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Old 3rd October 2017, 06:21 PM
penguin penguin is offline
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Next generation sequencing?

Does anyone know where I can find some details of whether and how they are using the Illimina Miseq platform for the mtdna tests? Read that somewhere once but can't remember where and don't think any more details were provided. (And if anyone knows/remembers when they switched over to current methodology and what they used before). I've looked through the dreadful "learning center" and googled it and checked for links on the main page but not finding stuff. Thanks.
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Old 3rd October 2017, 09:46 PM
KATM KATM is offline
mtDNA: K1a3 | Y-DNA: R-L1308*
 
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Quote:
Originally Posted by penguin View Post
Does anyone know where I can find some details of whether and how they are using the Illimina Miseq platform for the mtdna tests? Read that somewhere once but can't remember where and don't think any more details were provided. (And if anyone knows/remembers when they switched over to current methodology and what they used before). I've looked through the dreadful "learning center" and googled it and checked for links on the main page but not finding stuff. Thanks.
See my answer and another one to your other post on this topic in the "Grumbles and gripes" forum.
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Old 18th January 2018, 07:21 AM
chr chr is online now
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(the thread KATM mentions is named '"learning center" driving me nuts'.)

I can't currently find other first-hand and up-to-date information published by FTDNA about the technology used for mtDNA tests other than the ambiguous "Return-Policy" (https://www.familytreedna.com/privacy-policy - see section "MtDNA and Y-DNA Tests (Sanger and NextGen Sequencing)").

I asked the support whether my HVR2 region test - part of "mtFull Sequence" product - was done with "NGS sequencing with 2000+ coverage" and they confirmed. (The reason behind my question was that I wanted to get the C:T ratio of my detected heteroplasmy, and they also gave me the exact percentages for this position, which is great!)

So in my case I can be sure they used NGS; but it could be possible they still use Sanger (which I believe is still an equivalent test and not outdated) in some cases, i.e. for "mtDNA Plus", given that they split up the test in "HVR1", "HVR2" and "Coding Area", which would not be needed for NGS, but be typical for Sanger. They also use heteroplasmy detection thresholds that are typical for Sanger testing (but they may be doing so to maintain backwards-compatibility; and it also makes sense not to report every non-inherited micro-heteroplasmy, so they're probably doing it right). This is just my thoughts and I don't want to spread rumours. I asked them if they still use Sanger sequencing for mtDNA a week ago, and I will share the answer with you when I get it.

Unfortunately most of the mtDNA FAQs (in Learning Center/Expert's Handbook/mtDNA Tests) are still 'uh oh / Houston we have a problem', so that's of no help currently ... hope they fix it soon, (their) "team is actively investigating the issue and working towards a resolution."
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