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-   -   Distinguish sequencing errors and real mutations in mitochondria data (http://seqanswers.com/forums/showthread.php?t=76872)

cindylanzao 07-02-2017 06:24 PM

Distinguish sequencing errors and real mutations in mitochondria data
 
Hi,all

We are searching a silico method to distinguish sequencing errors and real mutations from mitochondria sequencing data. Please do consider that the heteroplasmy in mitochondria. Thanks!

Brian Bushnell 07-05-2017 10:54 AM

Is this question in the context of high-throughput sequencing? Or do you just mean, in general, you want to study mitochondrial and you have no data yet?

SNPsaurus 07-06-2017 04:13 PM

SNP callers like Lo-Freq are meant for mixed populations. We used it when developing PELE-Seq (paired-end low error sequencing) which is a wet lab approach to detecting low frequency mutations. We examined cancer mitochondrial genotypes and were able to detect sub-population heteroplasmy. You could detect heteroplasmy with just Lo-Freq, but would need to discard SNPs below ~1-5% depending on the read depth and quality.

cindylanzao 07-16-2017 07:33 PM

Quote:

Originally Posted by Brian Bushnell (Post 208963)
Is this question in the context of high-throughput sequencing? Or do you just mean, in general, you want to study mitochondrial and you have no data yet?

Yes, NGS data

cindylanzao 07-20-2017 12:30 AM

Quote:

Originally Posted by SNPsaurus (Post 209017)
SNP callers like Lo-Freq are meant for mixed populations. We used it when developing PELE-Seq (paired-end low error sequencing) which is a wet lab approach to detecting low frequency mutations. We examined cancer mitochondrial genotypes and were able to detect sub-population heteroplasmy. You could detect heteroplasmy with just Lo-Freq, but would need to discard SNPs below ~1-5% depending on the read depth and quality.

Thanks for your nice method recommendation. Another problem would be how to measure the heteroplasmy level of mitochondrial DNA. Thanks!


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