DNA Sequence Data

DNA Sequence Data

DNA Sequence Data

Introduction

What is DNA sequencing?

DNA sequencing, the process of determining the exact order of the 3 billion chemical building blocks (called bases and abbreviated A, T, C, and G) that make up the DNA of the 24 different human chromosomes, was the greatest technical challenge in the Human Genome Project. Achieving this goal has helped reveal the estimated 20,000-25,000 human genes within our DNA as well as the regions controlling them. The resulting DNA sequence maps are being used by 21st Century scientists to explore human biology and other complex phenomena.

Meeting Human Genome Project sequencing goals by 2003 required continual improvements in sequencing speed, reliability, and costs (Margulies M, Egholm M, Altman WE, et al (September 2005, 45-77)

Previously, standard methods were based on separating DNA fragments by gel electrophoresis, which was extremely labor intensive and expensive. Total sequencing output in the community was about 200 million base pairs for 1998. In January 2003, the DOE Joint Genome Institute alone sequenced 1.5 billion bases for the month. Gel-based sequencers use multiple tiny (capillary) tubes to run standard electrophoretic separations. These separations are much faster because the tubes dissipate heat well and allow the use of much higher electric fields to complete sequencing in shorter times. (Margulies M, Egholm M, Altman WE, et al (September 2005, 45-77)

Explanation

How is DNA sequencing done?

Chromosomes, which range in size from 50 million to 250 million bases, must first be broken into much shorter pieces (subcloning step).

Each short piece is used as a template to generate a set of fragments that differ in length from each other by a single base that will be identified in a later step (template preparation and sequencing reaction steps). (Shendure, J. 2005, 122-43)

What genomes have been sequenced completely?

The small genomes of several viruses and bacteria and the much larger genomes of three higher organisms have been completely sequenced; they are bakers' or brewers' yeast (Saccharomyces cerevisiae), the roundworm (Caenorhabditis elegans), and the fruit fly (Drosophila melanogaster). In October 2001, the draft sequence of the pufferfish Fugu rubripes, the first vertebrate after the human, was completed; and scientists finished the first genetic sequence of a plant, that of the weed Arabidopsis thaliana, in December 2000. Many more genome sequences have been completed since then. (Shendure, J. 2005, 122-43)

What happens now that the human genome sequence is completed?

The working-draft DNA sequence and the more polished 2003 version represent an enormous achievement, akin in scientific importance, some say, to developing the periodic table of elements. And, as in most major scientific advances, much work remains to realize the full potential of the accomplishment. Early explorations of the human genome, now joined by projects on the genomes of several other organisms, are generating data whose volume and complex analyses are unprecedented in biology. Genomic-scale technologies will be needed to study and compare entire genomes, sets of expressed RNAs or proteins, gene families from a large number of species, variation among individuals, and the classes of gene ...