A Protein Domain and Family Based Approach to Rare Variant Association Analysis

BackgroundIt has become common practice to analyse large scale sequencing data with statistical approaches based around the aggregation of rare variants within the same gene. We applied a novel approach to rare variant analysis by collapsing variants together using protein domain and family coordinates, regarded to be a more discrete definition of a biologically functional unit.MethodsUsing Pfam definitions, we collapsed rare variants (Minor Allele Frequency ≤ 1%) together in three different ways 1) variants within single genomic regions which map to individual protein domains 2) variants within two individual protein domain regions which are predicted to be responsible for a protein-protein interaction 3) all variants within combined regions from multiple genes responsible for coding the same protein domain (i.e. protein families). A conventional collapsing analysis using gene coordinates was also undertaken for comparison. We used UK10K sequence data and investigated associations between regions of variants and lipid traits using the sequence kernel association test (SKAT).ResultsWe observed no strong evidence of association between regions of variants based on Pfam domain definitions and lipid traits. Quantile-Quantile plots illustrated that the overall distributions of p-values from the protein domain analyses were comparable to that of a conventional gene-based approach. Deviations from this distribution suggested that collapsing by either protein domain or gene definitions may be favourable depending on the trait analysed.ConclusionWe have collapsed rare variants together using protein domain and family coordinates to present an alternative approach over collapsing across conventionally used gene-based regions. Although no strong evidence of association was detected in these analyses, future studies may still find value in adopting these approaches to detect previously unidentified association signals.     

Extraordinary Trypanosoma cruzi diversity within single mammalian reservoir hosts implies a mechanism of diversifying selection

Trypanosoma cruzi is an evolutionarily ancient parasitic protozoan endemic to the Americas. Multiple genetic and phenotypic markers indicate that this parasite is highly diverse, with several divergent and discrete major genotypes reported. Infection multiclonality has been observed among numerous metazoan and unicellular endoparasitic species. However, few studies report the complexity of mixed infections within an individual host in any detail or consider their ecological and biological implications. Here we report extraordinary genetic diversity within single reservoir hosts of T. cruzi I using nine polymorphic microsatellite markers across 211 clones from eight mammals from three different sylvatic foci in South America. Forty-nine distinct multilocus genotypes were defined, with as many as 10 isolated from the same host. We discuss our data in the light of previous population genetic studies of this and related parasitic protozoa and contrast high levels of diversity within each host with the precarious nature of T. cruzi contaminative vectorial transmission. Finally, we propose that non-neutral processes could easily account for the diversity we observe and suggest a functional link with survival in the host.     

Diagnosis of Coronary Heart Diseases Using Gene Expression Profiling; Stable Coronary Artery Disease,Cardiac Ischemia with and without Myocardial Necrosis

Cardiovascular disease (including coronary artery disease and myocardial infarction) is one of the leading causes of death in Europe, and is influenced by both environmental and genetic factors. With the recent advances in genomic tools and technologies there is potential to predict and diagnose heart disease using molecular data from analysis of blood cells. We analyzed gene expression data from blood samples taken from normal people (n = 21), non-significant coronary artery disease (n = 93), patients with unstable angina (n = 16), stable coronary artery disease (n = 14) and myocardial infarction (MI; n = 207). We used a feature selection approach to identify a set of gene expression variables which successfully differentiate different cardiovascular diseases. The initial features were discovered by fitting a linear model for each probe set across all arrays of normal individuals and patients with myocardial infarction. Three different feature optimisation algorithms were devised which identified two discriminating sets of genes, one using MI and normal controls (total genes = 6) and another one using MI and unstable angina patients (total genes = 7). In all our classification approaches we used a non-parametric k-nearest neighbour (KNN) classification method (k = 3). The results proved the diagnostic robustness of the final feature sets in discriminating patients with myocardial infarction from healthy controls. Interestingly it also showed efficacy in discriminating myocardial infarction patients from patients with clinical symptoms of cardiac ischemia but no myocardial necrosis or stable coronary artery disease, despite the influence of batch effects and different microarray gene chips and platforms.     

Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'

Background  

The frequency of a haplotype comprising one allele at each of two loci can be expressed as a cubic equation (the 'Hill equation'), the solution of which gives that frequency. Most haplotype and linkage disequilibrium analysis programs use iteration-based algorithms which substitute an estimate of haplotype frequency into the equation, producing a new estimate which is repeatedly fed back into the equation until the values converge to a maximum likelihood estimate (expectation-maximisation).     

Glycoprotein 63 (gp63) genes show gene conversion and reveal the evolution of Old World Leishmania

Species of the subgenus Leishmania (Leishmania) cause the debilitating disease leishmaniasis on four continents. Species grouped within the Leishmania donovani complex cause visceral leishmaniasis, a life-threatening disease, often associated with poverty, and affecting some 0.5 million people each year. The Leishmania glycoprotein GP63, or major surface protease, is a metalloprotease involved in parasite survival, infectivity and virulence. Here, we show that evolution of the gp63 multigene family is influenced by mosaic or fragmental gene conversion. This is a major evolutionary force for both homogenisation and for generating diversity, even in the absence of sexual reproduction. We propose here that the high GC content at the third codon position in the gp63 family of Old World Leishmania may be higher in multicopy regions, under the biased gene conversion model, because increased copy numbers may lead to increased rates of recombination. We confirm that one class of gp63 genes with an extended 3'end signal, gp63(EXT), reveals genetic groups within the complex and gives insights into evolution and host associations. Gp63(EXT) genes can also provide the basis for rapid and reliable genotyping of strains in the L. donovani complex. Our results confirmed that a more stringent definition of Leishmania infantum is required and that the species Leishmania archibaldi should be suppressed.     

Electromyographic studies of the syrinx in parrots (Aves,Psittacidae)

Summary The vocal organ (syrinx) of a bird may contain either extrinsic muscles alone or both extrinsic and intrinsic muscles. The former arise and insert on the trachea and affect the syrinx only indirectly; the latter also arise on the trachea but insert directly on syringeal elements. It is widely supposed that syringeal muscles can affect modulations of the sounds the birds make, and further, that the intrinsic muscles are closely associated with such a function. However, the exact roles of the two groups of muscles have not been directly observed.The psittacid syrinx, which has one (for practical purposes) pair of extrinsic and two pairs of intrinsic muscles, is about as simple as one can find in birds capable of uttering a wide variety of sounds. We have taken electromyograms from the syringeal muscles of five species of parrots. In all of these, the extrinsic sternotrachealis showed the simple activation pattern activity previously described from several non-passerine species that possess only extrinsic muscles. The intrinsic muscles, however, showed a variety of activity patterns. The relatively simple call of Cyanoliseus patagonus again showed the simple activation pattern. In Myiopsitta monachus, the muscles showed a string of pulses that matched to pulses of sound in a strongly amplitude modulated call. Agapornis roseicollis used at least two distinct patterns, each associated with a different call.The results are consistent with an hypothesis that, because of their indirect attachment of the syrinx, extrinsic muscles are poorly suited to the production of precise, rapid changes in syringeal action, but rather will function in an on-off switch capacity. Intrinsic muscles are so situated that, given proper neurological stimulus, they can effect a variety of alterations in the sound pattern. Hence, intrinsic muscles are necessary for the evolution of large vocabularies and variable vocal behavior.     

The physiological basis of slow locomotion in chamaeleons

The African chamaeleon, Chamaeleo senegalensis, will not move faster than approximately 0.1 m/second at 23 degrees C, whereas the lizard Agama agama, like most lizards its size, runs at speeds more than 10X as fast. To account for this difference, we measured various physiological parameters of the iliofibularis muscle of both lizards. The maximum speed of tetanic contraction of unloaded Chamaeleo muscle was half as fast as that of Agama muscle (2.5 vs. 5.8 resting lengths per second). Heavily loaded Chamaeleo iliofibularis contracted at nearly 1/4 the speed of Agama muscle. Time to peak isometric twitch tension and time to half relaxation were twice as long in Chamaeleo as in Agama (122 vs. 58 msec, and 168 vs. 81 msec). Much more of the Chamaeleo muscle consisted of tonic muscle fibers, and the Chamaeleo muscle, compared to Agama muscle, showed physiological evidence of having a significant amount of tonic fibers (potassium contracture and high tetanus to twitch ratios). Finally, the myofibrillar ATPase activity of the Chamaeleo muscle was 1/3 that of Agama muscle. Thus, these results show that the slow locomotion of old world chamaeleons can, in part, be explained by the physiology, biochemistry, and fiber-type distribution of their muscles.