What does Promethease do?
Promethease is a third party service which provides health related information based on DNA ancestry raw data from companies such as 23andme and others. After the brief FDA ban on 23andme, Promethease and other companies stepped in to fill the gap.
Post FDA ban, 23andMe could only provide the ancestry reports and the raw data information from the ancestry DNA test. The raw data file contains a list of rsIDs of SNPs. It also includes the relative chromosome position and the exact nucleotide base change at that position.
The 23andme raw data is of little use to people who do not have a background in genetics and biostatistics. However, the raw data file can be used to obtain health related information such as nutrient requirements, predispositions to complex and monogenic genetic conditions, allergies, carrier status, individual status of well-studied genes like MTHFR and BRCA1 and BRCA2 from service providers such as Promethease and Xcode Life.
Update: Late last year (2019) in September, MyHeritage acquired Promethease and SNPedia.
MyHeritage offered Promethease free of charge through the end of 2019 and continues to maintain SNPedia as a free resource for academic and non-profit users. For Non-European users, the DNA raw data will be shifted to MyHeritage into new accounts which will be created for them. However, the users will retain the ownership of their DNA raw data file and are free to delete it from MyHeritage’s server.
How to read Promethease results?
Promethease reports are based on SNPedia, a Wikipedia-styled repository. Promethease retrieves all relevant literature from the SNPedia database. This takes around 15 minutes. The report is organized in a single rs ID format. This means that the gene markers are listed by their dbSNP identifier with the potential risk provided next to it.
The red border indicates that the particular SNP has a bad implication for you. An explanation is provided in the grey box below with links to the respective references from SNPedia.
Sometimes you will see a similar passage below a gs ID. The gs IDs represent a genoset, which refers to a group of SNPs that affect the same phenotype (shown below). They may or may not mention the rsIDs of the SNP. Promethease is full of such terminologies that you may want to familiarize yourself with first before you dive into your reports. The adjoining table indicates the Repute, Magnitude and Geno time. Explanation for all three can be found here.
It is relevant to point out here that the Promethease report is not a result of analysis or algorithms. It is just a literature-retrieval system. Multiple polymorphisms influence human health conditions and traits. Predispositions to complex health conditions are analyzed using algorithms that take into account the combined effect of these polymorphisms.
A lot of conflicting information is published on these actively researched diseases on a regular basis. Interpreting these needs expert-curation. For example, if you select Acute Lymphoblastic Leukemia (ALL) from the side menu, Promethease might dig out 3 sources that indicate your increased risk for ALL (bad repute), 1 for decreased risk (good repute) and 2 which are neutral or repute not set. They are not weighed against each other to give you a strong case of yes or no.
What is Promethease Repute?
Repute according to the SNPedia website applies to a single genotype. The repute of a genotype maybe good, bad or not set. Since the Promethease report follows the single rsID format, the repute for each genotype is give in a table adjoining the passage along with magnitude and geno time. Unfortunately, this form of presenting can be misinterpreted by individuals who are using the Promethease report to make lifestyle alterations.
For example rs4132601(G;T) confers a bad repute for ALL according to the report. This does not mean that you rush off to an oncologist demanding an explanation. It only shows that there is literature evidence for that SNP to have a relatively strong genetic influence on ALL. Many diseases have multiple genetic components along with other external factors. Moreover, not all studies report the same findings. This may change when a larger study with a better sample population gives a different result.
If you do not want to see the repute color codes, you can choose the color-blind option and read your report without any visual bias.
23andMe Health Report vs Promethease Health Report vs Xcode Health Report
Human health is the manifestation of a complex interplay between genetics and the environment. In this light Promethease reports tend to set off a panic attack in people who do not have technical background. Health reports from Xcode Life and 23andMe
You can read a more in-depth comparative analysis between health reports from Xcode and Promethease or refer to the table below. Xcode now offers all the inherited health conditions covered in the 23andme health report in their Carrier Status report. The genetic risk factors covered in the 23andme health report is covered in the Xcode Health report.
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As often emphasized by genetic testing companies, the health related information provided by various third party providers are not for medical purposes. Only clinically certified tests can be used for such purposes. DNA ancestry tests such as those from 23andme, Ancestry DNA, Family Finder test from FTDNA are not clinically certified. Please bear in mind that the labs in which these tests are carried out may be certified, and many companies showcase this fact, but the certification of lab is not the same as the clinical certification of the test.
The only exception to this is a handful of traits reported by 23andme that are now FDA approved. All of the health traits reported by 23andme including the FDA approved traits are now covered in the Xcode Life health reports. One helpful consideration while evaluating the ancestry DNA tests is to look for the number of genetic markers being tested and the version of the chip. The 23andme v5 chip (GSA, Illumina) covers around 650,000 markers. Illumina has said that it is more health report-friendly than their OmniExpress versions that are still being used by companies like Ancestry DNA and Family Tree DNA. You can read more about the health markers covered in the 23andme v5 chip here. Living DNA also uses the same chip.
We recommend the 23andme ancestry test to clients who are interested in using the data for Xcode Life health reports. This is because of large number of health related markers present in the 23andme v5 chips which gives better health related information.