Last week I wrote about the results of my Family Finder autosomal DNA test by Family Tree DNA (see “A Review of Family Tree DNA’s Family Finder – Part I“). The Family Finder test uses a whole-genome SNP scan to find stretches of DNA shared by two individuals, thus identifying your genetic cousins (and will soon include the Population Finder analysis of admixture percentages). I currently have over 33 genetic cousins in Family Finder, and I’m working with them to identify our common ancestor(s).
The Affymetrix microarray chip used by FTDNA includes over 500,000 pairs of SNPs located on the X chromosome and the autosomes (no Y chromosome SNPs). Via SNPedia:
FamilyTreeDNA uses an Affymetrix Axiom CEU microarray chip with 3,269 SNPs removed (563,800 SNPs reported) for autosomal and X (but not Y or mitochondrial) ancestry testing for 9. Other sources have cited 548011 snps. This platform tests 1871 of the 12442 snps in SNPedia.
FTDNA states that the Family Finder test is not intended to be medical. From the FTDNA FAQ:
Question: Is the Family Finder test medical?
Answer: No, it is not.
This is entirely accurate of course; FTDNA does not analyze the test results for health, traits, or other medically-relevant information, and does not provide the user with any medical information or analysis tools that might reveal medical information.
However, when DNA is involved there is almost never any such thing as a completely non-medical test. It’s often impossible, at any given point in time, to know which of an individual’s SNPs might be affiliated – remotely or closely – with a medical state or condition. Ann Turner recently wrote the following at the Rootsweb GENEALOGY-DNA mailing list in response to another individual’s question:
Question: “I am wondering if FTDNA really left out the genes and just lists the intergenic areas?” Answer: “No, the claim was that they scrubbed medically significant SNPs. They still include over 1600 SNPs with entries in SNPedia, which would have some phenotype implications, according to an analysis posted at DNA-Forums: http://tinyurl.com/27slbj8.”
Indeed, as of August 3rd, 2010, there are 12,442 SNPs in SNPedia, of which a total of 1,871 are tested by Family Tree DNA’s Family Finder test.
Promethease Analysis
I was curious as to what information my Family Finder results might contain, so I ran my results through Promethease, a free software tool used to analyze whole-genome SNP scan results. From the Promethease website:
“Promethease is a tool to build a report based on SNPedia [an impressive database of annotated SNPs] and a file of genotypes [i.e., your Family Finder results]. Customers of testing services (23andMe, deCODEme, Navigenics, …) can use it to learn more about their DNA. It can also pool the data from multiple testing services. The program runs for approximately 3 hours. An optional payment per run unlocks extra features and reduces runtime to approximately 5 minutes.”
Similar to several of the other autosomal SNP scan testing companies, Family Tree DNA allows the customer to download their own DNA testing results. Autosomal results and X-chromosome results are separately downloaded as compressed files which can then be extracted for analysis. After downloading and installing Promethease, I ran the program using just my Family Finder results (after paying the for a faster runtime. I’m impatient.).
Promethease was indeed able to analyze my Family Finder results and returned a report that included 1881 annotated genotypes. Here, for example, is a screenshot from my results (click to embiggen):
In addition to the “most interesting snps” category, there are categories for “medicines”, “medical conditions” (below), and others. After clicking on “more” for each category, I receive more information about those annotated SNPs. To get an idea of what the full results look like, there are a number of people who have shared their real promethease reports.
Promethease also lets you upload your results from different companies, so I also analyzed my Family Finder results together with the results of my 23andMe test. Since there isn’t much overlap between the SNPs in the FTDNA test and the SNPs in the 23andMe test (see this ISOGG Wiki page for more information about FTDNA’s testing versus 23andMe’s testing, for example), I was able to extract information about 7691 of my personal genotypes using the SNPedia database (compared to 1881 genotypes with my Family Finder results alone). Thus it appears that the 23andMe results are more likely to contain SNPs that are annotated in SNPedia. This isn’t surprising considering that, according to reports, FTDNA designed their chip to contain fewer annotated SNPs.
My Results
Since I have taken whole-genome tests before and was familiar with both testing and the interpretation of results, my report was not surprising. Indeed, I was already aware of my increased risk of type-2 diabetes (see Personalized Genomics: A Very Personal Post ), as well as the fact that I’m “probably light-skinned” (see e.g., my bathroom mirror). However, it might not be clear to those taking these tests that the results contain a large amount of medically-relevant information. This can be problematic when considering the fact that Family Finder test-takers might share or reveal their data with other people. Indeed, even knowledge that you share a region of DNA with another person can reveal medically-relevant information that the two people share in that region.
On the other hand, this ability to apply Family Finder results to information in SNPedia will be of great interest to a number of test-takers who are interested in this type of genetic analysis. This type of “do-it-yourself biology” is becoming more and more popular everyday. Although there is still much debate regarding the utility of such information, exploring one’s genome can be highly interesting, informative, and interesting (and, to date, no one has adequately shown that exploring one’s genetic data is harmful for anything other than a tiny minority of people).
Conclusions
In conclusion, it is important for consumers to realize that ALL genomic information has the potential to reveal medically-relevant information (even Y-DNA and mtDNA results can include health information, for example). By no means, however, am I suggesting that people should forgo whole-genome SNP scans, or that governmental regulation is needed. Instead, I think it is vital that consumers understand the testing process and possible outcomes before testing, and I fully believe that it is the consumer, not the government, who should decided whether the consumer should or can undergo testing.
Indeed, rather than expend thousands of dollars in hearings, [faulty] investigations, and regulation, the government could use that money to fund programs that educate the population about genetics and DTC testing. After all, we are entering a future that will involve our personal genomes in many aspects of our lives.
I’m interested to hear your thoughts on this subject, so please feel free to leave a comment below.
(Disclaimer: Please note that I received my Family Finder test without charge from Family Tree DNA for purposes of this review. Regardless, I have attempted to review this product as honestly and as objectively as possible in order to provide valuable information about Family Finder to my readers. I am also a consultant for Pathway Genomics.)