A general Bayesian approach to analyzing diallel crosses of inbred strains

The classic diallel takes a set of parents and produces offspring from all possible mating pairs. Phenotype values among the offspring can then be related back to their respective parentage. When the parents are diploid, sexed, and inbred, the diallel can characterize aggregate effects of genetic background on a phenotype, revealing effects of strain dosage, heterosis, parent of origin, epistasis, and sex-specific versions thereof. However, its analysis is traditionally intricate, unforgiving of unplanned missing information, and highly sensitive to imbalance, making the diallel unapproachable to many geneticists. Nonetheless, imbalanced and incomplete diallels arise frequently, albeit unintentionally, as by-products of larger-scale experiments that collect F(1) data, for example, pilot studies or multiparent breeding efforts such as the Collaborative Cross or the Arabidopsis MAGIC lines. We present a general Bayesian model for analyzing diallel data on dioecious diploid inbred strains that cleanly decomposes the observed patterns of variation into biologically intuitive components, simultaneously models and accommodates outliers, and provides shrinkage estimates of effects that automatically incorporate uncertainty due to imbalance, missing data, and small sample size. We further present a model selection procedure for weighing evidence for or against the inclusion of those components in a predictive model. We evaluate our method through simulation and apply it to incomplete diallel data on the founders and F(1)'s of the Collaborative Cross, robustly characterizing the genetic architecture of 48 phenotypes.     

Mapping in Structured Populations by Resample Model Averaging

Highly recombinant populations derived from inbred lines, such as advanced intercross lines and heterogeneous stocks, can be used to map loci far more accurately than is possible with standard intercrosses. However, the varying degrees of relatedness that exist between individuals complicate analysis, potentially leading to many false positive signals. We describe a method to deal with these problems that does not require pedigree information and accounts for model uncertainty through model averaging. In our method, we select multiple quantitative trait loci (QTL) models using forward selection applied to resampled data sets obtained by nonparametric bootstrapping and subsampling. We provide model-averaged statistics about the probability of loci or of multilocus regions being included in model selection, and this leads to more accurate identification of QTL than by single-locus mapping. The generality of our approach means it can potentially be applied to any population of unknown structure.A number of experimental strategies for genetic mapping of complex traits in model organisms involve the use of highly recombinant populations derived from inbred lines. Examples are advanced intercross lines (AILs) (proposed by Darvasi and Soller 1995), where a pair of inbred progenitors are intercrossed for three or more generations, and heterogeneous stocks (HS) (Demarest et al. 1999), where a number, usually eight, of inbred strains are intercrossed for many generations. In theory, these strategies can achieve much higher-resolution mapping than is obtainable with standard inbred strain crosses because they accumulate a greater density of recombinants.It is often assumed that these populations can be analyzed as if the individuals were equally related, as in an F₂ cross, or unrelated, as in the case of a carefully ascertained human case–control association study. The simplifying assumptions are that family relations may be ignored and that each locus can be analyzed independently. However, it can easily be shown, for example by simulation, that these assumptions are false.What makes genetic association in an AIL or HS more complicated than in an F₂ cross? Advanced intercross lines are bred in maintenance populations of small to moderate size, typically between 20 and 50 mating pairs for n − 1 generations, and then bred out in a final generation to achieve a larger mapping population. The breeding strategy employed during the maintenance phase is usually chosen to minimize loss of genetic diversity and is similar to schemes used in the preservation of rare species. Completely random mating is inappropriate because, owing to the small number of individuals, it gives rise to an unacceptable number of matings between full sibs. Mating maximally unrelated individuals after Wright (1921) is optimal in the first few generations but rapidly contracts the network of unrelateds, making consanguineous breeding in later generations inevitable. More often schemes are chosen to balance convenience with minimal long-term inbreeding. In pseudorandom mating, mates are chosen at random, although mating to close relatives is forbidden. In regular systems such as circular mating, the population is maintained in a number of separate groups and males are transferred between groups in a predetermined pattern (Kimura and Crow 1963). Other more complex schemes based on minimizing coancestry are a sophistication of Wright''s method and may guard better against inbreeding (Caballero and Toro 2000) but are not to our knowledge used in the generation of populations bred for experimental mapping. Rockman and Kruglyak (2008) recently compared breeding schemes for the generation of recombinant inbred AILs (RIAILs) in terms of their ability to guard against allele-frequency drift and promote map expansion, finding that random-pair mating is superior to circular or random mating for producing panels of inbred lines for QTL mapping.One important consequence of these breeding schemes applied over multiple generations in a finite outbred population is the emergence of long-range correlations between genetic markers, such that, for example, it is sometimes possible to predict the genotype of a marker on chromosome 1 by the genotype on chromosome 5. These are due to partial fixation of pairs of haplotype blocks within subsets of the population. The exact pairings are stochastically determined, but some breeding designs are more susceptible to this effect than others. Consequently a single causal variant segregating in the cross will be confounded not only with neighboring loci [due to short-range linkage disequilibrium (LD)] but also with distant loci.HS populations have used similar breeding schemes to AILs (Valdar et al. 2006a) but differ from AILs in that they are descended from more than two inbred strains: typically, though not necessarily, eight. This adds a further level of complexity. Because the markers used for genotyping will have fewer alleles than the number of haplotypes segregating in the cross, individual markers typically do not unambiguously identify the underlying strain haplotype. In particular, unless all variants are genotyped, QTL will be missed by single-marker association analysis (Mott et al. 2000).Large-scale studies of HS, AILs, and similarly structured populations are also particularly susceptible to environment–genotype confounds that are avoidable in F₂''s, backcrosses, and simpler designs. With limited laboratory resources, inclusion of siblings in a genetic mapping study is often unavoidable. However, doing so introduces a level of clustering that can result in, for example, some families and alleles being oversampled in summer and undersampled in winter, which in turn can produce spurious genetic or family associations. The complex correlation structures present in AILs, HS, and related populations cause simplistic association methods to misclassify false signals as true QTL.These highly recombinant structured experimental populations resemble those found in plant and animal breeding where it is common to model the multiple levels of relatedness through variance components parameterized by the kinship matrix. Specifically, to account for effects from the rest of the genome the effect of a single locus is estimated simultaneously with one or more random intercept terms whose expected correlation structure is fixed given the pedigree and models the effects of overall genetic relatedness (Kennedy et al. 1992; Jannink et al. 2001; Zhao et al. 2007). Such approaches are highly applicable to HS and AIL populations, and control the false positive rate of association by diminishing the estimated effect and significance of loci that are predictive of family structure.However, two loci that are associated with the phenotype can be correlated with each other in a way that is not well explained by overall genetic relatedness. Moreover, it is plausible that a causal locus happens to be predictive of family structure and so is hard to detect under polygenic modeling. It is therefore useful to have complementary approaches that characterize the correlation structure between loci but that do not make strong assumptions about the relationship between the underlying population structure and the trait of interest.In this article we describe single-locus and multilocus approaches for dealing with both the detection and the subsequent characterization of location uncertainty of QTL segregating in structured populations. We expect our method to be particularly helpful in cases where the founders are known but the pedigree is not and where the population structure is expected to be smooth in the sense that any major structural features, such as gross environmental effects or strong subpopulation effects arising from combining separate populations at a late stage, are known or absent. We argue that when it comes to detecting QTL, a single-locus approach is inferior to one that models multiple loci, a view that has been advocated by several groups in animal and plant genetics (Jansen 1993; Zeng 1993; Sillanpaa and Arjas 1998; Broman and Speed 2002), and is one increasingly taken in human association (Balding 2006 and refs therein; Servin and Stephens 2007; Fridley 2008 and refs therein).     

Mitochondrial mismatch analysis is insensitive to the mutational process

Mismatch distributions are histograms showing the pattern of nucleotide (or restriction) site differences between pairs of individuals in a sample. They can be used to test hypotheses about the history of population size and subdivision (if selective neutrality is assumed) or about selection (if a constant population size is assumed). Previous work has assumed that mutations never strike the same site twice, an assumption that is called the model of infinite sites. Fortunately, the results are surprisingly robust even when this assumption is violated. We show here that (1) confidence regions inferred using the infinite- sites model differ little from those inferred using a model of finite sites with uniform site-specific mutation rates, and (2) even when site- specific mutation rates follow a gamma distribution, confidence regions are little changed until the gamma shape parameter falls well below its plausible range, to roughly 0.01. In addition, we evaluate and reject the proposition that mismatch waves are produced by pooling data from several subdivisions of a structured population.      

Study of the mechanism of vanadate inhibition of the dynein cross-bridge cycle in sea urchin sperm flagella

The effect of vanadate on the ATP-induced disruption of trypsin-treated axonemes and the ATP-induced straightening of rigor wave preparations of sea urchin sperm was investigated. Addition of ATP to a suspension of trypsin-treated axonemes results in a rapid decrease in turbidity (optical density measured at 350 nm) concomitant with the disruption of the axonemes by sliding between microtubules to form tangles of connected doublet microtubules (Summers and Gibbons, 1971; Sale and Satir, 1977). For axonemes digested to approximately 93 percent of their initial turbidity, 5 {muM} vanadate completely inhibits the ATP-induced decrease in turbidity and the axonemes maintain their structural integrity. However, with axonemes digested to approximately 80 percent of their initial turbidity, vanadate fails to inhibit the ATP-induced decrease in turbidity and the ATP-induced structural disruption of axonemes, even when the vanadate concentration is raised as high as 100 μm. For such axonemes digested to 80 percent of their initial turbidity, the form of ATP-induced structural changes, in the presence of 25 μM vanadate, was observed by dark-field light microscopy and revealed that the axonemes become disrupted into curved, isolated doublet microtubules, small groups of doublet microtubules, and “banana peel” structures in which tubules have peeled back from the axoneme. Addition of 5 μM ATP to rigor wave sperm, which were prepared by abrupt removal of ATP from reactivated sperm, causes straightening of the rigor waves within 1 min, and addition of more than 10 μM ATP causes resumption of flagellar beating. Addition of 40 μM vanadate to the rigor wave sperm does not inhibit straightening of the rigor waves of 2 μM-1 mM ATP, although oscillatory beating is completely inhibited. These results suggest that vanadate inhibits the mechanochemical cycle of dyein at a step subsequent to the MgATP(2-)-induced release of the bridged dynein arms.     

Strategies for mapping and cloning quantitative trait genes in rodents

Over the past 15 years, more than 2,000 quantitative trait loci (QTLs) have been identified in crosses between inbred strains of mice and rats, but less than 1% have been characterized at a molecular level. However, new resources, such as chromosome substitution strains and the proposed Collaborative Cross, together with new analytical tools, including probabilistic ancestral haplotype reconstruction in outbred mice, Yin-Yang crosses and in silico analysis of sequence variants in many inbred strains, could make QTL cloning tractable. We review the potential of these strategies to identify genes that underlie QTLs in rodents.     

Scoring residue conservation

The importance of a residue for maintaining the structure and function of a protein can usually be inferred from how conserved it appears in a multiple sequence alignment of that protein and its homologues. A reliable metric for quantifying residue conservation is desirable. Over the last two decades many such scores have been proposed, but none has emerged as a generally accepted standard. This work surveys the range of scores that biologists, biochemists, and, more recently, bioinformatics workers have developed, and reviews the intrinsic problems associated with developing and evaluating such a score. A general formula is proposed that may be used to compare the properties of different particular conservation scores or as a measure of conservation in its own right.     

Echocardiographic AV-interval optimization in patients with reduced left ventricular function

Background

Power Doppler (PD) has improved diagnostic capabilities of vascular sonography, mainly because it is independent from the angle of insonation. We evaluated this technique in a prospective comparison with conventional imaging, consisting in Duplex and Color Doppler, for the evaluation of Renal Artery (RA) stenosis.

Methods

Sensitivity, specificity and predictive values of PD and conventional imaging were assessed in a blinded fashion on eighteen patients, 9 with angiographic evidence of unilateral RA stenosis (hypertensive patients) and 9 with angiographically normal arteries (control group). PD images were interpreted with an angiography-like criteria.

Results

In the control group both techniques allowed correct visualization of 16 out of the 18 normal arteries (93% specificity). Only in five hypertensive patients RA stenosis was correctly identified with conventional technique (56% sensitivity and 86% negative predictive value); PD was successful in all hypertensive patients (100% sensitivity and negative predictive value), since the operators could obtain in each case of RA stenosis a sharp color signal of the whole vessel with a clear "minus" at the point of narrowing of the lumen. All results were statistically significant (p < 0.01).

Conclusions

This study demonstrates that PD is superior to conventional imaging, in terms of sensitivity and specificity, for the diagnosis of RA stenosis, because it allows a clear visualization of the whole stenotic vascular lumen. Especially if it is used in concert with the other sonographic techniques, PD can enable a more accurate imaging of renovascular disease with results that seem comparable to selective angiography.