It’s that time of year again! Genetic Genealogy enthusiasts have gathered at the Sheraton North Houston for the 9th Annual International Conference on Genetic Genealogy. This year lab tours were offered on Friday as well as Monday, which is great for those who plan to fly out on Sunday. Bennett Greenspan, President of Family Tree DNA, welcomed our group to the lab.
The lab at Family Tree DNA is a fully functional five or six day a week lab. Our first stop was the Pre-PCR area where DNA has not been amplified. Once DNA is amplified, it never returns to this area. Our group put on lab coats and anyone with open-toed shoes put on booties.
Bennett explained that all of the tubes have a red cap instead of the old tethered cap style. The machine shown below automatically fills each tube with the buffer that allows the sample to sit for long periods. The buffer arrests any potential for bacterial growth while the DNA is in the tube. About 400 per hour can be produced by this machine.
The next robot extracts approximately 600 samples per day during one normal shift. Around Christmas time the process is doubled in order to extract 1,200 samples per day.
The liquid handling robot takes DNA, puts it into a daughter plate, and puts a primer mix and a master mix in the well. Master mix is a neutral solution and the primer mix might be for any of the Y-DNA SNPs that have to be used for a confirmation purpose.
DNA samples that arrived yesterday or the day before that have not been put into a batch remain in the drawer. Often this drawer is full and during the busy season, the drawer below it gets full, too. This could cause up to two weeks delay for extractions and this is where that backup could begin.
Six plates of DNA are shaking on the shaker below. In the lab they put in Proteinase K, otherwise known as monosodium glutamate. This is used to rip open the cellular wall, allowing access to the DNA. There is a typical capacity of 600 per day. The kits shown above in the drawer did not make this batch and will be done during the next extraction.
Once the samples are extracted, they go into a $600,000 freezer that is also a robot. This maintains a temperature of -20 degrees and holds about 560,000 samples. It is currently half full. At the VA Hospital in Massachusetts, there is one of these one story higher and 32 feet long that holds 5 million DNA samples!
Every one of the hundreds of plates in the machine have a barcode so that the system knows which plate it is grabbing. It can change tools from a gripper to a puncher, which punches the sample out of the plate onto the deck. Then the robot will get a picking tool to pick up the individual sample out of the deck and put it into a daughter plate.
The plate shown below has several samples in it.
You can see on the bottom of the samples that there are two-dimensional barcodes on most of these samples. The two samples without barcodes are for quality control.
During he first week of November, Family Tree DNA was awarded certification by the College of American Pathologists. By the first of December they should have their document and then will be both a CAP and CLIA laboratory. In addition to being able to sequence for genealogy and anthropology, the lab will be able to do resequencing for cancer and provide tests of a medical basis. This gives them a lot of opportunities to be a viable and competitive company.
A reverse osmosis process is used to make water for the laboratory. This is great for cost as well as consistency.
Leaving the Pre-PCR area and heading into Post-PCR, the first machines we encountered were the 3730s. This technology is 15 years old and work is being moved away from these machines.
Chips are kept in freezers. Typically after a delivery, two freezers would be full.
The lab even has a dishwasher. No, it’s not what you might think. There are absolutely no snacks allowed! The dishwasher is used for glassware and plastic to be washed and sterilized.
Debra was hard at work when we visited the lab.
The Illumina IScan takes a chip with 12 samples on it. Twenty-four chips per liquid handling robot per day are done. This means that 576 samples per day are done. If they need to double production, someone needs to work a later shift. Normally everything is confined to a single shift but sometimes more shifts or more than five days per week are necessary during the holidays.
The MiSeq can run 96 samples at a time. The lab can process 576 samples in a week on the MiSeq. The up percentage is about 93%, which is amazing and has created great efficiencies in the lab.
The next two machines are also part of the Next Generation Sequencing. These machines can run the exomes and have greatly exceeded expectations, running hundreds of exomes since they were installed last year.
Full genomes can also be run. All 23 chromosomes create a file so large that it’s given on a hard drive. These files are hundreds of gigabytes in size. To load up this information and align it can be very time consuming. They did one that took 18 days! Hopefully the new staff will help to make this situation better over time. Exome orders are increasing despite the fact that Bennett tries to talk a lot of people out of ordering them. This machine is typically run two days per week with 16 exomes each. On occasion it’s run three days per week.
On occasion samples do fail when they are run. You can see on the screen below that one red spot is a fail. This will automatically be kicked out and rerun. If it fails again, they will look at how badly it failed to see what’s wrong with it. Maybe the DNA concentration was too weak. Sometimes the DNA sample is more bacteria than human DNA. If it fails a second time, the extra vial is tested. The failure rate with the buccal scrapes is 1.6-1.7%. Illumina says to expect a 2% failure rate.
Finally, we stopped to see the place where extra vials of DNA are stored. This is called the C Vial Storage Room. If the first DNA was a bad scrape or it’s been a lot of years, this sample can be used as backup. Each kit can be located by box and location number. As more kits come in, these boxes are refilled. There are currently 612,000 unextracted DNA samples waiting for use! This room does not need to be refrigerated because the DNA has not been extracted and is still in the buffer solution. This could sit for years in your car and it would be fine.
A big thank you to all of the staff at Family Tree DNA who continued working around our group while we came for a visit!!!
Now, for conference!
© 2013, Jennifer Zinck. All rights reserved.