Datapunk Opus 23 Pro

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LUMEN: Power over complexity

LUMEN is one of the most powerful apps in the Opus 23 Pro toolbox. This app allows you to examine the effects of multi-SNP, multi-gene consequences. Very few single SNPs exert their effects independently; they more typically interact through epistatic relationships (where the phenotypic expression of one gene influences the genotypic expression of another) or as a haplotype: a set of several SNPs, on a single chromatid of a chromosome pair that are associated statistically.

LUMEN does this by using algorithms, small step by step programs that run inside of LUMEN and that look at the logical result of multi-SNP combinations. This type of logic is essentially 'Boolean' in that its queries yield a yes or no answer. The combination of both allows LUMEN to provide you with insight into complex SNP arrangements and relationships that might otherwise escape detection.

Getting around in LUMEN

To start LUMEN, from the main menu bar at the top of the screen, hover over the Informatics link, and then scroll down to Algorithms. Click LUMEN. You will be presented with the Lumen index page.

LUMEN Index Page

Here you will find all the LUMEN algorithms grouped by general category. Each category is displayed as a half-pie chart depicting the distributions of the various algorithms in that category. The half-pie chart is color-coded and interactive.

LUMEN Category

The chart displays four types of algorithms: three that indicate algorithms returning a true value (green, orange and light gray) and one indicating algorithms that return a false value (dark gray).

The green-colored slice indicates algorithms that convey benefit (good repute) for which the client returned a true value
The orange-colored slice indicates algorithms that convey risk (bad repute) for which the client returned a true value
The light gray-colored slice indicates algorithms that have a neutral repute (i.e. they are not good or bad, such as one's blood type) for which the client returned a true value
The dark gray-colored slice indicates algorithms for which the client returned a false value

If you hover over any section of the sections, a tooltip will describe the type of result for the category and the number of outcomes. For example, out of a total of 31 algorithms classed as 'Autoimmune/ Inflammatory' eleven out of thirty-one algorithms returned a false value for the client (i.e. the algorithm did not apply to them).

Clicking on any pie slice will display the algorithms in that category. Clicking on the category name will display all the algorithms in that category, including those with a false result.

Let's click on the title (Autoimmune/ Inflammatory) and see what LUMEN can do.

Using LUMEN

Algorithms are displayed as individual boxes, one below the other. Let's examine one in detail:

The algorithm AG004 looks at three SNPs on three different genes to determine if the client's genotype may indicate an increased risk of allergic asthma. Starting from the top left, we see the now familiar NOTEPAD icon that would allow us to add a note about this algorithm. Next follows the algorithm ID and the conclusion summary.

Note: Many of these summaries are dynamic: for example, depending on this algorithm's outcome, it might have save 'Risk of...' or 'Increased risk of...' or 'Significantly increased risk of...'

Next we have a box with several details: If the selected algorithm has a bad repute it will be colored orange, if the algorithm results in some benefit, it will be colored green, and if the algorithm is neutral it will be colored gray. The Power Factor or magnitude is a number (1-10) added by the Opus 23 Pro curators. It reflects a combination of pathology severity, evidence basis and p-values and odds ratios when available. Next follows the genes included in the algorithm, and like most gene symbols in Opus 23 Pro, clicking on this will trigger an information pop-up.

If HapMap data on gene/ SNP frequencies are available they will be shown in a separate box directly underneath.

To the right is the interpretation abstract. This is usually a paragraph or two describing the algorithm and what are its criteria. When possible, a PubMed ID number is provided. Underneath the abstract will be a table showing the client's genotype for the SNPs involved, and like most rs ID numbers in Opus 23 Pro, clicking on this will trigger an information pop-up.

Variations in algorithm output

Depending on the type of criteria, LUMEN will sometimes present data in a table format. This is typically done in situations where an algorithm's SNPs outcome might convey benefit in one pathology but risk in another. Depending on the genes are SNPs, you might be alerted to the presence of other data available. For example, if there are natural products associated with any of the genes or SNPs in the algorithm you will see a link to a natural product:

Clicking on this link will trigger a pop-up and display any relevant information.

In addition, if any genes in the algorithm are included in MAPPER you will be alerted.

If you wish, LUMEN can return algorithms for which the client returned a false result. To distinguish there from true algorithms the algorithm box border is colored orange and a warning is displayed 'This algorithm is NOT TRUE for this client.' A false algorithm is also surrounded by an orange box.