Method and apparatus for image processing for massive parallel DNA sequencing

#This invention relates to a method and apparatus for image processing, and more particularly, this invention relates to a method and apparatus for processing image data generated by bioanalytical devices, such as DNA sequencers.

#The combined work of Avery et al, in 1944, and Watson and Crick in 1953, established that DNA contains the information that defines each organism, and that it is a long string of chemical building blocks—denoted by the letters A, T, C, G,—whose precise order, or “sequence”, is ultimately how this information is encoded. Since that point, it has been a major goal to develop ways to read this sequence, in order to eventually understand how it relates to the properties of different species, and of individuals within each species.

#In 1978, Sanger introduced the first practical biochemical technique for determining the sequence of DNA. This method was refined and automated, and was the basis for all practical DNA sequencing performed in the next 25 years, culminating in the publicly funded International Human Genome Project (and the privately funded parallel effort undertaken by Celera Corporation), which in 2003 produced a reference DNA sequence for the almost 3 billion letters long human genome. This effort required nearly a decade, and billions of dollars in equipment, labor and chemical reagents. Because the Sanger reaction is inherently serial, with each reaction producing only a few hundred letters of sequence, roughly about 100 million individual reactions had to be performed in the course of this effort, ultimately using thousands of semi-automated sequencing machines, each of which could perform thousands of separate reactions per day. Since the genomes of most species are large (tens of millions to billions of letters), Sanger sequencing to determine a reference sequence for a new species, or to obtain the sequence of a specific individual within a species, remains a massive and costly undertaking, even with all the technologically improvements made during the course of the Human genome Project.

#FIG. 1 illustrates an image produced by the ABI SOLiD system: a small portion of a real 2048×2048 pixel image from the ABI SOLiD system, showing approximately 100 beads.

#FIG. 2 illustrates a specific example of conducting a massively parallel DNA sequencing in the ABI SOLiD system: the DNA to be sequenced in fragmented into a pool of short fragments, which are then exposed to billions of microscopic beads, and processed so that a random fragment attaches to each bead and covers the bead with many copies of the initial fragment.

#FIG. 2a illustrates the next step continuing from FIG. 2: the DNA-carrying beads are immobilized onto a microscope slide surface, covered with a gasket that allows chemical reagents to be pumped in and out, and then undergo a series of chemical reactions which report sequence information in the form of a 4-color signal, which can be captured as microscope images of the slides.

#The detailed description set forth below is intended as a description of the presently exemplary device provided in accordance with aspects of the present invention and is not intended to represent the only forms in which the present invention may be prepared or utilized. It is to be understood, rather, that the same or equivalent functions and components may be accomplished by different embodiments that are also intended to be encompassed within the spirit and scope of the invention.

#Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this invention belongs. Although any methods, devices and materials similar or equivalent to those described can be used in the practice or testing of the invention, the exemplary methods, devices and materials are now described.

#All publications mentioned are incorporated by reference for the purpose of describing and disclosing, for example, the designs and methodologies that are described in the publications which might be used in connection with the presently described invention. The publications listed or discussed above, below and throughout the text are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention.