Identification of Medically Actionable Secondary Findings in the 1000 Genomes

The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.     

Skeletal muscle creatine kinase MB alterations in women marathon runners

Total creatine kinase (CK) and CK MB activities were determined in gastrocnemius muscle and serum obtained from 14 female marathon runners. The level of CK MB in muscle increased significantly (p less than 0.05) after chronic exercise training from 5.3% to 10.5% of the total CK activity, but not after acute exercise (post-marathon 8.9%). No significant differences in total CK activities were detected. However, the total CK activity in the muscles were significantly (p less than 0.05) less than those previously reported from the muscle of men runners (1800 U/g, 3000 U/g respectively). No significant correlation existed between fiber type and muscle CK MB activity. Additionally, trace amounts of mitochondrial CK and CK BB were present in muscle homogenates. A significant correlation was observed in the increase in mean serum total CK (597 UL-1) and CK MB (23 UL-1) activities 24 h after the race (r = 0.97, p less than 0.05). These results suggest that gastrocnemius muscle in women adapts to training with increased CK MB activities and imply that skeletal muscle is the major source of elevated serum CK MB activities in women marathon runners.     

Potential of Agrotis ipsilon nucleopolyhedrovirus for suppression of the black cutworm (Lepidoptera: Noctuidae) and effect of an optical brightener on virus efficacy.

Studies were performed in the laboratory, greenhouse and field to assess the potential of Agrotis ipsilon multicapsid nucleopolyhedrovirus (AgipMNPV) and a viral enhancing agent, M2R, for suppression of Agrotis ipsilon (Hufnagel). In laboratory droplet feeding bioassays, AgipMNPV was shown to be highly active against third-instar A. ipsilon. The optical brightener M2R significantly reduced LD50 estimates by approximately 160-fold, but had no direct effect on survival time estimates. In greenhouse trials, spray and bait formulations of AgipMNPV significantly reduced feeding damage to corn seedlings caused by third-instar A. ipsilon. In two sets of replicated field trials, bait formulations of AgipMNPV significantly reduced feeding damage to corn seedlings by third-instar A. ipsilon. However, there were no beneficial effects attributable to the inclusion of M2R in AgipMNPV formulations under greenhouse or field conditions. It seems likely that in an appropriately designed pest management program AgipMNPV could be used to suppress field populations of early and mid-instar A. ipsilon.     

Acanthocephaloides cyrusi n. sp. (Acanthocephala: Arhythmacanthidae) from southeast African teleost fishes

A new species,Acanthocephaloides cyrusi, is described from the fishesSolea bleekeri andPomadasys commersoni from Lake St. Lucia, Natal, South Africa. It is distinguished from the other species in the genus by the more marked sexual dimorphism in length, the arrangement of hooks, the proboscis with the longest hooks at the anterior-most extremity and the greater size of the proboscis hooks and body spines. An acanthella, which may represent this species, was found in the tanaidApseudes digitalis.     

Drug2ways: Reasoning over causal paths in biological networks for drug discovery

Elucidating the causal mechanisms responsible for disease can reveal potential therapeutic targets for pharmacological intervention and, accordingly, guide drug repositioning and discovery. In essence, the topology of a network can reveal the impact a drug candidate may have on a given biological state, leading the way for enhanced disease characterization and the design of advanced therapies. Network-based approaches, in particular, are highly suited for these purposes as they hold the capacity to identify the molecular mechanisms underlying disease. Here, we present drug2ways, a novel methodology that leverages multimodal causal networks for predicting drug candidates. Drug2ways implements an efficient algorithm which reasons over causal paths in large-scale biological networks to propose drug candidates for a given disease. We validate our approach using clinical trial information and demonstrate how drug2ways can be used for multiple applications to identify: i) single-target drug candidates, ii) candidates with polypharmacological properties that can optimize multiple targets, and iii) candidates for combination therapy. Finally, we make drug2ways available to the scientific community as a Python package that enables conducting these applications on multiple standard network formats.