One of the first things most people think about when it comes to genetic testing is privacy. These concerns are even more important when it comes to Whole Genome Sequencing (WGS), because unlike consumer genotyping (which only contains a tiny fraction of your DNA), Whole Genome Sequencing contains all of your DNA. We’ll go over privacy concerns first, and then we’ll tell you about all the different Whole Genome Sequencing options.
Privacy concerns and Direct-to-Consumer Testing
Some make the argument that it’s not safe to get sequencing or genotyping from third-party companies because their health data is at risk. While this is a valid concern, many don’t realize that you can always opt-out of genetic research and selling of your genetic data with virtually all companies that offer direct-to-consumer testing. Fortunately there are many US Federal and State privacy laws that are protective of privacy. According to the ACLU, “There are at least sixty bills pending in eighteen state legislatures that would provide protection against genetic discrimination in either the insurance or employment setting.” And there are even more strict European laws that 23andMe and other providers that do business in Europe have to adhere to.
There is also concern about health insurance discrimination. Under the Genetic Information Nondiscrimination Act (GINA), insurance companies are not allowed to discriminate based on genetic information. While certain states and regions have privacy protections, GINA does not protect consumers when it comes to life, disability, and long-term care insurance. This is something to be aware of.
In my personal experience, insurance companies will discriminate if it’s in the economic interest despite the laws stating that they are not allowed to. Proving discrimination can be a very hard thing to do. By getting tests direct-to-consumer, insurance providers or doctors do not have to see your testing unless you authorize them to. And when it comes to giving genetic data to other industries, it is of my opinion that you have the right to not disclose because of your right to privacy. However, I am sure my personal opinion is open to debate.
When I look at the big picture, I believe that when it comes to concerns about privacy, there may actually be more privacy by not going through your doctor and insurance — especially if your data is de-identified or on the blockchain.
If your primary concerns are about health and a healthcare provider accepting genetic testing data as valid, you may want to consider getting a test through a medical provider. However, testing through your provider often is not as comprehensive as testing through a direct-to-consumer Whole Genome Sequencing company. This may be due to the fact that medicine is on average 17 years behind translational research.
Choosing a Whole Genome Sequencing (WGS) Company
We are in the early days. The industry is rapidly evolving and start-ups come and go. For this reason, it’s possible that this post may be outdated in the matter of weeks or months.
There is Whole Genome Sequencing, and there is low-pass Whole Genome Sequencing. For sequencing with high quality and accuracy (up to 99.99%), you want to choose a company with 30x or greater sequencing. 30x means that the sequencing machines passed through all of your DNA approximately 30 times. Low-pass sequencing is innovative, but it comes at the expense of accuracy (about 99%). Low-pass sequencing has typically been offered at 0.4x, meaning the sequencing machines only pass through about 40% of your DNA once. An advanced method, called imputation, uses statistical methods to infer unobserved genotypes so you have many more variants than what was sequenced.
This is a complex and confusing subject, so if you feel lost about this technical jargon, you’re not alone! Basically, it’s an inexpensive way to get a lot more data than you can get from genotyping companies such as 23andMe and AncestryDNA.
Dante Labs is the first company I am going to mention because they are truly going for affordability, offering true clinical-grade sequencing and pushing down prices in the industry. This company has had a lot of start-up problems. In the past, they have taken 6 months or more to deliver results, and occasionally people have waited over a year. Now that they have moved their Sequencing center to Italy instead of outsourcing, their delivery times have drastically changed. There are now reports of people getting their data in as little as a couple weeks or couple months depending on how much you pay for expediency. However, with these changes, there have been some quality control issues where consumers weren’t getting exactly the product that was advertised. For example, they would order 30x sequencing, but maybe only get 15x or 20x data. To give a little bit of credit, Dante Labs is addressing these issues as they happen. If ordering through this company, I suggest joining the Dante Labs Customer Care (Official) Facebook group as well as the Dante Labs Customers (Unofficial) group for the best customer support.
Despite waiting 5 months or so, I am very happy with the quality of data I received from two kits I received Dante Labs. I have received all of my raw data including FASTQ, BAM, and VCF files. But each customer may have their own unique experience. If you are planning on purchasing, please be aware of the pros and cons of going with Dante Labs.
$299 plus subscription ($9.99/mo to $19.99/mo)
Nebula offers 30x clincal-grade Whole Genome Sequencing. Nebula is a Harvard-backed startup (George Church being the founder) with a very compelling platform. They are setting the stage to compete with leading consumer genotyping companies like 23andMe and AncestryDNA. Nebula provides relevant health information such as true polygenic risk scores for disease risk prediction and have a constantly updated research library and other exploration tools. Nebula was founded on the principles of privacy and they use blockchain technology for the security of your DNA data.
Nebula is coming out with Y-DNA and mtDNA Ancestry tools that utilize Family Tree DNA’s (FTDNA) enormous ancestry database. If the Ancestry tools are done well, Nebula may end up becoming the preferred WGS sequencing company for both amateur and professional genetic genealogists.
The cost of the subscription may seem like a lot considering that the popular consumer genotyping kits don’t require a subscription. You are paying for weekly updated reports based on the latest scientific discoveries. This should be appealing to those with a background or interest in scientific research and how it relates to their genome. However, if you are primarily interested in data, you can simply pay for the monthly subscription and cancel your account after you get the data.
Sanos Genetics shows promise to be more competent and more honest than Dante Labs, but it comes at a price! As of this post, Whole Genome Sequencing is being offered at £950 and Whole Exome Sequencing plus genotyping is £450. But if you upload data from 23andMe, AncestryDNA, or MyHeritage, there is a £125 pound discount. With the discount, Whole Genome Sequencing is £825 and Whole Exome Sequencing is £325.
Full Genomes Corp
This is definitely one of the more spendy options. But if money is not a huge concern and you want superb data, this may be a good choice.
30x Sequencing starts at $1150. And if you want the latest 250bp or linked-reads technology, the price currently comes in at $1800 and $2900 respectively. Optionally, if you want to save some money, they have a 20x product for $825 and a 15x product for $645.
Sure, you’ll probably get good data, but these prices probably are not in the range of the average consumer.
Veritas Genetics is not currently conducting business in the United States. Gencove, which offered a low-pass sequencing product is no longer selling to consumers.
This list takes a lot of time and is a work in progress. More companies will be added. If you want a company included, please post in the comments below.
In the meantime, if you want information about more Whole Genome Sequencing companies, check out this List of Personal Genome Sequencing and Interpretation Services from Harvard University.