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4 SAMPLE COLLECTION AND DATA MANAGEMENT
Pages 36-54

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From page 36...
... This chapter reflects the committee's thoughts on how those ends can be best served generally, but detailed guidance was not part of the committee's charge. Accordingly, given the importance of this potential resource, the committee recommends that a panel be convened to provide detailed guidance before a major sampling effort and specimen collection are begun.
From page 37...
... DNA can also be prepared from hair follicles, but the amount of DNA recoverable is less than that with buccal sampling. Transformed Cell Lines Peripheral blood can also be used as a source of white blood cells for the establishment of transformed cell lines.
From page 38...
... Transformed cell lines are preferred for collecting samples for human genetic-variation research. That is particularly true for populations that are small and hard to sample but that might yield interesting information about human prehistory.
From page 39...
... Moreover, B-cell cultures are not suitable for answering some fundamental biomedical questions about gene expression. Gene-expression profiles can differ among different transformed cell lines, so caution is in order if they are used to study phenotypic variations at the cellular level.
From page 41...
... The primers themselves can be inexpensively synthesized de novo or purchased commercially. Because SSLPs are highly informative, they are useful for a variety of human evolutionary studies, but they have a higher mutation rate than single-nucleotide substitutions.
From page 42...
... Each has a unique set of genetic characteristics, including mode of inheritance, mutation rate in male and female germ lines, and occurrence and rate of recombination. Each will provide a different view of human variation because they will illuminate the role of different genetic processes in the generation and maintenance of variation.
From page 43...
... PCR products can be analyzed with several electrophoretic methods that are capable of detecting simple nucleotide substitutions and insertion-deletion differences between different samples, for example, single-strand conformation polymorphism, density-gradient gel electrophoresis, and chemical cleavage. It should be noted that unless all measures of variation are at the level of a specific nucleotide sequence, there is always a chance that some allele-typing data will be compromised.
From page 44...
... RESEARCH-MATERIALS MANAGEMENT The specimens acquired in the course of a coordinated human genetic-variation research effort will be its most valuable and enduring resource. It can reasonably be expected that dramatic advances will occur in laboratory-analysis technologies because of current research investments in robotics, automation, and high-speed DNA-marker detection and DNA-sequencing methods.
From page 45...
... The most versatile model for a coordinated effort funded by US agencies would involve the establishment or designation of a relatively small number of regional centers, in different parts of the United States similar to the distribution of reagents used in the human genome project. Because the scope of human genome variation research is global, it would be optimal for the US effort to cooperate and consult at the international level with respect to establishing cen
From page 46...
... The raw data on allele typing will be the basis for all the scientific conclusions that follow from the human genome variation project, so it is critical that the allele-typing data be accurate. Because different laboratories might type different populations with the same genetic markers, accurate comparisons between populations depend on the accuracy of allele identification in each.
From page 47...
... The necessary data-management technologies and methods are relatively mature and economical, but the potentially sensitive nature of genetic information on persons and groups and the prospect that the data will be transported via public data networks, such as the Internet, might add requirements for information systems that support human genetic variation data management beyond the functions normally associated with collections of biologic data. The critical issue for data management is whether a data repository will contain information that can be used to link genetic data to specific individuals.
From page 48...
... The project should apply lessons learned in biologic naming systems; specifically, it should expect that the meaning of group names will change and that audit trails for relating prior definitions to current ones will need to be part of the data-repository design. To the extent that a human genetic variation data repository includes information sinkable to specific persons and adopts security measures to safeguard them the project will be undertaking a social experiment in determining the acceptability of strong security measures, access, and audit controls in a scientific
From page 49...
... In a manner analogous to licensing agreements for patent rights on products derived from human genetic variation (see chapter 5) , a decision will need to be made as to whether to hold copyright on the human genetic variation database.
From page 50...
... Obviously, the decreasing cost and increasing presence of microcomputers and digital-data networks argue for the creation of alternative pathways of data submission to a shared resource, including magnetic or optical media (floppy disks, recordable compact disk, or digital tape) , Internet file transfer protocol (ftp)
From page 51...
... The success and credibility of the work done by multiple participating sites, investigators, and laboratories will depend on proof that reasonable quality-control standards are in place and are implemented. COMMUNICATION VIA PUBLIC NETWORKS A coordinated human genetic variation research effort will benefit from the recent emergence and rapid growth of the global Internet, a network of networks that provides a communication path among computers that is widely accessible at academic institutions, businesses, and residences around the world.
From page 52...
... SECURITY ISSUES RELATED TO HUMAN GENETIC VARIATION DATA In a human genetic variation data resource, in which submitting investigators cannot even identify samples and records that they have submitted for purposes of linking to individually identifiable information, security risks are minimal. Where such links can be constructed or discovered, however, security takes on a much more prominent role in human genetic variation information systems des~gn.
From page 53...
... There are 5 basic types of security risks for personally identifiable data (Ford 1994~: · Disclosure loss of confidentiality or privacy · Modification loss of integrity · Fabrication loss of authenticity · Repudiation loss of attribution · Interruption loss of availability A credible model for human genetic variation data management will need to address each of those types of risk if the repository contains data that can be linked to specific persons. SUMMARY AND CONCLUSIONS The committee believes that at a stage when genotyping technology is evolving rapidly, it would be scientifically inappropriate and premature to designate a common core set of markers that is to be genotyped in all samples.
From page 54...
... The number of assays could be increased by a factor of 50-300 by multiplexing and using existing technologies designed for analysis of very small DNA samples. Transformed cell lines provide an essentially inexhaustible supply of DNA and are mandatory for some kinds of studies, but they require much more funding for their creation and maintenance.


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