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Genome-Wide Association Study

Genome-Wide Association Study. Brendan Burke and Kyle Steffen. Important New Tool in Genomic Medicine. GWAS is used to estimate disease risk and test SNPs( the most common type of genetic variation among people) for association to hundred, even thousands of people.

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Genome-Wide Association Study

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  1. Genome-Wide Association Study Brendan Burke and Kyle Steffen

  2. Important New Tool in Genomic Medicine • GWAS is used to estimate disease risk and test SNPs( the most common type of genetic variation among people) for association to hundred, even thousands of people. • It identifies a correlation between a genetic change in heredity and the incidence of a complex disease. • GWAS has increased our understanding of the pathophysiology of complex disease.

  3. General Procedure • Gather a group of people to be tested for the SNPs that you want to test. • As an example, in one the studies, they studied 2500 that had people that had Type 2 Diabetes and 2500 people who did not (as their control). The researchers then scanned their genomes to see which SNPs are present. • They found that people with Type 2 Diabetes have a unique set of SNPs in common and they located the QTLs( Quantitative Trait Loci) of those SNPs. They located the QTL of the SNPs • Then the researchers went to the QTL to see on the human genome map to see which genes are there. • They then attempted to link those unique SNPs to a known gene function.

  4. Common Disease-Common Variant Hypothesis • This hypothesis predicts that disease-causing alleles will be found in all human populations which manifest a given disease. • Common variants are known to exist in coding and regulatory sequences of genes. • Single nucleotide polymorphisms are valuable genomic signposts in the search for common variants that influence susceptibility to common diseases. • Common SNPs have been linked to diseases such as type 2 diabetes, Alzheimer’s, schizophrenia, and hypertension.

  5. GWAS Results • GWAS has over 1700 publications of their work • GWAS only publishes results that attempt to assay at least 100,000 SNPs. • Their publications are organized by date, most recent to least, and studies focusing only on candidate genes are excluded. • Their publications include over 250 human traits and diseases. • Also, there are over 7291 SNP-trait associations.

  6. Current GWAS Studies • Studies with Type 2 diabetes • Before the GWAS studies, only two loci were identified. • Now due to the GWAS studies, forty-four loci have been identified. • The loci are also known to connect with glucose metabolism pathways

  7. Current GWAS Studies continued • GWAS in Autoimmune Disease • If a person has an autoimmune disease the immune system mistakenly attacks itself, targeting the cells, tissues, and organs of a person’s own body. • Examples of Autoimmune diseases are Lupus, Multiple Sclerosis, and Rheumatoid Arthritis. • Before GWAS Studies, the genetic risk variants for autoimmune disease was only 15. • Now, because of the GWAS Studies, the risk variants has been increased to 68.

  8. GWAS Studies in Immune System Genes • Due to the GWAS Studies with the Immune Systems, 113 SNPs have been located. • 13 new regions have been discovered within the immune systems and most of these systems have genes with immune functions.

  9. GWAS Studies in Inflammatory Bowel Disease • The main forms of inflammatory bowel disease are Crohn’s disease and ulcerative colitis. • Inflammatory bowel diseases are considered autoimmune diseases, when the immune system attacks the digestive system. • The main difference between Crohn’s disease and ulcerative colitis is the location and nature of the inflammatory changes. • Inflammatory bowel disease is caused by concentrated milk fats, often found in processed foods.

  10. GIANT Studies • GIANT consortium is an international collaboration that seeks to identify genetic loci that modulate human body size and shape. • GIANT consortium is a collaboration of different groups, and their results represent their combined efforts. • Traits that have been studied are BMI, height, and waist circumference. • So far in their work, GIANT consortium have identified common genetic variants at hundreds of loci that are associated with anthropometric traits.

  11. Malaria Resistance Medication SNPs • Spontaneous mutations within SNPs would give an anti-malarial medication a reduced level of sensitivity. This can be caused by a single point mutation or multiple mutation • The resistance to anti-malarials may be increased by a process found in which a degree of phenotypic plasticity( the ability of an organism with a given genotype to change its phenotype in response to changes in the environment) was seen which allows the rapid development of resistance to a new drug, even if the drug has not been previously experienced.

  12. Blood Lipids • Blood lipids(such as cholesterol and triglycerides) are major risk factors found in patients that have heart disease. • Specific SNPs indicate that one does have heart disease. • Due to GWAS Studies, there are now 95 known SNPs that were associated with heart disease. • Before GWAS Studies, only 59 SNPs were associated with heart disease.

  13. SNPs and IQ • GWAS has explained that half the variation in I.Q. is due to the variation in genes. • Most of the genetic variation that is in this trait is due to numerous genes of little effect. • You inherit variants of these gens from both of your parents, and your own trait value is to a large extent both of your parents values. • This issue is not arguing whether intelligence is heritable, but how much you get from each of your parents.

  14. SNPs and Human Personality Traits • Studies have shown that there are no SNPs associated with any of the following personalities; Neuroticism, Extraversion, Openness, Agreeableness and Conscientiousness. • The genes that we inherit have no direct or indirect influence on our personalities. • Although there have been some tests on twins showing that genes do affect personalities, scientists have concluded it’s the environment they grow up in.

  15. SNPs and Human Personality Traits • There are five identified independent genetic loci associated with different facial phenotypes; PRDM16, PAX3, TP63, C5orf50, and COL17A1. • Three of these are involved in facial developments and diseases. • The other two are basically in charge of the facial developments. • This study may allow us to predict facial shape and details in the future.

  16. Questions • What does GWAS stand for? • What does QTL stand for? • How many risk variants have been identified for Autoimmune disease because of GWAS? • What are two example of Autoimmune diseases? • What is the overall purpose of GWAS?

  17. Bibliography • www.genome.gov/gwastudies/ • www.genome.gov • www.ncbi.nlm.nih.gov • www.ncbi.nlm.nhi.gov/pubmed/23017373 • www.biomedcentral.com/1471-2350/8/s1/s17 • www.broadinstitute.org/news/2898 • www.ncbi.nlm.nih.gov/pmc/articles/pmc2574810/

  18. THANK YOU THE END

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