A "quality-first" credo for the Human Genome Project

Comparing the whole-genome-shotgun and map-based sequences of the rice genome

The rice genome has now been sequenced using whole-genome-shotgun and map-based methods. The relative merits of the two methods are the subject of debate, as they were in the human genome project. In this Opinion article, we will show that the serious discrepancies between the resultant sequences are mostly found in the large transposable elements such as copia and gypsy that populate the intergenic regions of plant genomes. Differences in published gene counts and polymorphism rates are similarly resolved by considering how transposable elements affect the sequence analysis.

Strategies for the systematic sequencing of complex genomes

Recent spectacular advances in the technologies and strategies for DNA sequencing have profoundly accelerated the detailed analysis of genomes from myriad organisms. The past few years alone have seen the publication of near-complete or draft versions of the genome sequence of several well-studied, multicellular organisms - most notably, the human. As well as providing data of fundamental biological significance, these landmark accomplishments have yielded important strategic insights that are guiding current and future genome-sequencing projects.

Cross-talk filtering in four dye fluorescence-based DNA sequencing

We have addressed two important issues of nonlinear cross-talk and baseline adjustment in DNA data processing. An important aspect in the processing of the four-dye fluorescence-based data is the cross-talk filtering. Typically, a matrix M, which is a function of the fluorophores and the fluorescence detection system, is used in the multicomponent analysis. In this deconvolution process the matrix is applied directly to the raw signal, on a linear cross-talk assumption. This necessitates the signal to be aligned to the baseline before the filter is applied. The various techniques used for aligning the raw data have the negative effect of adding distortion to the signal. An algorithm for cross-talk removal is presented in this paper. The algorithm uses the intensity difference of the signal rather than the actual value itself, thus making the cross-talk removal possible before the base line adjustment. In addition, a supplementary filtering step is proposed in order to account for the nonlinear nature of the cross-talk. This second step is based on a matrix T that accounts for the correlation of each of the signals with the other three. The overall result is a more precise presentation of the DNA data and less information loss through filtering.

High-throughput DNA sequencing: a genomic data manufacturing process

The progress trends in automated DNA sequencing operation are reviewed. Technological development in sequencing instruments, enzymatic chemistry and robotic stations has resulted in ever-increasing capacity of sequence data production. This progress leads to a higher demand on laboratory information management and data quality assessment. High-throughput laboratories face the challenge of organizational management, as well as technology management. Engineering principles of process control should be adopted in this biological data manufacturing procedure. While various systems attempt to provide solutions to automate different parts of, or even the entire process, new technical advances will continue to change the paradigm and provide new challenges.

Analysis of the quality and utility of random shotgun sequencing at low redundancies

The currently favored approach for sequencing the human genome involves selecting representative large-insert clones (100-200 kb), randomly shearing this DNA to construct shotgun libraries, and then sequencing many different isolates from the library. This method, entitled directed random shotgun sequencing, requires highly redundant sequencing to obtain a complete and accurate finished consensus sequence. Recently it has been suggested that a rapidly generated lower redundancy sequence might be of use to the scientific community. Low-redundancy sequencing has been examined previously using simulated data sets. Here we utilize trace data from a number of projects submitted to GenBank to perform reconstruction experiments that mimic low-redundancy sequencing. These low-redundancy sequences have been examined for the completeness and quality of the consensus product, information content, and usefulness for interspecies comparisons. The data presented here suggest three different sequencing strategies, each with different utilities. (1) Nearly complete sequence data can be obtained by sequencing a random shotgun library at sixfold redundancy. This may therefore represent a good point to switch from a random to directed approach. (2) Sequencing can be performed with as little as twofold redundancy to find most of the information about exons, EST hits, and putative exon similarity matches. (3) To obtain contiguity of coding regions, sequencing at three- to fourfold redundancy would be appropriate. From these results, we suggest that a useful intermediate product for genome sequencing might be obtained by three- to fourfold redundancy. Such a product would allow a large amount of biologically useful data to be extracted while postponing the majority of work involved in producing a high quality consensus sequence.