From Genome Analysis Wiki
- David Schlessinger (National Institutes on Aging, Baltimore)
- Manuela Uda (National Research Center, Cagliari, Italy)
- Goncalo Abecasis (University of Michigan, Ann Arbor)
Genomewide Association Study
We carried out an initial genomewide association by genotyping 1405 samples with Affymetrix 500K SNP arrays. Then, because SardiNIA samples are closely related to each other, we were able to use these genotypes to impute the genomes of many close relatives who were genotyped with Affymetrix 10K SNP arrays. Typically, our SardiNIA GWAS analysis thus include approximately 4300 genotyped or imputed individuals. To learn more about the approach see Chen and Abecasis (2007) and Scuteri et al (2007).
Several ongoing experiments are expected to gradually improve our GWAS data. First, we expect to integrate Affymetrix 1M SNP chip genotypes into our analyses. Second, we plan to genotype all sampled individuals with the Metabochip, which includes 200,000 SNPs. This will enable us to fill in genotypes for relatives of those genotyped with denser arrays more accurately, because we will more precisely identify shared stretches of chromosome.
Medical Sequencing Project
We are sequencing the genomes of 1,000 individuals to learn about the genetics of blood lipid levels and personality.
If you are looking to learn about the project, I strongly recommend that you read the following papers
- Pilia G, Chen WM, Scuteri A, Orru M, Albai G, Dei M, Lai S, Usala G, Lai M, Loi P, Mameli C, Vacca L, Deiana M, Olla N, Masala M, Cao A, Najjar SS, Terracciano A, Nedorezov T, Sharov A, Zonderman AB, Abecasis GR, Costa P, Lakatta E and Schlessinger D (2006). Heritability of Cardiovascular and Personality Traits in 6,148 Sardinians. PLoS Genet 2:1207-1223 [Abstract and PDF]
- Scuteri A, Sanna S, Chen WM, Uda M, Albai G, Strait J, Najjar S, Nagarajah R, Orru M, Usala G, Dei M, Lai S, Maschio A, Busonero F, Mulas A, Ehret GB, Fink AA, Weder A, Cooper R, Galan P, Chakravarti A, Schlessinger D, Cao A, Lakatta E and Abecasis GR (2007). Genome Wide Association Scan shows Genetic Variants in the FTO gene are Associated with Obesity Related Traits PLoS Genetics 3:1200-10 [Abstract and PDF]
- Chen WM and Abecasis GR (2007). Family-based association tests for genomewide association scans. Am J Hum Genet 81:913-26 [Abstract and PDF]