag SNPs will it take to represent the human genome?” While estimates on that number range from 150,000 to 500,000 SNPs, his guess is that it might be about 300,000.

Emphasizing his point that SNP studies need to be validated, Dr. Chanock described the resequencing programs for cancer-risk genes developed at NCI.

The SNP500Cancer database—a central resource for sequence variation of SNPs—posts the results of resequence analysis of SNPs considered to be of immediate importance to molecular epidemiology cancer researchers, including estimated allele and genotype frequencies in four ethnic groups.

Also, Dr. Chanock said, a project within NCI's Cancer Genome Anatomy Program is resequencing genes altered in expression of breast cancer to define somatic mutations and linkage disequilibrium.

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Breast and Prostate Cancer Cohort Consortium

To speed the process of replication of results for candidate cancer-risk genes, NCI formed the Breast and Prostate Cancer Cohort Consortium. Speaking on behalf of the consortium, Dr. Hunter said that about 50 candidate genes are being resequenced in cases at the Whitehead Institute Genome Center, the French CEPH facility and the NCI Core Genotyping Facility.

SNPs will then be assessed in case-control pooled studies covering about 800,000 men and women.

Will the human gene variation HapMap ever actually be completed? Probably not, Dr. Chanock predicted.

“Haplotypes may never actually be finished, in the sense that they may get more and more refined.” As they do, he noted, more and more corroborative studies will also need to be done to determine what role—if any—different haplotypes play in cancer development and cancer susceptibility.

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For Further Information

More information about the:

▪ International HapMap Project is available at www.hapmap.org

▪ SNP500 cancer database is available at http://snp500cancer.nci.nih.gov

▪ Cancer Genome Anatomy Program is available at http://cgap.nci.nih.gov

© 2004 Lippincott Williams & Wilkins, Inc.

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