A common language for physical mapping of the human genome.

I N A REPORT ISSUED IN JANUARY 1988, THE NATIONAL Research Council (NRC) Committee on the Mapping and Sequencing of the Human Genome, on which the present authors served, recommended a staged mapping and sequencing project with early emphases on physical mapping of human DNA, mapping and sequencing of the genomes of model organisms, and the development of sequencing technology (1). As the Committee’s recommendations on physical mapping are beginning to be implemented on a substantial scale, it is timely to review these recommendations in the light of recent technical advances. In particular, the polymerase chain reaction (PCR) (2), a method that has only come into widespread use during the past 2 years, seems to us to offer a path toward a physical map that largely circumvents two problems that were prominent in the NRC Committee’s discussions. One of these was the difficulty of merging mapping data gathered by diverse methods in different laboratories into a consensus physical map. The second was the logistics and expense of managing the huge collections of cloned segments on which the mapping data would depend almost absolutely. By allowing short DNA sequences to be detected easily with high specificity and sensitivity, PCR makes practical the use of DNA sequence itself to define the basic landmarks on the physical map. We advocate the use of short tracts of single-copy DNA sequence (that is, sequences that occur only once in the genome) that can be easily recovered at any time by PCR as the landmarks that define position on the physical map. Construction of a physical map would then be seen as the determination of the order and spacing of DNA segments, each of which is identified uniquely by such a sequence. This will solve the problem of merging data from many sources, eliminate the need for large clone archives, and define a physical map that can evolve smoothly and naturally toward the ultimate goal of a complete DNA sequence of the human genome. Physical mapping: A hybrid technology. The physical map of the human genome envisioned by the NRC report as the precursor of sequencing was a hybrid of a “restriction map” and a “contig map.” Following the paradigm introduced by Nathans in the early 1970s for the case of SV4O, restriction maps show the order and distances between cleavage sites of site-specific restriction endonucleases (3). This type of mapping has been extended to much larger genomes, such as that of Escherichia coli, by exploiting the ability to separate very large restriction fragments with pulsed-field gel clectrophoresis (4). Contig maps represent the structure of contiguous regions of the genome by specifying the overlap relationships among a set of clones (5). Contig maps