Journal update 2/3: Alcohol consumption may influence the development and progression of epithelial ovarian cancer.

This study suggests that certain epigenetic factors and consumption of alcohol which have been previously found to suppress DNA methylation may influence the development and progression of epithelial ovarian cancer. They however note that there is no clear understanding whether these factors interact to affect the EOC risk. They performed a causal inference test (CIT) and the VanderWeele and Vansteelandt multiple mediator model to examine CpG sites that mediate the association between alcohol consumption and EOC risk. They found that decreased methylation at both CpGs was more common in cases who drank alcohol at the time of enrollment vs. those who did not.

Link: here

Joanne

Journal update 1/3: An epigenome study on trying to identify potential depression biomarkers

Depression is a common psychiatric disorder that has been linked to both genetic and environmental factors. It is important to identify potentially positive biomarkers for depression that can facilitate detection at an early stage. Previous studies have shown that the detailed etiology of depression remains unclear and there seems to be no validated biomarkers despite the numerous genetic and epigenetic studies that have been  performed. In this specific study scientists set out to investigate whether different levels of DNA methylation were associated with depressive tendencies. They performed an epigenome-wide association study (EWAS) of DNA methylation on subjects with or without depressive symptoms. They found that G-protein coupled receptor protein signaling pathways are involved in the pathogenesis of depression. This study however needs further research and validation by using a bigger sample size than the one used in this study.

Link: here

Joanne

Non-Potluck Post: Systemic sclerosis - A comparison of African-Americans and White populations

This paper represents the first gene-level analysis of GWAS data for systemic sclerosis. The goal of the paper was to analyze genetic susceptibility loci in systemic sclerosis at the gene level in order to determine if associations were shared in African American and White populations. In both racial groups, analysis integrated association statistics in a gene possibly containing multiple SNPs with "weak effect on disease risk." 4 genes were found to significantly associate with systemic sclerosis in Whites, but only one of these candidate genes was found to be significantly associated in African-Americans. The authors acknowledge that the sample size disparity in their study between Whites and African Americans was a problem, which calls out the need for this study to be replicated in order to validate the results.

Article here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189498#

Third post from PLoS ONE

Kim Foecke

Non-Potluck Post: Horse herpes

Equid herpesvirus 8 (EHV-8) is a viral agent present in multiple horse species which represents an understudied threat to livestock health. This study presents the first complete genome sequence of this virus. Analysis of the sequence indicate that the virus has undergone relatively little genetic diversification through time and across populations. The study also implicates the virus in fetal death in two studied animals, which they suggest warrants further study of the virus. Results could aid in developing treatments or preventative measures for the virus, with potential large implications for livestock health.

Article here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0192301#

Second post from PLoS ONE.

Kim Foecke

Non-Potluck Post: Plant Conservation Genetics

Bretschneidera sinensis is an endangered, protected wild plant in China. It is described as a "relic of the ancient Tertiary tropical flora" endemic to Asia. Before this study, little was known about its genetics and phylogeography. The goal of this paper was to figure out the current phylogeographic patterns and infer the past population dynamics of the plant, and to make recommendations for its conservation in certain regions of China. Results indicated 5 discrete and isolated historic populations and informed the selection of primary protection units. The study is a good example of the application of genetics to conservation of extant but endangered species.

Article here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189034#

First post from PLoS ONE.

Kim Foecke

Non-potluck post: Diversity and genomics research.

It is noted by Hindorff et al. (2018) that the majority of populations studied in Genome-Wide Association Studies (GWAS) are of European ancestry, meaning that there is an underrepresentation of populations with non-European ancestry. This lack of diversity has had particular implications for the clinical applications of genomic studies, as it can lead to the incorrect classification of particular genomic variations as pathogeneic, as opposed to being widespread in certain populations, when a sample from only one population or particular ancestry is considered (Hindorff et al. 2018). 

There have been some efforts to try to increase the diversity of the individuals sampled in genomic research, however, individual participation is also influenced by many factors such as socioeconomic background, potential negative associations with health care institutions, or linguistical barriers (Hindorff et al. 2018). Therefore, Hindorff et al. (2018) note that when designing studies to try to increase the diversity of genetic samples that these factors should be kept in mind. Hindorff et al. (2018) also suggest that increasing the diversity of populations sampled may have beneficial clinical implications due to the investigation and identification of novel variation, as well as causal variants for particular pathological conditions.  

Click here for the article.

References

Hindorff, L.A., Bonham V.L., Brody, L.C., Ginoza M.E.C., Hutter, C.M., Manolio T.A., and Green, E.D., 2018. Prioritizing diversity in human genomics research. Nature Reviews Genetics. 19: 175-185.

Second post from Nature Reviews Genetics.

Victoria Lockwood

Non-potluck post: Are Lethal Alleles Too Abundant in Humans?

It is generally known that lethal alleles are almost impossible to be eliminated from natural populations and many factors may contribute in their persistence in a population.

This article published in Trends in Genetics journal discusses variation in frequency of lethal alleles in humans and some contrasting findings are being reported. On one side, results suggest that lethal alleles can be retained and become abundant in a population. In contrast to this finding, other findings by Amorim and his colleagues propose that lethal alleles are generally rare as predicted by mutation-selection balance.

Here is the link to the full article: https://www.sciencedirect.com/science/article/pii/S0168952517302330

-Axelle

3rd non- potluck post

Publication from Trends in Genetics journal