Archon Genomics X PRIZE Validation Protocol

This document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies that emerge even after 2012

Assembly algorithms for next-generation sequencing data

AbstractThe emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly

Community Outreach through Genomics Education Partnership

The J Craig Venter Institute (JCVI) has recently partnered with undergraduate university faculty to expand the scope of education and outreach program as part of the NIAID’s BRC initiative, by joining forces with faculty members participating in the Genomics Education Partnership (GEP). The goal of the GEP is to provide opportunities for undergraduate students to participate in genomics research and gain hands on experience. Faculty members trained on annotation methodologies and tools during the Prokaryotic Annotation Workshop conducted at JCVI, impart their knowledge in the classroom as part of the semester course. As a pilot project, we are currently collaborating with 3 groups lead by a faculty member, spread across 3 universities in the community curation of bacterial genomes. Each participating undergraduate group collectively annotates a specific bacterial genome that was sequenced at JCVI and run through the automatic annotation pipeline. Remote access to genome sequence data, pre-computed gene predictions, search results, automatic annotation and bioinformatics analysis is provided through our web-based manual annotation tool, MANATEE. The students log into JCVI genome databases with user specific ids and password and learn to annotate single genes, entire metabolic pathways leading to analysis of a question that may be unique to the genome being analyzed. Users of the genome data receive dedicated support and guidance from our in house annotation experts on the usage of JCVI’s tools and annotation methodologies. Through this exercise, the undergraduate students are introduced to concepts of genomics and bioinformatics and gain deeper understanding of the concepts of cellular metabolism and disease pathology, which may lead them to making scientific research their career path. Some groups are focusing on genome specific pathways and plan to conduct wet lab experiments to understand unique genome features. We are highly encouraged that this model of web based, remote access, community annotation has been successful and propose to leverage the community of annotators to update annotations of pathogen genomes in Pathema-BRC

Expert Assertions Through Community Annotation Jamborees

Although there is significant optimism that community involvement can drive genome curation, results to date are disappointing. The Human Genome and Saccharomyces Genome Databases both tried community annotation experiments and few community contributions were obtained. JCVI’s own early experiences with community curation were also largely unsuccessful. Although community curation tools were publicly available on JCVI web resources and much effort was made by JCVI personnel to advertise these resources, little curation was actually submitted. Starting in late 2007, JCVI’s model for community curation changed. Instead of simply providing curation tools on websites and advertising their utility at meetings and conferences, JCVI instituted a community curation jamboree model. 

Annotation jamborees are an excellent form of outreach to the community. JCVI’s experience conducting jamborees is highly successful, demonstrating that jamborees are effective tools for incorporating expert annotation data into existing genome submissions, updating existing annotation, tagging annotation with updated experimental references and providing the community with opportunities to become familiar with JCVI’s annotation procedures and curation tools. Jamborees provide a means to directly interact with the community and integrate their research expertise into genomic data sets. Jamboree participants are encouraged to provide their expert input by focusing on their genes and gene families of interest, particularly those with supporting experimental evidence. Through JCVI’s NIAID Bioinformatics Resource Center, Pathema ("http://pathema.jcvi.org":http://pathema.jcvi.org), JCVI hosted two annotation jamborees incorporating expert annotation into Entamoeba and Burkholderia genome projects. These jamborees resulted in curation of 1,565 functional assignments, 3,499 Gene Ontology terms, 129 gene structures, and 296 experimental references for 11 genome projects representative of the Pathema data set. Researchers who contributed to annotation at these jamborees are being submitted as contributing authors on annotation update submissions made to GenBank for those organisms. Additionally, the annotation associated with the submission is recognized as part of community curation efforts and collaboration, and all updates and contributions are reflected on the Pathema web resource.

The networking and personal communication that occurs throughout a jamboree facilitates a forum for research and data exchange, solicitation of user feedback and the establishment of new community collaborations. Although integrating and updating annotation data is important, it is our experience that the interactions that occur and collaborations that are formed are the most beneficial long-term results of jamboree efforts. Collaborations we established as a direct result of jamboree activity include continued community annotation, custom data analyses and general informatics support not otherwise solicited by the researcher. For the jamborees JCVI recently hosted, we established successful collaborations with four researchers who continued to provide curation from their own institute

The Protein Naming Utility: a rules database for protein nomenclature

Generation of syntactically correct and unambiguous names for proteins is a challenging, yet vital task for functional annotation processes. Proteins are often named based on homology to known proteins, many of which have problematic names. To address the need to generate high-quality protein names, and capture our significant experience correcting protein names manually, we have developed the Protein Naming Utility (PNU, http://www.jcvi.org/pn-utility). The PNU is a web-based database for storing and applying naming rules to identify and correct syntactically incorrect protein names, or to replace synonyms with their preferred name. The PNU allows users to generate and manage collections of naming rules, optionally building upon the growing body of rules generated at the J. Craig Venter Institute (JCVI). Since communities often enforce disparate conventions for naming proteins, the PNU supports grouping rules into user-managed collections. Users can check their protein names against a selected PNU rule collection, generating both statistics and corrected names. The PNU can also be used to correct GenBank table files prior to submission to GenBank. Currently, the database features 3080 manual rules that have been entered by JCVI Bioinformatics Analysts as well as 7458 automatically imported names

Heterochromatic sequences in a Drosophila whole-genome shotgun assembly

BACKGROUND: Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it difficult to assemble and analyze. To better understand the heterochromatic component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly. RESULTS: WGS3, an improved whole-genome shotgun assembly, includes 20.7 Mb of draft-quality sequence not represented in the Release 3 sequence spanning the euchromatin. We annotated this sequence using the methods employed in the re-annotation of the Release 3 euchromatic sequence. This analysis predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Bacterial artificial chromosome (BAC)-based fluorescence in situ hybridization analysis was used to correlate the genomic sequence with the cytogenetic map in order to refine the genomic definition of the centric heterochromatin; on the basis of our cytological definition, the annotated Release 3 euchromatic sequence extends into the centric heterochromatin on each chromosome arm. CONCLUSIONS: Whole-genome shotgun assembly produced a reliable draft-quality sequence of a significant part of the Drosophila heterochromatin. Annotation of this sequence defined the intron-exon structures of 30 known protein-coding genes and 267 protein-coding gene models. The cytogenetic mapping suggests that an additional 150 predicted genes are located in heterochromatin at the base of the Release 3 euchromatic sequence. Our analysis suggests strategies for improving the sequence and annotation of the heterochromatic portions of the Drosophila and other complex genomes

Percutaneous transhepatic mitral commissurotomy

A novel, transhepatic approach to mitral valvuloplasty is described in a patient with an inferior vena caval filter. After transhepatic transseptal puncture, an Inoue dilatation catheter was passed through the hepatic parenchyma and across the atrial septum. Balloon mitral valvuloplasty was performed without complications. This approach should be considered when femoral venous access is restricted or is not feasible. © 1996 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/38224/1/22_ftp.pd

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation

BACKGROUND: The 50-year-old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome. RESULTS: The C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K+ channels. As a test of utility, RNA sequence data from Zika-infected cells were mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of nonhost reads. CONCLUSIONS: The C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease

Cortisol and externalizing behavior in children and adolescents: Mixed meta-analytic evidence for the inverse relation of basal cortisol and cortisol reactivity with externalizing behavior

An inverse relation between cortisol (re)activily and externalizing behavior has been hypothesized, but research findings seem equivocal. We tested this hypo(re)activity hypothesis in two meta-analyses, one for basal cortisol (k = 72 studies, N = 5,480) and one for cortisol reactivity to a stressor (k = 29 studies, N = 2,601). No association was found between cortisol reactivity and externalizing behaviors (r = -.04, 95% CI = -.11, .02). However, the relation between basal cortisol and externalizing behavior was significant but small (r = -.05, 95% CI = -.10, -.002). The age of the children significantly moderated this relation: Externalizing behavior was associated with higher basal cortisol (hyperactivity) in preschoolers (r =.09, 95% CI =.002, .17), and with lower basal cortisol (hypoactivity) in elementary school-aged children (r = -.14, 95% CI = -.19, -.08). There was no significant relation between cortisol and externalizing behavior in adolescents. © 2008 Wiley Periodicals, Inc