Genetic Data- Genotype
MeSH ID: D005838
Description:
The genetic constitution of the individual, comprising the alleles present at each genetic locus.
Best practice for sharing this type of data:
When possible the original data output should be shared (e.g. the Electrophoresis or sequencer output file). The scored genotypes should be shared as Tabular data, ensuring that the names for individual samples are consistent with those used in the article and in other related datasets. Tabular data should saved as a .txt or .csv file. The first row(s) should contain information about the dataset, such as the data file name, author, today's date, when the data within the file were last modified, and companion file names. Please also state which symbol has been used to denote missing data (NA is preferred). Column headings should describe the content of each column and contain only numbers, letters, and underscores - no spaces or special characters. Lowercase letters are preferred. Row names should be consistent with those used in the article and in other related datasets.
Most suitable repositories:
Genotype data may be added to Allele Frequency Net Database, ArrayExpress, NCBI Gene, Database of Genotypes and Phenotypes, NCBI Genome, European Variation Archive, Genomic Expression Archive, Japanese Genotype-Phenotype Archive, NCBI BioSample, Reference Sequence Database, Online Mendelian Inheritance in Man, The European Genome-Phenome Archive, and VectorBase.
Best practice for indicating re-use of existing data:
For public datasets please provide a DOI or other stable identified for the dataset itself *and* include a citation for the dataset in the reference list. Be sure to indicate exactly which data has been re-used, particularly when multiple versions of the dataset exist. In many cases, this is best achieved by sharing the code used to extract the part of the data that you analyzed. In some cases it may be best to share the exact dataset(s) you analyzed as well.
For access-controlled data authors should provide a link to instructions for obtaining access (e.g. here is the information page for ADNI (Alzheimer's Disease Neuroimaging Initiative): http://adni.loni.usc.edu/data-samples/access-data/).
When re-using a private dataset from a previous study please contact the data owners to discuss how the data can be made public.
