Automatic reading of DNA sequencing gel autoradiographs using a large format digital scanner

Abstract

We have developed a large format digital scanner for several applications in nucleic acid analysis. Here we describe the scanning of autoradiographs of DNA sequencing gels and a set of programs for reading the base sequence. The programs correct distortions in the gel, recognize bands by their characteristic shape and assign bases to bands by weighting band position and intensity. The sequence read in this way is as accurate as that read by an expert.

Imaging of DNA sequences with chemiluminescence.

“…Two methods using this approach with multiemission fluorescent labels allow the mixtures from base-specific reactions to be loaded as a single gel lane (3,4). Another, using 32p, requires multiple lanes (10,11).…”

Expanding Roles of Computers and Robotics in Biological Macromolecular Research

“…Several typ es of apparatus fo r fully automatic scanning of auto radiographs have been developed independently by Elder et al (40), by Hitachi Software Company, by Seiko Electronic and Instruments Company, and by Pharmacia Company (95,96,152, and references there in). All of these scanners use charge-coupled device (CCD) array cameras or CCD line sensors fo r digitizing electrophoresis signal bands.…”

“…All of these scanners use charge-coupled device (CCD) array cameras or CCD line sensors fo r digitizing electrophoresis signal bands. Elder (40) studied the basic principle and algorithm of the conversion of two dimensional tracks to one-dimensional ones fo r suppression of and cor rection fo r noise and distortions and fo r the registration of tracks and the identification of bands. The cu rrent perfo rmance of gel reading machines is 10--50 bp min-1 with a 1-2% error in the crowded band region.…”

Automated band mapping in electrophoretic gel images using background information

“…Systems to perform these tasks were developed soon after the introduction of large-format film scanners in the 1980s (1,2) and continue to facilitate what would otherwise be a rate-limiting step in sequence determination and assembly. Now a major challenge of genomics is the discovery of single-nucleotide differences, such as naturally occurring single-nucleotide polymorphisms (SNPs) and induced point mutations (3–5).…”