Great Genetics: PLOS ONE at ASHG

For the 2012 American Society for Human Genetics conference in San Francisco, we are highlighting a selection of recently published articles in the area.  In the last two years, PLOS ONE has published over 700 articles on human genetics; the eight summarized below are among the top 5% with regard to post-publication citations, HTML views, PDF downloads, and bookmarking.

Two of these papers address the genetic underpinnings of Alzheimer disease.  By mining genetic data, Jones et al. linked two physiological processes, cholesterol metabolism and the innate immune response, to late-onset Alzheimer disease development.  In a paper published in September of this year, Jun et al. discovered a correlation between the presence of cataracts and Alzheimer disease, and identified genetic variations in the gene encoding for the ?-catenin protein that may be the link between these two conditions.

Looking at another eye disorder, Nakano et al. investigated the genetic component of glaucoma.  Their research identified genetic variations among people of Japanese ancestry that are associated with certain types of glaucoma.

Another paper looked at the potential role of epigenetic modification in type 2 diabetes. Specifically, Bell et al. compared DNA from healthy women and women with type 2 diabetes and examined variations in DNA methylation, a chemical modification to the DNA that affects gene expression.  The analysis revealed significant methylation differences in regions of DNA previously associated with type 2 diabetes, suggesting that variations in DNA methylation may play a role in the disease.

Two studies considered variations in the number of repeats of specific DNA sequences, which can affect disease pathology and even drive evolution.  Valsesia et al. investigated DNA copy number variations and their effect on gene expression in seven different melanoma cell lines.  Their research identified candidate genes and molecular pathways involved in metastatic melanoma.  Zhang et al. compared the performance of four software programs in detecting copy number variations in DNA sequences longer than 1,000 bases.  The authors found inconsistency even among the most established programs, emphasizing the work that still needs to be done in this area.

Another paper addressed the issue of chromosome translocation, or the abnormal rearrangement of parts of chromosomes.  In a collaboration between biologists and physicists, Engreitz et al. showed that the three-dimensional organization of DNA in the cell nucleus may help explain certain chromosomal translocations linked to human disease.

Finally, using data from the Human Genome Diversity Project, Kirin et al. profiled the lengths and frequencies of DNA sequences that are identical on maternal and paternal chromosomes.  This large-scale analysis allowed the authors to make conclusions about historic and contemporary patterns of intra-communal parentage in different human populations.

If you are at the ASHG, we hope that you stop by the PLOS booth and meet some of the PLOS staff.  We will be at booth # 1606.  Also, if you have published in PLOS ONE, we have a stylish PLOS ONE author t-shirt to give you.  We look forward to seeing you there.

Acknowledgments:  Thank you to Martin Fenner for helping us with the article-level metrics analysis.  Thank you to Eric Martens and Matt Hodgkinson for designing the literature search and helping analyze the final results.  Finally, thank you to Camron Assadi for coordinating our efforts.

Image:  Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, et al. (2011) Network-Guided Analysis of Genes with Altered Somatic Copy Number and Gene Expression Reveals Pathways Commonly Perturbed in Metastatic Melanoma. PLoS ONE 6(4): e18369. doi:10.1371/journal.pone.0018369


Bell CG, Finer S, Lindgren CM, Wilson GA, Rakyan VK, et al. (2010) Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus. PLoS ONE 5(11): e14040. doi:10.1371/journal.pone.0014040

Engreitz JM, Agarwala V, Mirny LA (2012) Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease. PLoS ONE 7(9): e44196. doi:10.1371/journal.pone.0044196

Jones L, Holmans PA, Hamshere ML, Harold D, Moskvina V, et al. (2010) Genetic Evidence Implicates the Immune System and Cholesterol Metabolism in the Aetiology of Alzheimer’s Disease. PLoS ONE 5(11): e13950. doi:10.1371/journal.pone.0013950

Jun G, Moncaster JA, Koutras C, Seshadri S, Buros J, et al. (2012) ?-Catenin Is Genetically and Biologically Associated with Cortical Cataract and Future Alzheimer-Related Structural and Functional Brain Changes. PLoS ONE 7(9): e43728. doi:10.1371/journal.pone.0043728

Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, et al. (2010) Genomic Runs of Homozygosity Record Population History and Consanguinity. PLoS ONE 5(11): e13996. doi:10.1371/journal.pone.0013996

Nakano M, Ikeda Y, Tokuda Y, Fuwa M, Omi N, et al. (2012) Common Variants in CDKN2B-AS1 Associated with Optic-Nerve Vulnerability of Glaucoma Identified by Genome-Wide Association Studies in Japanese. PLoS ONE 7(3): e33389. doi:10.1371/journal.pone.0033389

Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, et al. (2011) Network-Guided Analysis of Genes with Altered Somatic Copy Number and Gene Expression Reveals Pathways Commonly Perturbed in Metastatic Melanoma. PLoS ONE 6(4): e18369. doi:10.1371/journal.pone.0018369

Zhang D, Qian Y, Akula N, Alliey-Rodriguez N, Tang J, et al. (2011) Accuracy of CNV Detection from GWAS Data. PLoS ONE 6(1): e14511. doi:10.1371/journal.pone.0014511

PLOS ONE News and Media Roundup

Lesions found on coral trout.

Last month, the media covered PLOS ONE papers on germs in airports, skin cancer in fish, a potentially life extending pill, and more!

Research by a team at MIT identified New York City’s JFK, Los Angeles’s LAX and Honolulu’s HNL as the nation’s airports most likely to influence the spread of a major pandemic in the first few days of an emerging disease. The team used geographical information, traffic structure and individual mobility patterns to model contagious disease dynamics through the air transportation network. The study was covered by NPR, CNN, and Wired.

A recent study comparing a hunter-gatherer population with a modern Western population found that daily energy expenditure between the two populations is not all that different; challenging the view that obesity in Western society is largely due to a lack of exercise.  This research may encourage shifting the focus of this debate to the importance of calorie consumption and was covered by The Atlantic, Mother Nature Network and the BBC.

Dark patches found on fish in the Great Barrier Reef have been identified as a deadly form of skin cancer, melanoma. “Evidence of Melanoma in Wild Marine Fish Populations” is the first published study of melanoma in a wild fish population but it is unlikely the problem is new. The Great Barrier Reef sits under the largest hole in the ozone, exposing fish populations there to high levels of UV radiation. The image above is Figure 1 of the manuscript. The study was covered by Science, LA Times and Scientific American.

Autistic children may benefit from getting a pet. According to this study by a French research team, children who received a pet around the age of five showed improved social skills, including increased ability to share with and comfort others, compared to autistic children who either grew up with a pet or never had one. US News, Fox and Time all covered this study.

Findings from the study “Randomized Polypill Crossover Trial in People Aged 50 and Over” suggest that people over fifty may benefit from taking a once daily “polypill” comprised of three blood pressure-lowering drugs and a cholesterol-lowering statin. Read more at CBS, Reuters and ABC.

For more in-depth coverage on news and blog articles about PLOS ONE papers, please visit our Media Tracking Project.