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.
It is usually downloadable in the form of a text, zip, or CSV file. When opened, you should see different columns that typically represent:
Most genetic ancestry testing companies let you download your DNA raw data file along with your ancestry test results, which can be analyzed to extract useful health information. Companies like AncestryDNA and 23andMe provide your DNA raw data in a text file format, which in some cases may be compressed as zip files when downloaded. Other companies like MyHeritage and FTDNA provide your DNA raw data in the CSV file format.
How to download raw data from 23andMe
How to download raw data from AncestryDNA
How to download raw data from Family Tree DNA (FTDNA)
There are many of you out there who uploaded your raw data to Promethease expecting to learn some insights on your health. As the name implies, the simplified Promethease report is a simplified version of your Promethease report.
The simplified Promethease report sources content from your Promethease report and organizes it in a topical, concise, easily readable and printable table format. [/vc_column_text][vc_column_text]In the Simplified Promethease report, all health category-related information is organized into a printable table.
The Simplified Promethease report has information from your Promethease report organized in the following topics.
Over the years, we have had several requests from our customers asking if we can re-interpret the Promethease report for them. The Promethease report is full of technical information that is difficult to interpret by non technical folks. We have taken this feedback and addressed this issue. The simplified Promethease report is topically organized, concise - giving you the most relevant information, and presented in a printable format.
You can receive your Simplified Promethease report by uploading your Promethease report to Xcode.Life website. Please select “Simplified Promethease” as the product option.
We have temporarily discontinued this report.
Clopidogrel or Plavix is a drug that is prescribed to help prevent blood clots. This is turn avoids blockage of blood flow that would otherwise lead to heart attack or stroke. The internal function of clopidogrel depends on how fast or slow it is metabolized by the system. The gene CYP2C19 is shown to have a strong influence in this regard. Certain genetic variants in the CYP2C19 gene reduces the activity of the CYP2C19 enzyme, causing individuals with such variants to be more prone to heart attack and stroke. Knowing in advance as to the nature of the CYP2C19 variant will help physicians prescribe a more accurate dose.
Once you upload your raw data from 23andMe, AncestryDNA or Family Tree DNA to the Plavix tool you will receive a report that includes 5 variants of the CYP2C19 gene. This gene encodes for a protein/enzyme that converts clopidogrel into its functional and active form. The variants *2, *3, *4 and *8 indicate reduced clopidogrel metabolism consequently lowering the efficiency of the drug. On the other hand, *17 variant is associated with increased clopidogrel metabolism. *1 is the neutral and the most commonly found version of CYP2C19.
Blood clotting is vital body function that prevents excessive loss of blood during injuries. However internal clots within a blood vessel can lead to heart attack or a stroke. Physicians prescribe clopidogrel (Plavix) for cases of internal clotting since this drug reduces the platelets, blood cells responsible for clotting, from sticking together.
Clopidogrel like several other drugs is enters the system in an inactive form. It is converted to its active form in the liver by enzymes. One of these enzymes, and the most important of them all is CYP2C19 encoded by the CYP2C19 gene. Polymorphisms in the CYP2C19 gene results in an increased or decreased protein function. This in turn influences the way clopidogrel is metabolised by the system.
Plavix is one of the most widely prescribed cardiovascular drug with more than 21 million prescriptions since its 1997 approval by the Food and Drug Administration (FDA). Prescribed in combination with aspirin, it helps reduce risk of heart attacks, treat chest pain, improve blood circulation to the limbs.
| CYP2C19 phenotype | Genotypes | Pharmacological implications | Therapeutic recommendations |
|---|---|---|---|
| Ultrarapid metabolizers | *1/*17, *17/*17 | Increased Platelet Inhibition. Decreased Platelet aggregation. | Standard Dosing |
| Extensive metabolizers | *1/*1 | Normal Platelet Inhibition. Normal Platelet Aggregation. | Standard Dosing |
| Intermediate metabolizers | *1/*2,*1/*3,*2/*17 | Reduced Platelet Inhibition. Increased Platelet Aggregation. Increased risk of CV events | Consider alternative antiplatelet agent such as prasugrel or ticagrelor |
| Poor metabolizers | *2/*2, *2/*3, *3/*3 | Significantly Reduced Platelet Inhibition. Increased Platelet Aggregation. Increased risk of CV events | Strongly recommended to consider alternative antiplatelet agent such as prasugrel or ticagrelor |
The Clinical Pharmacogenetics Implementation Consortium (CPIC) has developed certain guidelines that have been endorsed by several medical societies.They are designed to assist clinicians on how to use the results from genetic tests to determine the course of drug therapy for each patient. Genotype-based drug guidelines will help clinicians understand how a patient of a specific genotype would respond to or metabolize a particular drug. This will enable them to evaluate subsequent therapeutic options and to determine the dosage strength.
Important note: Your report may not contain all of the traits listed here depending upon the number of markers present in your raw data file.
A common aspect of a typical genetic ancestry report is understanding the population labels that match your DNA. This is expressed as a percentage value as many of you may have seen in your 23andme ancestry reports. When a report shows a relatively high percentage composition for a specific population then it is common to assume that you may have a recent ancestor from that population. A quick look at how companies come to these conclusions can help in understanding these results.
Ancestry testing companies use admixture mapping method for gene mapping. Different companies have a different technique. Companies like Xcode Life focus on South Asian ancestry while 23andme ancestry is mostly for the European population. While most companies rely on admixture, some have proprietary algorithms that utilize machine learning for their analysis.
23andme ancestry genetic testing uses a proprietary algorithm that determines your most recent ancestral location (within the last 3-5 generations). Following are some of the highlights of the 23andme ancestry analysis method:
It is extremely important that you understand the reference populations used in the classification, how population labels were determined, and what classification algorithm was used to determine your ancestry reports.
| Table comparing features of various service providers | ||||
|
Feature |
Xcode Life |
23andme | Ancestry DNA | Family Tree DNA |
| Ancestry composition | Focus on Global and South Asian ancestry composition | Focusses on Global population only | Focusses on Global population only | Focusses on Global population only |
| Mt haplogroup | YES | YES | NO | YES |
| Y haplogroup | YES | YES | NO | YES |
| DNA relatives | NO | YES | YES | YES |
| South Asian Ancestry breakdown | YES.
Detailed breakup for more than 40 ethnic groups in South, Central and East Asian Populations |
NO | NO | NO |
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.
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.
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.
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.
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.
| ATTRIBUTE | XCODE LIFE | PROMETHEASE |
|---|---|---|
| World Ranking on DNAtestingchoice.com | USA- #1 U.K- #1 129 reviews | U.K- #32 5 reviews |
| Description | Xcode Life is a global genetic testing company, specializing in a variety of genetic reports such as Nutrition, Health, Fitness, Skin, Allergy, among several others using raw data from any Ancestry company. | Promethease is a computer programme that was developed by SNPedia. It uses your genetic raw data to give you largely disease based reports.You will get to know which mutation confers what risk |
| Genetic raw data accepted from | ➤23andMe ➤ Ancestry.com ➤ Family tree DNA ➤ Genos ➤ DNA land ➤Genes for Good ➤My Heritage ➤WeGene ➤Helix.com ➤Living DNA ➤Ancestry.com ➤Living DNA ➤National Geographic and all other major international data providers. | ➤23andMe ➤Ancestry.com ➤Family tree DNA ➤Genos ➤DNA land ➤Genes for Good ➤My Heritage ➤WeGene |
| Ease of usage of report | The reports are on specific topics such as Nutrition, Allergy, skin, Fitness, health, precision medicine (drug sensitivity) and other topics. You don’t need the expertise to interpret the results as they are expert-curated. | Promethease results are do-it-yourself. This means that unless you are highly knowledgeable about the intricacies of SNPs and statistics, the process of interpreting their report can be cumbersome. |
| Recommendations | The report includes specific recommendations developed by a panel of experts. | Disease risk is communicated but no recommendations provided. |
| Focus areas | ➤Nutrition ➤Fitness ➤Health, ➤Precision Medicine ➤Carrier Status ➤Skincare ➤Ancestry ➤Weight Loss ➤Methylation and detox analysis ➤Allergies ➤ Breast cancer and BRCA | Promethease primarily focuses on Precision medicine and disease prediction. |
| Data safety | Client can delete their own information any time without having to secure permission from the company. | Deletes all data in 45 days |
| Organization of the report | The report is topical. The results are presented in a modular way. Example health, nutrition, fitness, Allergy etc. | The report is not segregated based on topics. You get to know which variants you carry and the odds ratio of developing the specific disease. |
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.
Some of you have tried multiple ancestry genetic tests to get the most accurate picture of your ancestry. Now that you want more health information from your DNA raw data you are unable to figure out which one works best.
This merger tool will remove those doubts. Simply upload the DNA raw data files that you have from different service providers. 15-20 minutes later a merged raw data file with more number of genetic markers will be sent to your registered email address. You can download that file and use it on third party DNA upload sites.
Some differences between AncestryDNA raw data and 23andme raw data are given below:
| Attribute | Ancestry DNA Raw Data | 23andMe Raw Data (v5) |
|---|---|---|
| Microarray chip | Illumina’ OmniExpress Chip | Illumina’s Global Screening Array |
| No. of genetic markers | ~700,000 | ~650,000 |
| Time taken to receive raw data file | 1- 24 hours | 1 hour |
| Format | txt | txt |
| Columns | rsID, chromosome number, chromosome position, allele 1 and allele 2 | rsID, chromosome number, chromosome position, genotype |
*Xcode Life does not have direct affiliate connections with any ancestry genetic testing service providers like 23andMe, Ancestry DNA, Family Tree DNA etc.
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