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  #1  
Old 10th July 2014, 09:21 AM
penguin penguin is offline
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Next generation sequencing?

Hi- does anyone want to comment on FTDNAs switch for mitochondrial dna analysis to Next Generation sequencing (Illimuna) from previously having used direct sequencing (Sanger)? For example, can they still cover all 16,000+ positions accurately?

I've seen the following on ftdna, but don't see any further details or a discussion:
--------------------
How do you perform mtDNA (mitochondrial DNA) tests?

Family Tree DNA currently uses next generation sequencing (NGS) technology to process all mtDNA tests. We use:

The Illumina MiSeq Platform
At greater than 2000X coverage

Note: Prior to April 2013, Family Tree DNA performed mitochondrial DNA (mtDNA) tests by direct (Sanger) sequencing.
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  #2  
Old 18th July 2014, 12:18 AM
fmoakes fmoakes is offline
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Quote:
Originally Posted by penguin View Post
Hi- does anyone want to comment on FTDNAs switch for mitochondrial dna analysis to Next Generation sequencing (Illimuna) from previously having used direct sequencing (Sanger)? For example, can they still cover all 16,000+ positions accurately?

I've seen the following on ftdna, but don't see any further details or a discussion:
--------------------
How do you perform mtDNA (mitochondrial DNA) tests?

Family Tree DNA currently uses next generation sequencing (NGS) technology to process all mtDNA tests. We use:

The Illumina MiSeq Platform
At greater than 2000X coverage

Note: Prior to April 2013, Family Tree DNA performed mitochondrial DNA (mtDNA) tests by direct (Sanger) sequencing.
http://res.illumina.com/documents/pr...troduction.pdf
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  #3  
Old 19th July 2014, 07:50 PM
penguin penguin is offline
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Thanks much. That was helpful. Do you (or anyone) know what coverage FTDNA uses? (for full mtdna, or even for their autosomal test)And optimally, if anyone knows that for 23andme too, it would be great to compare. I'm guessing its higher here at ftdna.
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  #4  
Old 20th July 2014, 09:20 AM
Ann Turner Ann Turner is offline
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Quote:
Originally Posted by penguin View Post
Thanks much. That was helpful. Do you (or anyone) know what coverage FTDNA uses? (for full mtdna, or even for their autosomal test)And optimally, if anyone knows that for 23andme too, it would be great to compare. I'm guessing its higher here at ftdna.
You're using the term coverage to mean how many times a given base position is read? That concept applies more to next generation sequencing (rather than the chip method for detecting known SNPs, used by 23andMe, AncestryDNA, or the Family Finder test at FTDNA). The chip method does have multiple chances to read a SNP, but that's part of the Illumina manufacturing process.

As stated in the FAQ, the NGS method for mtDNA has an average of 2000 reads per base position, achievable because there are hundreds or even thousands of mtDNA molecules in each cell. The NGS sequencing coverage for nuclear DNA is typically 30, 50, or 80X.
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  #5  
Old 9th January 2017, 04:03 AM
Schokolade Schokolade is offline
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NGS is much more sensitive than the old Sanger method and more powerful and accurate than chip method.
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  #6  
Old 9th January 2017, 10:43 AM
Schokolade Schokolade is offline
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As far as I know it seems that 23andme uses chips. At the moment FT DNA seems for me the best option.
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