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  • 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!

  • #2
    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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    • #3
      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.
      Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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      • #4
        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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        • #5
          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!

          Comment

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