Genetic Data- Single Nucleotide Polymorphism
MeSH ID: D020641
Description:
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
Best practice for sharing this type of data:
SNP data can be generated in many ways. In general, 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. Advice for SNP data generated by RAD or GBS can be found here
Most suitable repositories:
SNP data may be deposited into Database of Single Nucleotide Polymorphism, European Variation Archive, Reference Sequence Database, NCBI Gene, Genetic Testing Registry, NCBI Genome, Fungal and Oomycete Genomics Resource, Genomic Expression Archive, Mouse Genome Database, and WormBase.
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.
