(Cross posted to Azores, Madeira, and Island Routes) I found this to be one of the more interesting lectures and it really helps gain an understanding into what the lab goes through when extracting your DNA. Presented by Dr. Connie Bormans, lab manager
The DNA samples goes through 3 stages: Pre-analytic, Analytic, and Post Analytic. 1) Pre Analytic. This is the actual sample collection by the lab meaning that your sample was received and one vial goes to the lab and the other goes to storage. Problems encountered in this stage could be vials are received and someone has written some other code (kit number) over the bar coded kit number. Or it could be no swab in the tube, 2 swabs in one tube, little to no buffer in the tube (usually due to leakage or spillage). NOTE: They are changing the sticks that the swabs come on to try to eliminate some of these problems. Instead of a plunger where you push the end of the stick, you'll be able to snap it off at the black line. This is also going to allow full automation of this process. (Margaret-Brad is making a new video on this process, so if you will be so kind as to translate it into Portuguese when it becomes available) 2) Analytic: This stage has 3 parts. Extraction - The DNA is measured for concentration and purity. Any samples not passing this quality control stage are discarded and a new swab is requested. Storage & Retrieval - One active sample per customer may in the lab at all times. It's OK for multiple tests to compete for the same sample (ex: Family Finder and YDNA are both being run). Test processing - Different tests are run at different speeds (a Family Finder takes 2-3 weeks, one of the fastest tests to process). This includes the sample being prepared, the time on the machine, and analysis. Next Generation Sequencing tests (BigY) have additional quality control steps. 3) Post Analytical: This is where the data analysis and more quality control occurs. It depends on the test type and the number of samples in the batch. Some problems encountered in this stage are "dropouts" where the DNA is missing STRs or SNPs (for YDNA). The sample has to be requeued. Sometimes there's a failed reaction and they requeue it only once. If it fails a 2nd time, they will reextract again. If it's a poor quality sample the sample is requeued only once. Some other interesting information. Family Finder Call Rate. This is a quality control standard. How much data is there at that particular location in the DNA. The DNA MUST BE greater than 97%. If it is below 97% then they need to start over with a new extraction. If the sample fails repeatedly it could be degraded, sometimes there could be nulls, sometimes anomalies, the DNA looks contaminated, or the sample is not the correct gender. Family Finder predicts the gender and it must match the gender on the kit. If they don't match, it holds up the results in the whole batch (576-2000 samples). I spend a lot of time "fixing" the gender on the kits. My dad's DNA has been in the system for almost 10 years now. He is alive. It's his name and his picture on his account because it is his DNA. It all belongs to him. I just manage it. And one day, when he is not here, it will still be his name, his picture, and his DNA. NOTHING will change. You should do the same for the kits you manage. And the same for YDNA. The YDNA needs to be for a man. Don't go changing dear old Uncle Bob's picture and name that you manage for him because he has passed on. Leave it. It's Uncle Bob's DNA. You know how confusing it is to see that YDNA results are now in for Rosemarie Capodicci? I log in to my dad's kit and there's Rosemarie's picture and "she" has YDNA results? I have to email her to find out that it's her Uncle Bob and she's decided now to do YDNA on his sample. Now she needs to go back in and change his name back to Uncle Bob and his picture too. Leave it alone. For ALL Upgrades - When you order a 37 marker test (for example) and later you upgrade to 67 or 111, they actually rerun some markers from the previous test and the new results are compared. If differences exist, they will require review. That can hold up your results. BigY- Coverage must meet minimum. Low coverage are requeued. WHAT HAPPENS WITH THE VIALS: If you were to order every single test that FTDNA has to offer, they can get every single test out of one vial (assuming it was a good scraping). Every single test! Wow! Most of us don't run every single test at once. We run one test and at some point in time we chose a different type of test. They go back to the opened vial and use that one. Here's the thing: They are finding that the "shelf life" of an opened vial is about 2 years. Now I must say something about FTDNA: They always, always like to error on the side of caution. 2 years is probably a trouble free extraction. I've seen samples that are 8 years old run off of the same vial and they go through. However, it was difficult and there were problems with quality control and the call rate. I had marked the kit as deceased. The lab was willing to make concessions and they do this on a case by case basis. Unopened vials have almost infinite shelf life. It is very, very long. The buffer is the same one used by National Genographic out in the field - the hot, hot Sahara desert, the frozen North Pole, etc. It will preserve the DNA as its supposed to do. The current deep freezer was purchased in 2011. It has almost reached capacity. They are purchasing a new freezer. Other sources of DNA, such has hair, envelopes, teeth, etc. They are technically possible, but the success rate is just so low that FTDNA does not offer this type of testing (mentioned in another email on the Azores List). I will type up other conference notes as time permits during the week. Cheri Mello, Family Tree DNA Administrator (volunteer) -- You received this message because you are subscribed to the Google Groups "Azores Genealogy" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. Visit this group at https://groups.google.com/group/azores.
