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.     

Mechanisms of anti-atherosclerotic functions of soy-based diets

Soy-based diets have been reported to protect against the development of atherosclerosis. However, the underlying mechanism(s) for this protection remains unknown. Although atherosclerosis was traditionally considered a disease associated with impaired lipid metabolism, in recent years the inflammatory components of atherosclerosis have been explored. Recent studies have convincingly delineated that uncontrolled chronic inflammation is the principal contributing factor for the initiation and progression of atherosclerosis. Interaction between activated monocytes and vascular endothelial cells is an early event in atherogenesis. The adhesion of leukocytes, including monocytes, to the inflamed-vascular endothelium and their transmigration into intima initiate the inflammatory processes. Following transmigration, monocytes in the intima are transformed to macrophages, which take up oxidized-LDL (oxLDL) to generate lipid-laden macrophages, also known as foam cells. Hence, in this review article the inflammatory processes associated with atherosclerosis and possible anti-inflammatory functions of soy-based diets contributing to the prevention of atherosclerosis are presented.     

A Neural Network Model to Translate Brain Developmental Events across Mammalian Species

Translating the timing of brain developmental events across mammalian species using suitable models has provided unprecedented insights into neural development and evolution. More importantly, these models can prove to be useful abstractions and predict unknown events across species from known empirical event timing data retrieved from published literature. Such predictions can be especially useful since the distribution of the event timing data is skewed with a majority of events documented only across a few selected species. The present study investigates the choice of single hidden layer feed-forward neural networks (FFNN) for predicting the unknown events from the empirical data. A leave-one-out cross-validation approach is used to determine the optimal number of units in the hidden layer and the decay parameter for the FFNN. It is shown that unlike the present Finlay-Darlington (FD) model, FFNN does not impose any constraints on the functional form of the model and falls under the class of semiparametric regression models that can approximate any continuous function. The results from FFNN as well as FD model also indicate that a majority of events with large absolute prediction errors correspond to those of primates and late events comprising the tail of event timing data distribution with minimal representation in the empirical data. These results also indicate that accurate prediction of primate events may be challenging.     

Compromised base excision repair pathway in Mycobacterium tuberculosis imparts superior adaptability in the host

Tuberculosis caused by Mycobacterium tuberculosis (Mtb) is a significant public health concern, exacerbated by the emergence of drug-resistant TB. To combat the host’s dynamic environment, Mtb encodes multiple DNA repair enzymes that play a critical role in maintaining genomic integrity. Mtb possesses a GC-rich genome, rendering it highly susceptible to cytosine deaminations, resulting in the occurrence of uracils in the DNA. UDGs encoded by ung and udgB initiate the repair; hence we investigated the biological impact of deleting UDGs in the adaptation of pathogen. We generated gene replacement mutants of uracil DNA glycosylases, individually (RvΔung, RvΔudgB) or together (RvΔdKO). The double KO mutant, RvΔdKO exhibited remarkably higher spontaneous mutation rate, in the presence of antibiotics. Interestingly, RvΔdKO showed higher survival rates in guinea pigs and accumulated large number of SNPs as revealed by whole-genome sequence analysis. Competition assays revealed the superior fitness of RvΔdKO over Rv, both in ex vivo and in vivo conditions. We propose that compromised DNA repair results in the accumulation of mutations, and a subset of these drives adaptation in the host. Importantly, this property allowed us to utilize RvΔdKO for the facile identification of drug targets.     

Arsenate reductase activity in roots from the arsenic hyperaccumulator Pteris vittata utilizes both glutathione and dithiothreitol as reductants

Abstract

The role of glutathione and dithiothreitol as reductants supporting arsenate reductase activity in root extract from the arsenic hyperaccumulator Pteris vittata was examined. The two reductants in combination enhanced arsenate reduction in vitro more than glutathione alone. The implications of these results for in vivo arsenate reduction are discussed.     

DNMTs are required for delayed genome instability caused by radiation

The ability of ionizing radiation to initiate genomic instability has been harnessed in the clinic where the localized delivery of controlled doses of radiation is used to induce cell death in tumor cells. Though very effective as a therapy, tumor relapse can occur in vivo and its appearance has been attributed to the radio-resistance of cells with stem cell-like features. The molecular mechanisms underlying these phenomena are unclear but there is evidence suggesting an inverse correlation between radiation-induced genomic instability and global hypomethylation. To further investigate the relationship between DNA hypomethylation, radiosensitivity and genomic stability in stem-like cells we have studied mouse embryonic stem cells containing differing levels of DNA methylation due to the presence or absence of DNA methyltransferases. Unexpectedly, we found that global levels of methylation do not determine radiosensitivity. In particular, radiation-induced delayed genomic instability was observed at the Hprt gene locus only in wild-type cells. Furthermore, absence of Dnmt1 resulted in a 10-fold increase in de novo Hprt mutation rate, which was unaltered by radiation. Our data indicate that functional DNMTs are required for radiation-induced genomic instability, and that individual DNMTs play distinct roles in genome stability. We propose that DNMTS may contribute to the acquirement of radio-resistance in stem-like cells.