Detecting single fl uorescent molecules remains extremely challenging. Because some 5 percent are missed, more “reads” must be performed to fi ll in the resulting gap errors. That is why most groups fi rst copy, or amplify, the single DNA template of interest by a process called polymerase chain reaction (PCR). In this step, too, a variety of approaches have emerged that make the use of bacteria to generate DNA copies unnecessary. One cell-free amplifi cation method, developed by Eric Kawashima of the Serono Pharmaceutical Research Institute in Geneva, Alexander Chetverin of the Russian Academy of Sciences, and Mitra when he was at Harvard, creates individual colonies of polymerase—polonies—freely arrayed directly on the surface of a microscope slide or a layer of gel. A single template molecule undergoes PCR within each polony, producing millions of copies, which grow rather like a bacterial colony from the central original template. Because each resulting polony cluster is one micron wide and one femtoliter in volume, billions of them can fi t onto a single slide. A variation on this system fi rst produces polonies on tiny beads inside droplets within an emulsion. After the reaction millions of such beads, each bearing copies of a different template, can be placed in individual wells or immobilized by a gel where sequencing is performed on all of them simultaneously. These methods of template amplifi cation and of sequencing by base extension or by ligation are just a few representative examples of the approaches dozens of different academic and corporate research groups are taking to sequencing by synthesis. Still another technique, sequencing by hybridization, also uses fl uorescence to generate a visible signal and, like sequenc
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