Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms

Genome-wide association studies (GWAS) are widely used to search for genetic loci that underlie human disease. Another goal is to predict disease risk for different individuals given their genetic sequence. Such predictions could either be used as a “black box” in order to promote changes in life-style and screening for early diagnosis, or as a model that can be studied to better understand the mechanism of the disease. Current methods for risk prediction typically rank single nucleotide polymorphisms (SNPs) by the p-value of their association with the disease, and use the top-associated SNPs as input to a classification algorithm. However, the predictive power of such methods is relatively poor. To improve the predictive power, we devised BootRank, which uses bootstrapping in order to obtain a robust prioritization of SNPs for use in predictive models. We show that BootRank improves the ability to predict disease risk of unseen individuals in the Wellcome Trust Case Control Consortium (WTCCC) data and results in a more robust set of SNPs and a larger number of enriched pathways being associated with the different diseases. Finally, we show that combining BootRank with seven different classification algorithms improves performance compared to previous studies that used the WTCCC data. Notably, diseases for which BootRank results in the largest improvements were recently shown to have more heritability than previously thought, likely due to contributions from variants with low minimum allele frequency (MAF), suggesting that BootRank can be beneficial in cases where SNPs affecting the disease are poorly tagged or have low MAF. Overall, our results show that improving disease risk prediction from genotypic information may be a tangible goal, with potential implications for personalized disease screening and treatment.     

Fixated on fixation: using ChIP to interrogate the dynamics of chromatin interactions

A new study exploits the time-dependence of formaldehyde cross-linking in the commonly used chromatin immunoprecipitation (ChIP) assay to infer the on and off rates for site-specific chromatin interactions.     

Metabolic engineering in strawberry fruit uncovers a dormant biosynthetic pathway

Wild strawberry (Fragaria vesca) fruit contains several important phenylpropene aroma compounds such as eugenol, but cultivated varieties are mostly devoid of them. We have redirected the carbon flux in cultivated strawberry (Fragaria×ananassa) fruit from anthocyanin pigment biosynthesis to the production of acetates of hydroxycinnamyl alcohols, which serve as the precursors of the phenylpropenes, by downregulating the strawberry chalcone synthase (CHS) via RNAi-mediated gene silencing and, alternatively, by an antisense CHS construct. Simultaneous heterologous overexpression of a eugenol (EGS) and isoeugenol synthase (IGS) gene in the same cultivated strawberry fruits boosted the formation of eugenol, isoeugenol, and the related phenylpropenes chavicol and anol to concentrations orders of magnitude greater than their odor thresholds. The results show that Fragaria×ananassa still bears a phenylpropene biosynthetic pathway but the carbon flux is primarily directed to the formation of pigments. Thus, partial restoration of wild strawberry flavor in cultivated varieties is feasible by diverting the flavonoid pathway to phenylpropene synthesis through metabolic engineering.     

Anemia, iron deficiency, and stress fractures in female combatants during 16 months

Yanovich, R, Merkel, D, Israeli, E, Evans, RK, Erlich, T, and Moran, DS. Anemia, iron deficiency, and stress fractures in female combatants during 16 months. J Strength Cond Res 25(12): 3412-3421, 2011-The purpose of this study is to evaluate the hematological profile of military recruits in different settings and training programs and to investigate the link between anemia and iron deficiency with stress fracture (SF) occurrence. We surveyed 3 groups of recruits for 16 months: 221 women (F) and 78 men (M) from 3 different platoons of a gender-integrated combat battalion and a control group (CF) of 121 female soldiers from a noncombat unit. Data were fully collected upon induction and at 4 and 16 months from 48F, 21M, and 31CF. Blood tests, anthropometry, physical aerobic fitness, and SF occurrence were evaluated. On induction day, 18.0 and 19.0% of F and CF were found to be anemic, and 61.4 and 50.9%, respectively, were found to have iron deficiency, whereas 7.7% of M were found to be anemic and 10.2% iron deficient. During the 4 months of army basic training (ABT), anemia and iron deficiency prevalence did not change significantly in any group. After 16-months, anemia prevalence decreased by 8% among F and CF and abated in M. Iron deficiency was prevalent in 50.0, 59.4, and 18.8% of F, CF, and M, respectively. Stress fractures were diagnosed in 14 F during ABT, and they had a significantly higher prevalence (p < 0.05) of anemia and iron deficiency anemia compared to F without SFs. The observed link between anemia and iron deficiency on recruitment day and SFs suggests the importance of screening female combat recruits for these deficiencies. To minimize the health impact of army service on female soldiers, preventative measures related to anemia and iron deficiency should be administered. Further research is needed for evaluating the influence of low iron in kosher meat as a possible explanation for the high prevalence of iron deficiency among young Israeli recruits.     

Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules

Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other biomolecule structures. Created as a means for communicating biomolecule structures to a diverse scientific audience, Proteopedia (http://www.proteopedia.org) presents structural annotation in an intuitive, interactive format and allows members of the scientific community to easily contribute their own annotations. Here, we provide a status report on Proteopedia by describing advances in the web resource since its inception three and a half years ago, focusing on features of potential direct use to the scientific community. We discuss its progress as a collaborative 3D-encyclopedia of structures as well as its use as a complement to scientific publications and PowerPoint presentations. We also describe Proteopedia's use for 3D visualization in structure-related pedagogy.     

The relative importance of respiratory water loss in scorpions is correlated with species habitat type and activity pattern

Scorpions exhibit some of the lowest recorded water loss rates compared with those of other terrestrial arthropods of similar body size. Evaporative water loss (EWL) includes cuticular transpiration and respiratory water loss (RWL) from gas exchange surfaces, that is, book lung lamellae. Estimated fractions of cuticular and respiratory losses currently available from the literature show considerable variation, at least partly as a result of differences in methodology. This study reports RWL rates and their relative importance in scorpions from two families (Buthidae and Scorpionidae), including both xeric and mesic species (or subspecies). Two of the included Buthidae were surface-dwelling species, and another inhabits empty burrows of other terrestrial arthropods. This experimental design enabled correlating RWL importance with scorpion phylogeny, habitat type, and/or homing behavior. Buthidae species exhibited significantly lower EWL rates compared with those of Scorpionidae, whereas effects of habitat type and homing behavior were not significant. Resting RWL rates were not significantly affected by scorpion phylogeny, but rates for the xeric species (totaling ~10% of EWL rates at 30°C) were significantly lower compared with those of mesic species. These lower RWL values were correlated with significantly lower H(2)O/CO(2) emission rates in xeric species. The experimental setup and ~24-h duration of each individual recording allowed estimating the effect of interspecific variation in activity on RWL proportions. The high respiratory losses in active hydrated Scorpio maurus fuscus, totaling 30% of EWL, suggest that behavioral discretion in this species is a more likely mechanism for body water conservation under stressful conditions when compared with the responses of other studied species.     

Public response to an anthrax attack: reactions to mass prophylaxis in a scenario involving inhalation anthrax from an unidentified source

An attack with Bacillus anthracis ("anthrax") is a known threat to the United States. When weaponized, it can cause inhalation anthrax, the deadliest form of the disease. Due to the rapid course of inhalation anthrax, delays in initiation of antibiotics may decrease survival chances. Because a rapid response would require cooperation from the public, there is a need to understand the public's response to possible mass dispensing programs. To examine the public's response to a mass prophylaxis program, this study used a nationally representative poll of 1,092 adults, supplemented by a targeted focus on 3 metropolitan areas where anthrax attacks occurred in 2001: New York City (n=517), Washington, DC (n=509), and Trenton/Mercer County, NJ (n=507). The poll was built around a "worst-case scenario" in which cases of inhalation anthrax are discovered without an identified source and the entire population of a city or town is asked to receive antibiotic prophylaxis within a 48-hour period. Findings from this poll provide important signs of public willingness to comply with public health recommendations for obtaining antibiotics from a dispensing site, although they also indicate that public health officials may face several challenges to compliance, including misinformation about the contagiousness of inhalation anthrax; fears about personal safety in crowds; distrust of government agencies to provide sufficient, safe, and effective medicine; and hesitation about ingesting antibiotic pills after receiving them. In general, people living in areas where anthrax attacks occurred in 2001 had responses similar to those of the nation as a whole.     

Enhanced Localization of Genetic Samples through Linkage-Disequilibrium Correction

Characterizing the spatial patterns of genetic diversity in human populations has a wide range of applications, from detecting genetic mutations associated with disease to inferring human history. Current approaches, including the widely used principal-component analysis, are not suited for the analysis of linked markers, and local and long-range linkage disequilibrium (LD) can dramatically reduce the accuracy of spatial localization when unaccounted for. To overcome this, we have introduced an approach that performs spatial localization of individuals on the basis of their genetic data and explicitly models LD among markers by using a multivariate normal distribution. By leveraging external reference panels, we derive closed-form solutions to the optimization procedure to achieve a computationally efficient method that can handle large data sets. We validate the method on empirical data from a large sample of European individuals from the POPRES data set, as well as on a large sample of individuals of Spanish ancestry. First, we show that by modeling LD, we achieve accuracy superior to that of existing methods. Importantly, whereas other methods show decreased performance when dense marker panels are used in the inference, our approach improves in accuracy as more markers become available. Second, we show that accurate localization of genetic data can be achieved with only a part of the genome, and this could potentially enable the spatial localization of admixed samples that have a fraction of their genome originating from a given continent. Finally, we demonstrate that our approach is resistant to distortions resulting from long-range LD regions; such distortions can dramatically bias the results when unaccounted for.