Alan Medlar

Mutations in the autoregulatory domain of β-tubulin 4a cause hereditary dystonia

Dystonia type 4 (DYT4) was first described in a large family from Heacham in Norfolk with an autosomal dominantly inherited whispering dysphonia, generalized dystonia, and a characteristic hobby horse ataxic gait. We carried out a genetic linkage analysis in the extended DYT4 family that spanned 7 generations from England and Australia, revealing a single LOD score peak of 6.33 on chromosome 19p13.12‐13. Exome sequencing in 2 cousins identified a single cosegregating mutation (p.R2G) in the β‐tubulin 4a (TUBB4a) gene that was absent in a large number of controls. The mutation is highly conserved in the β‐tubulin autoregulatory MREI (methionine–arginine–glutamic acid–isoleucine) domain, highly expressed in the central nervous system, and extensive in vitro work has previously demonstrated that substitutions at residue 2, specifically R2G, disrupt the autoregulatory capability of the wild‐type β‐tubulin peptide, affirming the role of the cytoskeleton in dystonia pathogenesis. Ann Neurol 2013;73:546–553

Phospholipase A2 Receptor (PLA2R1) Sequence Variants in Idiopathic Membranous Nephropathy

The M-type receptor for phospholipase A2 (PLA2R1) is the major target antigen in idiopathic membranous nephropathy (iMN). Our recent genome-wide association study showed that genetic variants in an HLA-DQA1 and phospholipase A2 receptor (PLA2R1) allele associate most significantly with biopsy-proven iMN, suggesting that rare genetic variants within the coding region of the PLA2R1 gene may contribute to antibody formation. Here, we sequenced PLA2R1 in a cohort of 95 white patients with biopsy-proven iMN and assessed all 30 exons of PLA2R1, including canonical (GT-AG) splice sites, by Sanger sequencing. Sixty patients had anti-PLA2R1 in serum or detectable PLA2R1 antigen in kidney tissue. We identified 18 sequence variants, comprising 2 not previously described, 7 reported as rare variants (<1%) in the Single Nucleotide Polymorphism Database or the 1000 Genomes project, and 9 known to be common polymorphisms. Although we confirmed significant associations among 6 of the identified common variants and iMN, only 9 patients had the private or rare variants, and only 4 of these patients were among the 60 who were PLA2R positive. In conclusion, rare variants in the coding sequence of PLA2R1, including splice sites, are unlikely to explain the pathogenesis of iMN.

Nephrocalcinosis (enamel renal syndrome) caused by autosomal recessive FAM20A mutations.

Background/Aims: Calcium homeostasis requires regulated cellular and interstitial systems interacting to modulate the activity and movement of this ion. Disruption of these systems in the kidney results in nephrocalcinosis and nephrolithiasis, important medical problems whose pathogenesis is incompletely understood. Methods: We investigated 25 patients from 16 families with unexplained nephrocalcinosis and characteristic dental defects (amelogenesis imperfecta, gingival hyperplasia, impaired tooth eruption). To identify the causative gene, we performed genome-wide linkage analysis, exome capture, next-generation sequencing, and Sanger sequencing. Results: All patients had bi-allelic FAM20A mutations segregating with the disease; 20 different mutations were identified. Conclusions: This au-tosomal recessive disorder, also known as enamel renal syndrome, of FAM20A causes nephrocalcinosis and amelogenesis imperfecta. We speculate that all individuals with biallelic FAM20A mutations will eventually show nephrocalcinosis.

Autoinflammatory periodic fever, immunodeficiency, and thrombocytopenia (PFIT) caused by mutation in actin-regulatory gene WDR1.

The importance of actin dynamics in the activation of the inflammasome is becoming increasingly apparent. IL-1&bgr;, which is activated by the inflammasome, is known to be central to the pathogenesis of many monogenic autoinflammatory diseases. However, evidence from an autoinflammatory murine model indicates that IL-18, the other cytokine triggered by inflammasome activity, is important in its own right. In this model, autoinflammation was caused by mutation in the actin regulatory gene WDR1. We report a homozygous missense mutation in WDR1 in two siblings causing periodic fevers with immunodeficiency and thrombocytopenia. We found impaired actin dynamics in patient immune cells. Patients had high serum levels of IL-18, without a corresponding increase in IL-18–binding protein or IL-1&bgr;, and their cells also secreted more IL-18 but not IL-1&bgr; in culture. We found increased caspase-1 cleavage within patient monocytes indicative of increased inflammasome activity. We transfected HEK293T cells with pyrin and wild-type and mutated WDR1. Mutant protein formed aggregates that appeared to accumulate pyrin; this could potentially precipitate inflammasome assembly. We have extended the findings from the mouse model to highlight the importance of WDR1 and actin regulation in the activation of the inflammasome, and in human autoinflammation.

Beyond Relevance: Adapting Exploration/Exploitation in Information Retrieval

We present a novel adaptation technique for search engines to better support information-seeking activities that include both lookup and exploratory tasks. Building on previous findings, we describe (1) a classifier that recognizes task type (lookup vs. exploratory) as a user is searching and (2) a reinforcement learning based search engine that adapts accordingly the balance of exploration/exploitation in ranking the documents. This allows supporting both task types surreptitiously without changing the familiar list-based interface. Search results include more diverse results when users are exploring and more precise results for lookup tasks. Users found more useful results in exploratory tasks when compared to a base-line system, which is specifically tuned for lookup tasks.

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization

Wasabi is an open source, web-based environment for evolutionary sequence analysis. Wasabi visualizes sequence data together with a phylogenetic tree within a modern, user-friendly interface: The interface hides extraneous options, supports context sensitive menus, drag-and-drop editing, and displays additional information, such as ancestral sequences, associated with specific tree nodes. The Wasabi environment supports reproducibility by automatically storing intermediate analysis steps and includes built-in functions to share data between users and publish analysis results. For computational analysis, Wasabi supports PRANK and PAGAN for phylogeny-aware alignment and alignment extension, and it can be easily extended with other tools. Along with drag-and-drop import of local files, Wasabi can access remote data through URL and import sequence data, GeneTrees and EPO alignments directly from Ensembl. To demonstrate a typical workflow using Wasabi, we reproduce key findings from recent comparative genomics studies, including a reanalysis of the EGLN1 gene from the tiger genome study: These case studies can be browsed within Wasabi at http://wasabiapp.org:8000?id=usecases. Wasabi runs inside a web browser and does not require any installation. One can start using it at http://wasabiapp.org. All source code is licensed under the AGPLv3.

Balancing Exploration and Exploitation: Empirical Parameterization of Exploratory Search Systems

Exploratory searches are where a user has insufficient knowledge to define exact search criteria or does not otherwise know what they are looking for. Reinforcement learning techniques have demonstrated great potential for supporting exploratory search in information retrieval systems as they allow the system to trade-off exploration (presenting the user with alternatives topics) and exploitation (moving toward more specific topics). Users of such systems, however, often feel that the system is not responsive to user needs. This problem is not an inherent feature of such systems, but is caused by the exploration rate parameter being inappropriately tuned for a given system, dataset or user. We present a user study to analyze how different exploration rates affect search performance, user satisfaction, and the number of documents selected. We show that the tradeoff between exploration and exploitation can be modelled as a direct relationship between the exploration rate parameter from the reinforcement learning algorithm and the number of relevant documents returned to the user over the course of a search session. We define the optimal exploration/exploitation trade-off as where this relationship is maximised and show this point to be broadly concordant with user satisfaction and performance.

SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU

MOTIVATION Linkage analysis remains an important tool in elucidating the genetic component of disease and has become even more important with the advent of whole exome sequencing, enabling the user to focus on only those genomic regions co-segregating with Mendelian traits. Unfortunately, methods to perform multipoint linkage analysis scale poorly with either the number of markers or with the size of the pedigree. Large pedigrees with many markers can only be evaluated with Markov chain Monte Carlo (MCMC) methods that are slow to converge and, as no attempts have been made to exploit parallelism, massively underuse available processing power. Here, we describe SWIFTLINK, a novel application that performs MCMC linkage analysis by spreading the computational burden between multiple processor cores and a graphics processing unit (GPU) simultaneously. SWIFTLINK was designed around the concept of explicitly matching the characteristics of an algorithm with the underlying computer architecture to maximize performance. RESULTS We implement our approach using existing Gibbs samplers redesigned for parallel hardware. We applied SWIFTLINK to a real-world dataset, performing parametric multipoint linkage analysis on a highly consanguineous pedigree with EAST syndrome, containing 28 members, where a subset of individuals were genotyped with single nucleotide polymorphisms (SNPs). In our experiments with a four core CPU and GPU, SWIFTLINK achieves a 8.5× speed-up over the single-threaded version and a 109× speed-up over the popular linkage analysis program SIMWALK. AVAILABILITY SWIFTLINK is available at https://github.com/ajm/swiftlink. All source code is licensed under GPLv3.

Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus).

While it is known that intestinal parasite communities vary in their composition over time, there is a lack of studies addressing how variation in component communities (between-hosts) manifests in infracommunities (within-host) during the host lifespan. In this study, we investigate the changes in the intestinal parasite infracommunities in wild-living rufous mouse lemurs (Microcebus rufus) from Ranomafana National Park in southeastern Madagascar from 2010 to 2012. We used high-throughput barcoding of the 18S rRNA gene to interrogate parasite community structure. Our results show that in these nematode communities, there were two frequently occurring putative species and four rarer putative species. All putative species were randomly distributed over host individuals and they did not occur in clear temporal patterns. For the individuals caught in at least two different years, there was high turnover of putative species and high variation in fecal egg counts. Our study shows that while there was remarkable variation in infracommunities over time, the component community was relatively stable. Nevertheless, the patterns of prevalence varied substantially between years in each component community.

Séance: reference-based phylogenetic analysis for 18S rRNA studies

BackgroundMarker gene studies often use short amplicons spanning one or more hypervariable regions from an rRNA gene to interrogate the community structure of uncultured environmental samples. Target regions are chosen for their discriminatory power, but the limited phylogenetic signal of short high-throughput sequencing reads precludes accurate phylogenetic analysis. This is particularly unfortunate in the study of microscopic eukaryotes where horizontal gene flow is limited and the rRNA gene is expected to accurately reflect the species phylogeny. A promising alternative to full phylogenetic analysis is phylogenetic placement, where a reference phylogeny is inferred using the complete marker gene and iteratively extended with the short sequences from a metagenetic sample under study.ResultsBased on the phylogenetic placement approach we built Séance, a community analysis pipeline focused on the analysis of 18S marker gene data. Séance combines the alignment extension and phylogenetic placement capabilities of the Pagan multiple sequence alignment program with a suite of tools to preprocess, cluster and visualise datasets composed of many samples. We showcase Séance by analysing 454 data from a longitudinal study of intestinal parasite communities in wild rufous mouse lemurs (Microcebus rufus) as well as in simulation. We demonstrate both improved OTU picking at higher levels of sequence similarity for 454 data and show the accuracy of phylogenetic placement to be comparable to maximum likelihood methods for lower numbers of taxa.ConclusionsSéance is an open source community analysis pipeline that provides reference-based phylogenetic analysis for rRNA marker gene studies. Whilst in this article we focus on studying nematodes using the 18S marker gene, the concepts are generic and reference data for alternative marker genes can be easily created. Séance can be downloaded from http://wasabiapp.org/software/seance/.