Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Coverage depth vs mutation frequency

    Hello,

    the group I am working in is preparing for some targeted (~50 genes) analysis of variations on tumor samples using the Ion Torrent platform. As the number of chips needs to be minimized due to cost, we were trying to design the experiment to obtain the best results out of our limitations.

    This brings us to the problem: determining the optimal coverage depth per mutation frequency. In other words, what is a good coverage depth to detect mutations with these frequencies:
    • 20%
    • 10%
    • 5%


    Is there any publication or reference where I can get an ideal grasp of this so we can adjust the experiment design accordingly? Thanks in advance.

  • #2
    hi, just wondering if you ever got through figuring this out. I would really appreciate your thoughts on how we could address the same problem that we have right now.

    thanks

    Comment


    • #3
      In my simple view of statistics, I would calculate it like this:
      A mutation at 10% frequency has a .1 chance of being seen by a read.
      So a .9 chance of not being seen. The chance of it not being seen in 10 reads is .9^10 = .35 (35%).

      To see 95% of the mutations at 10% frequency, you would solve:
      .05 (5% chance of not being seen) = .9^X
      X = log .05 / log .9 = 28X coverage.

      This is idealized and doesn't take into account variation in coverage, etc. Unfortunately, if the average coverage is 28X, then regions of higher coverage won't have much higher chances of seeing the mutation (40X coverage will have a 99% chance instead of a 95% chance), but regions of lower coverage will have much worse performance (15X coverage will see only 80% of the mutations).
      Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Latest Developments in Precision Medicine
        by seqadmin



        Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

        Somatic Genomics
        “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
        05-24-2024, 01:16 PM
      • seqadmin
        Recent Advances in Sequencing Analysis Tools
        by seqadmin


        The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
        05-06-2024, 07:48 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 05-24-2024, 07:15 AM
      0 responses
      195 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 10:28 AM
      0 responses
      217 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 07:35 AM
      0 responses
      219 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-22-2024, 02:06 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Working...
      X