Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
In this issue...
HGP and the Private Sector
In the News
Ethical, Legal, and Social Issues
Web, Publications, Resources
Meeting Calendars & Acronyms
International SNP Meetings
Some 100 invited international researchers from industry and academia attended the Second International Meeting on Single Nucleotide Polymorphism (SNP) and Complex Genome Analysis held in Munich, Germany, in September 1999. Below is a summary of meeting highlights with updates from the September 2000 meeting in Taos, New Mexico.
The overall tone of the 1999 meeting showed that SNP research still lacks a solid consensus about how best to proceedand this is at a time when vast sums of money are being spent on public and private SNP programs. This state of affairs is only partially improved today. SNP discovery alone will not determine how and whether SNPs should be used. Instead, this knowledge has to come from empirically determined guidelines and studies based upon best guesses and theory using the latest technologies.
SNP Scoring and Detection
Two principal approaches to SNP scoring are in individual reactions and in a multiplexed fashion, usually achieved by using immobilized oligonucleotides on microarrays. The requirement for PCR before the detection reaction remains a major bottleneck. Simultaneous analysis of pooled DNA samples may be useful for increasing throughput and decreasing the cost of SNP scoring in association studies.
Diseases and Phenotypes
If there is no initial linkage to guide the search, however, the current answer seems to be to make educated guesses about which genes are likely to be important. Presenters summarized attempts to do this for Alzheimers disease, schizophrenia, dyslexia, and substance dependence. These studies began with a strong prior belief in the relevance of the tested candidate gene. Other presented data showed how intricate estimations of haplotype configurations, regression, and cladistic analyses can lead toward the precise intragenic location of the pathogenic allele and genotype combinations. This evolutionary perspective was a key take-home message.
The emphasis of most SNP research on tools and genotyping (finding the link between marker and pathogenic allele) was contrasted with the relative lack of attention to careful study design and sample ascertainment (finding the link between pathogenic allele and disease). Many case-control association studies may be futile because the lack of even rare families segregating the disease could indicate too-high genetic complexity.
Databases and Bioinformatics
Many groups endeavor to mine SNPs from EST data, but measuring allele frequencies in silico is difficult, and many rare alleles might be among them. Prediction accuracy is estimated at only 60% to 80% in most cases, although this identifies gene candidates for further investigation. Others are attempting to map large numbers of SNPs onto human chromosomes and three-dimensional protein structures to understand phenotypic differences and human evolution using SNP data.
Intellectual Property, Commerce
In the first situation, proprietary rights to the important SNPs are expected to generate profits via licensing. In the third instance, profits can be generated over shorter times by sales and licensing of patented technologies. But the greatest business success from SNP knowledge may be realized only if and when solid correlations between SNPs and gene function are determined.
A key question is whether the most obvious and rewarding SNPs (from a cost-benefit standpoint) already have been discovered and patented or if latecomers still have a good chance of finding valuable SNPs. [Reported by Anthony Brookes; Center for Genomics Research; Karolinska Institute; Stockholm, Sweden (firstname.lastname@example.org)]
Detailed 1999 Meeting Report
September 2000 Meeting: http://brookes.cgb.ki.se/snp2000/abstracts.htm
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The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.
Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.