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Genes for Good

From SNPedia


After answering (how many?) survey questions on Facebook, you are able to get free genetic testing which gives you your raw data. This data is compatible with Promethease.

They offer several downloads. Promethease understands any of the files in either VCF or 23andMe format.

Some of their files are imputed. These give the largest report, but since some of your genotypes have been 'imputed' they are assumed, and may not be true. Individuals from ethnic groups which were not part of the Genes for Good training sets can expect more errors than people from similar ethnic groups. It's unclear exactly what groups were used for training, but it's safe to assume western europeans are well represented.

Files that don't mentioned 'imputed' should only include genotypes which were actually observed. This results in a smaller promethease report, but with higher confidence.

Some of their files also indicate 'noY_noMT' indicating that SNPs from these haploid chromosomes are not included. Without them it is impossible to see any data reloated to your haplogroups.

For a small ($2) additional fee, you can combine (pool) additional files together, which might let you have the best of both worlds.

As for how to interpret a pooled report.

Notice that many of your genos say 'count 2'. Those were in both files. The ones that were only in one file, don't say that. Since we expect everything from the original file, to be in the imputed, that is enough to let you know what's imputed.

In practice there are a few genos that differ between the files. This relates mostly to different representations of the same information. ie, 23andMe like to use II or DD or DI to indicate indel for Indels. Genes for Good will usually use the actual genotype so you'll probably see (for example) rs1234(G;G) or rs1234(;) or rs1234(-;G). By clicking the checkbox for conflicts, you can find these.

See also VCF