Identification of Polycystic Kidney Disease 1 Like 1 Gene Variants in Children With Biliary Atresia Splenic Malformation Syndrome.

Biliary atresia (BA) is the most common cause of end-stage liver disease in children and the primary indication for pediatric liver transplantation, yet underlying etiologies remain unknown. Approximately 10% of infants affected by BA exhibit various laterality defects (heterotaxy) including splenic abnormalities and complex cardiac malformations-a distinctive subgroup commonly referred to as the biliary atresia splenic malformation (BASM) syndrome. We hypothesized that genetic factors linking laterality features with the etiopathogenesis of BA in BASM patients could be identified through whole-exome sequencing (WES) of an affected cohort. DNA specimens from 67 BASM subjects, including 58 patient-parent trios, from the National Institute of Diabetes and Digestive and Kidney Diseases-supported Childhood Liver Disease Research Network (ChiLDReN) underwent WES. Candidate gene variants derived from a prespecified set of 2,016 genes associated with ciliary dysgenesis and/or dysfunction or cholestasis were prioritized according to pathogenicity, population frequency, and mode of inheritance. Five BASM subjects harbored rare and potentially deleterious biallelic variants in polycystic kidney disease 1 like 1 (PKD1L1), a gene associated with ciliary calcium signaling and embryonic laterality determination in fish, mice, and humans. Heterozygous PKD1L1 variants were found in 3 additional subjects. Immunohistochemical analysis of liver from the one BASM subject available revealed decreased PKD1L1 expression in bile duct epithelium when compared to normal livers and livers affected by other noncholestatic diseases. Conclusion: WES identified biallelic and heterozygous PKD1L1 variants of interest in 8 BASM subjects from the ChiLDReN data set; the dual roles for PKD1L1 in laterality determination and ciliary function suggest that PKD1L1 is a biologically plausible, cholangiocyte-expressed candidate gene for the BASM syndrome.

The relationship between common risk factors and the pathology of pressure ulcer development: a systematic review.

OBJECTIVE: The aim of this systematic review was to examine the associations and relationship between commonly cited risk factors and the pathology of pressure ulcer (PU) development. METHOD: Using systematic review methodology, original research studies, prospective design and human studies written in English were included. The search was conducted in March 2018, using Ovid, Ovid EMBASE and CINAHL databases. Data were extracted using a pre-designed extraction tool and all included studies were quality appraised using the evidence-based librarianship critical appraisal. RESULTS: A total of 382 records were identified, of which five met the inclusion criteria. The studies were conducted between 1994 and 2017. Most studies were conducted in hospital and geriatric wards. The mean sample size was 96±145.7 participants. Ischaemia, recovery of blood flow and pathological impact of pressure and shear was mainly found as the cited risk factor and PU aetiology. CONCLUSION: This review systematically analysed five papers exploring the relationship between risk factors for PU development and aetiology. It identified many risk factors and underlying pathological mechanisms that interact in the development of PU including ischaemia, stress, recovery of blood flow, tissue hypoxia and the pathological impact of pressure and shear. There are several pathways in which these pathological mechanisms contribute to PU development and identifying these could establish potential ways of preventing or treating the development of PU for patients.

Ankle Fracture Detection Utilizing a Convolutional Neural Network Ensemble Implemented with a Small Sample, De Novo Training, and Multiview Incorporation.

To determine whether we could train convolutional neural network (CNN) models de novo with a small dataset, a total of 596 normal and abnormal ankle cases were collected and processed. Single- and multiview models were created to determine the effect of multiple views. Data augmentation was performed during training. The Inception V3, Resnet, and Xception convolutional neural networks were constructed utilizing the Python programming language with Tensorflow as the framework. Training was performed using single radiographic views. Measured output metrics were accuracy, positive predictive value (PPV), negative predictive value (NPV), sensitivity, and specificity. Model outputs were evaluated using both one and three radiographic views. Ensembles were created from a combination of CNNs after training. A voting method was implemented to consolidate the output from the three views and model ensemble. For single radiographic views, the ensemble of all 5 models produced the best accuracy at 76%. When all three views for a single case were utilized, the ensemble of all models resulted in the best output metrics with an accuracy of 81%. Despite our small dataset size, by utilizing an ensemble of models and 3 views for each case, we achieved an accuracy of 81%, which was in line with the accuracy of other models using a much higher number of cases with pre-trained models and models which implemented manual feature extraction.

The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool.

BACKGROUND: Prioritization of sequence variants for diagnosis and discovery of Mendelian diseases is challenging, especially in large collections of whole genome sequences (WGS). Fast, scalable solutions are needed for discovery research, for clinical applications, and for curation of massive public variant repositories such as dbSNP and gnomAD. In response, we have developed VVP, the VAAST Variant Prioritizer. VVP is ultrafast, scales to even the largest variant repositories and genome collections, and its outputs are designed to simplify clinical interpretation of variants of uncertain significance. RESULTS: We show that scoring the entire contents of dbSNP (> 155 million variants) requires only 95 min using a machine with 4 cpus and 16 GB of RAM, and that a 60X WGS can be processed in less than 5 min. We also demonstrate that VVP can score variants anywhere in the genome, regardless of type, effect, or location. It does so by integrating sequence conservation, the type of sequence change, allele frequencies, variant burden, and zygosity. Finally, we also show that VVP scores are consistently accurate, and easily interpreted, traits not shared by many commonly used tools such as SIFT and CADD. CONCLUSIONS: VVP provides rapid and scalable means to prioritize any sequence variant, anywhere in the genome, and its scores are designed to facilitate variant interpretation using ACMG and NHS guidelines. These traits make it well suited for operation on very large collections of WGS sequences.

TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome.

TBX3 is a member of the T-box family of transcription factors with critical roles in development, oncogenesis, cell fate, and tissue homeostasis. TBX3 mutations in humans cause complex congenital malformations and Ulnar-mammary syndrome. Previous investigations into TBX3 function focused on its activity as a transcriptional repressor. We used an unbiased proteomic approach to identify TBX3 interacting proteins in vivo and discovered that TBX3 interacts with multiple mRNA splicing factors and RNA metabolic proteins. We discovered that TBX3 regulates alternative splicing in vivo and can promote or inhibit splicing depending on context and transcript. TBX3 associates with alternatively spliced mRNAs and binds RNA directly. TBX3 binds RNAs containing TBX binding motifs, and these motifs are required for regulation of splicing. Our study reveals that TBX3 mutations seen in humans with UMS disrupt its splicing regulatory function. The pleiotropic effects of TBX3 mutations in humans and mice likely result from disrupting at least two molecular functions of this protein: transcriptional regulation and pre-mRNA splicing.

Large-Scale Synthesis of Helicene-Like Molecules for the Design of Enantiopure Thin Films with Strong Chiroptical Activity.

Helicenes are fascinating molecules owing to their unusual properties and applications in many fields from catalysis to organic electronics. Herein, we report a straightforward pathway for the synthesis of helicene-like molecules on a gram scale in an enantiopure form. Thin-film materials with good propagating optical properties and very high chiroptical responses have been grown by using pulsed laser ablation without altering the structure or the enantiopurity of the molecules. Moreover, electronic and vibrational circular dichroism spectroscopies coupled with theoretical calculations enabled some dependences of the chiroptical properties with the structure to be highlighted, for example, effects of rigidification, aromatization, or the state of matter (liquid versus solid).

Is lipid correction necessary in the stable isotope analysis of fish tissues?

RATIONALE: Stable isotope analysis (SIA) is a powerful tool for examining diet and food-web dynamics. SIA assumes "you are what you eat" relative to carbon (C) and nitrogen (N). However, fractionation of carbon during lipid synthesis violates this assumption; high-lipid tissues do not reflect δ(13) C values of diet and therefore have the potential to skew mixing model results and diet interpretations, making corrections necessary. METHODS: Brook Trout (Salvelinus fontinalis) white muscle and liver samples from several fish species representing the temperate North American cold- and warm-water fish community were corrected for lipids via chemical lipid extraction and mathematical lipid normalization. To assess the accuracy of model-predicted lipid-free δ(13) C values calculated from four normalization models, we compared model-predicted values with those measured after lipid extraction. RESULTS: We found that chemical lipid extraction is unnecessary for Brook Trout white muscle tissue with low initial lipid content. However, in tissues with C:N ratios greater than 3.5, lipid extraction increased δ(13) C values in fish liver by more than 1.0 ‰, indicating that liver lipid content is sufficient to bias δ(13) C values. We also found that lipids were accurately accounted for with mathematical normalization and recommend that tissues with C:N ratios greater than 3.5 be corrected mathematically. CONCLUSIONS: Our findings indicate that mathematical normalization is sufficient to account for bias in δ(13) C values associated with lipid content in fish tissues when C:N ratios are above 3.5. C:N ratios below 3.5 indicate that tissues have insufficient levels of lipid to bias the δ(13) C values. Generally, these findings support the use of more timely and cost-effective processing and analysis methods in future aquatic food-web studies utilizing SIA. Copyright © 2016 John Wiley & Sons, Ltd.

Ruthenium-Grafted Vinylhelicenes: Chiroptical Properties and Redox Switching.

The properties of mono- and bis-Ru-vinyl[6]helicene complexes (2 a and 2 b, respectively), recently synthesized by using molecular engineering of helicenes based on the grafting of lateral organometallic substituents on the π-helical backbone through a vinyl bridge, are presented. These helicene derivatives are thoroughly characterized, with special attention given to their chiroptical properties and redox switching activity. The UV/Vis and electronic circular dichroism (ECD) spectra of P and M enantiopure species, both in the neutral and oxidized states ([2 a](·+), [2 b](·+), and [2 b](2+)), are analyzed with the aid of quantum-chemical calculations. The extended π-conjugation facilitated by the vinyl moiety, clearly visible in the electronic structures of 2 a,b, introduces new active bands in the ECD spectra that consequently lead to a significant increase in optical rotation of Ru-vinylhelicenes compared with the organic precursors. The vibrational circular dichroism (VCD) spectra were measured and calculated for both the organic and organometallic species and constitute the first examples of VCD for metal-based helicene derivatives. Finally, the redox-triggered chiroptical switching activity of 2 a,b is examined in detail by using ECD spectroscopy. The modifications of the ECD spectra in the UV/Vis and NIR region are well reproduced and rationalized by calculations.

Acid/base-triggered switching of circularly polarized luminescence and electronic circular dichroism in organic and organometallic helicenes.

Electronic circular dichroism and circularly polarized luminescence acid/base switching activity has been demonstrated in helicene-bipyridine proligand 1 a and in its "rollover" cycloplatinated derivative 2 a. Whereas proligand 1 a displays a strong bathochromic shift (>160 nm) of the nonpolarized and circularly polarized luminescence upon protonation, complex 2 a displays slightly stronger emission. This strikingly different behavior between singlet emission in the organic helicene and triplet emission in the organometallic derivative has been rationalized by using quantum-chemical calculations. The very large bathochromic shift of the emission observed upon protonation of azahelicene-bipyridine 1 a has been attributed to the decrease in aromaticity (promoting a charge-transfer-type transition rather than a π-π* transition) as well as an increase in the HOMO-LUMO character of the transition and stabilization of the LUMO level upon protonation.

Effect of mixing, concentration and temperature on the formation of mesostructured solutions and their role in the nucleation of DL-valine crystals.

We report investigations on the formation of mesostructured solutions in DL-valine-water-2-propanol mixtures, and the crystallization of DL-valine from these solutions. Mesostructured liquid phases, similar to those previously observed in aqueous solutions of glycine and DL-alanine, were observed using Dynamic Light Scattering and Brownian microscopy, in both undersaturated and supersaturated solutions below a certain transition temperature. Careful experimentation was used to demonstrate that the optically clear mesostructured liquid phase, comprising colloidal mesoscale clusters dispersed within bulk solution, is thermodynamically stable and present in equilibrium with the solid phase at saturation conditions. Solutions prepared by slow cooling contained mesoscale clusters with a narrow size distribution and a mean hydrodynamic diameter of around 200 nm. Solutions of identical composition prepared by rapid isothermal mixing of valine aqueous solutions with 2-propanol contained mesoscale clusters which were significantly larger than those observed in slowly cooled solutions. The presence of larger mesoscale clusters was found to correspond to faster nucleation. Observed induction times were strongly dependent on the rapid initial mixing step, although solutions were left undisturbed afterwards and the induction times observed were up to two orders of magnitude longer than the initial mixing period. We propose that mesoscale clusters above a certain critical size are likely to be the location of productive nucleation events.

Transfer of microcystin from freshwater lakes to Puget Sound, WA and toxin accumulation in marine mussels (Mytilus trossulus).

Many eutrophic inland freshwater lakes in the Puget Sound Washington region produce toxic cyanobacteria blooms annually. While such blooms in lakes tend to be viewed as a localized phenomenon, there is significant potential for downstream export of toxins to freshwater streams, and marine and brackish water environments. However, monitoring for cyanotoxins typically associated with freshwaters, such as the hepatotoxin, microcystin (MC) in marine receiving waters is rare. In 2013 we studied four eutrophic Puget Sound area lakes to assess both toxin transport to marine waters and its potential accumulation in marine shellfish, specifically mussels. Shellfish beds are extensive throughout Puget Sound, and recreational harvest occurs downstream of our study lakes, so a study goal was to also assess if shellfish consumption poses a human health risk for MC exposure. We confirm, for the first time, freshwater to marine transfer of MCs in Puget Sound with subsequent bioaccumulation of MC by mussels. ELISA analysis estimated maximum MC concentrations in source lakes of 2700 µg/L, up to 0.34 µg/L in marine waters and 6.5 µg/kg in mussels. Confirmatory analyses by LC-MS/MS on water and mussel samples identified MC-LA as the major toxin. Although we found relatively low MC levels in mussels, our study implies that potential concern for human food safety is justified and warrants further investigation.

Identifying best methods for routine ELISA detection of microcystin in seafood.

Ingestion of water contaminated with the cyanotoxin, microcystin (MC), can pose serious health risks to humans. MC is also known to accumulate in seafood; however, this exposure pathway is much less understood. A fundamental element of this uncertainty is related to analytical difficulties. Commercially available enzyme-linked immunosorbent assays (ELISAs) offer one of the best options for routine MC detection, but methods of detecting MC in tissue are far from standardized. We spiked freshwater finfish and marine mussel tissues with MC, then compared recovery rates using four different preparation protocols and two ELISA types (polyclonal anti-MC-ADDA/direct monoclonal (DM)). Preparation protocol, type of ELISA, and seafood tissue variety significantly affected MC detection. This is the first known study to use DM ELISA for tissue analyses, and our findings demonstrate that DM ELISA combined with a short solvent extraction results in fewer false positives than other commonly used methods. This method can be used for rapid and reliable MC detection in seafood.

VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix.

The need for improved algorithmic support for variant prioritization and disease-gene identification in personal genomes data is widely acknowledged. We previously presented the Variant Annotation, Analysis, and Search Tool (VAAST), which employs an aggregative variant association test that combines both amino acid substitution (AAS) and allele frequencies. Here we describe and benchmark VAAST 2.0, which uses a novel conservation-controlled AAS matrix (CASM), to incorporate information about phylogenetic conservation. We show that the CASM approach improves VAAST's variant prioritization accuracy compared to its previous implementation, and compared to SIFT, PolyPhen-2, and MutationTaster. We also show that VAAST 2.0 outperforms KBAC, WSS, SKAT, and variable threshold (VT) using published case-control datasets for Crohn disease (NOD2), hypertriglyceridemia (LPL), and breast cancer (CHEK2). VAAST 2.0 also improves search accuracy on simulated datasets across a wide range of allele frequencies, population-attributable disease risks, and allelic heterogeneity, factors that compromise the accuracies of other aggregative variant association tests. We also demonstrate that, although most aggregative variant association tests are designed for common genetic diseases, these tests can be easily adopted as rare Mendelian disease-gene finders with a simple ranking-by-statistical-significance protocol, and the performance compares very favorably to state-of-art filtering approaches. The latter, despite their popularity, have suboptimal performance especially with the increasing case sample size.

Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency.

We have identified two families with a previously undescribed lethal X-linked disorder of infancy; the disorder comprises a distinct combination of an aged appearance, craniofacial anomalies, hypotonia, global developmental delays, cryptorchidism, and cardiac arrhythmias. Using X chromosome exon sequencing and a recently developed probabilistic algorithm aimed at discovering disease-causing variants, we identified in one family a c.109T>C (p.Ser37Pro) variant in NAA10, a gene encoding the catalytic subunit of the major human N-terminal acetyltransferase (NAT). A parallel effort on a second unrelated family converged on the same variant. The absence of this variant in controls, the amino acid conservation of this region of the protein, the predicted disruptive change, and the co-occurrence in two unrelated families with the same rare disorder suggest that this is the pathogenic mutation. We confirmed this by demonstrating a significantly impaired biochemical activity of the mutant hNaa10p, and from this we conclude that a reduction in acetylation by hNaa10p causes this disease. Here we provide evidence of a human genetic disorder resulting from direct impairment of N-terminal acetylation, one of the most common protein modifications in humans.

A probabilistic disease-gene finder for personal genomes.

VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds on existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and noncoding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology. Here we demonstrate its ability to identify damaged genes using small cohorts (n = 3) of unrelated individuals, wherein no two share the same deleterious variants, and for common, multigenic diseases using as few as 150 cases.

Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention.

OBJECTIVE: We hypothesized that genetic variation affects responsiveness to 17-alpha hydroxyprogesterone caproate (17P) for recurrent preterm birth prevention. STUDY DESIGN: Women of European ancestry with ≥1 spontaneous singleton preterm birth at <34 weeks' gestation who received 17P were recruited prospectively and classified as a 17P responder or nonresponder by the difference in delivery gestational age between 17P-treated and -untreated pregnancies. Samples underwent whole exome sequencing. Coding variants were compared between responders and nonresponders with the use of the Variant Annotation, Analysis, and Search Tool (VAAST), which is a probabilistic search tool for the identification of disease-causing variants, and were compared with a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway candidate gene list. Genes with the highest VAAST scores were then classified by the online Protein ANalysis THrough Evolutionary Relationships (PANTHER) system into known gene ontology molecular functions and biologic processes. Gene distributions within these classifications were compared with an online reference population to identify over- and under- represented gene sets. RESULTS: Fifty women (9 nonresponders) were included. Responders delivered 9.2 weeks longer with 17P vs 1.3 weeks' gestation for nonresponders (P < .001). A genome-wide search for genetic differences implicated the NOS1 gene to be the most likely associated gene from among genes on the KEGG candidate gene list (P < .00095). PANTHER analysis revealed several over-represented gene ontology categories that included cell adhesion, cell communication, signal transduction, nitric oxide signal transduction, and receptor activity (all with significant Bonferroni-corrected probability values). CONCLUSION: We identified sets of over-represented genes in key processes among responders to 17P, which is the first step in the application of pharmacogenomics to preterm birth prevention.

Self-Adjuvanting Calcium-Phosphate-Coated Microcrystal-Based Vaccines Induce Pyroptosis in Human and Livestock Immune Cells.

Successful vaccines require adjuvants able to activate the innate immune system, eliciting antigen-specific immune responses and B-cell-mediated antibody production. However, unwanted secondary effects and the lack of effectiveness of traditional adjuvants has prompted investigation into novel adjuvants in recent years. Protein-coated microcrystals modified with calcium phosphate (CaP-PCMCs) in which vaccine antigens are co-immobilised within amino acid crystals represent one of these promising self-adjuvanting vaccine delivery systems. CaP-PCMCs has been shown to enhance antigen-specific IgG responses in mouse models; however, the exact mechanism of action of these microcrystals is currently unclear. Here, we set out to investigate this mechanism by studying the interaction between CaP-PCMCs and mammalian immune cells in an in vitro system. Incubation of cells with CaP-PCMCs induced rapid pyroptosis of peripheral blood mononuclear cells and monocyte-derived dendritic cells from cattle, sheep and humans, which was accompanied by the release of interleukin-1ß and the activation of Caspase-1. We show that this pyroptotic event was cell-CaP-PCMCs contact dependent, and neither soluble calcium nor microcrystals without CaP (soluble PCMCs) induced pyroptosis. Our results corroborate CaP-PCMCs as a promising delivery system for vaccine antigens, showing great potential for subunit vaccines where the enhancement or find tuning of adaptive immunity is required.

DIS3 Variants are Associated With Primary Ovarian Insufficiency: Importance of Transcription/Translation in Oogenesis.

CONTEXT: A genetic etiology accounts for the majority of unexplained primary ovarian insufficiency (POI). OBJECTIVE: We hypothesized a genetic cause of POI for a sister pair with primary amenorrhea. DESIGN: The study was an observational study. Subjects were recruited at an academic institution. SUBJECTS: Subjects were sisters with primary amenorrhea caused by POI and their parents. Additional subjects included women with POI analyzed previously (n = 291). Controls were recruited for health in old age or were from the 1000 Genomes Project (total n = 233). INTERVENTION: We performed whole exome sequencing, and data were analyzed using the Pedigree Variant Annotation, Analysis and Search Tool, which identifies genes harboring pathogenic variants in families. We performed functional studies in a Drosophila melanogaster model. MAIN OUTCOME: Genes with rare pathogenic variants were identified. RESULTS: The sisters carried compound heterozygous variants in DIS3. The sisters did not carry additional rare variants that were absent in publicly available datasets. DIS3 knockdown in the ovary of D. melanogaster resulted in lack of oocyte production and severe infertility. CONCLUSIONS: Compound heterozygous variants in highly conserved amino acids in DIS3 and failure of oocyte production in a functional model suggest that mutations in DIS3 cause POI. DIS3 is a 3' to 5' exoribonuclease that is the catalytic subunit of the exosome involved in RNA degradation and metabolism in the nucleus. The findings provide further evidence that mutations in genes important for transcription and translation are associated with POI.

Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning.

BACKGROUND: Rapidly and efficiently identifying critically ill infants for whole genome sequencing (WGS) is a costly and challenging task currently performed by scarce, highly trained experts and is a major bottleneck for application of WGS in the NICU. There is a dire need for automated means to prioritize patients for WGS. METHODS: Institutional databases of electronic health records (EHRs) are logical starting points for identifying patients with undiagnosed Mendelian diseases. We have developed automated means to prioritize patients for rapid and whole genome sequencing (rWGS and WGS) directly from clinical notes. Our approach combines a clinical natural language processing (CNLP) workflow with a machine learning-based prioritization tool named Mendelian Phenotype Search Engine (MPSE). RESULTS: MPSE accurately and robustly identified NICU patients selected for WGS by clinical experts from Rady Children's Hospital in San Diego (AUC 0.86) and the University of Utah (AUC 0.85). In addition to effectively identifying patients for WGS, MPSE scores also strongly prioritize diagnostic cases over non-diagnostic cases, with projected diagnostic yields exceeding 50% throughout the first and second quartiles of score-ranked patients. CONCLUSIONS: Our results indicate that an automated pipeline for selecting acutely ill infants in neonatal intensive care units (NICU) for WGS can meet or exceed diagnostic yields obtained through current selection procedures, which require time-consuming manual review of clinical notes and histories by specialized personnel.

SOBA: sequence ontology bioinformatics analysis.

The advent of cheaper, faster sequencing technologies has pushed the task of sequence annotation from the exclusive domain of large-scale multi-national sequencing projects to that of research laboratories and small consortia. The bioinformatics burden placed on these laboratories, some with very little programming experience can be daunting. Fortunately, there exist software libraries and pipelines designed with these groups in mind, to ease the transition from an assembled genome to an annotated and accessible genome resource. We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.