Friday Five #11: GWAS, Ebola, babies, and Snoop

1) Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application (Need access to read the whole article). This is an excellent review article about what to do with GWAS results or how to go about taking the next step. The authors make a good point that GWAS is the tip of the iceberg and what is really needed is a fundamental understanding of the biology involved not just the genetic variants.

Genome-wide association studies (GWAS) have rapidly become a standard method for disease gene discovery. A substantial number of recent GWAS indicate that for most disorders, only a few common variants are implicated and the associated SNPs explain only a small fraction of the genetic risk. This review is written from the viewpoint that findings from the GWAS provide preliminary genetic information that is available for additional analysis by statistical procedures that accumulate evidence, and that these secondary analyses are very likely to provide valuable information that will help prioritize the strongest constellations of results. We review and discuss three analytic methods to combine preliminary GWAS statistics to identify genes, alleles, and pathways for deeper investigations. Meta-analysis seeks to pool information from multiple GWAS to increase the chances of finding true positives among the false positives and provides a way to combine associations across GWAS, even when the original data are unavailable. Testing for epistasis within a single GWAS study can identify the stronger results that are revealed when genes interact. Pathway analysis of GWAS results is used to prioritize genes and pathways within a biological context. Following a GWAS, association results can be assigned to pathways and tested in aggregate with computational tools and pathway databases. Reviews of published methods with recommendations for their application are provided within the framework for each approach.

2) Genome Study Provides a Census of Early Humans A NYT article regarding a PNAS study that looks at the number of ancient humans around and suggest the effective population size was small, around 18,500. Basically, they looked at Alu inserts, which are a type of retroelement and are unique to primate genomes.

3) Researcher Discovers Ebola's Deadly Secret: A cool (yes I'm a nerd) Science Daily article that demonstrates how Ebola is able to fool the host cell defense mechanism and identifies the protein involved (VP35).

4) Birth Weights Fell From 1990 to 2005: Looks at a downward secular trend in the birthweight of babies. They noted that "The lower-birth-weight trend couldn't be explained by common factors such as how much weight mothers gained during pregnancy, whether the delivery was induced or by cesarean section, the amount of prenatal care, or maternal-health issues such as smoking and hypertension, researchers said". However, I wonder if they accounted for the age of the mother, which wouldn't suprise me to much if that is the case as demonstrated by this article.

5) Snoop Dogg Shocked by Genealogy Results: From Eastman's Online Genealogy Newsletter (best viewed in Firefox of Chrome). Funny but I wonder if his results will change.

Project 365 Day 31: Science Thursday

As part of returning this blog to things a little more scientific and to help me look at things outside of articles in genetics and anthropology I decided to do a little thing called Science Thursday where I take a recent research article that has peaked my interest in the last week. This is one from PLOS Medicine on Plague, Past, Present, and Future. The gist of this article is that plague is still a serious problem worldwide. Granted cart loads of people aren't being wheeled and city's burned but it still remains a viable public health concern. Figure 1 from there article shows the reservoir where plaque still resides. Yes, the US is one of them mostly in the west. The figure also show plague cases and countries that have reported them.



There are three types of plague: 1) bubonic, the one that cause the black death in Europe and two others pandemics Justinian and 19th century China one and is still the most common form of plaque; 2) septicaemic which involves an infection of the blood; and 3) pneumonic which is transmitted directly from human to human (if you remember the movie Outbreak it is airborne and by the way that is New World Monkey). The last two are almost always fatal without antibiotics.

The article points out that it is impossible to eradicate plaque because it found in wild rodents, which are difficult to exterminate therefore the current outbreak approach is reactive rather than proactive. The major point of this article is more of reminder that plaque is still with us and not to forget that it takes the right conditions to spread like wildfire.

Plague: Past, Present, and Future Stenseth NC, Atshabar BB, Begon M, Belmain SR, Bertherat E, et al. PLoS Medicine Vol. 5, No. 1, e3 doi:10.1371/journal.pmed.0050003