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1. How to read your Promethease report?

To read your Promethease review report you will need to ensure that you are accustomed to some of the terms that are found in their report like magnitude and repute. It is difficult to sift through thousands of pages in your report. Once you organize the pages as per your unique needs it becomes a relatively easy task to. 

2. What is Promethease?

Promethease allows users to analyze their genetic data and compare personal genomics results against the SNPedia database. SNPedia is a wiki-styled genetic data repository. 

Though popular, it is often criticized for being too technical and difficult to read. You can take a look at Promethease's sample report here.

Promethease is a do-it-yourself (DIY) tool for health genetic information from 23andMe raw data. It is a third party online tool that provides consumers information about their genetic variants and how they affect your health. After 23andme FDA ban on providing health reports, people started using tools like Promethease to get more information from their DNA raw data, other than just locating distant cousins. Though Promethease is a good tool built on a repository like SNPedia there are a number of factors to consider before you decide to upload your raw data to Promethease. Promethease is popular as a low-cost offering, but it’s also very technical and disease-centric. There are many alternatives to Promethease to analyze your 23andme raw data, that are easy to follow and understand. Below we present a feature by feature comparison between Promethease and Xcode Life Sciences.

3. How did Promethease gain popularity?

Promethease was one of the early companies to offer DNA raw data analysis based on 23andMe, Ancestry DNA raw data. 

What is DNA Raw Data?

A DNA raw data is a file that contains information about your genetic variants. These are called single nucleotide polymorphisms or SNPs and account for the differences in different traits like eye and hair color, height, and skin pigmentation across individuals. Your ancestry DNA raw data is a lab-generated text file. It is usually in the following two formats

The whole-genome files have a size of 80-90 GB (30x). All the top consumer genetic testing companies like 23andMe, AncestryDNA, Family Tree DNA enable their customers to [download their raw data](https://www.xcode.life/23andme-raw-data/download-23andme-dna-raw-data-third-3rd-party-tool) directly from the website or request a download. 

The raw data from different ancestry DNA testing companies have different numbers of genetic markers depending on the microarray chip used. For example, the 23andMe raw data has around 650,000 SNPs in its v5 chip and AncestryDNA has around 700,000 SNPs

When the FDA (briefly) banned 23andMe from providing health reports, Promethease was the only alternative and gained popularity because of its free service and low turnaround time.

Promethease is criticized for its user-unfriendly interface based on several user reviews. Some well-known competitors for this tool are Xcode Life, Codegen, Interpretive, Nutrahacker, and GEDMatch.

Update: In 2019, 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. The raw data of Non-European users has been shifted to MyHeritage into new accounts created for them. However, users retain ownership of their DNA raw data file and are free to delete it from MyHeritage's server.

4. How long does it take to get my Promethease reports?

Promethease takes approximately 20 minutes to generate health report from your raw data.

5. What does Promethease provide?

Promethease offers health reports based on 23andme, Ancestry DNA, Family Tree DNA, and other ancestry raw DNA data providers for a price of $12. Once you upload your DNA raw data, you will get your report in about 20 minutes.

Earlier, the reports were offered free or at a discount. So many users tried them due to the free/low-cost aspect and the high accuracy that the vastness of their content seemed to imply. However, the reports left individuals more confused than clear. 

So if you have a Promethease report that you still cannot make heads or tails of, read on.

6. What exactly do you get to know from a Promethease report?

Promethease is a wiki-style collection of peer-curated genetic information in contrast to expert-curated reports like Xcode Life's reports. You can search genes/variants/diseases as you would on Wikipedia. The results are pages of information. This is great for people who have degrees in genetics and want to learn about all the diseases they can get.

However, if you want organized information that you can use in specific aspects of your daily life, such as Nutrition, Fitness, or Ancestry, to enhance your health and wellbeing, then you may not find the Promethease reports all that helpful. Promethease's emphasis seems to be largely on the different diseases that one can get.

7. How to read my Promethease report?

Once you transfer your DNA raw data to Promethease, you will get a lengthy report. Though it may look like a massive report on the face of it, the amount of potentially useful information in the Promethease report is quite limited. Understanding and interpreting this report is a challenge. 

Let's break it down:

The total number of entries in a typical Promethease report = Approximately 25,000

Number of entries

The "Summary" component of the Promethease report is where the information pertaining to your genotype is given. This column, for the vast majority of the entries, has information that will not be useful to most people. It contains many terms that carry no useful information for the regular user.

The number of entries remaining after removing empty entries (no annotation) and terms such as "common in ClinVar," "common on affy axiom," "none," and "complete genomics,"," is 1482.

On further removal of more such terms (normal, common, etc.), you will be left with ~800 entries.

> So, only about 800 entries out of 25,000 (~ 3%) are potentially informative entries in the Promethease report.

8. Will getting the health test from 23andme give me better results?

A lot of people think that getting the additional health report from 23andme will help them get better results. That is not true! Whether you order the Health report or the Ancestry report from 23andme, the raw data you receive is the same!

9. How does Promethease work?

This third party DNA raw data analysis tool, is a literature retrieval system from SNPedia which is a Wikipedia style repository where people can add information. It is not a systematic risk assessment tool. For example, for Alzheimer’s disease (AD), you will not get a summary of your risk for developing AD. Instead, you will get a list of scientific literature that is available that indicates or does not indicate your risk for AD for a specific variant. For a particular disease or trait, if there are 15 articles that report on that particular DNA location, based on your SNPs 2 information sources might indicate an increased risk, 5 might be neutral, and 3 towards the lower side. Promethease does not summarise these for you. Rather it returns all these 10 articles and makes you do the interpreting yourself. This is the major reason why many individuals are alarmed and confused by their Promethease report.

10. How accurate is Promethease?

The vast majority of human traits are polygenic, meaning, several genes contribute towards that trait. Even if one carries a disease variant, they may also be carrying variants that reduce the risk of disease. Even in the case of Monogenic conditions- where one single gene leads to disease, scientist have found individuals carrying these deadly mutations but apparently healthy with no sign of disease. In a majority of the cases, the genetic risk is a small contributor towards the overall risk of that disease/condition. So, one must consider all of these things in interpreting their report. 

11. Where does Promethease get all its information?

Promethease only relies on SNPedia. Several other notable and high scientific authority tools are left out from the Promethease reports.

12. How do I filter through the Promethease report?

It is impractical to sift through the dump of information that you get (anticipate about 48,000 rows of data). The tool is equipped with different kinds of filters aimed at assisting you. Some of them are gene names, haplogroup names, diseases, drug names (referred to as “medicines”), medical conditions, names of genes and race.

13. What is magnitude in Promethease?

Magnitude is a subjective parameter that measures the interest level of the information. Here is the table partially resourced from the SNPedia website that describes what each numerical value indicates.

[table id=1 responsive=scroll/]

14. What is Promethease repute?

Good repute: The variation has a positive influence on you.

Not set: There is no verified information on the nature of the variation.

Bad repute: The variation has a negative influence on you.

According to the SNPedia website, it is better to leave the repute as “Not Set” as all genotypes have a little of both the “good” and “bad” repute.

15. What are ClinVar diseases?

This option allows you to see only the SNPs present in ClinVar. ClinVar is a freely accessible public archive of information on genetic variations specifically with clinical implications. It is maintained by the National Institute of Health (NIH). When you filter using this option you will find all the medical conditions that have been formally labeled by ClinVar.

16. How is Xcode Life different from Promethease?

How is Xcode Life Report different from the Promethease report?

Xcode Life puts together expert-curated references of variant annotations from several large databases and leading scientific journals. 

The information is then organized systematically into topical reports such as Nutrition, Health, Fitness, Skin, Allergy, Ancestry, etc. 

Each report is further organized into traits, which provide actionable insights into your genetic type along with specific recommendations. Xcode reports are easily readable, understandable, and implementable. 

The core philosophy of Xcode reports, in contrast to Promethease's voluminous coverage of diseases, is to empower the user with actionable genetic information that they can use to enhance health and wellbeing. Each report is reasonably priced at around $20; additionally, there are package discounts if the user buys multiple reports together.

If you are not looking for anything specific and just want to satisfy your curiosity, then Promethease may be the way to go. Even then, it is very likely that you will be left scratching your head with a vast load of information that you can't make sense of. But, if you want specific, organized, and actionable insights from your genetic data about your health and wellbeing, then you certainly must try the Xcode Health reports.

[table id=2]

Summary

There you have it! With information, free is not always good and useful. A lot of users come to Xcode after having tried Promethease for $5. If you just want to satisfy your curiosity and not really looking for anything specific, then Promethease may be the way to go. But, if you want specific, organized, and actionable insights from your genetic data about your health and wellbeing, then you certainly must try the Xcode Health reports!

About Xcode Life

Updated on January 15th, 2022

1. How to read your Promethease report?

To read your Promethease review report you will need to ensure that you are accustomed to some of the terms that are found in their report like magnitude and repute. It is difficult to sift through thousands of pages in your report. Once you organize the pages as per your unique needs it becomes a relatively easy task to. 

2. What is Promethease?

Promethease is a do-it-yourself (DIY) tool for health genetic information from 23andMe raw data. It is a third party online tool that provides consumers information about their genetic variants and how they affect your health. After 23andme FDA ban on providing health reports, people started using tools like Promethease to get more information from their DNA raw data, other than just locating distant cousins. Though Promethease is a good tool built on a repository like SNPedia there are a number of factors to consider before you decide to upload your raw data to Promethease. Promethease is popular as a low-cost offering, but it’s also very technical and disease-centric. There are many alternatives to Promethease to analyze your 23andme raw data, that are easy to follow and understand. Below we present a feature by feature comparison between Promethease and Xcode Life Sciences.

3. How did Promethease gain popularity?

Promethease was one of the early companies to offer health reports based on 23andme data. When the FDA (briefly) banned 23andme from providing health reports, Promethease was the only alternative and gained popularity because of its (almost) free service.

4. How long does it take to get my Promethease reports?

Promethease takes approximately 20 minutes to generate health report from your raw data.

5. What does Promethease provide?

Promethease provides health report for $5 based on 23andme, Ancestry DNA, Family Tree DNA. Promethease provides the genetic risk for a number of diseases. Many users try the Promethease reports due to the cost aspect. However, there are several reports of panicked and confused Promethease users online.

6. What exactly do you get to know from a Promethease report?

Promethease is a wiki-style collection of peer curated (not expert-curated) genetic information. You can search `genes/variants/diseases’ as you would in Wikipedia. A Promethease report is essentially a data dump, leaving the user to wade through a whole lot of science, statistics, charts, and graphs. This is great for people who want to geek out and want to learn about all sorts of diseases they can get!!

However, if you want organized information that you can use in specific aspects of daily life such as Nutrition, Fitness, Personalized medicine, etc., to enhance your health and wellbeing, then you may not find the Promethease reports all that helpful. Promethease’ emphasis largely seems to be the variety of different diseases that one can get.

7. How do I understand my Promethease report?

Please be aware that your report may cause you anxiety. Many individuals carry risk variants that will not manifest in the form of a disease. Promethease report will indicate that your risk for several diseases is several times higher than the normal population- be prepared!  You will find many forums on the internet where users have shared their experience of being alarmed by their Promethease report and did further testing for that condition.

8. Will getting the health test from 23andme give me better results?

A lot of people think that getting the additional health report from 23andme will help them get better results. That is not true! Whether you order the Health report or the Ancestry report from 23andme, the raw data you receive is the same!

9. How does Promethease work?

This third party DNA raw data analysis tool, is a literature retrieval system from SNPedia which is a Wikipedia style repository where people can add information. It is not a systematic risk assessment tool. For example, for Alzheimer’s disease (AD), you will not get a summary of your risk for developing AD. Instead, you will get a list of scientific literature that is available that indicates or does not indicate your risk for AD for a specific variant. For a particular disease or trait, if there are 15 articles that report on that particular DNA location, based on your SNPs 2 information sources might indicate an increased risk, 5 might be neutral, and 3 towards the lower side. Promethease does not summarise these for you. Rather it returns all these 10 articles and makes you do the interpreting yourself. This is the major reason why many individuals are alarmed and confused by their Promethease report.

10. How accurate is Promethease?

The vast majority of human traits are polygenic, meaning, several genes contribute towards that trait. Even if one carries a disease variant, they may also be carrying variants that reduce the risk of disease. Even in the case of Monogenic conditions- where one single gene leads to disease, scientist have found individuals carrying these deadly mutations but apparently healthy with no sign of disease. In a majority of the cases, the genetic risk is a small contributor towards the overall risk of that disease/condition. So, one must consider all of these things in interpreting their report. 

11. Where does Promethease get all its information?

Promethease only relies on SNPedia. Several other notable and high scientific authority tools are left out from the Promethease reports.

12. How do I filter through the Promethease report?

It is impractical to sift through the dump of information that you get (anticipate about 48,000 rows of data). The tool is equipped with different kinds of filters aimed at assisting you. Some of them are gene names, haplogroup names, diseases, drug names (referred to as “medicines”), medical conditions, names of genes and race.

13. What is magnitude in Promethease?

Magnitude is a subjective parameter that measures the interest level of the information. Here is the table partially resourced from the SNPedia website that describes what each numerical value indicates.

[table id=1 responsive=scroll/]

14. What is Promethease repute?

Good repute: The variation has a positive influence on you.

Not set: There is no verified information on the nature of the variation.

Bad repute: The variation has a negative influence on you.

According to the SNPedia website, it is better to leave the repute as “Not Set” as all genotypes have a little of both the “good” and “bad” repute.

15. What are ClinVar diseases?

This option allows you to see only the SNPs present in ClinVar. ClinVar is a freely accessible public archive of information on genetic variations specifically with clinical implications. It is maintained by the National Institute of Health (NIH). When you filter using this option you will find all the medical conditions that have been formally labeled by ClinVar.

16. How is Xcode Life different from Promethease?

Xcode Life, on the other hand, includes expert-curated references not just from SNPedia but also from several large and high scientific authority databases, including UK biobank, Clinvar, OMIM, and leading scientific journals to name a few,  to curate the variant annotations. Disease risk is indicated as an average of all variants the individual carries and not a single variant. In this methodology, unless the individual truly carries a combination of several high-risk variants, their result will not be indicated as high risk.

The information is then organized systematically into topical reports such as Nutrition, Health, Precision Medicine, Fertility, Fitness, Skin, Allergy, etc. Each report is further organized into traits, which provide actionable insights into your genetic type along with specific recommendations for you. Xcode reports are easily readable, understandable and implementable. The core philosophy of Xcode reports is to empower the user with actionable genetic information that they can use to enhance health and wellbeing.

As an alternative to this third party tool, many people use 23andme raw data analysis and interpretation third-party tools and services.  One such provider is Xcode Life which is a global genetics and bioinformatics company which specializes in 23andme raw data analysis and interpretation using genetic raw data from all major international data providers such as 23andme, Family Tree DNA (FTDNA), AncestryDNA.com, Helix.com, Living DNA, National Geographic and others . Xcode Life provides all the information and much more, but there are key differences for you to note. These reports come with DNA raw data analysis and interpretation and specific recommendations for people with your genetic type. Counseling is also available, upon request. Xcode provides reports to individuals and professional practitioners such as physicians, surgeons, nutritionists, sports trainers, chiropractic and other professionals. These reports are focused and consumer-friendly and are designed specifically for practical use. 

[table id=2 responsive=scroll/]

Summary

There you have it! With information, free is not always good and useful. A lot of users come to Xcode after having tried Promethease for $5. If you just want to satisfy your curiosity and not really looking for anything specific, then Promethease may be the way to go. But, if you want specific, organized and actionable insights from your genetic data about your health and wellbeing, then you certainly must try the Xcode Health reports!!

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