Your Genetic Genealogist: A Visit to Family Tree DNA's State-of-the ...

I have been a bit behind in my postings, but I didn't want to miss the chance to write about the incredible lab tour of Family Tree DNA's awesome facility, which was definitely one of the highlights of the 2012 FTDNA Administrator's Conference for me. I don't know if you all realize it, but Family Tree DNA is the ONLY company in the field that has their very own lab. They process everything from start to finish in their state-of-the-art facility in Houston for the thousands of different DNA tests that they offer. (Thomas Krahn notes that the individual Y-SNP tests alone number over 2900!) Some people might find it comforting to know that when ordering a test through FTDNA, this very trustworthy company is the sole handler of their DNA sample.?
This lab is even capable of processing exome and whole genome sequences. (These are available through Family Tree DNA's sister division DNA DTC, both a part of Gene by Gene). Max Blankfeld proudly told me that almost immediately after the announcement, they were already receiving orders for both tests. This is really exciting if you think about it. The first company to offer genetic genealogy testing is, according to The Genomics Law Report, also the only company currently offering these advanced tests-of-the-future in a "truly direct-to-consumer manner".? ("Gene By Gene probably does represent, however, the only commercial company currently offering a whole genome sequence in a truly direct-to-consumer (DTC) manner." DNA DTC: The Return of Direct to Consumer Whole Genome Sequencing, Dan Vorhaus, November 29, 2012)

Okay, on to the lab tour! Tim Janzen has kindly shared both his notes and his photos with my readers. I have added to Tim's notes just a bit, but most of what you see below was written by him. (I lost my notes and, although I did use some of them, the photos from my cell phone aren't as nice as Tim's photos from a "real" camera!)
On November 12, 2012, Family Tree DNA graciously allowed approximately 30 attendees from the FTDNA conference to take one-hour tours of their laboratory facilities in Houston, Texas. Bennett Greenspan, the president of FTDNA, primarily led the tours and Max Blankfeld led some supplemental tours (for those of us who showed up late!). The tour participants all donned lab jackets for the tour, making us feel very official (I got to be Thomas Krahn). Bennett explained the functions of a number of very important pieces of DNA equipment as he took us through the lab.? (Update - Thomas Krahn has added some very interesting and educational commentary throughout this post. I have added it below or just after what it is referencing. Thanks Thomas!)
One of the first pieces of equipment we viewed is used to extract the DNA from samples that are sent to FTDNA. The DNA is extracted through an automated process. Ninety-six samples can be processed at a time. FTDNA can complete 600 extractions per day and has a 98.8% success rate of extracting DNA on the first try.??

Another piece of equipment held primers that are used to test for specific short tandem repeat (STR) tests and single nucleotide polymorphism (SNP) tests. (Note from Thomas Krahn: We're taking the DNA from the DNA tubes and transferring? them to a reaction plate which contains the primers and the rest of the PCR assay. In a previous step the primers were distributed in the correct wells by automatically picking the correct primer pair so that the customer gets the segment sequenced where the marker is located that he's interested in.)This process is also entirely robotized so that multiple tests can be run at a time. The lab must repeatedly change the plastic covers on the pipettes to ensure that DNA from two different samples is never mixed as part of the testing. (Note from Thomas: We use the covers just as a precaution. In case a droplet is released from the pipetting tips during the movement of the robot we want to make sure that the primer assays are not contaminated with human DNA. With lids the primer library is safe. We would easily recognize such a contamination because of mixed basecalls, however primers are expensive and we want to protect the primer library from such a contamination. The chance that DNA samples mix is pretty small because we reduce the speed of the robot drastically while we have the tips over the DNA plate. In any case such a cross contamination could probably not be prevented with a lid method. The pipetting tip is discarded after the DNA from one person is distributed into all the assays that he ordered. Each DNA sample gets a brand new tip so that cross-contamination through the tip itself can be excluded.)

Bennett Greenspan proudly showed off the robotic DNA storage freezer that the company purchased in autumn of 2011. It was designed and manufactured by the engineering company Matrical Bioscience in Spokane, Washington. This piece of equipment took many months to design and build. After it had been built, it was disassembled and shipped to Houston. The installation process in the FTDNA lab took approximately 6 weeks. This chamber stores multiple small trays that hold 96 DNA samples each. The samples are held in small vials about 3/4 inch in height and about 3/8 inch in diameter.? The trays holding the samples are about 4 inches by 7 inches in size. There are thousands of trays stacked on top of each other in a -20 degrees Celsius chamber approximately 5 feet by 8 feet in size. A robot inside this chamber retrieves DNA samples from the approximately 175,000 samples that are stored there in a very strictly regimented and automated fashion. (Note from Thomas: I have just made a query and there are currently 173,012 DNA tubes in the store. However more than 50% of them have been added during the last year. 500,000 is the approximate number when the store is 100% full. We have rigorously sorted out empty and bad tubes from our repository in the past and we run regular compression procedures so that the racks are not half empty.) This robot is wired to a computer station outside the room. At the computer terminal a lab technician can enter a series of kit numbers for DNA samples for which additional testing has been ordered. The technician can then leave the area to do other things while the robot automatically retrieves the samples that were chosen. Ninety-six samples can be retrieved at a time and the retrieval process takes approximately 30 minutes. When the retrieval process has been completed the technician then returns to the storage unit, picks up the tray of samples and takes it to another piece of equipment for the additional testing that the customer has ordered, such as upgraded STR panels or individual SNP tests.

The functions of other pieces of equipment in the lab were also explained by Bennett. One machine is used for mitochondrial DNA sequencing. There is also another piece of equipment that is used to lyse the cells in each of the DNA samples and prepare them for extraction of the DNA. Additionally, Bennett showed us a room that contains thousands of DNA samples that have not yet been processed. These samples are held in long-term storage at room temperature for eventual use by customers who wish to order additional testing.?

Bennett also took us to a different room where the Geno 2.0 SNP chip tests are being processed. Approximately 154,000 SNPs are tested on a single chip for the Geno 2.0 test. Considering this, the chips are relatively small at approximately 1 inch by 4 inches in size. The actual scanning area is only 5mm by 5mm per assay. (Note from Thomas: On one of those glass slides there are 12 samples processed simultaneously.) At the time we were there, thousands of chips were being processed.??

Bennett showed us the new sequencing machines that were recently purchased so that the company can do large-scale complete genome sequencing.?The two new Illumina HiSeq 2000 machines can sequence 10 times as much as the Applied Biosystems DNA Analyzers are capable of using 454 sequencing and can sequence a complete genome in three runs. These machines are approximately 2000 times as efficient as using the primers used in Walk Through the Y testing and are 100 times as efficient as the Applied Biosystems 454 sequencer. (Note from Thomas: The HiSeq instruments are producing more sequences so that you get a higher coverage. If the machines are also more "efficient" for finding new mutations by the same scaling factor is still to be demonstrated. Simply scaling the average coverage of 400 KB from the WTY times 2000 would yield 800 MB, however the Y chromosome is only 50 MB long and only 20 MB can be effectively aligned to the reference sequence. To overcome this problem you'll want to enrich for target specific DNA and you'll want to barcode several samples so that they can be pooled together on one instrument run. This again reduces the "efficiency" by quite some significant percentage.) FTDNA has two new Illumina MiSeq DNA sequencers as well. The lab now has the capability to sequence six whole genomes in two weeks and 64 exomes at 80x coverage in one week.
The FTDNA lab tour was an exciting experience. It was very interesting to see all of the technicians at work running the various DNA tests that we as FTDNA customers have ordered. I was incredibly impressed by their vast array of state-of-the-art equipment. Hopefully, Bennett and the rest of his lab staff will continue to allow these tours for attendees at future FTDNA conferences. If you haven't seen it yet, it is well worth your time and I highly recommend it.

The following may be overkill for some of you. If so, I will just say goodbye to you here. However, if you are like me and you just can't get enough or want to gain a better understanding of how this all works from the inside, here is a series of photos from the lab tour.??

Comment from Thomas: FTDNA's automated equipment that is used to combine genomic DNA with primers to prepare a PCR assay. An in-house developed software controlls the pipetting steps so that the ordered assay is run with the correct DNA.

Comment from Thomas: This is the only step that still needs to be processed manually because we haven't found a robot that is able to remove the cotton swab from the vial yet.

Comment from Thomas: (This is) where the individual DNA sample tubes are re-arranged to the position where they will be processed in the assay. We try to prevent thaw and freeze cycles wherever possible because they will degrade DNA. So instead of taking out a complete plate (where we may only need a single sample) and thaw it completely, we use this technology of re-arraying tubes in the frozen state so that only the processed samples will be thawed and all other samples will stay frozen. The DNA samples/plates are actually stored in the back compartment and on the left side. Those areas are not clearly visible in the image.?


Comment from Thomas: The recipe for the liquid in the sample vials is optimized for long term storage under a large variety of storage conditions. Essentially the high salt concentration will suck out all water from inside the cheek cells (by osmosis) so that the cells form compact clumps and conserve their ingredients. This makes the sample more resistant to mechanical shearing and the high salt concentration also inhibits growth of micro-organisms that could digest the cells. The downside of this is that we need to use harsh mechanical forces when we enzymatically want to open the cells to extract the DNA. Shaking a 2 ml sample tube in an upright position doesn't really move the liquid in the tube a lot. Therefore we turn the tubes horizontally and shake them along the tube axis where the liquid has a longer path to accelerate. This method has been proven to be very effective.







Comment from Thomas: Before we dispose the chips to the glass recycling facility, we temporarily store them for a few weeks. During a 48-hour time frame they are still good and since they are barcoded we may have the chance in rare cases to re-scan a chip in case some bad read happened at the scanner.



Comment from Thomas: In order to get ultrapure water for molecular genetic assays (such as PCR) the tap water needs to pass through several steps:
1.) Pre-filter to remove particles such as sand and rust from pipes
2.) Membrane filters to get rid of small particulate material
3.) Ion exchangers to remove Ions and salts
4.) Reverse osmosis to remove organic compounds. At this stage we use the water for general cleaning purpose such as for the lab dishwasher and for rinsing flasks. However to get PCR grade water we continue with:
5.) Another step of ion exchange and reverse osmosis in a laboratory grade water purification system to remove any contamination coming from the plastic tube piping internal of the lab.
6.) Then the water passes a sterile filter before it is bottled in a glass flask to remove bacteria and other micro-organisms.
7.) Finally the bottled water is heat sterilized in an autoclave at a temperature that should degrade all possible DNA chains that may have survived to this point.

We also have a room with two air compressors that supply compressed air for the robots. One of them is a backup system because at an interruption all robots will stand still. They are in a separate room across the hallway because they're quite noisy and produce a lot of heat.

Comment from Thomas: Each lane represents a sequencing trace where the bases are displayed in 4 different colors. This display format gives the technician a quick overview about the quality of the complete run. The fluorescence intensities are digitized by a analog to digital converter so that it can be saved on a computer, but they still represent analog measurement values. When talking about a digital output the impression could arise that the display shows the scored base-calls which is really processed in a later step.

















Thanks to Tim and Rachel Janzen for sharing their photos, Tim for helping to write this and to FTDNA for the spectacular tour.

Source: http://www.yourgeneticgenealogist.com/2013/02/visiting-family-tree-dnas-state-of-art.html

Bosses Day 2012 Arlen Specter Winsor McCay Amanda Todd washington nationals Gary Collins bus driver uppercut