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Genos exome:FAQ

From SNPedia

This page aims to answer the most common questions a current or potential Promethease user might have about the Genos exome sequencing service; Genos also maintains their own FAQ page here.

General[edit]

What's an exome?[edit]

Your exome is the subset (~1.5%) of your genome that contains most of the gene sequences that encode proteins. Since most of the medically interesting DNA variants are found in genes, your exome may represent the most interesting part of your genome.

What does exome sequencing give you that you can't get from microarray (DNA chip) based products?[edit]

DNA chip manufacturers choose which variants will be placed on a given chip version. Once made, that DNA chip can return results for the variants on it, but if a variant isn't on it, it won't be tested and there won't be any data for it.
Sequencing determines the order of the DNA bases in the regions sequenced. For exome sequencing, that means the protein-encoding regions of most genes. Your exome sequence will include variants that have never been seen before, or who's significance may only be discovered in the future. Sequence therefore becomes more interesting over time as new discoveries are published.

What do microarray based products offer that exome sequencing doesn't?[edit]

Microarray manufacturers can sample any part of the genome they wish, up to the capacity of their chip (currently around 1,000,000 variants), so a variant can usually be represented on a chip no matter where it's from in your genome. Microarray technology is also more mature and is currently less expensive than sequencing.
Exome sequencing offers lower coverage of the non-coding regions of your genome, so important variants that may be in regulatory regions or in-between genes are unlikely to be covered.
Ultimately, all of your DNA will be important to have sequenced, but currently such 'whole genome sequence' is significantly more expensive than exome sequencing.

Promethease Reports from Genos data[edit]

How much of SNPedia (or ClinVar) is represented in a Genos-based Promethease report?[edit]

Promethease reports run with data provided by Genos yield ~42,000 genotypes, of which 34,000 are from ClinVar. Other details are reported on our Testing and Genos pages, and a sample Genos report is available here.

Can Promethease reports from Genos data report on novel variants?[edit]

Not at this time. When the algorithms for predicting how beneficial or how damaging novel variants become better, we anticipate adding this feature.

File Formats[edit]

Which file format on the Genos website do I need to use to make a Promethease report?[edit]

Select the 'Promethease-compatible', .tsv file format, as explained in more detail here.