Genome-wide association study

In genetic epidemiology, a genome-wide association study (GWA study) - also known as whole genome association study (WGA study) - is an examination of genetic variation across the human genome, designed to identify genetic associations with observable traits, such as blood pressure or weight, or why some people get a disease or condition.Cite journal| doi = 10.1001/jama.299.11.1335| volume = 299| issue = 11| pages = 1335–44 |author= Pearson TA, Manolio TA | title = How to interpret a genome-wide association study| journal = JAMA| date = 2008 |doi=10.1001/jama.299.11.1335 |pmid=18349094 | url = http://jama.ama-assn.org/cgi/content/full/299/11/1335]

The completion of the Human Genome Project in 2003 made it possible to find the genetic contributions to common diseases and analyze whole-genome samples for genetic variations that contribute to their onset.

These studies require two groups of participants: people with the disease and similar people without. After obtaining samples from each participant, the set of markers such as SNPs are scanned into computers. The computers survey each participant's genome for markers of genetic variation.

If genetic variations are more frequent in people with the disease, the variations are said to be "associated" with the disease. The associated genetic variations are then considered pointers to the region of the human genome where the disease-causing problem resides. Since the entire genome is analysed for the genetic associations of a particular disease, this technique allows the genetics of a disease to be investigated in a non-hypothesis-driven manner.

Background

Humans differ in genetic makeup by only 0.1%, but that small part of the genome contains the key differences that can determine a person’s susceptibility to disease. GWA studies allow researchers to identify factors in many areas, including asthma, cancer, diabetes, heart disease and mental illness research and clinical care.

As people have migrated and married over generations, it has become more difficult to limit studies to biological data; for example, people with tuberculosis moving to Colorado might lead to conclusions that Colorado people are biologically inclined to Tuberculosis if correction for population stratification is not properly factored in. [cite press release |url=http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1841 |title= Taking geography out of genetics |publisher= Broad Institute |date=2006-07-31 |accessdate=2008-06-19]

uccesses

In 2005 it was learned through a small scale GWA Studies that age-related macular degeneration is associated with variation in the gene for complement factor H, which produces a protein that regulates inflammation.

The first major GWA was published in Nature in February 2007 by Robert Sladek "et al." in a study searching for type II diabetes variants. [cite journal |author= Sladek R, Rocheleau G, Rung J, "et al." |title= A genome-wide association study identifies novel risk loci for type 2 diabetes |journal=Nature |volume=445 |issue=7130 |pages=881–5 |date=2007 |pmid=17293876 |doi=10.1038/nature05616] The work was mainly carried out the Genome Quebec centre in McGill University although it included collaboration with scientists at Imperial College London and other research institutions.The group tested 392'935 single-nucleotide polymorphisms and identified several associations, among others in the genes called TCF7L2 and SLC30A8.

In 2007 the Wellcome Trust Case Control Consortium carried out genome-wide association studies for the diseases coronary heart disease, type 1 diabetes, type 2 diabetes, rheumatoid arthritis, Crohn's disease, bipolar disorder and hypertension. This study was successful in uncovering many new disease genes underlying these diseases. [cite press release |url=http://www.wtccc.org.uk/info/070606.shtml |title= Largest ever study of genetics of common diseases published today |publisher= Wellcome Trust Case Control Consortium |date=2007-06-06 |accessdate=2008-06-19]

Problems

Some critics of GWA studies regard them as extremely expensive "factory science". Alternatives such as linkage analysis have advantages over GWAs such as robustness to allelic heterogeneity.

Robert Elston is a prominent proponent of linkage, although he does accept association may occasionally be useful.

According to Pearson and Manolio's assessment of the technique, "the GWA approach can also be problematic because the massive number of statistical tests performed presents an unprecedented potential for false-positive results".

References

External links

* [http://www.cancer.gov/Templates/db_alpha.aspx?CdrID=561726 Whole genome association study] entry in the public domain NCI Dictionary of Cancer Terms.
* [http://www.genome.gov/17516714 Whole genome association studies] (NIH release)
* [http://www.genome.gov/20019523 Genome-wide association studies] (NIH fact sheet)