Toby Bloom

Evaluation of 16s rDNA-based community profiling for human microbiome research

The Human Microbiome Project will establish a reference data set for analysis of the microbiome of healthy adults by surveying multiple body sites from 300 people and generating data from over 12,000 samples. To characterize these samples, the participating sequencing centers evaluated and adopted 16S rDNA community profiling protocols for ABI 3730 and 454 FLX Titanium sequencing. In the course of establishing protocols, we examined the performance and error characteristics of each technology, and the relationship of sequence error to the utility of 16S rDNA regions for classification- and OTU-based analysis of community structure. The data production protocols used for this work are those used by the participating centers to produce 16S rDNA sequence for the Human Microbiome Project. Thus, these results can be informative for interpreting the large body of clinical 16S rDNA data produced for this project.

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome. It is also enriched in segmental duplications, ranking third in density among the autosomes. Here we report a finished sequence for human chromosome 17, as well as a structural comparison with the finished sequence for mouse chromosome 11, the first finished mouse chromosome. Comparison of the orthologous regions reveals striking differences. In contrast to the typical pattern seen in mammalian evolution, the human sequence has undergone extensive intrachromosomal rearrangement, whereas the mouse sequence has been remarkably stable. Moreover, although the human sequence has a high density of segmental duplication, the mouse sequence has a very low density. Notably, these segmental duplications correspond closely to the sites of structural rearrangement, demonstrating a link between duplication and rearrangement. Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome.

Issues in the design of object-oriented database programming languages

We see a trend toward extending object-oriented languages in the direction of databases, and, at the same time, toward extending database systems with object-oriented ideas. On the surface, these two activities seem to be moving in a consistent direction. However, at a deeper level, we see difficulties that may inhibit their ending up at the same point. We feel that many of these difficulties are a result of the underlying assumptions that are inherent in the fields of programming language and database systems research. Many of these assumptions are historical and contribute to a set of cultural biases that often prevent the two communities from interacting as effectively as possible. The purpose of this paper is to try to uncover some of the cultural presuppositions that have inhibited development of a fully integrated database programming language. We have identified database and language features that seem to be difficult to reconcile. We try to uncover the basic problems in these two areas that these features were intended to solve. In order to resolve these problems, we attempt to distinguish fundamental differences from historical artifacts.

Evaluating synchronization mechanisms

In recent years, many high-level synchronization constructs have been proposed. Each claims to satisfy criteria such as expressive power, ease of use, and modifiability. Because these terms are so imprecise, we have no good methods for evaluating how well these mechanisms actually meet such requirements. This paper presents a methodology for performing such an evaluation. Synchronization problems are categorized according to some basic properties, and this categorization is used in formulating more precise definitions of the criteria mentioned, and in devising techniques for assessing how well those criteria are met.

Analysis of the DNA sequence and duplication history of human chromosome 15

Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.

Human chromosome 11 DNA sequence and analysis including novel gene identification

Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here—nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence—provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena.

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

ABSTRACT Tilapia are an important global food source due to their omnivorous diet, tolerance for high-density aquaculture, and relative disease resistance. Since 2009, tilapia aquaculture has been threatened by mass die-offs in farmed fish in Israel and Ecuador. Here we report evidence implicating a novel orthomyxo-like virus in these outbreaks. The tilapia lake virus (TiLV) has a 10-segment, negative-sense RNA genome. The largest segment, segment 1, contains an open reading frame with weak sequence homology to the influenza C virus PB1 subunit. The other nine segments showed no homology to other viruses but have conserved, complementary sequences at their 5′ and 3′ termini, consistent with the genome organization found in other orthomyxoviruses. In situ hybridization indicates TiLV replication and transcription at sites of pathology in the liver and central nervous system of tilapia with disease. IMPORTANCE The economic impact of worldwide trade in tilapia is estimated at

Managing data from high-throughput genomic processing: a case study

7.5 billion U.S. dollars (USD) annually. The infectious agent implicated in mass tilapia die-offs in two continents poses a threat to the global tilapia industry, which not only provides inexpensive dietary protein but also is a major employer in the developing world. Here we report characterization of the causative agent as a novel orthomyxo-like virus, tilapia lake virus (TiLV). We also describe complete genomic and protein sequences that will facilitate TiLV detection and containment and enable vaccine development. The economic impact of worldwide trade in tilapia is estimated at

Whole-genome bisulfite sequencing with improved accuracy and cost

7.5 billion U.S. dollars (USD) annually. The infectious agent implicated in mass tilapia die-offs in two continents poses a threat to the global tilapia industry, which not only provides inexpensive dietary protein but also is a major employer in the developing world. Here we report characterization of the causative agent as a novel orthomyxo-like virus, tilapia lake virus (TiLV). We also describe complete genomic and protein sequences that will facilitate TiLV detection and containment and enable vaccine development.

WHOLE GENOME BISULPHITE SEQUENCING USING THE ILLUMINA HISEQ X SYSTEM

Genomic data has become the canonical example of very large, very complex data sets. As such, there has been significant interest in ways to provide targeted database support to address issues that arise in genomic processing. Whether genomic data is truly a special case, or just another application area exhibiting problems common to other domains, is an as yet unanswered question. In this abstract, we explore the structure and processing requirements of a large-scale genome sequencing center, as a case study of the issues that arise in genomic data managements, and as a means to compare those issues with those that arise in other domains.