There's no right or wrong way to filter through the results of raw genomic data and no professional standards or guidelines about how to do. So I've come up with my own strategy for how to do it out of necessity. It's a common request I receive, and in my quest to help people get proper genetic counseling and the appropriate follow-up testing and/or recommendations, I'm happy to try to help.
There are many reasons you should not rely on a Promethease report or consider raw data to be accurate health information, which I've written about in prior blog posts (and posted a video on YouTube) in the past:
But don't just take my word for it! Also consider the warnings from the companies and tools themselves, like this fine print on one page of the 23andMe website:
"This data has undergone a general quality review; however, only a subset of markers have been individually validated for accuracy. As such, the data from 23andMe's Browse Raw Data feature is suitable only for research, educational, and informational use and not for medical, diagnostic or other use."
I know many people will try to make use of their raw data anyway, so here is my guidance for the folks turning to Pomethease. **Again, I want to emphasize this is only one approach, and until there are standards I am not claiming this guidance as personalized medical advice for readers in any way.**
Brianne's Five Steps to Filtering a Promethease Report
- Scroll down to the bottom of the report page and set the visualization tool to the "color blind" setting.
- Set “Magnitude” at a minimum of 3.0 and leave maximum at its standard setting (4+).
- Turn on the “ClinVar” button.
- Scroll down to the bottom to the ethnicity section (at the bottom right), and uncheck all the ethnicities that do not describe you.
- If you used a raw data file from recent testing at Ancestry.com (v2), be aware there are many false positives ("miscalls") that seem to be creeping up. Miscalls happen with other company's data as well, so read through to see if any of your markers are referred to as “miscalls” in the Promethease report for the particular company you used.
The first step is optional, but I recommend it because I've found that viewing the genetic markers listed on a Promethease report using the default color setting (red is listed as "bad" and green as "good") can be psychologically misleading and distressing to some people. This report isn't diagnosing you with medical issues, nor is it predicting your future. The genetic markers ("SNPs" or "snips") are simply risk-adjusters. And on top of that, raw data findings can be wrong.
If you have any markers still remaining after filtering -- and especially if any relate to conditions already in your personal or family medical history -- I recommend you consider scheduling follow-up with a genetic counselor who is familiar with raw data and third party tool reports. You might have to shop around to find one because there aren't too many of us (at least not yet).
Genome Medical is one service that will see patients with questions about specific SNPs/raw data markers associated with health conditions. Genome Medical offers counseling via phone or video and can discuss the potential impact of that marker on your health and order follow-up confirmation testing if appropriate. They do not currently work with patients to filter data or review the entire raw data file, so you will need to have already done the filtering process yourself.
If you are someone who prefers an in-person type of interaction, you might search for a genetic counselor at a clinic near you. Start at findageneticcounselor.com and search based on location or the genetic counselor specialty (cancer, cardiovascular, reproductive, etc.). Some geographical areas and hospital systems may have a genetic counselor able to assist you and others may not.
Want help with the filtering process or a better understanding of the different filters and why they matter? I'm happy to assist. My schedule will open up again for these types of referrals at the end of the spring, so check back for my calendar to be reposted in May 2018, if you don't mind waiting.