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Old 07-02-2017, 06:24 PM   #1
cindylanzao
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Default 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!
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Old 07-05-2017, 10:54 AM   #2
Brian Bushnell
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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?
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Old 07-06-2017, 04:13 PM   #3
SNPsaurus
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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.
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Old 07-16-2017, 07:33 PM   #4
cindylanzao
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Quote:
Originally Posted by Brian Bushnell View Post
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
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Old 07-20-2017, 12:30 AM   #5
cindylanzao
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Quote:
Originally Posted by SNPsaurus View Post
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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