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A New Map of the Human Genome Promises Medical Advances Contribution of the Hong Kong HapMap Group

27 Oct 2005

The International HapMap Consortium today (1 p.m. EASTERN, Wed., Oct. 26) announced a comprehensive catalogue of human genetic variation, a landmark achievement that is already accelerating the search for genes involved in common diseases, such as asthma, diabetes, cancer and heart disease. The Hong Kong HapMap Group, as a partner of the Chinese HapMap Consortium (CHMC), contributed to the mapping of 2.5% of the whole human genome.

The new map concentrates on genomic locations where people differ from each other. These genetic differences explain largely why some people are more prone than others to develop diseases such as cancer, heart disease and schizophrenia. This makes it a different undertaking to its predecessor, the Human Genome Project, which generated a complete sequence of the human genome. The main features of the HapMap project will be published in a landmark article by the magazine, Nature. [Please refer to the Notes at the end for an abstract]

The Hong Kong HapMap Group, led by Principal Investigator Professor Lap-Chee Tsui, took responsibility for generating the genetic data for most of the short arm of chromosome 3, amounting to 2.5% of the genome. The work was completed on schedule by the Genome Research Centre at the University of Hong Kong, and amounted to the assaying of over 30,000 genetic markers on all of the samples. Members of the Hong Kong HapMap Group specialising in bioinformatics and statistics also participated in the Data Analysis Group of the HapMap Project by developing software for selecting variable sites for genetic studies and for measuring the genetic relatedness between pairs of individuals.

Professor Tsui provided some comments on this project:

o "The scene is set for some major and exciting discoveries to be made and these will lead to effective prevention of diseases and better treatments for patients."

o "Now that we have the HapMap, especially of the Chinese population, and the expertise gained by our participation in it, we have a unique opportunity to be at the forefront of genetic research into the most important diseases in Southeast Asia. For studies on Chinese and Japanese samples, the amount of work may be reduced by as much as 10-fold."

o "Some of these genomic regions show evidence of 'selection' and it will be interesting to find out if and why selection had indeed occurred, and whether they display strong racial specificity."

o "The Genome Research Centre and its collaborators are already using the HapMap to look for genes for schizophrenia, diabetes, osteoporosis and lumbar disc degeneration in specific genomic regions. We are now planning to conduct genetic studies on a genome-wide scale for these diseases as well as others such as breast and colorectal cancers."

o "I am very happy that we participated in this project, as we have not only established the high-throughout genotyping technology, but also obtained the valuable information on how to design disease studies in the future. In terms of disease gene identification, I am really happy that my previous work (on cystic fibrosis) had provided important framework for today’s strategy."

The project represents a productive collaboration between HKU and two sister institutions, CUHK and HKUST. Professor Tsui expressed his gratitude to UGC (University Grants Committee) and ITF (Innovation and Technology Fund) for funding this project and to the research staff at the HKU Genome Research Centre for their hard work.

For details of the HapMap Project, please visit http://www.hapmap.org.

Telephone interviews with Professor Lap-Chee Tsui or Professor Pak Sham may be arranged please contact Ms Cherry Cheung, Senior Press Officer, the University of Hong Kong at 2859 2606.

27 October 2005 1:00am

NOTES

1. The full name of the HapMap Project is the "International Haplotype Map Project".

2. The HapMap Project was launched on Oct. 29, 2002, by the U.S. National Human Genome Research Institute (NHGRI), with a timeline for completion of 3 years.

3. The completion of the HapMap Project is being announced on Oct 26, 2005, in Salt Lake City, Utah, U.S.A.

4. The participating countries in the HapMap Project are USA, UK, Japan, Canada, China and Nigeria, with China completing 10% of the map.

5. The China HapMap Consortium (CHMC) was established on March 28th, 2003, and consists of the Beijing Genomics Institute, the Chinese National Human Genome Centre at Beijing, the Chinese National Human Genome Centre at Shanghai, and the Hong Kong HapMap Group. The CHMC was funded by the Chinese Ministry of Science and Technology, Chinese Academy of Sciences, Natural Science Foundation of China.

6. The Hong Kong HapMap Group comprises of the University of Hong Kong, the Chinese University of Hong Kong and the Hong Kong University of Science and Technology.

7. Professor Lap-Chee Tsui is the Chairman of the Steering Committee of the Genome Research Centre at HKU and Principal Investigator of the Hong Kong HapMap Group. [Please refer to supplementary information enclosed for the full list of participants in the Hong Kong HapMap Group]

8. Funding for the Hong Kong HapMap Group was provided by the University Grants Committee (HK$25 million) and the Innovation and Technology Fund (HK$10 million).

9. A string of variants on a short genomic segment is called a haplotype, and it is the characterization of all common haplotypes and their frequencies that gives the HapMap its name. The number of different haplotypes actually present in a human population is often far fewer than the expected number that would be observed if genetic variants combine freely with each other. This reduced haplotype diversity is a result of the recent expansion of human populations from a small number of shared ancestors from Africa, and is most marked in genomic segments called haplotype blocks, separated by gaps where genetic material has been historically reshuffled. The greatest practical use of the HapMap is in the identification of clans of close-knit variable sites, where each clan can be effectively represented by just a single site, helping to cut down the cost of genetic studies. For the Asian population, over 72% of the 1 million variable sites of the Phase 1 HapMap belong to the 100,000 largest clans; the corresponding figures for the European and African populations being 68% and 47%, respectively.

10. The Abstract of the article entitled "A haplotype map of the human genome", by the International HapMap Consortium, to be published in the 27 October issue of Nature magazine:

A haplotype map of the human genome
The International HapMap Consortium

ABSTRACT

Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.