What is needed for a genetic study?
|“Sufficient” number of high-quality sequencing/genotype data||Amount needed can vary from one proband and a few family members (for very rare Mendelian disorders) to thousands of cases and controls (for certain common complex disorder/traits)|
|List of candidate genes||Websites such as http://omim.org/ and http://ghr.nlm.nih.gov/; and software such as SNPs3D can be helpful|
|Identification of variant calling tool||Such as in Table 2|
|Identification of variant effect predictor tool||Such as in Table 3; tools usually require conversion of VCF to VEP format (Ensembl website)|
|Knowledge of human population variation databases||That is, HapMap, 1000 Genomes Project, EVS, dbSNP, and internal databases|
|Knowledge of databases storing information about genes and their products||That is, OMIM, Gene (NCBI), GeneCards, Unigene (NCBI), GEO Profiles (NCBI), HomoloGene (NCBI), and Mouse knockout databases (such as http://www.informatics.jax.org/, http://www.tigm.org/database/ and http://www.nc3rs.org.uk/category.asp?catID=8). Search the literature using PubMed and/or Web of Science.|
|The most important factors when carrying out a genetic association study are (i) the availability of reliable data (ii) bioinformatics and biological expertise, and (iii) careful planning.|