INTRODUCTION The completion of the first draft of the Human Genome Project in 2001, and subsequent refinements since then, have stimulated an explosion of research about the human genome, the inherent variability of DNA sequences among humans, and the relationship of sequence variation to human health. The scientific impact of this research in understanding the pathophysiology of disease and in...

The Bonobo Genome Consortium generated DNA sequencing reads representing the genome of a single bonobo individual. The data consisted of almost 270 million fragment sequences generated on FLX machines from 454 Life Sciences. The fragments derived from FLX standard and Titanium chemistries, and from paired and unpaired protocols. The data was assembled at the J. Craig Venter Institute with the o...

We are resubmitting as an attachment a white paper requesting an 8-fold coverage draft genome sequence for the opisthobranch mollusc, Aplysia californica. As described in the proposal, Aplysia is a major model organism for studies in cellular, molecular and behavioral neuroscience, integrative physiology and system biology. It is also ideally placed taxonomically to serve as an important organi...

Next-generation sequencing technology has enabled genome-wide analysis of 5mC nucleotides at single-nucleotide resolution. Previous methods for whole-genome bisulfite sequencing (WGBS) yielded reduced genomic representation due to required DNA shearing, ligation of methylated sequencing adapters, and bisulfite conversion of unmethylated cytidine residues prior to sequencing. One disadvantage of...

DNA sequencing can be used to gain important information on genes, genetic variation and gene function for biological and medical studies. The growing collection of publicly available reference genome sequences will underpin a new era of whole genome re-sequencing, but sequencing costs need to fall and throughput needs to rise by several orders of magnitude. Novel technologies are being develop...

Sequence of the chimpanzee (Pan troglodytes) genome should be a high priority. The chimpanzee genome sequence will have a major impact on our understanding of human disease, human evolution, and human population genetics. We propose that the first phase of a project to obtain chimpanzee sequence consist of 3-4X whole-genome shotgun coverage, with the sequence obtained from multiple individuals ...

New technologies for DNA sequencing, coupled with advanced analytical approaches, are now providing unprecedented speed and precision in decoding human genomes. This combination of technology and analysis, when applied to the study of cancer genomes, is revealing specific and novel information about the fundamental genetic mechanisms that underlie cancer's development and progression. This revi...

Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x cove...

The motivation for sequencing genomes is rather direct. According to the central dogma of biology, elements of the genome are translated via several mechanisms into the structure and function of organisms. But in order to study genomes, we must first sequence them. Whole Genome Shotgun (WGS) is a successful method for sequencing genomes. This lecture we will discuss how WGS works, some of the c...